@article{KundeMartinsPremieretal.2019, author = {Kunde, Miriam N. and Martins, Renata Filipa and Premier, Joe and Fickel, J{\"o}rns and F{\"o}rster, Daniel W.}, title = {Population and landscape genetic analysis of the Malayan sun bear Helarctos malayanus}, series = {Conservation genetics}, volume = {21}, journal = {Conservation genetics}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {1566-0621}, doi = {10.1007/s10592-019-01233-w}, pages = {123 -- 135}, year = {2019}, abstract = {Conservation genetics can provide data needed by conservation practitioners for their decisions regarding the management of vulnerable or endangered species, such as the sun bear Helarctos malayanus. Throughout its range, the sun bear is threatened by loss and fragmentation of its habitat and the illegal trade of both live bears and bear parts. Sharply declining population numbers and population sizes, and a lack of natural dispersal between populations all threaten the genetic diversity of the remaining populations of this species. In this first population genetics study of sun bears using microsatellite markers, we analyzed 68 sun bear samples from Cambodia to investigate population structure and genetic diversity. We found evidence for two genetically distinct populations in the West and East of Cambodia. Ongoing or recent gene flow between these populations does not appear sufficient to alleviate loss of diversity in these populations, one of which (West Cambodia) is characterized by significant inbreeding. We were able to assign 85\% of sun bears of unknown origin to one of the two populations with high confidence (assignment probability >= 85\%), providing valuable information for future bear reintroduction programs. Further, our results suggest that developed land (mostly agricultural mosaics) acts as a barrier to gene flow for sun bears in Cambodia. We highlight that regional sun bear conservation action plans should consider promoting population connectivity and enforcing wildlife protection of this threatened species.}, language = {en} } @article{MartinHerppichRoscheretal.2019, author = {Martin, Craig E. and Herppich, Werner B. and Roscher, Yvonne and Burkart, Michael}, title = {Relationships between leaf succulence and Crassulacean acid metabolism in the genus Sansevieria (Asparagaceae)}, series = {Flora : morphology, distribution, functional ecology of plants}, volume = {261}, journal = {Flora : morphology, distribution, functional ecology of plants}, publisher = {Elsevier}, address = {M{\"u}nchen}, issn = {0367-2530}, doi = {10.1016/j.flora.2019.151489}, pages = {8}, year = {2019}, abstract = {Relationships between different measures of succulence and Crassulacean acid metabolism (CAM; defined here as nocturnal increases in tissue acidity) were investigated in leaves of ten species of Sansevieria under greenhouse conditions. CAM was found in seven of the ten species investigated, and CAM correlated negatively with leaf thickness and leaf hydrenchyma/chlorenchyma ratio. Similarly, CAM correlated negatively with leaf water content, but only when expressed on a fresh mass basis. CAM was not correlated with "mesophyll succulence", but weakly with leaf chlorophyll concentration. These results indicate that CAM is associated more with "all-cell succulence" and not with the amount of leaf hydrenchyma in the genus Sansevieria. The findings of this study emphasize the importance of defining the nature of "leaf succulence" in studies of photosynthetic pathways and leaf morphology. Evidence is also provided that CAM and succulence arose multiple times in the genus Sansevieria.}, language = {en} } @article{KlopschBaldermannHanschenetal.2019, author = {Klopsch, Rebecca and Baldermann, Susanne and Hanschen, Franziska S. and Voss, Alexander and Rohn, Sascha and Schreiner, Monika and Neugart, Susanne}, title = {Brassica-enriched wheat bread: Unraveling the impact of ontogeny and breadmaking on bioactive secondary plant metabolites of pak choi and kale}, series = {Food chemistry}, volume = {295}, journal = {Food chemistry}, publisher = {Elsevier}, address = {Oxford}, issn = {0308-8146}, doi = {10.1016/j.foodchem.2019.05.113}, pages = {412 -- 422}, year = {2019}, abstract = {Consumption of Brassica vegetables is linked to health benefits, as they contain high concentrations of the following secondary plant metabolites (SPMs): glucosinolate breakdown products, carotenoids, chlorophylls, and phenolic compounds. Especially Brassica vegetables are consumed as microgreens (developed cotyledons). It was investigated how different ontogenetic stages (microgreens or leaves) of pak choi (Brassica rapa subsp. chinensis) and kale (Brassica oleracea var. sabellica) differ in their SPM concentration. The impact of breadmaking on SPMs in microgreens (7 days) and leaves (14 days) in pak choi and kale as a supplement in mixed wheat bread was assessed. In leaves, carotenoids, chlorophylls, and phenolic compounds were higher compared to those of microgreens. Breadmaking caused a decrease of SPMs. Chlorophyll degradation was observed, leading to pheophytin and pyropheophytin formation. In kale, sinapoylgentiobiose, a hydroxycinnamic acid derivative, concentration increased. Thus, leaves of Brassica species are suitable as natural ingredients for enhancing bioactive SPM concentrations in bread.}, language = {en} } @article{HeslopWinkelAnthonyetal.2019, author = {Heslop, J. K. and Winkel, Matthias and Anthony, K. M. Walter and Spencer, R. G. M. and Podgorski, D. C. and Zito, P. and Kholodov, A. and Zhang, M. and Liebner, Susanne}, title = {Increasing organic carbon biolability with depth in yedoma permafrost}, series = {Journal of geophysical research : Biogeosciences}, volume = {124}, journal = {Journal of geophysical research : Biogeosciences}, number = {7}, publisher = {American Geophysical Union}, address = {Washington}, issn = {2169-8953}, doi = {10.1029/2018JG004712}, pages = {2021 -- 2038}, year = {2019}, abstract = {Permafrost thaw subjects previously frozen organic carbon (OC) to microbial decomposition, generating the greenhouse gases (GHG) carbon dioxide (CO2) and methane (CH4) and fueling a positive climate feedback. Over one quarter of permafrost OC is stored in deep, ice-rich Pleistocene-aged yedoma permafrost deposits. We used a combination of anaerobic incubations, microbial sequencing, and ultrahigh-resolution mass spectrometry to show yedoma OC biolability increases with depth along a 12-m yedoma profile. In incubations at 3 degrees C and 13 degrees C, GHG production per unit OC at 12-versus 1.3-m depth was 4.6 and 20.5 times greater, respectively. Bacterial diversity decreased with depth and we detected methanogens at all our sampled depths, suggesting that in situ microbial communities are equipped to metabolize thawed OC into CH4. We concurrently observed an increase in the relative abundance of reduced, saturated OC compounds, which corresponded to high proportions of C mineralization and positively correlated with anaerobic GHG production potentials and higher proportions of OC being mineralized as CH4. Taking into account the higher global warming potential (GWP) of CH4 compared to CO2, thawed yedoma sediments in our study had 2 times higher GWP at 12-versus 9.0-m depth at 3 degrees C and 15 times higher GWP at 13 degrees C. Considering that yedoma is vulnerable to processes that thaw deep OC, our findings imply that it is important to account for this increasing GHG production and GWP with depth to better understand the disproportionate impact of yedoma on the magnitude of the permafrost carbon feedback.}, language = {en} } @phdthesis{Tong2019, author = {Tong, Hao}, title = {Dissection of genetic architecture of intermediate phenotypes and predictions in plants}, school = {Universit{\"a}t Potsdam}, pages = {127}, year = {2019}, abstract = {Determining the relationship between genotype and phenotype is the key to understand the plasticity and robustness of phenotypes in nature. While the directly observable plant phenotypes (e.g. agronomic, yield and stress resistance traits) have been well-investigated, there is still a lack in our knowledge about the genetic basis of intermediate phenotypes, such as metabolic phenotypes. Dissecting the links between genotype and phenotype depends on suitable statistical models. The state-of-the-art models are developed for directly observable phenotypes, regardless the characteristics of intermediate phenotypes. This thesis aims to fill the gaps in understanding genetic architecture of intermediate phenotypes, and how they tie to composite traits, namely plant growth. The metabolite levels and reaction fluxes, as two aspects of metabolic phenotypes, are shaped by the interrelated chemical reactions formed in genome-scale metabolic network. Here, I attempt to answer the question: Can the knowledge of underlying genome-scale metabolic network improve the model performance for prediction of metabolic phenotypes and associated plant growth? To this end, two projects are investigated in this thesis. Firstly, we propose an approach that couples genomic selection with genome-scale metabolic network and metabolic profiles in Arabidopsis thaliana to predict growth. This project is the first integration of genomic data with fluxes predicted based on constraint-based modeling framework and data on biomass composition. We demonstrate that our approach leads to a considerable increase of prediction accuracy in comparison to the state-of-the-art methods in both within and across environment predictions. Therefore, our work paves the way for combining knowledge on metabolic mechanisms in the statistical approach underlying genomic selection to increase the efficiency of future plant breeding approaches. Secondly, we investigate how reliable is genomic selection for metabolite levels, and which single nucleotide polymorphisms (SNPs), obtained from different neighborhoods of a given metabolic network, contribute most to the accuracy of prediction. The results show that the local structure of first and second neighborhoods are not sufficient for predicting the genetic basis of metabolite levels in Zea mays. Furthermore, we find that the enzymatic SNPs can capture most the genetic variance and the contribution of non-enzymatic SNPs is in fact small. To comprehensively understand the genetic architecture of metabolic phenotypes, I extend my study to a local Arabidopsis thaliana population and their hybrids. We analyze the genetic architecture in primary and secondary metabolism as well as in growth. In comparison to primary metabolites, compounds from secondary metabolism were more variable and show more non-additive inheritance patterns which could be attributed to epistasis. Therefore, our study demonstrates that heterozygosity in local Arabidopsis thaliana population generates metabolic variation and may impact several tasks directly linked to metabolism. The studies in this thesis improve the knowledge of genetic architecture of metabolic phenotypes in both inbreed and hybrid population. The approaches I proposed to integrate genome-scale metabolic network with genomic data provide the opportunity to obtain mechanistic insights about the determinants of agronomically important polygenic traits.}, language = {en} } @article{LangaryNikoloski2019, author = {Langary, Damoun and Nikoloski, Zoran}, title = {Inference of chemical reaction networks based on concentration profiles using an optimization framework}, series = {Chaos : an interdisciplinary journal of nonlinear science}, volume = {29}, journal = {Chaos : an interdisciplinary journal of nonlinear science}, number = {11}, publisher = {American Institute of Physics}, address = {Melville}, issn = {1054-1500}, doi = {10.1063/1.5120598}, pages = {12}, year = {2019}, abstract = {Understanding the structure of reaction networks along with the underlying kinetics that lead to particular concentration readouts of the participating components is the first step toward optimization and control of (bio-)chemical processes. Yet, solutions to the problem of inferring the structure of reaction networks, i.e., characterizing the stoichiometry of the participating reactions provided concentration profiles of the participating components, remain elusive. Here, we present an approach to infer the stoichiometric subspace of a chemical reaction network from steady-state concentration data profiles obtained from a continuous isothermal reactor. The subsequent problem of finding reactions consistent with the observed subspace is cast as a series of mixed-integer linear programs whose solution generates potential reaction vectors together with a measure of their likelihood. We demonstrate the efficiency and applicability of the proposed approach using data obtained from synthetic reaction networks and from a well-established biological model for the Calvin-Benson cycle. Furthermore, we investigate the effect of missing information, in the form of unmeasured species or insufficient diversity within the data set, on the ability to accurately reconstruct the network reactions. The proposed framework is, in principle, applicable to many other reaction systems, thus providing future extensions to understanding reaction networks guiding chemical reactors and complex biological mixtures. (C) 2019 Author(s).}, language = {en} } @article{SongLiNowaketal.2019, author = {Song, Yu and Li, Gang and Nowak, Jacqueline and Zhang, Xiaoqing and Xu, Dongbei and Yang, Xiujuan and Huang, Guoqiang and Liang, Wanqi and Yang, Litao and Wang, Canhua and Bulone, Vincent and Nikoloski, Zoran and Hu, Jianping and Persson, Staffan and Zhang, Dabing}, title = {The Rice Actin-Binding Protein RMD Regulates Light-Dependent Shoot Gravitropism}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {181}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.19.00497}, pages = {630 -- 644}, year = {2019}, abstract = {Light and gravity are two key determinants in orientating plant stems for proper growth and development. The organization and dynamics of the actin cytoskeleton are essential for cell biology and critically regulated by actin-binding proteins. However, the role of actin cytoskeleton in shoot negative gravitropism remains controversial. In this work, we report that the actin-binding protein Rice Morphology Determinant (RMD) promotes reorganization of the actin cytoskeleton in rice (Oryza sativa) shoots. The changes in actin organization are associated with the ability of the rice shoots to respond to negative gravitropism. Here, light-grown rmd mutant shoots exhibited agravitropic phenotypes. By contrast, etiolated rmd shoots displayed normal negative shoot gravitropism. Furthermore, we show that RMD maintains an actin configuration that promotes statolith mobility in gravisensing endodermal cells, and for proper auxin distribution in light-grown, but not dark-grown, shoots. RMD gene expression is diurnally controlled and directly repressed by the phytochrome-interacting factor-like protein OsPIL16. Consequently, overexpression of OsPIL16 led to gravisensing and actin patterning defects that phenocopied the rmd mutant. Our findings outline a mechanism that links light signaling and gravity perception for straight shoot growth in rice.}, language = {en} } @article{YuWuNowaketal.2019, author = {Yu, Yanjun and Wu, Shenjie and Nowak, Jacqueline and Wang, Guangda and Han, Libo and Feng, Zhidi and Mendrinna, Amelie and Ma, Yinping and Wang, Huan and Zhang, Xiaxia and Tian, Juan and Dong, Li and Nikoloski, Zoran and Persson, Staffan and Kong, Zhaosheng}, title = {Live-cell imaging of the cytoskeleton in elongating cotton fibres}, series = {Nature plants}, volume = {5}, journal = {Nature plants}, number = {5}, publisher = {Nature Publ. Group}, address = {London}, issn = {2055-026X}, doi = {10.1038/s41477-019-0418-8}, pages = {498 -- 504}, year = {2019}, abstract = {Cotton (Gossypium hirsutum) fibres consist of single cells that grow in a highly polarized manner, assumed to be controlled by the cytoskeleton(1-3). However, how the cytoskeletal organization and dynamics underpin fibre development remains unexplored. Moreover, it is unclear whether cotton fibres expand via tip growth or diffuse growth(2-4). We generated stable transgenic cotton plants expressing fluorescent markers of the actin and microtubule cytoskeleton. Live-cell imaging revealed that elongating cotton fibres assemble a cortical filamentous actin network that extends along the cell axis to finally form actin strands with closed loops in the tapered fibre tip. Analyses of F-actin network properties indicate that cotton fibres have a unique actin organization that blends features of both diffuse and tip growth modes. Interestingly, typical actin organization and endosomal vesicle aggregation found in tip-growing cell apices were not observed in fibre tips. Instead, endomembrane compartments were evenly distributed along the elongating fibre cells and moved bi-directionally along the fibre shank to the fibre tip. Moreover, plus-end tracked microtubules transversely encircled elongating fibre shanks, reminiscent of diffusely growing cells. Collectively, our findings indicate that cotton fibres elongate via a unique tip-biased diffuse growth mode.}, language = {en} } @article{AngeleskaNikoloski2019, author = {Angeleska, Angela and Nikoloski, Zoran}, title = {Coherent network partitions}, series = {Discrete applied mathematics}, volume = {266}, journal = {Discrete applied mathematics}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0166-218X}, doi = {10.1016/j.dam.2019.02.048}, pages = {283 -- 290}, year = {2019}, abstract = {Graph clustering is widely applied in the analysis of cellular networks reconstructed from large-scale data or obtained from experimental evidence. Here we introduce a new type of graph clustering based on the concept of coherent partition. A coherent partition of a graph G is a partition of the vertices of G that yields only disconnected subgraphs in the complement of G. The coherence number of G is then the size of the smallest edge cut inducing a coherent partition. A coherent partition of G is optimal if the size of the inducing edge cut is the coherence number of G. Given a graph G, we study coherent partitions and the coherence number in connection to (bi)clique partitions and the (bi)clique cover number. We show that the problem of finding the coherence number is NP-hard, but is of polynomial time complexity for trees. We also discuss the relation between coherent partitions and prominent graph clustering quality measures.}, language = {en} } @article{HaberlandHampeAutenriethetal.2019, author = {Haberland, Christian and Hampe, Oliver and Autenrieth, Marijke and Voss, Manja}, title = {Balaenoptera borealis Lesson, 1828}, series = {Mammalia}, volume = {83}, journal = {Mammalia}, number = {4}, publisher = {De Gruyter}, address = {Berlin}, issn = {0025-1461}, doi = {10.1515/mammalia-2017-0149}, pages = {343 -- 351}, year = {2019}, abstract = {The whereabouts of the Balaenoptera borealis holotype, the skeleton of a 1819 stranded specimen, have been unknown since the World War II (WWII). Due to nomenclatural confusion, deficient documentation, and finally WWII bombing, which destroyed predominantly cetacean material in the Museum fib Naturkunde Berlin (MfN), the type skeleton of the sei whale sank into oblivion. Construction activities enabled a recent search and study on the remaining whale material. Here, we provide evidence that the type specimen was not destroyed. On the basis of species-wide and individual characters of the type material such as the shape of cranial elements and the pattern of the maxillary foramina, we show that the skull and mandibles, the vertebral column (except the atlas), and the ribs of the holotype remain intact. Further evidence that these skeletal remains belong to the previously missing holotype is provided by the characteristics of the spine. In addition, we analyzed ancient DNA from bone samples and confirm they are B. borealis, and the occurrence of same mitochondrial haplotypes indicate that the bones belong to the same individual. Additionally, a blue inscription was discovered at the caudal epiphysis of a thoracic vertebra; historical research matched this inscription with the material belonging to the former Anatomical-Zootomical Museum, from which the holotype was once bought.}, language = {en} }