Browsing by Subject "FRAGMENTS"

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  • Fondi, Marco; Karkman, Antti; Tamminen, Manu V.; Bosi, Emanuele; Virta, Marko; Fani, Renato; Alm, Eric; McInerney, James O. (2016)
    The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as everything is everywhere but the environment selects." While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge.
  • Nasibullin, R. T.; Valiev, R. R.; Faiskanova, K. M.; Stepanova, E.; Cherepanov, V. N.; Filimonov, V. D.; Sundholm, D. (2019)
    Acetyl protecting groups are commonly used in carbohydrate chemistry. Partially acetylated arylglycosides are not only useful building blocks in syntheses, but they are also substantial for plant metabolism. Nonselective base catalysis is often used for removing the acetyl groups. Even though acid-catalyzed deacetylation might be more selective, it is seldom used in carbohydrate chemistry, because it has not been thoroughly investigated. In this work, we study the acid-catalyzed deacetylation of per-acetylated phenyl glycosides experimentally and computationally by using density functional theory (DFT) calculations. Based on quantum modeling, we design a general scheme for the stepwise acid-catalyzed deacetylation of arylglycosides per-acetates. The approach can also be applied on gluco- and galactopyranosides. We have studied the deacetylation reaction in solvents of different polarity and found that the activation barriers of the stepwise deacetylation mechanism increase with increasing polarity of the solvent.
  • Kyro, Kukka; Brenneisen, Stephan; Kotze, D. Johan; Szallies, Alexander; Gerner, Magdalena; Lehvavirta, Susanna (2018)
    Green roofs are a promising tool to return nature to cities and mitigate biodiversity loss brought about by urbanization. Yet, we lack basic information on how green roofs contribute to biodiversity and how their placement in the urban landscape affects different taxa and community composition. We studied the effects of local and landscape variables on beetle communities on green roofs. We expected that both local roof characteristics and urban landscape composition shape communities, but that their relative importance depends on species characteristics. Using pitfall traps, we collected beetles during two consecutive years from 17 green roofs in Basel, Switzerland. We evaluated the contribution of six local and six landscape variables to beetle community structure and to the responses of individual species. Communities on the roofs consisted of mobile and open dry-habitat species, with both local and landscape variables playing a role in structuring these communities. At the individual species level, local roof variables were more important than characteristics of the surrounding urban landscape. The most influential factors affecting the abundances of beetle species were vegetation, described as forb and grass cover (mainly positive), and roof age (mainly negative). Therefore, we suggest that the careful planning of green roofs with diverse vegetation is essential to increase their value as habitat for beetles. In addition, while beetle communities on green roofs can be diverse regardless of their placement in the urban landscape, the lack of wingless species indicates the need to increase the connectivity of green roofs to ground level habitats.
  • Kalendar, Ruslan; Shustov, Alexandr; Schulman, Alan (2021)
    Genome walking (GW), a strategy for capturing previously unsequenced DNA fragments that exist in proximity to a known sequence tag, is currently predominantly based on PCR. Recently developed PCR-based methods allow for combining of sequence-specific primers with designed capturing primers capable of annealing to unknown DNA targets, which offer the rapidity and effectiveness of PCR. This study presents a methodological improvement to the previously described GW technique known as Palindromic Sequence-Targeted PCR (PST-PCR). Like PST-PCR, this new method (called PST-PCR v.2) relies on targeting of capturing primers to palindromic sequences arbitrarily present in natural DNA templates. PST-PCR v.2 consists of two rounds of PCR. The first round uses a combination of one sequence-specific primer with one capturing (PST) primer. The second round uses a combination of a single (preferred) or two universal primers; one anneals to a 5’ tail attached to the sequence-specific primer and the other anneals to a different 5’ tail attached to the PST primer. The key advantage of PST-PCR v.2 is the convenience of using a single universal primer with invariable sequences in GW processes involving various templates. The entire procedure takes approximately 2–3 hours to produce the amplified PCR fragment, which contains a portion of a template flanked by the sequence-specific and capturing primers. PST-PCR v.2 is highly suitable for simultaneous work with multiple samples. For this reason, PST-PCR v.2 can be applied beyond the classical task of GW for studies in population genetics, in which PST-PCR v.2 is a preferred alternative to amplified fragment length polymorphism (AFLP) or next-generation sequencing. Furthermore, the conditions for PST-PCR v.2 are easier to optimize, as only one sequence-specific primer is used. This reduces non-specific Random Amplified Polymorphic DNA (RAPD)-like amplification and formation of non-templated amplification. Importantly, akin to the previous version, PST-PCR v.2 is not sensitive to template DNA sequence complexity or quality. This study illustrates the utility of PST-PCR v.2 for transposon display, which is a method to characterize inter- or intra-specific variability related to transposon integration sites. The Ac transposon sequence in the corn (Zea mays) genome was used as a sequence tag during the transposon display procedure to characterize the Ac integration sites.
  • Kalendar, Ruslan; Shustov, Alexandr; Seppänen, Mervi Mirjam; Schulman, Alan Howard; Stoddard, Frederick Lothrop (2019)
    Genome walking (GW) refers to the capture and sequencing of unknown regions in a long DNA molecule that are adjacent to a region with a known sequence. A novel PCR-based method, palindromic sequence-targeted PCR (PST-PCR), was developed. PST-PCR is based on a distinctive design of walking primers and special thermal cycling conditions. The walking primers (PST primers) match palindromic sequences (PST sites) that are randomly distributed in natural DNA. The PST primers have palindromic sequences at their 3’ ends. Upstream of the palindromes there is a degenerate sequence (8-12 nucleotides long); defined adapters are present at the 5’-termini. The thermal cycling profile has a linear amplification phase and an exponential amplification phase differing in annealing temperature. Changing the annealing temperature to switch the amplification phases at a defined cycle controls the balance between sensitivity and specificity. In contrast to traditional genome walking methods, PST-PCR is rapid (two to three hours to produce GW fragments) as it uses only one or two PCR rounds. Using PST-PCR, previously unknown regions (the promoter and intron 1) of the VRN1 gene of Timothy-grass (Phleum pratense L.) were captured for sequencing. In our experience, PST-PCR had higher throughput and greater convenience in comparison to other GW methods.
  • Oszkiewicz, Dagmara; Kryszczynska, Agnieszka; Kankiewicz, Pawel; Moskovitz, Nicholas A.; Skiff, Brian A.; Leith, Thomas B.; Durech, Josef; Wlodarczyk, Ireneusz; Marciniak, Anna; Geier, Stefan; Fedorets, Grigori; Troianskyi, Volodymyr; Fohring, Dora (2019)
    Context. Asteroid (2579) Spartacus is a small V-type object located in the inner main belt. This object shows spectral characteristics unusual for typical Vestoids, which may indicate an origin deeper than average within Vesta or an origin from an altogether different parent body. Aims. Our main goal is to study the origin of Spartacus. We derive the spin of Spartacus and a convex shape model of Spartacus in order to increase the knowledge of the body's physical properties. The rotational parameters are then used to investigate dynamical evolution of the object as well as to distinguish regions sampled by spectral observations to determine whether its surface displays heterogeneity. Methods. We collected lightcurves available from the literature (oppositions of 2009, 2012) and obtained additional photometric observations at various telescopes in 2016, 2017, and 2018. We used the lightcurve inversion method to derive a spin and convex shape model. We have collected spectral observations over two rotational periods of Spartacus and determined its spectral parameters using the modified Gaussian model (MGM). We then dynamically integrated the orbital elements of Spartacus, taking into account existing information, including its thermal properties, size and the derived spin axis orientation. Results. We find two models for (2579) Spartacus: (a) lambda = 312 degrees +/- 5 degrees, beta = -57 degrees +/- 5 degrees and (b) lambda = 113 degrees +/- 5 degrees, beta = -60 degrees +/- 5 degrees both retrograde. We find that the drift direction for Spartacus is consistent with separation from Vesta, and after a backward integration of 1 Gyr the asteroid reaches the boundary of the family. We did not observe spectral variations with rotation, thus the body most likely has a homogeneous surface. Additionally, new spectral analysis indicates that the 1.0 and 2.0 mu m band centers are within ranges that are typical for Vestoids while the area ratio of these bands is about half that of typical Vestoids. Conclusions. The asteroid (2579) Spartacus is in retrograde rotation and has a drift direction consistent with an origin from Vesta. The revised spectral band centers are within ranges typical for Vestoids, while band area ratio (BAR) is unusually low compared to that of other V-types. The dynamical model shows that the asteroid could have migrated to its current location from the edges of the Vesta family within 1 Gyr, but an origin from an earlier impact on Vesta could also be plausible.
  • Sablok, Gaurav; Yang, Kun; Chen, Rui; Wen, Xiaopeng (2017)
    Among several smallRNAs classes, microRNAs play an important role in controlling the post-transcriptional events. Next generation sequencing has played a major role in extending the landscape of miRNAs and revealing their spatio-temporal roles in development and abiotic stress. Lateral evolution of these smallRNAs classes have widely been seen with the recently emerging knowledge on tRNA derived smallRNAs. In the present perspective, we discussed classification, identification and roles of tRNA derived smallRNAs across plants and their potential involvement in abiotic and biotic stresses.