TY - JOUR A1 - Yuan, Jun-Xia A1 - Hou, Xin-Dong A1 - Barlow, Axel A1 - Preick, Michaela A1 - Taron, Ulrike H. A1 - Alberti, Federica A1 - Basler, Nikolas A1 - Deng, Tao A1 - Lai, Xu-Long A1 - Hofreiter, Michael A1 - Sheng, Gui-Lian T1 - Molecular identification of late and terminal Pleistocene Equus ovodovi from northeastern China JF - PLOS ONE N2 - The extant diversity of horses (family Equidae) represents a small fraction of that occurring over their evolutionary history. One such lost lineage is the subgenus Sussemionus, which is thought to have become extinct during the Middle Pleistocene. However, recent molecular studies and morphological analysis have revealed that one of their representatives, E. ovodovi, did exist in Siberia during the Late Pleistocene. Fossil materials of E. ovodovi have thus far only been found in Russia. In this study, we extracted DNA from three equid fossil specimens excavated from northeastern China dated at 12,770-12,596, 29,525-28,887 and 40,201-38,848 cal. yBP, respectively, and retrieved three near-complete mitochondrial genomes from the specimens. Phylogenetic analyses cluster the Chinese haplotypes together with previously published Russian E. ovodovi, strongly supporting the assignment of these samples to this taxon. The molecular identification of E. ovodovi in northeastern China extends the known geographical range of this fossil species by several thousand kilometers to the east. The estimated coalescence time of all E. ovodovi haplotypes is approximately 199 Kya, with the Chinese haplotypes coalescing approximately 130 Kya. With a radiocarbon age of 12,770-12,596 cal. yBP, the youngest sample in this study represents the first E. ovodovi sample dating to the terminal Pleistocene, moving the extinction date of this species forwards considerably compared to previously documented fossils. Overall, comparison of our three mitochondrial genomes with the two published ones suggests a genetic diversity similar to several extant species of the genus Equus. Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0216883 SN - 1932-6203 VL - 14 IS - 5 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Yuan, Junxia A1 - Sheng, Guilian A1 - Preick, Michaela A1 - Sun, Boyang A1 - Hou, Xindong A1 - Chen, Shungang A1 - Taron, Ulrike Helene A1 - Barlow, Axel A1 - Wang, Linying A1 - Hu, Jiaming A1 - Deng, Tao A1 - Lai, Xulong A1 - Hofreiter, Michael T1 - Mitochondrial genomes of Late Pleistocene caballine horses from China belong to a separate clade JF - Quaternary science reviews : the international multidisciplinary research and review journal N2 - There were several species of Equus in northern China during the Late Pleistocene, including Equus przewalskii and Equus dalianensis. A number of morphological studies have been carried out on E. przewalskii and E. dalianensis, but their evolutionary history is still unresolved. In this study, we retrieved near-complete mitochondrial genomes from E. dalianensis and E. przewalskii specimens excavated from Late Pleistocene strata in northeastern China. Phylogenetic analyses revealed that caballoid horses were divided into two subclades: the New World and the Old World caballine horse subclades. The Old World caballine horses comprise of two deep phylogenetic lineages, with modern and ancient Equus caballus and modern E. przewalskii forming lineage I, and the individuals in this study together with one Yakut specimen forming lineage II. Our results indicate that Chinese Late Pleistocene caballoid horses showed a closer relationship to other Eurasian caballine horses than that to Pleistocene horses from North America. In addition, phylogenetic analyses suggested a close relationship between E. dalianensis and the Chinese fossil E. przewalskii, in agreement with previous researches based on morphological analyses. Interestingly, E. dalianensis and the fossil E. przewalskii were intermixed rather than split into distinct lineages, suggesting either that gene flow existed between these two species or that morphology-based species assignment of palaeontological specimens is not always correct. Moreover, Bayesian analysis showed that the divergence time between the New World and the Old World caballoid horses was at 1.02 Ma (95% CI: 0.86-1.24 Ma), and the two Old World lineages (I & II) split at 0.88 Ma (95% CI: 0.69-1.13 Ma), which indicates that caballoid horses seem to have evolved into different populations in the Old World soon after they migrated from North America via the Bering Land Bridge. Finally, the TMRCA of E. dalianensis was estimated at 0.20 Ma (95% CI: 0.15-0.28 Ma), and it showed a relative low genetic diversity compared with other Equus species. KW - Equus dalianensis KW - Equus przewalskii KW - Pleistocene caballine horses KW - ancient DNA KW - phylogenetic relationship KW - divergence time Y1 - 2020 U6 - https://doi.org/10.1016/j.quascirev.2020.106691 SN - 0277-3791 VL - 250 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Yuryev, Ruslan A1 - Kasche, Volker A1 - Ignatova, Zoya A1 - Galunsky, Boris T1 - Improved A. faecalis penicillin amidase mutant retains the thermodynamic and pH stability of the wild type enzyme N2 - Penicillin amidase from Alacaligenes faecalis is an attractive biocatalyst for hydrolysis of penicillin G for production of 6-aminopenicillanic acid, which is used in the synthesis of semi-synthetic beta-lactam antibiotics. Recently a mutant of this enzyme with extended C-terminus of the A-chain comprising parts of the connecting linker peptide was constructed. Its turnover number for the hydrolysis of penicillin G was 140 s(-1), about twice of the value for the wild-type enzyme (80 s(-1)). At the same time the specificity constant was improved about three-fold. The wild- type and the mutant enzymes showed similar pH stability suggesting that the linker peptide fragment covalently attached to the A-chain does not alter the electrostatic interactions in the protein core. Although the global stability of A. faecalis wild-type enzyme and the T206GS213G variant does not differ, the presence of the linker fragment stabilizes the domains interface, as evidenced by the monophasic transition of the mutant enzyme from folded to unfolded state during urea-induced denaturation. The high stability and activity of the mutant enzyme provides a rationale to use it as a biocatalyst in the industrial processes, where the enzyme must be more robust to fluctuations in the operational conditions. Y1 - 2010 UR - http://springerlink.metapress.com/content/1573-4943/ U6 - https://doi.org/10.1007/s10930-010-9238-4 SN - 1572-3887 ER - TY - JOUR A1 - Zabihi, Fatemeh A1 - Graff, Patrick A1 - Schumacher, Fabian A1 - Kleuser, Burkhard A1 - Hedtrich, Sarah A1 - Haag, Rainer T1 - Synthesis of poly(lactide-co-glycerol) as a biodegradable and biocompatible polymer with high loading capacity for dermal drug delivery JF - Nanoscale N2 - Due to the low cutaneous bioavailability of tacrolimus (TAC), penetration enhancers are used to improve its penetration into the skin. However, poor loading capacity, non-biodegradability, toxicity, and in some cases inefficient skin penetration are challenging issues that hamper their applications for the dermal TAC delivery. Here we present poly(lactide-co-glycerol) (PLG) as a water soluble, biodegradable, and biocompatible TAC-carrier with high loading capacity (14.5% w/w for TAC) and high drug delivery efficiencies into the skin. PLG was synthesized by cationic ring-opening copolymerization of a mixture of glycidol and lactide and showed 35 nm and 300 nm average sizes in aqueous solutions before and after loading of TAC, respectively. Delivery experiments on human skin, quantified by fluorescence microscopy and LC-MS/MS, showed a high ability for PLG to deposit Nile red and TAC into the stratum corneum and viable epidermis of skin in comparison with Protopic (R) (0.03% w/w, TAC ointment). The cutaneous distribution profile of delivered TAC proved that 80%, 16%, and 4% of the cutaneous drug level was deposited in the stratum corneum, viable epidermis, and upper dermis, respectively. TAC delivered by PLG was able to efficiently decrease the IL-2 and TSLP expressions in human skin models. Taking advantage of the excellent physicochemical and biological properties of PLG, it can be used for efficient dermal TAC delivery and potential treatment of inflammatory skin diseases. Y1 - 2018 U6 - https://doi.org/10.1039/c8nr05536j SN - 2040-3364 SN - 2040-3372 VL - 10 IS - 35 SP - 16848 EP - 16856 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Zaccheus, Mona V. A1 - Bröker, Nina Kristin A1 - Lundborg, Magnus A1 - Uetrecht, Charlotte A1 - Barbirz, Stefanie A1 - Widmalm, Goran T1 - Structural studies of the O-antigen polysaccharide from Escherichia coli TD2158 having O18 serogroup specificity and aspects of its interaction with the tailspike endoglycosidase of the infecting bacteriophage HK620 JF - Carbohydrate research N2 - We have analyzed the O-antigen polysaccharide of the previously uncharacterized Escherichia coli strain TD2158 which is a host of bacteriophage HK620. This bacteriophage recognizes and cleaves the polysaccharide with its tailspike protein (TSP). The polysaccharide preparation as well as oligosaccharides obtained from HK620TSP endoglycosidase digests were analyzed with NMR spectroscopy. Additionally, sugar analysis was performed on the O-antigen polysaccharide and MALDI-TOF MS was used in oligosaccharide analysis. The present study revealed a heterogeneous polysaccharide with a hexasaccharide repeating unit of the following structure: alpha-D-Glcp-(1 -> 6) vertical bar vertical bar 2)-alpha-L-Rhap-(1 -> 6)-alpha-D-Glcp-(1 -> 4)-alpha-D-Galp-(1 -> 3)-alpha-D-GlcpNAc- (1 ->vertical bar beta-D-Glcp/beta-D-GlcpNAc-(1 -> 3) A repeating unit with a D-GlcNAc substitution of D-Gal has been described earlier as characteristic for serogroup O18A1. Accordingly, we termed repeating units with D-Glc substitution at D-Gal as O18A2. NMR analyses of the polysaccharide confirmed that O18A1- and O18A2-type repeats were present in a 1:1 ratio. However, HK620TSP preferentially bound the D-GlcNAc- substituted O18A1-type repeating units in its high affinity binding pocket with a dissociation constant of 140 mu M and disfavored the O18A2-type having a beta-D-Glcp-(1 -> 3)-linked group. As a result, in hexasaccharide preparations, O18A1 and O18A2 repeats were present in a 9: 1 ratio stressing the clear preference of O18A1- type repeats to be cleaved by HK620TSP. KW - Escherichia coli KW - Tailspike KW - Endoglycosidase KW - Lipopolysaccharide KW - NMR KW - Mass spectrometry Y1 - 2012 U6 - https://doi.org/10.1016/j.carres.2012.05.022 SN - 0008-6215 VL - 357 IS - 8 SP - 118 EP - 125 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Zakharova, A. A1 - Nikoloski, Zoran A1 - Koseska, Aneta T1 - Dimensionality reduction of bistable biological systems JF - Bulletin of mathematical biology : official journal of the Society for Mathematical Biology N2 - Time hierarchies, arising as a result of interactions between system's components, represent a ubiquitous property of dynamical biological systems. In addition, biological systems have been attributed switch-like properties modulating the response to various stimuli across different organisms and environmental conditions. Therefore, establishing the interplay between these features of system dynamics renders itself a challenging question of practical interest in biology. Existing methods are suitable for systems with one stable steady state employed as a well-defined reference. In such systems, the characterization of the time hierarchies has already been used for determining the components that contribute to the dynamics of biological systems. However, the application of these methods to bistable nonlinear systems is impeded due to their inherent dependence on the reference state, which in this case is no longer unique. Here, we extend the applicability of the reference-state analysis by proposing, analyzing, and applying a novel method, which allows investigation of the time hierarchies in systems exhibiting bistability. The proposed method is in turn used in identifying the components, other than reactions, which determine the systemic dynamical properties. We demonstrate that in biological systems of varying levels of complexity and spanning different biological levels, the method can be effectively employed for model simplification while ensuring preservation of qualitative dynamical properties (i.e., bistability). Finally, by establishing a connection between techniques from nonlinear dynamics and multivariate statistics, the proposed approach provides the basis for extending reference-based analysis to bistable systems. KW - Bistability KW - Time-scales hierarchy KW - Similarity transformation KW - Canonical correlation analysis KW - Dimensionality reduction Y1 - 2013 U6 - https://doi.org/10.1007/s11538-013-9807-8 SN - 0092-8240 VL - 75 IS - 3 SP - 373 EP - 392 PB - Springer CY - New York ER - TY - JOUR A1 - Zancolli, Giulia A1 - Baker, Timothy G. A1 - Barlow, Axel A1 - Bradley, Rebecca K. A1 - Calvete, Juan J. A1 - Carter, Kimberley C. A1 - de Jager, Kaylah A1 - Owens, John Benjamin A1 - Price, Jenny Forrester A1 - Sanz, Libia A1 - Scholes-Higham, Amy A1 - Shier, Liam A1 - Wood, Liam A1 - Wüster, Catharine E. A1 - Wüster, Wolfgang T1 - Is Hybridization a Source of Adaptive Venom Variation in Rattlesnakes? A Test, Using a Crotalus scutulatus x viridis Hybrid Zone in Southwestern New Mexico JF - Toxins N2 - Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species. KW - adaptation KW - Crotalus KW - evolution KW - hybridization KW - introgression KW - Mojave toxin KW - molecular evolution KW - venom Y1 - 2016 U6 - https://doi.org/10.3390/toxins8060188 SN - 2072-6651 VL - 8 PB - MDPI CY - Basel ER - TY - JOUR A1 - Zappa, Luca A1 - Schlaffer, Stefan A1 - Brocca, Luca A1 - Vreugdenhil, Mariette A1 - Nendel, Claas A1 - Dorigo, Wouter T1 - How accurately can we retrieve irrigation timing and water amounts from (satellite) soil moisture? JF - International journal of applied earth observation and geoinformation N2 - While ensuring food security worldwide, irrigation is altering the water cycle and generating numerous environmental side effects. As detailed knowledge about the timing and the amounts of water used for irrigation over large areas is still lacking, remotely sensed soil moisture has proved potential to fill this gap. However, the spatial resolution and revisit time of current satellite products represent a major limitation to accurately estimating irrigation. This work aims to systematically quantify their impact on the retrieved irrigation information, hence assessing the value of satellite soil moisture for estimating irrigation timing and water amounts. In a real-world experiment, we modeled soil moisture using actual irrigation and meteorological data, obtained from farmers and weather stations, respectively. Modeled soil moisture was compared against various remotely sensed products differing in terms of spatio-temporal resolution to test the hypothesis that high-resolution observations can disclose the irrigation signal from individual fields while coarse-scale satellite products cannot. Then, in a synthetic experiment, we systematically investigated the effect of soil moisture spatial and temporal resolution on the accuracy of irrigation estimates. The analysis was further elaborated by considering different irrigation scenarios and by adding realistic amounts of random errors in the soil moisture time series. We show that coarse-scale remotely sensed soil moisture products achieve higher correlations with rainfed simulations, while high-resolution satellite observations agree significantly better with irrigated simulations, suggesting that high-resolution satellite soil moisture can inform on field-scale (similar to 40 ha) irrigation. A thorough analysis of the synthetic dataset showed that satisfactory results, both in terms of detection (F-score > 0.8) and quantification (Pearson's correlation > 0.8), are found for noise-free soil moisture observations either with a temporal sampling up to 3 days or if at least one-third of the pixel covers the irrigated field(s). However, irrigation water amounts are systematically underestimated for temporal samplings of more than one day, and decrease proportionally to the spatial resolution, i.e., coarsening the pixel size leads to larger irrigation underestimations. Although lower spatial and temporal resolutions decrease the detection and quantification accuracies (e.g., R between 0.6 and 1 depending on the irrigation rate and spatio-temporal resolution), random errors in the soil moisture time series have a stronger negative impact (Pearson R always smaller than 0.85). As expected, better performances are found for higher irrigation rates, i.e. when more water is supplied during an irrigation event. Despite the potentially large underestimations, our results suggest that high-resolution satellite soil moisture has the potential to track and quantify irrigation, especially over regions where large volumes of irrigation water are applied to the fields, and given that low errors affect the soil moisture observations. KW - remote sensing KW - soil moisture KW - irrigation KW - detection KW - quantification KW - sentinel-1 Y1 - 2022 U6 - https://doi.org/10.1016/j.jag.2022.102979 SN - 1569-8432 SN - 1872-826X VL - 113 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Zarattini, Paola A1 - Mura, Graziella A1 - Ketmaier, Valerio T1 - Intra-specific variability in the thirteen known populations of the fairy shrimp Chirocephalus ruffoi (Crustacea: Anostraca) - resting egg morphometrics and mitochondrial DNA reveal decoupled patterns of deep divergence JF - Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica N2 - Chirocephalus ruffoi is a fairy shrimp endemic to the Italian peninsula, where it is known only from thirteen high mountain locations. Twelve of these are in the Northern Apennines while the thirteenth is about 700 km away in the Calabrian Apennines (Southern Italy). We quantified degree of genetic divergence within the species by sequencing a fragment of the mitochondrial DNA encoding for Cytochrome Oxidase I. We then combined genetic data with the re-analysis of two different datasets on the morphometrics of the resting eggs (cysts) produced by the species as an adaptation to survive seasonal droughts. Genetic data revealed profound divergence; we identified four clusters of haplotypes within the species phylogeography, three in the Northern Apennines and one in the Calabrian Apennines with most of the genetic variation (a parts per thousand 70%) being apportioned among haplogroups. We found high variability in cyst morphometrics, especially in cyst size and height of the spines ornamenting the surface. Genetic and morphometric data are decoupled suggesting that cyst morphology is either under selection or a plastic trait. We, therefore, caution against using cyst morphology for taxonomic purposes in anostracans. KW - Anostraca KW - Resting eggs KW - Morphometrics KW - Cytochrome oxidase I KW - Population structure Y1 - 2013 U6 - https://doi.org/10.1007/s10750-013-1487-8 SN - 0018-8158 VL - 713 IS - 1 SP - 19 EP - 34 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Zaupa, Alessandro A1 - Neffe, Axel T. A1 - Pierce, Benjamin F. A1 - Nöchel, Ulrich A1 - Lendlein, Andreas T1 - Influence of tyrosine-derived moieties and drying conditions on the formation of helices in gelatin JF - Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences N2 - The single and triple helical organization of protein chains strongly influences the mechanical properties of gelatin-based materials. A chemical method for obtaining different degrees of helical organization in gelatin is covalent functionalization, while a physical method for achieving the same goal is the variation of the drying conditions of gelatin solutions. Here we explored how the introduction of desaminotyrosine (DAT) and desaminotyrosyl tyrosine (DATT) linked to lysine residues of gelatin influenced the kinetics and thermodynamic equilibrium of the helicalization process of single and triple helices following different drying conditions. Drying at a temperature above. the helix-to-coil transition temperature of gelatin (T > T-c, called nu(short)) generally resulted in gelatins with relatively lower triple helical content (X-c,X-t = 1-2%) than lower temperature drying (T < T-c, called nu(long)) (X-c,X-t = 8-10%), where the DAT(T) functional groups generally disrupted helix formation. While different helical contents affected the thermal transition temperatures only slightly, the mechanical properties were strongly affected for swollen hydrogels (E = 4-13 kPa for samples treated by nu(long) and E = 120-700 kPa for samples treated by nu(short)). This study shows that side group functionalization and different drying conditions are viable options to control the helicalization and macroscopic properties of gelatin-based materials. Y1 - 2011 U6 - https://doi.org/10.1021/bm101029k SN - 1525-7797 VL - 12 IS - 1 SP - 75 EP - 81 PB - American Chemical Society CY - Washington ER -