@article{StraubePreickNayloretal.2021, author = {Straube, Nicolas and Preick, Michaela and Naylor, Gavin J. P. and Hofreiter, Michael}, title = {Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae)}, series = {Royal Society Open Science}, volume = {8}, journal = {Royal Society Open Science}, number = {9}, publisher = {Royal Society}, address = {London}, issn = {2054-5703}, doi = {10.1098/rsos.210474}, pages = {13}, year = {2021}, abstract = {After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus, in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has 12 times coverage and a length of 16 741 bp. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the shortfin smooth lantern shark Etmopterus joungi. Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet collection type specimen for taxonomy.}, language = {en} } @article{AndreevRaschkeBiskabornetal.2021, author = {Andreev, Andrei and Raschke, Elena and Biskaborn, Boris and Vyse, Stuart Andrew and Courtin, J{\´e}r{\´e}my and B{\"o}hmer, Thomas and Stoof-Leichsenring, Kathleen R. and Kruse, Stefan and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike}, title = {Late Pleistocene to Holocene vegetation and climate changes in northwestern Chukotka (Far East Russia) deduced from lakes Ilirney and Rauchuagytgyn pollen records}, series = {Boreas : an international journal of quaternary research}, volume = {50}, journal = {Boreas : an international journal of quaternary research}, number = {3}, publisher = {Wiley-Blackwell}, address = {Oxford [u.a.]}, issn = {0300-9483}, doi = {10.1111/bor.12521}, pages = {652 -- 670}, year = {2021}, abstract = {This paper presents two new pollen records and quantitative climate reconstructions from northern Chukotka documenting environmental changes over the last 27.9 ka. Open tundra- and steppe-like habitats dominated between 27.9 and 18.7 cal. ka BP. Betula and Alnus shrubs might have grown in sheltered microhabitats but disappeared after 18.7 cal. ka BP. Although the climate was rather harsh, local herb-dominated communities supported herbivores as is evident by the presence of coprophilous spores in the sediments. The increase in Salix and Cyperaceae similar to 16.1 cal. ka BP suggests climate amelioration. Shrub Betula appeared similar to 15.9 cal. ka BP, and became dominant after similar to 15.52 cal. ka BP, whilst typical steppe communities drastically reduced. Very high presence of Botryococcus in the Lateglacial sediments reflects widespread shallow habitats, probably due to lake level increase. Shrub Alnus became common after similar to 13 cal. ka BP reflecting further climate amelioration. Simultaneously, herb communities gradually decreased in the vegetation reaching a minimum similar to 11.8 cal. ka BP. A gradual decrease of algae remains suggests a reduction of shallow-water habitats. Shrubby and graminoid tundra was dominant similar to 11.8-11.1 cal. ka BP, later Salix stands significantly decreased. The forest-tundra ecotone established in the Early Holocene, shortly after 11.1 cal. ka BP. Low contents of green algae in the Early Holocene sediments likely reflect deeper aquatic conditions. The most favourable climate conditions were between similar to 10.6 and 7 cal. ka BP. Vegetation became similar to the modern after similar to 7 cal. ka BP but Pinus pumila came to the Ilirney area at about 1.2 cal. ka BP. It is important to emphasize that the study area provided refugia for Betula and Alnus during MIS 2. It is also notable that our records do not reflect evidence of Younger Dryas cooling, which is inconsistent with some regional environmental records but in good accordance with some others.}, language = {en} } @article{HuChengXuetal.2021, author = {Hu, Ting-Li and Cheng, Feng and Xu, Zhen and Chen, Zhong-Zheng and Yu, Lei and Ban, Qian and Li, Chun-Lin and Pan, Tao and Zhang, Bao-Wei}, title = {Molecular and morphological evidence for a new species of the genus Typhlomys (Rodentia: Platacanthomyidae)}, series = {Zoological research : ZR = Dongwuxue-yanjiu : jikan / published by Kunming Institute of Zoology, Chinese Academy of Sciences, Zhongguo Kexueyuan Kunming Dongwu Yanjiusuo zhuban, Dongwuxue-yanjiu Bianji Weiyuanhui bianji}, volume = {42}, journal = {Zoological research : ZR = Dongwuxue-yanjiu : jikan / published by Kunming Institute of Zoology, Chinese Academy of Sciences, Zhongguo Kexueyuan Kunming Dongwu Yanjiusuo zhuban, Dongwuxue-yanjiu Bianji Weiyuanhui bianji}, number = {1}, publisher = {Yunnan Renmin Chubanshe}, address = {Kunming}, issn = {2095-8137}, doi = {10.24272/j.issn.2095-8137.2020.132}, pages = {100 -- 107}, year = {2021}, abstract = {In this study, we reassessed the taxonomic position of Typhlomys (Rodentia: Platacanthomyidae) from Huangshan, Anhui, China, based on morphological and molecular evidence. Results suggested that Typhlomys is comprised of up to six species, including four currently recognized species ( Typhlomys cinereus, T. chapensis, T. daloushanensis, and T. nanus), one unconfirmed candidate species, and one new species ( Typhlomys huangshanensis sp. nov.). Morphological analyses further supported the designation of the Huangshan specimens found at mid-elevations in the southern Huangshan Mountains (600 m to 1 200 m a.s.l.) as a new species.}, language = {en} } @article{TungSunWangetal.2021, author = {Tung, Wing Tai and Sun, Xianlei and Wang, Weiwei and Xu, Xun and Ma, Nan and Lendlein, Andreas}, title = {Structure, mechanical properties and degradation behavior of electrospun PEEU fiber meshes and films}, series = {MRS advances : a journal of the Materials Research Society (MRS)}, volume = {6}, journal = {MRS advances : a journal of the Materials Research Society (MRS)}, number = {10}, publisher = {Springer Nature Switzerland AG}, address = {Cham}, issn = {2059-8521}, doi = {10.1557/s43580-020-00001-0}, pages = {276 -- 282}, year = {2021}, abstract = {The capability of a degradable implant to provide mechanical support depends on its degradation behavior. Hydrolytic degradation was studied for a polyesteretherurethane (PEEU70), which consists of poly(p-dioxanone) (PPDO) and poly(epsilon-caprolactone) (PCL) segments with a weight ratio of 70:30 linked by diurethane junction units. PEEU70 samples prepared in the form of meshes with average fiber diameters of 1.5 mu m (mesh1.5) and 1.2 mu m (mesh1.2), and films were sterilized and incubated in PBS at 37 degrees C with 5 vol\% CO2 supply for 1 to 6 weeks. Degradation features, such as cracks or wrinkles, became apparent from week 4 for all samples. Mass loss was found to be 11 wt\%, 6 wt\%, and 4 wt\% for mesh1.2, mesh1.5, and films at week 6. The elongation at break decreased to under 20\% in two weeks for mesh1.2. In case of the other two samples, this level of degradation was achieved after 4 weeks. The weight average molecular weight of both PEEU70 mesh and film samples decreased to below 30 kg/mol when elongation at break dropped below 20\%. The time period of sustained mechanical stability of PEEU70-based meshes depends on the fiber diameter and molecular weight.}, language = {en} } @article{XuNieWangetal.2021, author = {Xu, Xun and Nie, Yan and Wang, Weiwei and Ullah, Imran and Tung, Wing Tai and Ma, Nan and Lendlein, Andreas}, title = {Generation of 2.5D lung bud organoids from human induced pluripotent stem cells}, series = {Clinical hemorheology and microcirculation : blood flow and vessels}, volume = {79}, journal = {Clinical hemorheology and microcirculation : blood flow and vessels}, number = {1}, publisher = {IOS Press}, address = {Amsterdam}, issn = {1386-0291}, doi = {10.3233/CH-219111}, pages = {217 -- 230}, year = {2021}, abstract = {Human induced pluripotent stem cells (hiPSCs) are a promising cell source to generate the patient-specific lung organoid given their superior differentiation potential. However, the current 3D cell culture approach is tedious and time-consuming with a low success rate and high batch-to-batch variability. Here, we explored the establishment of lung bud organoids by systematically adjusting the initial confluence levels and homogeneity of cell distribution. The efficiency of single cell seeding and clump seeding was compared. Instead of the traditional 3D culture, we established a 2.5D organoid culture to enable the direct monitoring of the internal structure via microscopy. It was found that the cell confluence and distribution prior to induction were two key parameters, which strongly affected hiPSC differentiation trajectories. Lung bud organoids with positive expression of NKX 2.1, in a single-cell seeding group with homogeneously distributed hiPSCs at 70\% confluence (SC 70\% hom) or a clump seeding group with heterogeneously distributed cells at 90\% confluence (CL 90\% het), can be observed as early as 9 days post induction. These results suggest that a successful lung bud organoid formation with single-cell seeding of hiPSCs requires a moderate confluence and homogeneous distribution of cells, while high confluence would be a prominent factor to promote the lung organoid formation when seeding hiPSCs as clumps. 2.5D organoids generated with defined culture conditions could become a simple, efficient, and valuable tool facilitating drug screening, disease modeling and personalized medicine.}, language = {en} } @article{RutschmannChenZhouetal.2021, author = {Rutschmann, Sereina and Chen, Ping and Zhou, Changfa and Monaghan, Michael T.}, title = {Three mitochondrial genomes of early-winged insects (Ephemeroptera: Baetidae and Leptophlebiidae)}, series = {Mitochondrial DNA Part B}, volume = {6}, journal = {Mitochondrial DNA Part B}, number = {10}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {2380-2359}, doi = {10.1080/23802359.2021.1974966}, pages = {2969 -- 2971}, year = {2021}, abstract = {Mayflies (Ephemeroptera) are a semi-aquatic insect order with comparatively few genomic data available despite their phylogenetic position at the root of the winged-insects and possession of ancestral traits. Here, we provide three mitochondrial genomes (mtgenomes) from representatives of the two most species-rich families, Baetis rutilocylindratus and Cloeon dipterum (Baetidae), and Habrophlebiodes zijinensis (Leptophlebiidae). All mtgenomes had a complete set of 13 protein-coding genes and a conserved orientation except for two inverted tRNAs in H. zijinensis. Phylogenetic reconstructions using 21 mayfly mtgenomes and representatives of seven additional orders recovered both Baetidae and Leptophlebiidae as well supported monophyletic clades, with Ephemeroptera as the sister-taxon to all other winged insects (i.e. Odonata and Neoptera).}, language = {en} } @article{OmranianAngeleskaNikoloski2021, author = {Omranian, Sara and Angeleska, Angela and Nikoloski, Zoran}, title = {PC2P}, series = {Bioinformatics}, volume = {37}, journal = {Bioinformatics}, number = {1}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btaa1089}, pages = {73 -- 81}, year = {2021}, abstract = {Motivation: Prediction of protein complexes from protein-protein interaction (PPI) networks is an important problem in systems biology, as they control different cellular functions. The existing solutions employ algorithms for network community detection that identify dense subgraphs in PPI networks. However, gold standards in yeast and human indicate that protein complexes can also induce sparse subgraphs, introducing further challenges in protein complex prediction. Results: To address this issue, we formalize protein complexes as biclique spanned subgraphs, which include both sparse and dense subgraphs. We then cast the problem of protein complex prediction as a network partitioning into biclique spanned subgraphs with removal of minimum number of edges, called coherent partition. Since finding a coherent partition is a computationally intractable problem, we devise a parameter-free greedy approximation algorithm, termed Protein Complexes from Coherent Partition (PC2P), based on key properties of biclique spanned subgraphs. Through comparison with nine contenders, we demonstrate that PC2P: (i) successfully identifies modular structure in networks, as a prerequisite for protein complex prediction, (ii) outperforms the existing solutions with respect to a composite score of five performance measures on 75\% and 100\% of the analyzed PPI networks and gold standards in yeast and human, respectively, and (iii,iv) does not compromise GO semantic similarity and enrichment score of the predicted protein complexes. Therefore, our study demonstrates that clustering of networks in terms of biclique spanned subgraphs is a promising framework for detection of complexes in PPI networks.}, language = {en} } @article{NwosuRoeserYangetal.2021, author = {Nwosu, Ebuka Canisius and Roeser, Patricia Angelika and Yang, Sizhong and Ganzert, Lars and Dellwig, Olaf and Pinkerneil, Sylvia and Brauer, Achim and Dittmann, Elke and Wagner, Dirk and Liebner, Susanne}, title = {From water into sediment-tracing freshwater cyanobacteria via DNA analyses}, series = {Microorganisms : open access journal}, volume = {9}, journal = {Microorganisms : open access journal}, number = {8}, publisher = {MDPI}, address = {Basel}, issn = {2076-2607}, doi = {10.3390/microorganisms9081778}, pages = {20}, year = {2021}, abstract = {Sedimentary ancient DNA-based studies have been used to probe centuries of climate and environmental changes and how they affected cyanobacterial assemblages in temperate lakes. Due to cyanobacteria containing potential bloom-forming and toxin-producing taxa, their approximate reconstruction from sediments is crucial, especially in lakes lacking long-term monitoring data. To extend the resolution of sediment record interpretation, we used high-throughput sequencing, amplicon sequence variant (ASV) analysis, and quantitative PCR to compare pelagic cyanobacterial composition to that in sediment traps (collected monthly) and surface sediments in Lake Tiefer See. Cyanobacterial composition, species richness, and evenness was not significantly different among the pelagic depths, sediment traps and surface sediments (p > 0.05), indicating that the cyanobacteria in the sediments reflected the cyanobacterial assemblage in the water column. However, total cyanobacterial abundances (qPCR) decreased from the metalimnion down the water column. The aggregate-forming (Aphanizomenon) and colony-forming taxa (Snowella) showed pronounced sedimentation. In contrast, Planktothrix was only very poorly represented in sediment traps (meta- and hypolimnion) and surface sediments, despite its highest relative abundance at the thermocline (10 m water depth) during periods of lake stratification (May-October). We conclude that this skewed representation in taxonomic abundances reflects taphonomic processes, which should be considered in future DNA-based paleolimnological investigations.}, language = {en} } @article{NieWangXuetal.2021, author = {Nie, Yan and Wang, Weiwei and Xu, Xun and Ma, Nan and Lendlein, Andreas}, title = {The response of human induced pluripotent stem cells to cyclic temperature changes explored by BIO-AFM}, series = {MRS advances : a journal of the Materials Research Society (MRS)}, volume = {6}, journal = {MRS advances : a journal of the Materials Research Society (MRS)}, number = {31}, publisher = {Springer}, address = {Cham}, issn = {2059-8521}, doi = {10.1557/s43580-021-00110-4}, pages = {745 -- 749}, year = {2021}, abstract = {Human induced pluripotent stem cells (hiPSCs) are highly sensitive to extrinsic physical and biochemical signals from their extracellular microenvironments. In this study, we analyzed the effect of cyclic temperature changes on hiPSCs behaviors, especially by means of scanning force microscopy (BIO-AFM). The alternation in cellular mechanics, as well as the secretion and pattern of deposition of extracellular matrix (ECM) protein in hiPSCs were evaluated. The arrangement of the actin cytoskeleton changed with the variation of the temperature. The rearranged cytoskeleton architecture led to the subsequent changes in cell mechanics (Young's modulus of hiPSCs). With the exposure to the cyclic cold stimuli, an increase in the average surface roughness (Ra) and roughness mean square (RMS) was detected. This observation might be at least in part due to the upregulated secretion of Laminin alpha 5 during repeated temporary cooling. The expression of pluripotent markers, NANOG and SOX2, was not impaired in hiPSCs, when exposed to the cyclic cold stimuli for 24 h. Our findings provide an insight into the effect of temperature on the hiPSC behaviors, which may contribute to a better understanding of the application of locally controlled therapeutic hypothermia.}, language = {en} } @article{LozanoAguilarTriguerosOnandiaetal.2021, author = {Lozano, Yudi M. and Aguilar-Trigueros, Carlos A. and Onandia, Gabriela and Maaß, Stefanie and Zhao, Tingting and Rillig, Matthias C.}, title = {Effects of microplastics and drought on soil ecosystem functions and multifunctionality}, series = {Journal of applied ecology : an official journal of the British Ecological Society}, volume = {58}, journal = {Journal of applied ecology : an official journal of the British Ecological Society}, number = {5}, publisher = {Wiley-Blackwell}, address = {Oxford [u.a.]}, issn = {1365-2664}, doi = {10.1111/1365-2664.13839}, pages = {988 -- 996}, year = {2021}, abstract = {1. Microplastics in soils have become an important threat for terrestrial systems as they may potentially alter the geochemical/biophysical soil environment and can interact with drought. As microplastics may affect soil water content, this could exacerbate the well-known negative effects of drought on ecosystem functionality. Thus, functions including litter decomposition, soil aggregation or those related with nutrient cycling can be altered. Despite this potential interaction, we know relatively little about how microplastics, under different soil water conditions, affect ecosystem functions and multifunctionality. 2. To address this gap, we performed an experiment using grassland plant communities growing in microcosms. Microplastic fibres (absent, present) and soil water conditions (well-watered, drought) were applied in a fully factorial design. At harvest, we measured soil ecosystem functions related to nutrient cycling (beta-glucosaminidase, beta-D-cellobiosidase, phosphatase, beta-glucosidase enzymes), respiration, nutrient retention, pH, litter decomposition and soil aggregation (water stable aggregates). As terrestrial systems provide these functions simultaneously, we also assessed ecosystem multifunctionality, an index that encompasses the array of ecosystem functions measured here. 3. We found that the interaction between microplastic fibres and drought affected ecosystem functions and multifunctionality. Drought had negatively affected nutrient cycling by decreasing enzymatic activities by up to similar to 39\%, while microplastics increased soil aggregation by similar to 18\%, soil pH by similar to 4\% and nutrient retention by up to similar to 70\% by diminishing nutrient leaching. Microplastic fibres also impacted soil enzymes, respiration and ecosystem multifunctionality, but importantly, the direction of these effects depended on soil water status. That is, under well-watered conditions, these functions decreased with microplastic fibres by up to similar to 34\% while under drought they had similar values irrespective of the microplastic presence, or tended to increase with microplastics. Litter decomposition had a contrary pattern increasing with microplastics by similar to 6\% under well-watered conditions while decreasing to a similar percentage under drought. 4. Synthesis and applications. Single ecosystem functions can be positively or negatively affected by microplastics fibres depending on soil water status. However, our results suggest that microplastic fibres may cause negative effects on ecosystem soil multifunctionality of a similar magnitude as drought. Thus, strategies to counteract this new global change factor are necessary.}, language = {en} }