TY  - JOUR
A1  - Shikangalah, Rosemary
A1  - Mapani, Benjamin
A1  - Mapaure, Isaac
A1  - Herzschuh, Ulrike
T1  - Responsiveness of Dichrostachys cinerea to seasonal variations in temperature and rainfall in central Namibia
JF  - Flora
N2  - Woody plants provide natural archives of climatic variation which can be investigated by applying dendroclimatological methods. Such studies are limited in Southern Africa but have great potential of improving our understanding of past climates and plant functional adaptations in the region. This study therefore investigated the responsiveness of Dichrostachys cinerea to seasonal variations in temperature and rainfall at two sites in central Namibia, Waterberg and Kuzikus. Dichrostachys cinerea is one of the encroacher species thriving well in Namibia. A moving correlation and response function analysis were used to test its responsiveness to seasonal climatic variations over time. Dichrostachys cinerea growth rings showed relationships to late summer warming, lasting up to half of the rainy season. The results also revealed that past temperatures had been fluctuating and their influence on growth rings had been intensifying over the years, but to varying extents between the two sites. Temperature was a more important determinant of ring growth at the drier site (Kuzikus), while rainfall was more important at the wetter site (Waterberg). Growth ring responsiveness to rainfall was not immediate but showed a rather lagged pattern. We conclude that D. cinerea differentially responds to variations in rainfall and temperature across short climatic gradients. This study showed that the species, due to its somewhat wide ecological amplitude, has great potential for dendroclimatological studies in tropical regions.
KW  - Dendroclimatology
KW  - Dichrostachys cinerea
KW  - Growth rings
KW  - Namibia
KW  - Seasonal variation
Y1  - 2021
U6  - https://doi.org/10.1016/j.flora.2021.151974
SN  - 0367-2530
SN  - 1618-0585
VL  - 286
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - López-Sánchez, Aida
A1  - Bareth, Georg
A1  - Bolten, Andreas
A1  - Rose, Laura E.
A1  - Mansfeldt, Tim
A1  - Sapp, Melanie
A1  - Linstädter, Anja
T1  - Effects of declining oak vitality on ecosystem multifunctionality
BT  - lessons from a Spanish oak woodland
JF  - Forest ecology and management
N2  - Mediterranean oak woodlands are currently facing unprecedented degradation threats from oak decline. The Iberian oak decline "Seca", related to Phytophthora infection, causes crown defoliation that may adversely affect ecosystem services (ESs). We aim to improve our understanding of how Seca-induced declines in crown foliation affect the provision of multiple ecosystem services from understory vegetation. We selected holm (Quercus ilex) and cork oak (Q. suber) trees in a Spanish oak woodland and evaluated three proxies of canopy effects. One proxy (crown defoliation) solely captured Seca-dependent effects, one proxy solely captured Seca-independent effects (tree dimensions such as diameter and height), while the third proxy (tree vigor) captured overall canopy effects. We then used the best-performing proxies to assess canopy effects on key ecosystem services (ESs) such as aboveground net primary production (ANPP), grass and legume biomass, species diversity, litter decomposition rates, and a combined index of ecosystem multifunctionality. <br /> We found that both types of canopy effects (i.e. Seca-dependent and Seca-independent effects) were related, indicating that ANPP was disproportionally more affected by Seca when defoliated trees were large. Responses of other ESs were mostly not significant, although lower species diversity was found under trees with intermediate vigor. Our results underline that a Seca-related decline in canopy density triggered a homogenization of ecosystem service delivery on the ecosystem scale. The ecosystem functions (EFs) under trees of low vigor are similar to that in adjacent open microsites indicating that the presence of vigorous (i.e. old and vital) trees is critical for maintaining EFs at a landscape level. Our results also highlight the importance of quantifying not only defoliation but also tree dimensions as both factors jointly and interactively modify canopy effects on ecosystem multifunctionality.
KW  - ANPP
KW  - Decomposition
KW  - Microsite degradation
KW  - Herb diversity
KW  - Seca
Y1  - 2021
U6  - https://doi.org/10.1016/j.foreco.2021.118927
SN  - 0378-1127
SN  - 1872-7042
VL  - 484
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Sedaghatmehr, Mastoureh
A1  - Thirumalaikumar, Venkatesh P.
A1  - Kamranfar, Iman
A1  - Schulz, Karina
A1  - Müller-Röber, Bernd
A1  - Sampathkumar, Arun
A1  - Balazadeh, Salma
T1  - Autophagy complements metalloprotease FtsH6 in degrading plastid heat shock protein HSP21 during heat stress recovery
JF  - The journal of experimental botany : an official publication of the Society for Experimental Biology and of the Federation of European Societies of Plant Physiology
N2  - Moderate and temporary heat stresses prime plants to tolerate, and survive, a subsequent severe heat stress. Such acquired thermotolerance can be maintained for several days under normal growth conditions, and can create a heat stress memory. We recently demonstrated that plastid-localized small heat shock protein 21 ( HSP21) is a key component of heat stress memory in Arabidopsis thaliana. A sustained high abundance of HSP21 during the heat stress recovery phase extends heat stress memory. The level of HSP21 is negatively controlled by plastid-localized metalloprotease FtsH6 during heat stress recovery. Here, we demonstrate that autophagy, a cellular recycling mechanism, exerts additional control over HSP21 degradation. Genetic and chemical disruption of both metalloprotease activity and autophagy trigger superior HSP21 accumulation, thereby improving memory. Furthermore, we provide evidence that autophagy cargo receptor ATG8-INTERACTING PROTEIN1 (ATI1) is associated with heat stress memory. ATI1 bodies co-localize with both autophagosomes and HSP21, and their abundance and transport to the vacuole increase during heat stress recovery. Together, our results provide new insights into the module for control of the regulation of heat stress memory, in which two distinct protein degradation pathways act in concert to degrade HSP21, thereby enabling cells to recover from the heat stress effect at the cost of reducing the heat stress memory.
KW  - Arabidopsis thaliana
KW  - ATI1
KW  - FtsH6
KW  - heat stress
KW  - HSP21
KW  - plastid
KW  - selective autophagy
KW  - stress memory
KW  - stress recovery
Y1  - 2021
U6  - https://doi.org/10.1093/jxb/erab304
SN  - 0022-0957
SN  - 1460-2431
VL  - 72
IS  - 21
SP  - 7498
EP  - 7513
PB  - Oxford University Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Gorin, Vladislav A.
A1  - Scherz, Mark D.
A1  - Korost, Dmitry V.
A1  - Poyarkov, Nikolay A.
T1  - Consequences of parallel miniaturisation in Microhylinae (Anura, Microhylidae), with the description of a new genus of diminutive South East Asian frogs
JF  - Zoosystematics and evolution : Mitteilungen aus dem Museum für Naturkunde in Berlin
N2  - The genus Microhyla Tschudi, 1838 includes 52 species and is one of the most diverse genera of the family Microhylidae, being the most species-rich taxon of the Asian subfamily Microhylinae. The recent, rapid description of numerous new species of Microhyla with complex phylogenetic relationships has made the taxonomy of the group especially challenging. Several recent phylogenetic studies suggested paraphyly of Microhyla with respect to Glyphoglossus Gunther, 1869, and revealed three major phylogenetic lineages of mid-Eocene origin within this assemblage. However, comprehensive works assessing morphological variation among and within these lineages are absent. In the present study we investigate the generic taxonomy of Microhyla-Glyphoglossus assemblage based on a new phylogeny including 57 species, comparative morphological analysis of skeletons from cleared-and-stained specimens for 23 species, and detailed descriptions of generalized osteology based on volume-rendered micro-CT scans for five speciesal-together representing all major lineages within the group. The results confirm three highly divergent and well-supported clades that correspond with external and osteological morphological characteristics, as well as respective geographic distribution. Accordingly, acknowledging ancient divergence between these lineages and their significant morphological differentiation, we propose to consider these three lineages as distinct genera: Microhyla sensu stricto, Glyphoglossus, and a newly described genus, Nanohyla gen. nov.
KW  - Amphibians
KW  - integrative taxonomy
KW  - narrow-mouthed frogs
KW  - micro-computed tomography
KW  - Nanohyla gen. nov
KW  - osteology
KW  - sexual dimorphism
KW  - taxonomic revision
Y1  - 2021
U6  - https://doi.org/10.3897/zse.97.57968
SN  - 1860-0743
SN  - 1435-1935
VL  - 97
IS  - 1
SP  - 21
EP  - 54
PB  - Pensoft Publishers
CY  - Sofia
ER  - 
TY  - JOUR
A1  - Schmidt, Sabrina
A1  - Reil, Daniela
A1  - Jeske, Kathrin
A1  - Drewes, Stephan
A1  - Rosenfeld, Ulrike
A1  - Fischer, Stefan
A1  - Spierling, Nastasja G.
A1  - Labutin, Anton
A1  - Heckel, Gerald
A1  - Jacob, Jens
A1  - Ulrich, Rainer G.
A1  - Imholt, Christian
T1  - Spatial and temporal dynamics and molecular evolution of Tula orthohantavirus in German vole populations
JF  - Viruses / Molecular Diversity Preservation International (MDPI)
N2  - Tula orthohantavirus (TULV) is a rodent-borne hantavirus with broad geographical distribution in Europe. Its major reservoir is the common vole (Microtus arvalis), but TULV has also been detected in closely related vole species. Given the large distributional range and high amplitude population dynamics of common voles, this host-pathogen complex presents an ideal system to study the complex mechanisms of pathogen transmission in a wild rodent reservoir. We investigated the dynamics of TULV prevalence and the subsequent potential effects on the molecular evolution of TULV in common voles of the Central evolutionary lineage. Rodents were trapped for three years in four regions of Germany and samples were analyzed for the presence of TULV-reactive antibodies and TULV RNA with subsequent sequence determination. The results show that individual (sex) and population-level factors (abundance) of hosts were significant predictors of local TULV dynamics. At the large geographic scale, different phylogenetic TULV clades and an overall isolation-by-distance pattern in virus sequences were detected, while at the small scale (<4 km) this depended on the study area. In combination with an overall delayed density dependence, our results highlight that frequent, localized bottleneck events for the common vole and TULV do occur and can be offset by local recolonization dynamics.
KW  - rodents
KW  - hantavirus
KW  - monitoring
KW  - population dynamics
KW  - common vole
KW  - field vole
KW  - water vole
KW  - phylogeny
KW  - molecular evolution
Y1  - 2021
U6  - https://doi.org/10.3390/v13061132
SN  - 1999-4915
VL  - 13
IS  - 6
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Straube, Nicolas
A1  - Preick, Michaela
A1  - Naylor, Gavin J. P.
A1  - Hofreiter, Michael
T1  - Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae)
JF  - Royal Society Open Science
N2  - 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.
KW  - museum specimens
KW  - archival DNA
KW  - deep-sea sharks
KW  - Etmopterus pusillus
KW  - Etmopterus joungi
KW  - taxonomy
Y1  - 2021
U6  - https://doi.org/10.1098/rsos.210474
SN  - 2054-5703
VL  - 8
IS  - 9
PB  - Royal Society
CY  - London
ER  - 
TY  - JOUR
A1  - Andreev, Andrei
A1  - Raschke, Elena
A1  - Biskaborn, Boris
A1  - Vyse, Stuart Andrew
A1  - Courtin, Jérémy
A1  - Böhmer, Thomas
A1  - Stoof-Leichsenring, Kathleen R.
A1  - Kruse, Stefan
A1  - Pestryakova, Luidmila Agafyevna
A1  - Herzschuh, Ulrike
T1  - Late Pleistocene to Holocene vegetation and climate changes in northwestern Chukotka (Far East Russia) deduced from lakes Ilirney and Rauchuagytgyn pollen records
JF  - Boreas : an international journal of quaternary research
N2  - 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.
Y1  - 2021
U6  - https://doi.org/10.1111/bor.12521
SN  - 0300-9483
SN  - 1502-3885
VL  - 50
IS  - 3
SP  - 652
EP  - 670
PB  - Wiley-Blackwell
CY  - Oxford [u.a.]
ER  - 
TY  - JOUR
A1  - Hu, Ting-Li
A1  - Cheng, Feng
A1  - Xu, Zhen
A1  - Chen, Zhong-Zheng
A1  - Yu, Lei
A1  - Ban, Qian
A1  - Li, Chun-Lin
A1  - Pan, Tao
A1  - Zhang, Bao-Wei
T1  - Molecular and morphological evidence for a new species of the genus Typhlomys (Rodentia: Platacanthomyidae)
JF  - 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
N2  - 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.
KW  - Morphology
KW  - Phylogenetics
KW  - Species delimitation
KW  - Taxonomy
Y1  - 2021
U6  - https://doi.org/10.24272/j.issn.2095-8137.2020.132
SN  - 2095-8137
VL  - 42
IS  - 1
SP  - 100
EP  - 107
PB  - Yunnan Renmin Chubanshe
CY  - Kunming
ER  - 
TY  - JOUR
A1  - Tung, Wing Tai
A1  - Sun, Xianlei
A1  - Wang, Weiwei
A1  - Xu, Xun
A1  - Ma, Nan
A1  - Lendlein, Andreas
T1  - Structure, mechanical properties and degradation behavior of electrospun PEEU fiber meshes and films
JF  - MRS advances : a journal of the Materials Research Society (MRS)
N2  - 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.
Y1  - 2021
U6  - https://doi.org/10.1557/s43580-020-00001-0
SN  - 2059-8521
VL  - 6
IS  - 10
SP  - 276
EP  - 282
PB  - Springer Nature Switzerland AG
CY  - Cham
ER  - 
TY  - JOUR
A1  - Xu, Xun
A1  - Nie, Yan
A1  - Wang, Weiwei
A1  - Ullah, Imran
A1  - Tung, Wing Tai
A1  - Ma, Nan
A1  - Lendlein, Andreas
T1  - Generation of 2.5D lung bud organoids from human induced pluripotent stem cells
JF  - Clinical hemorheology and microcirculation : blood flow and vessels
N2  - 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.
KW  - lung organoid
KW  - human induced pluripotent stem cell
KW  - cell culture
Y1  - 2021
U6  - https://doi.org/10.3233/CH-219111
SN  - 1386-0291
SN  - 1875-8622
VL  - 79
IS  - 1
SP  - 217
EP  - 230
PB  - IOS Press
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Rutschmann, Sereina
A1  - Chen, Ping
A1  - Zhou, Changfa
A1  - Monaghan, Michael T.
T1  - Three mitochondrial genomes of early-winged insects (Ephemeroptera: Baetidae and Leptophlebiidae)
JF  - Mitochondrial DNA Part B
N2  - 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).
KW  - Baetis
KW  - Cloeon
KW  - Habrophlebiodes
KW  - mayfly
KW  - mitochondrial phylogeny
Y1  - 2021
U6  - https://doi.org/10.1080/23802359.2021.1974966
SN  - 2380-2359
VL  - 6
IS  - 10
SP  - 2969
EP  - 2971
PB  - Routledge, Taylor & Francis Group
CY  - Abingdon
ER  - 
TY  - JOUR
A1  - Omranian, Sara
A1  - Angeleska, Angela
A1  - Nikoloski, Zoran
T1  - PC2P
BT  - parameter-free network-based prediction of protein complexes
JF  - Bioinformatics
N2  - 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.
Y1  - 2021
U6  - https://doi.org/10.1093/bioinformatics/btaa1089
SN  - 1367-4811
VL  - 37
IS  - 1
SP  - 73
EP  - 81
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Nwosu, Ebuka Canisius
A1  - Roeser, Patricia Angelika
A1  - Yang, Sizhong
A1  - Ganzert, Lars
A1  - Dellwig, Olaf
A1  - Pinkerneil, Sylvia
A1  - Brauer, Achim
A1  - Dittmann, Elke
A1  - Wagner, Dirk
A1  - Liebner, Susanne
T1  - From water into sediment-tracing freshwater cyanobacteria via DNA analyses
JF  - Microorganisms : open access journal
N2  - 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.
KW  - Aphanizomenon
KW  - Planktothrix
KW  - Snowella
KW  - cyanobacteria sedimentation
KW  - lake monitoring
KW  - sedimentary ancient DNA
KW  - sediment traps
KW  - environmental reconstruction
Y1  - 2021
U6  - https://doi.org/10.3390/microorganisms9081778
SN  - 2076-2607
VL  - 9
IS  - 8
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Nie, Yan
A1  - Wang, Weiwei
A1  - Xu, Xun
A1  - Ma, Nan
A1  - Lendlein, Andreas
T1  - The response of human induced pluripotent stem cells to cyclic temperature changes explored by BIO-AFM
JF  - MRS advances : a journal of the Materials Research Society (MRS)
N2  - 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.
Y1  - 2021
U6  - https://doi.org/10.1557/s43580-021-00110-4
SN  - 2059-8521
VL  - 6
IS  - 31
SP  - 745
EP  - 749
PB  - Springer
CY  - Cham
ER  - 
TY  - JOUR
A1  - Lozano, Yudi M.
A1  - Aguilar-Trigueros, Carlos A.
A1  - Onandia, Gabriela
A1  - Maaß, Stefanie
A1  - Zhao, Tingting
A1  - Rillig, Matthias C.
T1  - Effects of microplastics and drought on soil ecosystem functions and multifunctionality
JF  - Journal of applied ecology : an official journal of the British Ecological Society
N2  - 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.
KW  - enzymatic activities
KW  - grasslands ecosystem
KW  - litter decomposition
KW  - nutrient cycling
KW  - nutrient leaching
KW  - soil aggregation
KW  - soil pH
KW  - soil respiration
Y1  - 2021
U6  - https://doi.org/10.1111/1365-2664.13839
SN  - 1365-2664
VL  - 58
IS  - 5
SP  - 988
EP  - 996
PB  - Wiley-Blackwell
CY  - Oxford [u.a.]
ER  - 
TY  - JOUR
A1  - Huang, Lixing
A1  - Qiao, Ying
A1  - Xu, Wei
A1  - Gong, Linfeng
A1  - He, Rongchao
A1  - Qi, Weilu
A1  - Gao, Qiancheng
A1  - Cai, Hongyan
A1  - Grossart, Hans-Peter
A1  - Yan, Qingpi
T1  - Full-length transcriptome
BT  - a reliable alternative for single-cell RNA-seq analysis in the spleen of teleost without reference genome
JF  - Frontiers in immunology
N2  - Fish is considered as a supreme model for clarifying the evolution and regulatory mechanism of vertebrate immunity. However, the knowledge of distinct immune cell populations in fish is still limited, and further development of techniques advancing the identification of fish immune cell populations and their functions are required. Single cell RNA-seq (scRNA-seq) has provided a new approach for effective in-depth identification and characterization of cell subpopulations. Current approaches for scRNA-seq data analysis usually rely on comparison with a reference genome and hence are not suited for samples without any reference genome, which is currently very common in fish research. Here, we present an alternative, i.e. scRNA-seq data analysis with a full-length transcriptome as a reference, and evaluate this approach on samples from Epinephelus coioides-a teleost without any published genome. We show that it reconstructs well most of the present transcripts in the scRNA-seq data achieving a sensitivity equivalent to approaches relying on genome alignments of related species. Based on cell heterogeneity and known markers, we characterized four cell types: T cells, B cells, monocytes/macrophages (Mo/M phi) and NCC (non-specific cytotoxic cells). Further analysis indicated the presence of two subsets of Mo/M phi including M1 and M2 type, as well as four subsets in B cells, i.e. mature B cells, immature B cells, pre B cells and early-pre B cells. Our research will provide new clues for understanding biological characteristics, development and function of immune cell populations of teleost. Furthermore, our approach provides a reliable alternative for scRNA-seq data analysis in teleost for which no reference genome is currently available.
KW  - scRNA-seq
KW  - full-length transcriptome
KW  - immune cell population
KW  - teleost
KW  - infection
Y1  - 2021
U6  - https://doi.org/10.3389/fimmu.2021.737332
SN  - 1664-3224
VL  - 12
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Nwosu, Ebuka Canisius
A1  - Brauer, Achim
A1  - Kaiser, Jérôme
A1  - Horn, Fabian
A1  - Wagner, Dirk
A1  - Liebner, Susanne
T1  - Evaluating sedimentary DNA for tracing changes in cyanobacteria dynamics from sediments spanning the last 350 years of Lake Tiefer See, NE Germany
JF  - Journal of paleolimnology
N2  - Since the beginning of the Anthropocene, lacustrine biodiversity has been influenced by climate change and human activities. These factors advance the spread of harmful cyanobacteria in lakes around the world, which affects water quality and impairs the aquatic food chain. In this study, we assessed changes in cyanobacterial community dynamics via sedimentary DNA (sedaDNA) from well-dated lake sediments of Lake Tiefer See, which is part of the Klocksin Lake Chain spanning the last 350 years. Our diversity and community analysis revealed that cyanobacterial communities form clusters according to the presence or absence of varves. Based on distance-based redundancy and variation partitioning analyses (dbRDA and VPA) we identified that intensified lake circulation inferred from vegetation openness reconstructions, delta C-13 data (a proxy for varve preservation) and total nitrogen content were abiotic factors that significantly explained the variation in the reconstructed cyanobacterial community from Lake Tiefer See sediments. Operational taxonomic units (OTUs) assigned to Microcystis sp. and Aphanizomenon sp. were identified as potential eutrophication-driven taxa of growing importance since circa common era (ca. CE) 1920 till present. This result is corroborated by a cyanobacteria lipid biomarker analysis. Furthermore, we suggest that stronger lake circulation as indicated by non-varved sediments favoured the deposition of the non-photosynthetic cyanobacteria sister clade Sericytochromatia, whereas lake bottom anoxia as indicated by subrecent- and recent varves favoured the Melainabacteria in sediments. Our findings highlight the potential of high-resolution amplicon sequencing in investigating the dynamics of past cyanobacterial communities in lake sediments and show that lake circulation, anoxic conditions, and human-induced eutrophication are main factors explaining variations in the cyanobacteria community in Lake Tiefer See during the last 350 years.
KW  - Late Holocene
KW  - Methylheptadecanes
KW  - Varves
KW  - Anthropocene
KW  - Sericytochromatia
KW  - Melainabacteria
Y1  - 2021
U6  - https://doi.org/10.1007/s10933-021-00206-9
SN  - 0921-2728
SN  - 1573-0417
VL  - 66
IS  - 3
SP  - 279
EP  - 296
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Glückler, Ramesh
A1  - Herzschuh, Ulrike
A1  - Kruse, Stefan
A1  - Andreev, Andrei
A1  - Vyse, Stuart Andrew
A1  - Winkler, Bettina
A1  - Biskaborn, Boris
A1  - Pestryakova, Luidmila Agafyevna
A1  - Dietze, Elisabeth
T1  - Wildfire history of the boreal forest of south-western Yakutia (Siberia) over the last two millennia documented by a lake-sediment charcoal record
JF  - Biogeosciences : BG / European Geosciences Union
N2  - Wildfires, as a key disturbance in forest ecosystems, are shaping the world's boreal landscapes. Changes in fire regimes are closely linked to a wide array of environmental factors, such as vegetation composition, climate change, and human activity. Arctic and boreal regions and, in particular, Siberian boreal forests are experiencing rising air and ground temperatures with the subsequent degradation of permafrost soils leading to shifts in tree cover and species composition. Compared to the boreal zones of North America or Europe, little is known about how such environmental changes might influence long-term fire regimes in Russia. The larch-dominated eastern Siberian deciduous boreal forests differ markedly from the composition of other boreal forests, yet data about past fire regimes remain sparse. Here, we present a high-resolution macroscopic charcoal record from lacustrine sediments of Lake Khamra (southwest Yakutia, Siberia) spanning the last ca. 2200 years, including information about charcoal particle sizes and morphotypes. Our results reveal a phase of increased charcoal accumulation between 600 and 900 CE, indicative of relatively high amounts of burnt biomass and high fire frequencies. This is followed by an almost 900-year-long period of low charcoal accumulation without significant peaks likely corresponding to cooler climate conditions. After 1750 CE fire frequencies and the relative amount of biomass burnt start to increase again, coinciding with a warming climate and increased anthropogenic land development after Russian colonization. In the 20th century, total charcoal accumulation decreases again to very low levels despite higher fire frequency, potentially reflecting a change in fire management strategies and/or a shift of the fire regime towards more frequent but smaller fires. A similar pattern for different charcoal morphotypes and comparison to a pollen and non-pollen palynomorph (NPP) record from the same sediment core indicate that broad-scale changes in vegetation composition were probably not a major driver of recorded fire regime changes. Instead, the fire regime of the last two millennia at Lake Khamra seems to be controlled mainly by a combination of short-term climate variability and anthropogenic fire ignition and suppression.
Y1  - 2021
U6  - https://doi.org/10.5194/bg-18-4185-2021
SN  - 1726-4170
SN  - 1726-4189
VL  - 18
IS  - 13
SP  - 4185
EP  - 4209
PB  - Copernicus
CY  - Göttingen
ER  - 
TY  - JOUR
A1  - Courtin, Jérémy
A1  - Andreev, Andrei
A1  - Raschke, Elena
A1  - Bala, Sarah
A1  - Biskaborn, Boris
A1  - Liu, Sisi
A1  - Zimmermann, Heike
A1  - Diekmann, Bernhard
A1  - Stoof-Leichsenring, Kathleen R.
A1  - Pestryakova, Luidmila Agafyevna
A1  - Herzschuh, Ulrike
T1  - Vegetation changes in Southeastern Siberia during the late pleistocene and the holocene
JF  - Frontiers in Ecology and Evolution
N2  - Relationships between climate, species composition, and species richness are of particular importance for understanding how boreal ecosystems will respond to ongoing climate change. This study aims to reconstruct changes in terrestrial vegetation composition and taxa richness during the glacial Late Pleistocene and the interglacial Holocene in the sparsely studied southeastern Yakutia (Siberia) by using pollen and sedimentary ancient DNA (sedaDNA) records. Pollen and sedaDNA metabarcoding data using the trnL g and h markers were obtained from a sediment core from Lake Bolshoe Toko. Both proxies were used to reconstruct the vegetation composition, while metabarcoding data were also used to investigate changes in plant taxa richness. The combination of pollen and sedaDNA approaches allows a robust estimation of regional and local past terrestrial vegetation composition around Bolshoe Toko during the last similar to 35,000 years. Both proxies suggest that during the Late Pleistocene, southeastern Siberia was covered by open steppe-tundra dominated by graminoids and forbs with patches of shrubs, confirming that steppe-tundra extended far south in Siberia. Both proxies show disturbance at the transition between the Late Pleistocene and the Holocene suggesting a period with scarce vegetation, changes in the hydrochemical conditions in the lake, and in sedimentation rates. Both proxies document drastic changes in vegetation composition in the early Holocene with an increased number of trees and shrubs and the appearance of new tree taxa in the lake's vicinity. The sedaDNA method suggests that the Late Pleistocene steppe-tundra vegetation supported a higher number of terrestrial plant taxa than the forested Holocene. This could be explained, for example, by the "keystone herbivore" hypothesis, which suggests that Late Pleistocene megaherbivores were able to maintain a high plant diversity. This is discussed in the light of the data with the broadly accepted species-area hypothesis as steppe-tundra covered such an extensive area during the Late Pleistocene.
KW  - last glacial
KW  - Holocene
KW  - Lake Bolshoe Toko
KW  - paleoenvironments
KW  - sedimentary ancient DNA
KW  - metabarcoding
KW  - trnL
KW  - pollen
Y1  - 2021
U6  - https://doi.org/10.3389/fevo.2021.625096
SN  - 2296-701X
VL  - 9
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Calderan-Rodrigues, Maria Juliana
A1  - Luzarowski, Marcin
A1  - Monte-Bello, Carolina Cassano
A1  - Minen, Romina Ines
A1  - Zühlke, Boris M.
A1  - Nikoloski, Zoran
A1  - Skirycz, Aleksandra
A1  - Caldana, Camila
T1  - Proteogenic dipeptides are characterized by diel fluctuations and target of rapamycin complex-signaling dependency in the model plant Arabidopsis thaliana
JF  - Frontiers in plant science : FPLS
N2  - As autotrophic organisms, plants capture light energy to convert carbon dioxide into ATP, nicotinamide adenine dinucleotide phosphate (NADPH), and sugars, which are essential for the biosynthesis of building blocks, storage, and growth. At night, metabolism and growth can be sustained by mobilizing carbon (C) reserves. In response to changing environmental conditions, such as light-dark cycles, the small-molecule regulation of enzymatic activities is critical for reprogramming cellular metabolism. We have recently demonstrated that proteogenic dipeptides, protein degradation products, act as metabolic switches at the interface of proteostasis and central metabolism in both plants and yeast. Dipeptides accumulate in response to the environmental changes and act via direct binding and regulation of critical enzymatic activities, enabling C flux distribution. Here, we provide evidence pointing to the involvement of dipeptides in the metabolic rewiring characteristics for the day-night cycle in plants. Specifically, we measured the abundance of 13 amino acids and 179 dipeptides over short- (SD) and long-day (LD) diel cycles, each with different light intensities. Of the measured dipeptides, 38 and eight were characterized by day-night oscillation in SD and LD, respectively, reaching maximum accumulation at the end of the day and then gradually falling in the night. Not only the number of dipeptides, but also the amplitude of the oscillation was higher in SD compared with LD conditions. Notably, rhythmic dipeptides were enriched in the glucogenic amino acids that can be converted into glucose. Considering the known role of Target of Rapamycin (TOR) signaling in regulating both autophagy and metabolism, we subsequently investigated whether diurnal fluctuations of dipeptides levels are dependent on the TOR Complex (TORC). The Raptor1b mutant (raptor1b), known for the substantial reduction of TOR kinase activity, was characterized by the augmented accumulation of dipeptides, which is especially pronounced under LD conditions. We were particularly intrigued by the group of 16 dipeptides, which, based on their oscillation under SD conditions and accumulation in raptor1b, can be associated with limited C availability or photoperiod. By mining existing protein-metabolite interaction data, we delineated putative protein interactors for a representative dipeptide Pro-Gln. The obtained list included enzymes of C and amino acid metabolism, which are also linked to the TORC-mediated metabolic network. Based on the obtained results, we speculate that the diurnal accumulation of dipeptides contributes to its metabolic adaptation in response to changes in C availability. We hypothesize that dipeptides would act as alternative respiratory substrates and by directly modulating the activity of the focal enzymes.
KW  - dipeptide
KW  - diel cycle
KW  - metabolism
KW  - TOR signaling
KW  - protein-metabolite
KW  - interactions
KW  - carbon limitation
KW  - amino acid
Y1  - 2021
U6  - https://doi.org/10.3389/fpls.2021.758933
SN  - 1664-462X
VL  - 12
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Friedrich, Thomas
A1  - Oberkofler, Vicky
A1  - Trindade, Inês
A1  - Altmann, Simone
A1  - Brzezinka, Krzysztof
A1  - Lämke, Jörn S.
A1  - Gorka, Michal
A1  - Kappel, Christian
A1  - Sokolowska, Ewelina
A1  - Skirycz, Aleksandra
A1  - Graf, Alexander
A1  - Bäurle, Isabel
T1  - Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis
JF  - Nature Communications
N2  - Adaptive plasticity in stress responses is a key element of plant survival strategies. For instance, moderate heat stress (HS) primes a plant to acquire thermotolerance, which allows subsequent survival of more severe HS conditions. Acquired thermotolerance is actively maintained over several days (HS memory) and involves the sustained induction of memory-related genes. Here we show that FORGETTER3/ HEAT SHOCK TRANSCRIPTION FACTOR A3 (FGT3/HSFA3) is specifically required for physiological HS memory and maintaining high memory-gene expression during the days following a HS exposure. HSFA3 mediates HS memory by direct transcriptional activation of memory-related genes after return to normal growth temperatures. HSFA3 binds HSFA2, and in vivo both proteins form heteromeric complexes with additional HSFs. Our results indicate that only complexes containing both HSFA2 and HSFA3 efficiently promote transcriptional memory by positively influencing histone H3 lysine 4 (H3K4) hyper-methylation. In summary, our work defines the major HSF complex controlling transcriptional memory and elucidates the in vivo dynamics of HSF complexes during somatic stress memory. Moderate heat stress primes plants to acquire tolerance to subsequent, more severe heat stress. Here the authors show that the HSFA3 transcription factor forms a heteromeric complex with HSFA2 to sustain activated transcription of genes required for acquired thermotolerance by promoting H3K4 hyper-methylation.
Y1  - 2021
U6  - https://doi.org/10.1038/s41467-021-23786-6
SN  - 2041-1723
VL  - 12
IS  - 1
PB  - Nature Publishing Group UK
CY  - [London]
ER  - 
TY  - JOUR
A1  - Carpio Arias, Tannia Valeria
A1  - Arias Mogrovejo, Diana Carolina
A1  - Nicolalde Cifuentes, Tomás Marcelo
A1  - Tapia Veloz, Estephany Carolina
A1  - Zeeuw, Chris I. de
A1  - Vinueza Veloz, Maria Fernanda
T1  - Sleep quality does not mediate the negative effects of chronodisruption on body composition and metabolic syndrome in healthcare workers in Ecuador
JF  - Diabetes & metabolic syndrome : clinical research & reviews ; the official journal of DiabetesIndia
N2  - Background and aims: 
The objective of the present work was to determine to what extent sleep quality may mediate the association between chronodisruption (CD) and metabolic syndrome (MS), and between CD and body composition (BC). 

Methodology:
Cross-sectional study which included 300 adult health workers, 150 of whom were night shift workers and thereby exposed to CD. Diagnosis of MS was made based on Adult Treatment Panel III criteria. Sleep quality was measured using the Pittsburgh Sleep Quality Index. Body mass index (BMI), fat mass percentage, and visceral fat percentage were measured as indicators of body composition (BC). Data were analyzed using logistic, linear regression and structural equation models. 

Results: 
The odds of health workers exposed to CD to suffer MS was 22.13 (IC95 8.68-66.07) when the model was adjusted for age, gender, physical activity and energy consumption. CD was also significantly associated with an increase in fat mass and visceral fat percentages, but not to BMI. Surprisingly, there was not enough evidence supporting the hypothesis that sleep quality contributes to the association between CD and MS or between CD and BC. 

Conclusions:
Sleep quality does not mediate the negative effects of CD on MS nor on BC.
KW  - Shift work
KW  - Metabolic syndrome
KW  - Sleep quality
KW  - Chronodisruption
KW  - Body composition
Y1  - 2021
U6  - https://doi.org/10.1016/j.dsx.2021.01.017
SN  - 1871-4021
SN  - 1878-0334
VL  - 15
IS  - 1
SP  - 397
EP  - 402
PB  - Elsevier
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - Scharnweber, Inga Kristin
A1  - Chaguaceda, Fernando
A1  - Eklöv, Peter
T1  - Fatty acid accumulation in feeding types of a natural freshwater fish population
JF  - Oecologia / in cooperation with the International Association for Ecology, Intecol
N2  - Fatty acids are widely used to study trophic interactions in food web assemblages. Generally, it is assumed that there is a very small modification of fatty acids from one trophic step to another, making them suitable as trophic biomarkers. However, recent literature provides evidence that many fishes possess genes encoding enzymes with a role in bioconversion, thus the capability for bioconversion might be more widespread than previously assumed. Nonetheless, empirical evidence for biosynthesis occurring in natural populations remains scarce. In this study, we investigated different feeding types of perch (Perca fluviatilis) that are specialized on specific resources with different levels of highly unsaturated fatty acids (HUFAs), and analyzed the change between HUFA proportions in perch muscle tissue compared to their resources. Perch showed matching levels to their resources for EPA, but ARA and especially DHA were accumulated. Compound-specific stable isotope analyses helped us to identify the origin of HUFA carbon. Our results suggest that perch obtain a substantial amount of DHA via bioconversion when feeding on DHA-poor benthic resources. Thus, our data indicate the capability of bioconversion of HUFAs in a natural freshwater fish population.
KW  - Fatty acid conversion
KW  - Compound-specific stable isotope analysis
KW  - Docosahexaenoic acid
KW  - Bioconversion
KW  - Trophic upgrading
Y1  - 2021
U6  - https://doi.org/10.1007/s00442-021-04913-y
SN  - 0029-8549
SN  - 1432-1939
VL  - 196
IS  - 1
SP  - 53
EP  - 63
PB  - Springer
CY  - Berlin ; Heidelberg [u.a.]
ER  - 
TY  - JOUR
A1  - Zimmermann, Heike
A1  - Stoof-Leichsenring, Kathleen R.
A1  - Kruse, Stefan
A1  - Nürnberg, Dirk
A1  - Tiedemann, Ralf
A1  - Herzschuh, Ulrike
T1  - Sedimentary ancient DNA from the subarctic North Pacific
BT  - How sea ice, salinity, and insolation dynamics have shaped diatom composition and richness over the past 20,000 years
JF  - Paleoceanography and paleoclimatology
N2  - We traced diatom composition and diversity through time using diatom-derived sedimentary ancient DNA (sedaDNA) from eastern continental slope sediments off Kamchatka (North Pacific) by applying a short, diatom-specific marker on 63 samples in a DNA metabarcoding approach. The sequences were assigned to diatoms that are common in the area and characteristic of cold water. SedaDNA allowed us to observe shifts of potential lineages from species of the genus Chaetoceros that can be related to different climatic phases, suggesting that pre-adapted ecotypes might have played a role in the long-term success of species in areas of changing environmental conditions. These sedaDNA results complement our understanding of the long-term history of diatom assemblages and their general relationship to environmental conditions of the past. Sea-ice diatoms (Pauliella taeniata [Grunow] Round & Basson, Attheya septentrionalis [ostrup] R. M. Crawford and Nitzschia frigida [Grunow]) detected during the late glacial and Younger Dryas are in agreement with previous sea-ice reconstructions. A positive correlation between pennate diatom richness and the sea-ice proxy IP25 suggests that sea ice fosters pennate diatom richness, whereas a negative correlation with June insolation and temperature points to unfavorable conditions during the Holocene. A sharp increase in proportions of freshwater diatoms at similar to 11.1 cal kyr BP implies the influence of terrestrial runoff and coincides with the loss of 42% of diatom sequence variants. We assume that reduced salinity at this time stabilized vertical stratification which limited the replenishment of nutrients in the euphotic zone.
KW  - Bacillariophyceae
KW  - DNA metabarcoding
KW  - glacial / interglacial transition
KW  - northwestern Pacific
KW  - richness
KW  - sedaDNA
Y1  - 2021
U6  - https://doi.org/10.1029/2020PA004091
SN  - 2572-4525
VL  - 36
IS  - 4
PB  - Wiley
CY  - Hoboken, NJ
ER  - 
TY  - JOUR
A1  - Nwosu, Ebuka Canisius
A1  - Roeser, Patricia Angelika
A1  - Yang, Sizhong
A1  - Pinkerneil, Sylvia
A1  - Ganzert, Lars
A1  - Dittmann, Elke
A1  - Brauer, Achim
A1  - Wagner, Dirk
A1  - Liebner, Susanne
T1  - Species-level spatio-temporal dynamics of cyanobacteria in a hard-water temperate lake in the Southern Baltics
JF  - Frontiers in microbiology
N2  - Cyanobacteria are important primary producers in temperate freshwater ecosystems. However, studies on the seasonal and spatial distribution of cyanobacteria in deep lakes based on high-throughput DNA sequencing are still rare. In this study, we combined monthly water sampling and monitoring in 2019, amplicon sequence variants analysis (ASVs; a proxy for different species) and quantitative PCR targeting overall cyanobacteria abundance to describe the seasonal and spatial dynamics of cyanobacteria in the deep hard-water oligo-mesotrophic Lake Tiefer See, NE Germany. We observed significant seasonal variation in the cyanobacterial community composition (p < 0.05) in the epi- and metalimnion layers, but not in the hypolimnion. In winter-when the water column is mixed-picocyanobacteria (Synechococcus and Cyanobium) were dominant. With the onset of stratification in late spring, we observed potential niche specialization and coexistence among the cyanobacteria taxa driven mainly by light and nutrient dynamics. Specifically, ASVs assigned to picocyanobacteria and the genus Planktothrix were the main contributors to the formation of deep chlorophyll maxima along a light gradient. While Synechococcus and different Cyanobium ASVs were abundant in the epilimnion up to the base of the euphotic zone from spring to fall, Planktothrix mainly occurred in the metalimnetic layer below the euphotic zone where also overall cyanobacteria abundance was highest in summer. Our data revealed two potentially psychrotolerant (cold-adapted) Cyanobium species that appear to cope well under conditions of lower hypolimnetic water temperature and light as well as increasing sediment-released phosphate in the deeper waters in summer. The potential cold-adapted Cyanobium species were also dominant throughout the water column in fall and winter. Furthermore, Snowella and Microcystis-related ASVs were abundant in the water column during the onset of fall turnover. Altogether, these findings suggest previously unascertained and considerable spatiotemporal changes in the community of cyanobacteria on the species level especially within the genus Cyanobium in deep hard-water temperate lakes.
KW  - Cyanobium
KW  - picocyanobacteria diversity
KW  - amplicon sequencing
KW  - lake monitoring
KW  - ecological succession
KW  - lake stratification
KW  - psychrotolerant
Y1  - 2021
U6  - https://doi.org/10.3389/fmicb.2021.761259
SN  - 1664-302X
VL  - 12
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Lozada-Gobilard, Sissi Donna
A1  - Jeltsch, Florian
A1  - Zhu, Jinlei
T1  - High matrix vegetation decreases mean seed dispersal distance but increases long wind dispersal probability connecting local plant populations in agricultural landscapes
JF  - Agriculture, ecosystems & environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere
N2  - Seed dispersal plays an important role in population dynamics in agricultural ecosystems, but the effects of surrounding vegetation height on seed dispersal and population connectivity on the landscape scale have rarely been studied. Understanding the effects of surrounding vegetation height on seed dispersal will provide important information for land-use management in agricultural landscapes to prevent the spread of undesired weeds or enhance functional connectivity. We used two model species, Phragmites australis and Typha latifolia, growing in small natural ponds known as kettle holes, in an agricultural landscape to evaluate the effects of surrounding vegetation height on wind dispersal and population connectivity between kettle holes. Seed dispersal distance and the probability of long-distance dispersal (LDD) were simulated with the mechanistic WALD model under three scenarios of "low", "dynamic" and "high" surrounding vegetation height. Connectivity between the origin and target kettle holes was quantified with a connectivity index adapted from Hanski and Thomas (1994). Our results show that mean seed dispersal distance decreases with the height of surrounding matrix vegetation, but the probability of long-distance dispersal (LDD) increases with vegetation height. This indicates an important vegetation-based trade-off between mean dispersal distance and LDD, which has an impact on connectivity. Matrix vegetation height has a negative effect on mean seed dispersal distance but a positive effect on the probability of LDD. This positive effect and its impact on connectivity provide novel insights into landscape level (meta-)population and community dynamics - a change in matrix vegetation height by land-use or climatic changes could strongly affect the spread and connectivity of wind-dispersed plants. The opposite effect of vegetation height on mean seed dispersal distance and the probability of LDD should therefore be considered in management and analyses of future land-use and climate change effects.
KW  - Seed dispersal by wind
KW  - Long-distance seed dispersal
KW  - Matrix vegetation
KW  - Kettle holes
KW  - Agricultural landscapes
KW  - Metapopulation dynamics
Y1  - 2021
U6  - https://doi.org/10.1016/j.agee.2021.107678
SN  - 0167-8809
SN  - 1873-2305
VL  - 322
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Scheffler, Christiane
A1  - Bogin, Barry
A1  - Hermanussen, Michael
T1  - Catch-up growth is a better indicator of undernutrition than thresholds for stunting
JF  - Public health nutrition : PHN / The Nutrition Society
N2  - Objective: 
Stunting (height-for-age < −2 SD) is one of the forms of undernutrition and is frequent among children of low- and middle-income countries. But stunting perSe is not a synonym of undernutrition. We investigated association between body height and indicators of energetic undernutrition at three critical thresholds for thinness used in public health: (1) BMI SDS < −2; (2) mid-upper arm circumference divided by height (MUAC (mm) × 10/height (cm) < 1·36) and (3) mean skinfold thickness (SF) < 7 mm and to question the reliability of thresholds as indicators of undernutrition.

Design: 
Cross-sectional study; breakpoint analysis.

Setting: 
Rural and urban regions of Indonesia and Guatemala – different socio-economic status (SES).

Participants:
1716 Indonesian children (6·0–13·2 years) and 3838 Guatemalan children (4·0–18·9 years) with up to 50 % stunted children.

Results: 
When separating the regression of BMI, MUAC or SF, on height into distinguishable segments (breakpoint analysis), we failed to detect relevant associations between height, and BMI, MUAC or SF, even in the thinnest and shortest children. For BMI and SF, the breakpoint analysis either failed to reach statistical significance or distinguished at breakpoints above critical thresholds. For MUAC, the breakpoint analysis yielded negative associations between MUAC/h and height in thin individuals. Only in high SES Guatemalan children, SF and height appeared mildly associated with R2 = 0·017.

Conclusions: 
Currently used lower thresholds of height-for-age (stunting) do not show relevant associations with anthropometric indicators of energetic undernutrition. We recommend using the catch-up growth spurt during early re-feeding instead as immediate and sensitive indicator of past undernourishment. We discuss the primacy of education and social-economic-political-emotional circumstances as responsible factors for stunting.
KW  - no threshold for stunting
KW  - catch-up growth
KW  - social-economic-political-emotional
KW  - (SEPE) factors
Y1  - 2020
U6  - https://doi.org/10.1017/S1368980020003067
SN  - 1475-2727
SN  - 1368-9800
VL  - 24
IS  - 1
SP  - 52
EP  - 61
PB  - Cambridge University Press
CY  - Cambridge ; New York, NY
ER  - 
TY  - JOUR
A1  - Omranian, Sara
A1  - Angeleska, Angela
A1  - Nikoloski, Zoran
T1  - Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient
JF  - Computational and structural biotechnology journal
N2  - Identification of protein complexes from protein-protein interaction (PPI) networks is a key problem in PPI mining, solved by parameter-dependent approaches that suffer from small recall rates. Here we introduce GCC-v, a family of efficient, parameter-free algorithms to accurately predict protein complexes using the (weighted) clustering coefficient of proteins in PPI networks. Through comparative analyses with gold standards and PPI networks from Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens, we demonstrate that GCC-v outperforms twelve state-of-the-art approaches for identification of protein complexes with respect to twelve performance measures in at least 85.71% of scenarios. We also show that GCC-v results in the exact recovery of similar to 35% of protein complexes in a pan-plant PPI network and discover 144 new protein complexes in Arabidopsis thaliana, with high support from GO semantic similarity. Our results indicate that findings from GCC-v are robust to network perturbations, which has direct implications to assess the impact of the PPI network quality on the predicted protein complexes. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
KW  - Protein complexes
KW  - Protein-protein interaction
KW  - Network clustering
KW  - Species comparison
Y1  - 2021
U6  - https://doi.org/10.1016/j.csbj.2021.09.014
SN  - 2001-0370
VL  - 19
SP  - 5255
EP  - 5263
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Hampf, Anna
A1  - Nendel, Claas
A1  - Strey, Simone
A1  - Strey, Robert
T1  - Biotic yield losses in the Southern Amazon, Brazil
BT  - making use of smartphone-assisted plant disease diagnosis data
JF  - Frontiers in plant science : FPLS
N2  - Pathogens and animal pests (P&A) are a major threat to global food security as they directly affect the quantity and quality of food. The Southern Amazon, Brazil's largest domestic region for soybean, maize and cotton production, is particularly vulnerable to the outbreak of P&A due to its (sub)tropical climate and intensive farming systems. However, little is known about the spatial distribution of P&A and the related yield losses. Machine learning approaches for the automated recognition of plant diseases can help to overcome this research gap. The main objectives of this study are to (1) evaluate the performance of Convolutional Neural Networks (ConvNets) in classifying P&A, (2) map the spatial distribution of P&A in the Southern Amazon, and (3) quantify perceived yield and economic losses for the main soybean and maize P&A. The objectives were addressed by making use of data collected with the smartphone application Plantix. The core of the app's functioning is the automated recognition of plant diseases via ConvNets. Data on expected yield losses were gathered through a short survey included in an "expert" version of the application, which was distributed among agronomists. Between 2016 and 2020, Plantix users collected approximately 78,000 georeferenced P&A images in the Southern Amazon. The study results indicate a high performance of the trained ConvNets in classifying 420 different crop-disease combinations. Spatial distribution maps and expert-based yield loss estimates indicate that maize rust, bacterial stalk rot and the fall armyworm are among the most severe maize P&A, whereas soybean is mainly affected by P&A like anthracnose, downy mildew, frogeye leaf spot, stink bugs and brown spot. Perceived soybean and maize yield losses amount to 12 and 16%, respectively, resulting in annual yield losses of approximately 3.75 million tonnes for each crop and economic losses of US$2 billion for both crops together. The high level of accuracy of the trained ConvNets, when paired with widespread use from following a citizen-science approach, results in a data source that will shed new light on yield loss estimates, e.g., for the analysis of yield gaps and the development of measures to minimise them.
KW  - plant pathology
KW  - animal pests
KW  - pathogens
KW  - machine learning
KW  - digital
KW  - image processing
KW  - disease diagnosis
KW  - crowdsourcing
KW  - crop losses
Y1  - 2021
U6  - https://doi.org/10.3389/fpls.2021.621168
SN  - 1664-462X
VL  - 12
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Caserta, Giorgio
A1  - Zhang, Xiaorong
A1  - Yarman, Aysu
A1  - Supala, Eszter
A1  - Wollenberger, Ulla
A1  - Gyurcsányi, Róbert  E.
A1  - Zebger, Ingo
A1  - Scheller, Frieder W.
T1  - Insights in electrosynthesis, target binding, and stability of peptide-imprinted polymer nanofilms
JF  - Electrochimica acta : the journal of the International Society of Electrochemistry (ISE)
N2  - Molecularly imprinted polymer (MIP) nanofilms have been successfully implemented for the recognition of different target molecules: however, the underlying mechanistic details remained vague. 
This paper provides new insights in the preparation and binding mechanism of electrosynthesized peptide-imprinted polymer nanofilms for selective recognition of the terminal pentapeptides of the beta-chains of human adult hemoglobin, HbA, and its glycated form HbA1c. 
To differentiate between peptides differing solely in a glucose adduct MIP nanofilms were prepared by a two-step hierarchical electrosynthesis that involves first the chemisorption of a cysteinyl derivative of the pentapeptide followed by electropolymerization of scopoletin. 
This approach was compared with a random single-step electrosynthesis using scopo-letin/pentapeptide mixtures. Electrochemical monitoring of the peptide binding to the MIP nanofilms by means of redox probe gating revealed a superior affinity of the hierarchical approach with a Kd value of 64.6 nM towards the related target. 
Changes in the electrosynthesized non-imprinted polymer and MIP nanofilms during chemical, electrochemical template removal and rebinding were substantiated in situ by monitoring the characteristic bands of both target peptides and polymer with surface enhanced infrared absorption spectroscopy. 
This rational approach led to MIPs with excellent selectivity and provided key mechanistic insights with respect to electrosynthesis, rebinding and stability of the formed MIPs.
KW  - SEIRA spectroelectrochemistry
KW  - peptide imprinting
KW  - electrosynthesis
KW  - MIP
KW  - glycated peptide
Y1  - 2021
U6  - https://doi.org/10.1016/j.electacta.2021.138236
SN  - 0013-4686
SN  - 1873-3859
VL  - 381
PB  - Elsevier
CY  - New York, NY [u.a.]
ER  - 
TY  - JOUR
A1  - Yarman, Aysu
A1  - Kurbanoğlu, Sevinç
A1  - Zebger, Ingo
A1  - Scheller, Frieder W.
T1  - Simple and robust
BT  - the claims of protein sensing by molecularly imprinted polymers
JF  - Sensors and actuators : B, Chemical : an international journal devoted to research and development of chemical transducers
N2  - A spectrum of 7562 publications on Molecularly Imprinted Polymers (MIPs) has been presented in literature within the last ten years (Scopus, September 7, 2020). Around 10 % of the papers published on MIPs describe the recognition of proteins. The straightforward synthesis of MIPs is a significant advantage as compared with the preparation of enzymes or antibodies. MIPs have been synthesized from only one up to six functional monomers while proteins are made up of 20 natural amino acids. Furthermore, they can be synthesized against structures of low immunogenicity and allow multi-analyte measurements via multi-target synthesis. Electrochemical methods allow simple polymer synthesis, removal of the template and readout. Among the different sensor configurations electrochemical MIP-sensors provide the broadest spectrum of protein analytes. The sensitivity of MIP-sensors is sufficiently high for biomarkers in the sub-nanomolar region, nevertheless the cross-reactivity of highly abundant proteins in human serum is still a challenge. MIPs for proteins offer innovative tools not only for clinical and environmental analysis, but also for bioimaging, therapy and protein engineering.
KW  - Molecularly imprinted polymer
KW  - Plastibodies
KW  - Functional scaffolds
KW  - Biomimetic sensors
KW  - Proteins
Y1  - 2021
U6  - https://doi.org/10.1016/j.snb.2020.129369
SN  - 0925-4005
SN  - 1873-3077
VL  - 330
PB  - Elsevier Science
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - Tran, V. Phuong
A1  - Tamura, Yui
A1  - Pham, Van-Cuong
A1  - Elhussiny, Mohamed Z.
A1  - Han, Guofeng
A1  - Sur Chowdhury, Vishwajit
A1  - Furuse, Mitsuhiro
T1  - Neuropeptide Y modifies a part of diencephalic catecholamine but not indolamine metabolism in chicks depending on feeding status
JF  - Neuropeptides
N2  - The role of the monoaminergic system in the feeding behavior of neonatal chicks has been reported, but the functional relationship between the metabolism of monoamines and appetite-related neuropeptides is still unclear. This study aimed to investigate the changes in catecholamine and indolamine metabolism in response to the central action of neuropeptide Y (NPY) in different feeding statuses and the underlying mechanisms. In Experiment 1, the diencephalic concentrations of amino acids and monoamines following the intracerebroventricular (ICV) injection of NPY (375 pmol/10 mu l/chick), saline solution under ad libitum, and fasting conditions for 30 min were determined. Central NPY significantly decreased L-tyrosine concentration, the precursor of catecholamines under feeding condition, but not under fasting condition. Central NPY significantly increased dopamine metabolites, including 3,4-dihydroxyphenylacetic acid and homovanillic acid (HVA). The concentration of 3-methoxy-4-hydroxyphenylglycol was significantly reduced under feeding condition, but did not change under fasting condition by NPY. However, no effects of NPY on indolamine metabolism were found in either feeding status. Therefore, the mechanism of action of catecholamines with central NPY under feeding condition was elucidated in Experiment 2. Central NPY significantly attenuated diencephalic gene expression of catecholaminergic synthetic enzymes, such as tyrosine hydroxylase, L-aromatic amino acid decarboxylase, and GTP cyclohydrolase I after 30 min of feeding. In Experiment 3, co-injection of alpha-methyl-L-tyrosine, an inhibitor of tyrosine hydroxylase with NPY, moderately attenuated the orexigenic effect of NPY, accompanied by a significant positive correlation between food intake and HVA levels. In Experiment 4, there was a significant interaction between NPY and clorgyline, an inhibitor of monoamine oxidase A with ICV co-injection which implies that co-existence of NPY and clorgyline enhances the orexigenic effect of NPY. In conclusion, central NPY modifies a part of catecholamine metabolism, which is illustrated by the involvement of dopamine transmission and metabolism under feeding but not fasting conditions.
KW  - Neuropeptide Y
KW  - Feeding behavior
KW  - Neonatal chick
KW  - CNS
KW  - Catecholamines
Y1  - 2021
U6  - https://doi.org/10.1016/j.npep.2021.102169
SN  - 0143-4179
SN  - 1532-2785
VL  - 89
PB  - Elsevier
CY  - New York, NY
ER  - 
TY  - JOUR
A1  - Kürschner, Tobias
A1  - Scherer, Cédric
A1  - Radchuk, Viktoriia
A1  - Blaum, Niels
A1  - Kramer-Schadt, Stephanie
T1  - Movement can mediate temporal mismatches between resource availability and biological events in host-pathogen interactions
JF  - Ecology and evolution
N2  - Global change is shifting the timing of biological events, leading to temporal mismatches between biological events and resource availability. These temporal mismatches can threaten species' populations. Importantly, temporal mismatches not only exert strong pressures on the population dynamics of the focal species, but can also lead to substantial changes in pairwise species interactions such as host-pathogen systems. We adapted an established individual-based model of host-pathogen dynamics. The model describes a viral agent in a social host, while accounting for the host's explicit movement decisions. We aimed to investigate how temporal mismatches between seasonal resource availability and host life-history events affect host-pathogen coexistence, that is, disease persistence. Seasonal resource fluctuations only increased coexistence probability when in synchrony with the hosts' biological events. However, a temporal mismatch reduced host-pathogen coexistence, but only marginally. In tandem with an increasing temporal mismatch, our model showed a shift in the spatial distribution of infected hosts. It shifted from an even distribution under synchronous conditions toward the formation of disease hotspots, when host life history and resource availability mismatched completely. The spatial restriction of infected hosts to small hotspots in the landscape initially suggested a lower coexistence probability due to the critical loss of susceptible host individuals within those hotspots. However, the surrounding landscape facilitated demographic rescue through habitat-dependent movement. Our work demonstrates that the negative effects of temporal mismatches between host resource availability and host life history on host-pathogen coexistence can be reduced through the formation of temporary disease hotspots and host movement decisions, with implications for disease management under disturbances and global change.
KW  - classical swine fever
KW  - dynamic landscapes
KW  - global change
KW  - host– pathogen dynamics
KW  - individual‐ based model
KW  - movement ecology
Y1  - 2021
U6  - https://doi.org/10.1002/ece3.7478
SN  - 2045-7758
VL  - 11
IS  - 10
SP  - 5728
EP  - 5741
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Kaech, Heidi
A1  - Dennis, Alice B.
A1  - Vorburger, Christoph
T1  - Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa
JF  - BMC genomics
N2  - Background
Secondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins. These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly.

Results
We used RNA-Seq to generate hypotheses on why four of these strains inflict such different costs to A. fabae. We found different H. defensa strains to cause strain-specific changes in aphid gene expression, but little effect of H. defensa on gene expression of the primary endosymbiont, Buchnera aphidicola. The highly costly and over-replicating H. defensa strain H85 was associated with strongly reduced aphid expression of hemocytin, a marker of hemocytes in Drosophila. The closely related strain H15 was associated with downregulation of ubiquitin-related modifier 1, which is related to nutrient-sensing and oxidative stress in other organisms. Strain H402 was associated with strong differential regulation of a set of hypothetical proteins, the majority of which were only differentially regulated in presence of H402.

Conclusions
Overall, our results suggest that costs of different strains of H. defensa are likely caused by different mechanisms, and that these costs are imposed by interacting with the host rather than the host's obligatory endosymbiont B. aphidicola.
KW  - Aphis fabae
KW  - Buchnera
KW  - Cost of resistance
KW  - Hamiltonella
KW  - Host-symbiont interaction
KW  - RNA-Seq
KW  - Symbiosis
Y1  - 2021
U6  - https://doi.org/10.1186/s12864-021-07742-8
SN  - 1471-2164
VL  - 22
IS  - 1
PB  - BioMed Central
CY  - London
ER  - 
TY  - JOUR
A1  - Korniienko, Yevheniia
A1  - Nguyen, Linh
A1  - Baumgartner, Stephanie
A1  - Vater, Marianne
A1  - Tiedemann, Ralph
A1  - Kirschbaum, Frank
T1  - Correction to: Intragenus F1-hybrids of African weakly electric fish (Mormyridae: Campylomormyrus tamandua male x C. compressirostris female) are fertile (vol 206, pg 571, 2020)
JF  - Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology
Y1  - 2021
U6  - https://doi.org/10.1007/s00359-021-01513-2
SN  - 0340-7594
SN  - 1432-1351
VL  - 207
IS  - 6
SP  - 773
EP  - 773
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Olas, Justyna Jadwiga
A1  - Apelt, Federico
A1  - Watanabe, Mutsumi
A1  - Höfgen, Rainer
A1  - Wahl, Vanessa
T1  - Developmental stage-specific metabolite signatures in Arabidopsis thaliana under optimal and mild nitrogen limitation
JF  - Plant science : an international journal of experimental plant biology
N2  - Metabolites influence flowering time, and thus are among the major determinants of yield. Despite the reported role of trehalose 6-phosphate and nitrate signaling on the transition from the vegetative to the reproductive phase, little is known about other metabolites contributing and responding to developmental phase changes. To increase our understanding which metabolic traits change throughout development in Arabidopsis thaliana and to identify metabolic markers for the vegetative and reproductive phases, especially among individual amino acids (AA), we profiled metabolites of plants grown in optimal (ON) and limited nitrogen (N) (LN) conditions, the latter providing a mild but consistent limitation of N. We found that although LN plants adapt their growth to a decreased level of N, their metabolite profiles are strongly distinct from ON plant profiles, with N as the driving factor for the observed differences. We demonstrate that the vegetative and the reproductive phase are not only marked by growth parameters such as biomass and rosette area, but also by specific metabolite signatures including specific single AA. In summary, we identified N-dependent and -independent indicators manifesting developmental stages, indicating that the plant's metabolic status also reports on the developmental phases.
KW  - Amino acids
KW  - Floral induction
KW  - Flowering time
KW  - Nitrogen
KW  - Metabolites
KW  - Vegetative phase
KW  - Reproductive phase
Y1  - 2021
U6  - https://doi.org/10.1016/j.plantsci.2020.110746
SN  - 0168-9452
SN  - 1873-2259
VL  - 303
PB  - Elsevier Science
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - Wendt, Martin
A1  - Senftleben, Nele
A1  - Gros, Patrick
A1  - Schmitt, Thomas
T1  - Coping with environmental extremes
BT  - population ecology and behavioural adaptation of Erebia pronoe, an Alpine butterfly species
JF  - Insects : open access journal
N2  - Simple Summary:& nbsp;High alpine meadows are home to numerous endemic butterfly species. A combination of climate change and changes in agricultural practices has led to a severe decline in many species. A seemingly unaffected representative of this habitat is Erebia pronoe. We studied the behaviour, resource use and population structure of this species to explain its resilience and estimate its future survival potential. This species shows pronounced protandry in combination with serial eclosion. Males were significantly more active and mobile and were also caught significantly more often than females, resulting in a pronounced shift in sex ratio in the predicted population structure. The adults use a wide range of nectar plants and establish homeranges in areas of high habitat quality. Thus, Erebia pronoe adults use a wide array of resources combined with a slight specialisation to avoid niche overlap with closely related species. The resulting ecological flexibility seems to be an adaptation to unpredictable environmental conditions, which should be the result of a long-lasting adaptation process. Moreover, the combination of opportunism and modest specialisation should also be a good basis for coping with future changes caused by climate and land-use change.</p> <br /> <br></p> <br /> A mark-recapture study of the nominotypical Erebia pronoe in the Alps was conducted to survey its ecological demands and characteristics. Population structure analysis revealed a combination of protandry (one-week earlier eclosion of males) and serial eclosion. Significant differences between both sexes were found in population density (males: 580/ha & PLUSMN; 37 SE; females: 241/ha & PLUSMN; 66 SE), sex-ratio (2.4) and behaviour (57.7 vs. 11.9% flying). Both sexes used a wide range of nectar plants (Asteraceae, 77.3%; Dipsacaceae, 12.3%; Gentianaceae, 9.7%). The use of nectar plants shows a non-specific spectrum, which, however, completely avoids overlap with the locally co-occurring species Erebia nivalis. Movement patterns show the establishment of homeranges, which significantly limits the migration potential. Due to its broad ecological niche, E. pronoe will probably be able to react plastically to the consequences of climate change. The formation of high population densities, the unconcerned endangerment status, the unspecific resource spectrum and the sedentary character of the species make E. pronoe a potential indicator of the quality and general resource occurrence of alpine rupicolous grasslands.
KW  - mark-release-recapture
KW  - movement patterns
KW  - opportunistic behaviour
KW  - partial protandry
KW  - population demography
Y1  - 2021
U6  - https://doi.org/10.3390/insects12100896
SN  - 2075-4450
VL  - 12
IS  - 10
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Angeleska, Angela
A1  - Omranian, Sara
A1  - Nikoloski, Zoran
T1  - Coherent network partitions
BT  - Characterizations with cographs and prime graphs
JF  - Theoretical computer science : the journal of the EATCS
N2  - We continue to study coherent partitions of graphs whereby the vertex set is partitioned into subsets that induce biclique spanned subgraphs. The problem of identifying the minimum number of edges to obtain biclique spanned connected components (CNP), called the coherence number, is NP-hard even on bipartite graphs. Here, we propose a graph transformation geared towards obtaining an O (log n)-approximation algorithm for the CNP on a bipartite graph with n vertices. The transformation is inspired by a new characterization of biclique spanned subgraphs. In addition, we study coherent partitions on prime graphs, and show that finding coherent partitions reduces to the problem of finding coherent partitions in a prime graph. Therefore, these results provide future directions for approximation algorithms for the coherence number of a given graph.
KW  - Graph partitions
KW  - Network clustering
KW  - Cographs
KW  - Coherent partition
KW  - Prime graphs
Y1  - 2021
U6  - https://doi.org/10.1016/j.tcs.2021.10.002
SN  - 0304-3975
VL  - 894
SP  - 3
EP  - 11
PB  - Elsevier
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - Yan, Jiawei
A1  - Frøkjær, Emil Egede
A1  - Engelbrekt, Christian
A1  - Leimkühler, Silke
A1  - Ulstrup, Jens
A1  - Wollenberger, Ulla
A1  - Xiao, Xinxin
A1  - Zhang, Jingdong
T1  - Voltammetry and single-molecule in situ scanning tunnelling microscopy of the redox metalloenzyme human sulfite oxidase
JF  - ChemElectroChem
N2  - Human sulfite oxidase (hSO) is a homodimeric two-domain enzyme central in the biological sulfur cycle. A pyranopterin molybdenum cofactor (Moco) is the catalytic site and a heme b(5) group located in the N-terminal domain. The two domains are connected by a flexible linker region. Electrons produced at the Moco in sulfite oxidation, are relayed via heme b(5) to electron acceptors or an electrode surface. Inter-domain conformational changes between an open and a closed enzyme conformation, allowing "gated" electron transfer has been suggested. We first recorded cyclic voltammetry (CV) of hSO on single-crystal Au(111)-electrode surfaces modified by self-assembled monolayers (SAMs) both of a short rigid thiol, cysteamine and of a longer structurally flexible thiol, omega-amino-octanethiol (AOT). hSO on cysteamine SAMs displays a well-defined pair of voltammetric peaks around -0.207 V vs. SCE in the absence of sulfite substrate, but no electrocatalysis. hSO on AOT SAMs displays well-defined electrocatalysis, but only "fair" quality voltammetry in the absence of sulfite. We recorded next in situ scanning tunnelling spectroscopy (STS) of hSO on AOT modified Au(111)-electrodes, disclosing, a 2-5 % surface coverage of strong molecular scale contrasts, assigned to single hSO molecules, notably with no contrast difference in the absence and presence of sulfite. In situ STS corroborated this observation with a sigmoidal tunnelling current/overpotential correlation.
KW  - cyclic voltammetry
KW  - human sulfite oxidase
KW  - in  situ scanning
KW  - tunnelling spectroscopy
KW  - self-assembled molecular monolayers
KW  - single-crystal gold electrodes
Y1  - 2021
U6  - https://doi.org/10.1002/celc.202001258
SN  - 2196-0216
VL  - 8
IS  - 1
SP  - 164
EP  - 171
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Tadjoung Waffo, Armel Franklin
A1  - Mitrova, Biljana
A1  - Tiedemann, Kim
A1  - Iobbi-Nivol, Chantal
A1  - Leimkühler, Silke
A1  - Wollenberger, Ulla
T1  - Electrochemical trimethylamine n-oxide biosensor with enzyme-based oxygen-scavenging membrane for long-term operation under ambient air
JF  - Biosensors : open access journal
N2  - An amperometric trimethylamine N-oxide (TMAO) biosensor is reported, where TMAO reductase (TorA) and glucose oxidase (GOD) and catalase (Cat) were immobilized on the electrode surface, enabling measurements of mediated enzymatic TMAO reduction at low potential under ambient air conditions. The oxygen anti-interference membrane composed of GOD, Cat and polyvinyl alcohol (PVA) hydrogel, together with glucose concentration, was optimized until the O-2 reduction current of a Clark-type electrode was completely suppressed for at least 3 h. For the preparation of the TMAO biosensor, Escherichia coli TorA was purified under anaerobic conditions and immobilized on the surface of a carbon electrode and covered by the optimized O-2 scavenging membrane. The TMAO sensor operates at a potential of -0.8 V vs. Ag/AgCl (1 M KCl), where the reduction of methylviologen (MV) is recorded. The sensor signal depends linearly on TMAO concentrations between 2 mu M and 15 mM, with a sensitivity of 2.75 +/- 1.7 mu A/mM. The developed biosensor is characterized by a response time of about 33 s and an operational stability over 3 weeks. Furthermore, measurements of TMAO concentration were performed in 10% human serum, where the lowest detectable concentration is of 10 mu M TMAO.
KW  - trimethylamine N-oxide
KW  - biosensor
KW  - TMAO-reductase
KW  - oxygen scavenger
KW  - immobilized enzyme
KW  - multienzyme electrode
KW  - viologen
Y1  - 2021
U6  - https://doi.org/10.3390/bios11040098
SN  - 2079-6374
VL  - 11
IS  - 4
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Scheffler, Christiane
A1  - Hermanussen, Michael
A1  - Rogol, Alan D.
T1  - Stunting
BT  - historical lessons that catch-up growth tells us for mapping growth restoration
JF  - Archives of disease in childhood : a peer review journal for health professionals and researchers covering conception to adolescence
Y1  - 2020
U6  - https://doi.org/10.1136/archdischild-2020-319240
SN  - 0003-9888
SN  - 1468-2044
VL  - 106
IS  - 8
SP  - 819
EP  - 820
PB  - BMJ Publishing Group
CY  - London
ER  - 
TY  - JOUR
A1  - Sandhage-Hofmann, Alexandra
A1  - Linstädter, Anja
A1  - Kindermann, Liana
A1  - Angombe, Simon
A1  - Amelung, Wulf
T1  - Conservation with elevated elephant densities sequesters carbon in soils despite losses of woody biomass
JF  - Global change biology
N2  - Nature conservation and restoration in terrestrial ecosystems is often focused on increasing the numbers of megafauna, expecting them to have positive impacts on ecological self-regulation processes and biodiversity. In sub-Saharan Africa, conservation efforts also aspire to protect and enhance biodiversity with particular focus on elephants. However, elephant browsing carries the risk of woody biomass losses. In this context, little is known about how increasing elephant numbers affects carbon stocks in soils, including the subsoils. We hypothesized that (1) increasing numbers of elephants reduce tree biomass, and thus the amount of C stored therein, resulting (2) in a loss of soil organic carbon (SOC). If true, a negative carbon footprint could limit the sustainability of elephant conservation from a global carbon perspective. To test these hypotheses, we selected plots of low, medium, and high elephant densities in two national parks and adjacent conservancies in the Namibian component of the Kavango Zambezi Transfrontier Area (KAZA), and quantified carbon storage in both woody vegetation and soils (1 m). Analyses were supplemented by the assessment of soil carbon isotopic composition. We found that increasing elephant densities resulted in a loss of tree carbon storage by 6.4 t ha(-1). However, and in contrast to our second hypothesis, SOC stocks increased by 4.7 t ha(-1) with increasing elephant densities. These higher SOC stocks were mainly found in the topsoil (0-30 cm) and were largely due to the formation of SOC from woody biomass. A second carbon input source into the soils was megaherbivore dung, which contributed with 0.02-0.323 t C ha(-1) year(-1) to ecosystem carbon storage in the low and high elephant density plots, respectively. Consequently, increasing elephant density does not necessarily lead to a negative C footprint, as soil carbon sequestration and transient C storage in dung almost compensate for losses in tree biomass.
KW  - carbon sequestration
KW  - conservation
KW  - elephants
KW  - soil organic carbon
KW  - woody biomass
Y1  - 2021
U6  - https://doi.org/10.1111/gcb.15779
SN  - 1354-1013
SN  - 1365-2486
VL  - 27
IS  - 19
SP  - 4601
EP  - 4614
PB  - Blackwell Science
CY  - Oxford [u.a.]
ER  - 
TY  - JOUR
A1  - Kindermann, Liana
A1  - Dobler, Magnus
A1  - Niedeggen, Daniela
A1  - Linstädter, Anja
T1  - A new protocol for estimation of woody aboveground biomass in disturbance-prone ecosystems
JF  - Ecological indicators : integrating monitoring, assessment and management
N2  - Almost one third of global drylands are open forests and savannas, which are typically shaped by frequent natural disturbances such as wildfire and herbivory. Studies on ecosystem functions and services of woody vegetation require robust estimates of aboveground biomass (AGB). However, most methods have been developed for comparatively undisturbed forest ecosystems. As they are not tailored to accurately quantify AGB of small and irregular growth forms, their application on these growth forms may lead to unreliable or even biased AGB estimates in disturbance-prone dryland ecosystems. Moreover, these methods cannot quantify AGB losses caused by disturbance agents. Here we propose a methodology to estimate individual-and stand-level woody AGB in disturbance-prone ecosystems. It consists of flexible field sampling routines and estimation workflows for six growth classes, delineated by size and damage criteria. It also comprises a detailed damage assessment, harnessing the ecological archive of woody growth for past disturbances. 

Based on large inventories collected along steep gradients of elephant disturbances in African dryland ecosystems, we compared the AGB estimates generated with our proposed method against estimates from a less adapted forest inventory method. We evaluated the necessary stepwise procedures of method adaptation and analyzed each step's effect on stand-level AGB estimation. We further explored additional advantages of our proposed method with regard to disturbance impact quantification. Results indicate that a majority of growth forms and individuals in savanna vegetation could only be assessed if methods of AGB estimation were adapted to the conditions of a disturbance-prone ecosystem. Furthermore, our damage assessment demonstrated that one third to half of all woody AGB was lost to disturbances. Consequently, less adapted methods may be insufficient and are likely to render inaccurate AGB estimations.

Our proposed method has the potential to accurately quantify woody AGB in disturbance-prone ecosystems, as well as AGB losses. Our method is more time consuming than conventional allometric approaches, yet it can cover sufficient areas within reasonable timespans, and can also be easily adapted to alternative sampling schemes.
KW  - Damage assessment
KW  - Disturbance impacts
KW  - Tree growth classes
KW  - Method
KW  - comparison
KW  - Flexible sampling strategy
KW  - Tree allometry
KW  - Woody
KW  - aboveground biomass
Y1  - 2021
U6  - https://doi.org/10.1016/j.ecolind.2021.108466
SN  - 1470-160X
SN  - 1872-7034
VL  - 135
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Soeriyadi, Angela H.
A1  - Ongley, Sarah E.
A1  - Kehr, Jan-Christoph
A1  - Pickford, Russel
A1  - Dittmann, Elke
A1  - Neilan, Brett A.
T1  - Tailoring enzyme stringency masks the multispecificity of a lyngbyatoxin (indolactam alkaloid) nonribosomal peptide synthetase
JF  - ChemBioChem
N2  - Indolactam alkaloids are activators of protein kinase C (PKC) and are of pharmacological interest for the treatment of pathologies involving PKC dysregulation. The marine cyanobacterial nonribosomal peptide synthetase (NRPS) pathway for lyngbyatoxin biosynthesis, which we previously expressed in E. coli, was studied for its amenability towards the biosynthesis of indolactam variants. Modification of culture conditions for our E. coli heterologous expression host and analysis of pathway products suggested the native lyngbyatoxin pathway NRPS does possess a degree of relaxed specificity. Site-directed mutagenesis of two positions within the adenylation domain (A-domain) substrate-binding pocket was performed, resulting in an alteration of substrate preference between valine, isoleucine, and leucine. We observed relative congruence of in vitro substrate activation by the LtxA NRPS to in vivo product formation. While there was a preference for isoleucine over leucine, the substitution of alternative tailoring domains may unveil the true in vivo effects of the mutations introduced herein.
KW  - a domain
KW  - indolactams
KW  - MbtH
KW  - natural products
KW  - teleocidin
Y1  - 2021
U6  - https://doi.org/10.1002/cbic.202100574
SN  - 1439-4227
SN  - 1439-7633
VL  - 23
IS  - 3
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Malchow, Anne-Kathleen
A1  - Bocedi, Greta
A1  - Palmer, Stephen C. F.
A1  - Travis, Justin M. J.
A1  - Zurell, Damaris
T1  - RangeShiftR
BT  - an R package for individual-based simulation of spatial changes
JF  - Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos
N2  - Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.
KW  - connectivity
KW  - conservation
KW  - dispersal
KW  - evolution
KW  - population dynamics
KW  - range dynamics
Y1  - 2021
U6  - https://doi.org/10.1111/ecog.05689
SN  - 1600-0587
VL  - 44
IS  - 10
SP  - 1443
EP  - 1452
PB  - Wiley-Blackwell
CY  - Oxford [u.a.]
ER  - 
TY  - JOUR
A1  - Zhang, Xiaorong
A1  - Caserta, Giorgio
A1  - Yarman, Aysu
A1  - Supala, Eszter
A1  - Tadjoung Waffo, Armel Franklin
A1  - Wollenberger, Ulla
A1  - Gyurcsanyi, Robert E.
A1  - Zebger, Ingo
A1  - Scheller, Frieder W.
T1  - "Out of Pocket" protein binding
BT  - a dilemma of epitope imprinted polymers revealed for human hemoglobin
JF  - Chemosensors
N2  - The epitope imprinting approach applies exposed peptides as templates to synthesize Molecularly Imprinted Polymers (MIPs) for the recognition of the parent protein. While generally the template protein binding to such MIPs is considered to occur via the epitope-shaped cavities, unspecific interactions of the analyte with non-imprinted polymer as well as the detection method used may add to the complexity and interpretation of the target rebinding. To get new insights on the effects governing the rebinding of analytes, we electrosynthesized two epitope-imprinted polymers using the N-terminal pentapeptide VHLTP-amide of human hemoglobin (HbA) as the template. MIPs were prepared either by single-step electrosynthesis of scopoletin/pentapeptide mixtures or electropolymerization was performed after chemisorption of the cysteine extended VHLTP peptide. Rebinding of the target peptide and the parent HbA protein to the MIP nanofilms was quantified by square wave voltammetry using a redox probe gating, surface enhanced infrared absorption spectroscopy, and atomic force microscopy. While binding of the pentapeptide shows large influence of the amino acid sequence, all three methods revealed strong non-specific binding of HbA to both polyscopoletin-based MIPs with even higher affinities than the target peptides.
KW  - Molecularly Imprinted Polymers
KW  - epitope imprinting
KW  - non-specific
KW  - binding
KW  - redox gating
KW  - SEIRA spectroelectrochemistry
Y1  - 2021
U6  - https://doi.org/10.3390/chemosensors9060128
SN  - 2227-9040
VL  - 9
IS  - 6
PB  - MDPI
CY  - Basel
ER  - 
TY  - CHAP
A1  - Dennis, Alice B.
A1  - Inäbnit, Thomas
T1  - Physiological and genomic variation among cryptic species of a marsh snail (Melampus bidentatus)
T2  - Integrative and comparative biology / Society of Integrative and Comparative Biology
Y1  - 2021
U6  - https://doi.org/10.1093/icb/icab001
SN  - 1540-7063
SN  - 1557-7023
VL  - 61
SP  - E195
EP  - E196
PB  - Oxford University Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Qiu, Liang
A1  - Zhang, Haoran
A1  - Bick, Thomas
A1  - Martin, Johannes
A1  - Wendler, Petra
A1  - Böker, Alexander
A1  - Glebe, Ulrich
A1  - Xing, Chengfen
T1  - Construction of highly ordered glyco-inside nano-assemblies through RAFT dispersion polymerization of galactose-decorated monomer
JF  - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition
N2  - Glyco-assemblies derived from amphiphilic sugar-decorated block copolymers (ASBCs) have emerged prominently due to their wide application, for example, in biomedicine and as drug carriers. However, to efficiently construct these glyco-assemblies is still a challenge. Herein, we report an efficient technology for the synthesis of glyco-inside nano-assemblies by utilizing RAFT polymerization of a galactose-decorated methacrylate for polymerization-induced self-assembly (PISA). Using this approach, a series of highly ordered glyco-inside nano-assemblies containing intermediate morphologies were fabricated by adjusting the length of the hydrophobic glycoblock and the polymerization solids content. A specific morphology of complex vesicles was captured during the PISA process and the formation mechanism is explained by the morphology of its precursor and intermediate. Thus, this method establishes a powerful route to fabricate glyco-assemblies with tunable morphologies and variable sizes, which is significant to enable the large-scale fabrication and wide application of glyco-assemblies.
KW  - galactose-decorated monomer
KW  - glyco-inside nano-assemblies
KW  - morphology
KW  - evolution
KW  - PISA
KW  - RAFT dispersion polymerization
Y1  - 2021
U6  - https://doi.org/10.1002/anie.202015692
SN  - 1433-7851
SN  - 1521-3773
VL  - 60
IS  - 20
SP  - 11098
EP  - 11103
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - De Sousa Mota, Cristiano
A1  - Diniz, Ana
A1  - Coelho, Catarina
A1  - Santos-Silva, Teresa
A1  - Esmaeeli Moghaddam Tabalvandani, Mariam
A1  - Leimkühler, Silke
A1  - Cabrita, Eurico J.
A1  - Marcelo, Filipa
A1  - Romão, Maria João
T1  - Interrogating the inhibition mechanisms of human aldehyde oxidase by X-ray crystallography and NMR spectroscopy
BT  - the raloxifene case
JF  - Journal of medicinal chemistry / American Chemical Society
N2  - Human aldehyde oxidase (hAOX1) is mainly present in the liver and has an emerging role in drug metabolism, since it accepts a wide range of molecules as substrates and inhibitors. Herein, we employed an integrative approach by combining NMR, X-ray crystallography, and enzyme inhibition kinetics to understand the inhibition modes of three hAOX1 inhibitors-thioridazine, benzamidine, and raloxifene. These integrative data indicate that thioridazine is a noncompetitive inhibitor, while benzamidine presents a mixed type of inhibition. Additionally, we describe the first crystal structure of hAOX1 in complex with raloxifene. Raloxifene binds tightly at the entrance of the substrate tunnel, stabilizing the flexible entrance gates and elucidating an unusual substrate-dependent mechanism of inhibition with potential impact on drug-drug interactions. This study can be considered as a proof-of-concept for an efficient experimental screening of prospective substrates and inhibitors of hAOX1 relevant in drug discovery.
Y1  - 2021
U6  - https://doi.org/10.1021/acs.jmedchem.1c01125
SN  - 0022-2623
SN  - 1520-4804
VL  - 64
IS  - 17
SP  - 13025
EP  - 13037
PB  - American Chemical Society
CY  - Washington
ER  - 
TY  - JOUR
A1  - Brandes, Stefanie
A1  - Sicks, Florian
A1  - Berger, Anne
T1  - Behaviour classification on giraffes (Giraffa camelopardalis) using machine learning algorithms on triaxial acceleration data of two commonly used GPS devices and its possible application for their management and conservation
JF  - Sensors
N2  - Averting today's loss of biodiversity and ecosystem services can be achieved through conservation efforts, especially of keystone species. Giraffes (Giraffa camelopardalis) play an important role in sustaining Africa's ecosystems, but are 'vulnerable' according to the IUCN Red List since 2016. Monitoring an animal's behavior in the wild helps to develop and assess their conservation management. One mechanism for remote tracking of wildlife behavior is to attach accelerometers to animals to record their body movement. We tested two different commercially available high-resolution accelerometers, e-obs and Africa Wildlife Tracking (AWT), attached to the top of the heads of three captive giraffes and analyzed the accuracy of automatic behavior classifications, focused on the Random Forests algorithm. For both accelerometers, behaviors of lower variety in head and neck movements could be better predicted (i.e., feeding above eye level, mean prediction accuracy e-obs/AWT: 97.6%/99.7%; drinking: 96.7%/97.0%) than those with a higher variety of body postures (such as standing: 90.7-91.0%/75.2-76.7%; rumination: 89.6-91.6%/53.5-86.5%). Nonetheless both devices come with limitations and especially the AWT needs technological adaptations before applying it on animals in the wild. Nevertheless, looking at the prediction results, both are promising accelerometers for behavioral classification of giraffes. Therefore, these devices when applied to free-ranging animals, in combination with GPS tracking, can contribute greatly to the conservation of giraffes.
KW  - giraffe
KW  - triaxial acceleration
KW  - machine learning
KW  - random forests
KW  - behavior classification
KW  - giraffe conservation
Y1  - 2021
U6  - https://doi.org/10.3390/s21062229
SN  - 1424-8220
VL  - 21
IS  - 6
PB  - MDPI
CY  - Basel
ER  -