### Recent Submissions

• Journal Article

#### Studded leather collars are very effective in protecting cattle from leopard (Panthera pardus) attacks ﻿

Ecological Solutions and Evidence 2020; 1(1) p.1-9: Art. e12013
1. Human‐wildlife conflicts are widespread, particularly with big cats which can kill domestic livestock and create a counteraction between conservation and local livelihoods, especially near protected areas. Minimisation of livestock losses caused by big cats and other predators is essential to mitigate conflicts and promote socially acceptable conservation. As big cats usually kill by throat bites, protective collars represent a potentially effective non‐lethal intervention to prevent livestock depredation, yet the application and effectiveness estimation of these tools are very limited. 2. In this study, for the first time we measured the effectiveness of studded leather collars in protecting cattle from leopard (Panthera pardus) attacks. We conducted a randomised controlled experiment during 14 months to collar 202 heads and leave uncollared 258 heads grazing in forests and belonging to 27 owners from eight villages near three protected areas in Mazandaran Province, northern Iran. 3. Our results show that none of collared cattle and nine uncollared cattle were lost to leopard depredation, meaning that collars caused a zero relative risk of damage and a perfect 100% damage reduction. Most losses occurred in summer and autumn due to lush vegetation attracting more cattle, long daytime allowing movements deep into leopard habitats and dense cover favouring leopard hunts from ambush. Losses were recorded in only six owners and four villages, suggesting local rarity and patchy distribution of leopards. 4. We suggest that collars can be successfully applied to cattle freely grazing in habitats of leopards or other felids for a long time and thus remaining persistently exposed to depredation. As grazing cattle are usually not supervised by shepherds or dogs, collars can be the only practical protection tool. Production and sales of collars can become a sustainable small‐scale business for farmers to further boost conservation and rural livelihoods.
• Journal Article

#### On the Leucanthemopsis alpina (L.) Heywood growing in the Illyrian region ﻿

PhytoKeys 2020; 161 p.27-40
Leucanthemopsis alpina (L.) Heywood (Asteraceae, Anthemideae) is a small, caespitose plant growing in high alpine environments in all the main southern European mountain ranges. However, the species status in the Balkan Peninsula (and especially in the Dinaric Alps) is not very well known. Surrounding this area, different L. alpina subspecies are found in the Eastern Alps and in the Carpathians. These subspecies differ from one another, both morphologically and in chromosome number. The present study aims to better characterise the populations of L. alpina in the Illyrian and Balkan regions by undertaking a comprehensive survey of herbarium collections for the species in this area, by applying flow cytometry for ploidy determination and by sequencing of two chloroplast markers. Results from our investigation suggest that the only population of the species in the Dinaric Alps is found in the Vranica Mts (Bosnia and Herzegovina). This population consists of diploid plants (unlike tetraploid populations from the Eastern Alps) that are slightly distinct genetically from those of the subspecies growing in the Eastern Alps and the Tatra Mts. Both the ploidy and their genetic distinction indicate that Vranica Mts most probably served as a refugium for the species during the Pleistocene glaciations. Considering its isolated geographical range and its genetic distinction, the population of L. alpina growing in the Vranica Mts should be considered as a separate subspecies.
• Journal Article

#### Quantitative Modelling and Perspective Taking: Two Competencies of Decision Making for Sustainable Development ﻿

Sustainability 2020; 12(17) p.1-32: Art. 6980
Land use change, natural resource use and climate change are challenging Sustainable Development issues (SDGs 13–15). Fostering the competencies to deal with such issues is one core task for current educational endeavors. Among these competencies, decision-making competencies are central. In detail, we investigate how learners evaluate alternative decision-making options to improve existing competence models. We exemplify our competence modelling approach using the designation of a Marine Protected Area. The cross-sectional sample consists of secondary school students and student teachers (N = 760). Partial Credit modelling shows that quantitative modelling of decision-making options is a different competence dimension than perspective taking if contextualized for Sustainable Development. In quantitative modelling, mathematical modelling is used to evaluate and reflect on decision-making options. Perspective taking covers the ability to consider different normative perspectives on Sustainable Development issues. Both dimensions show plausible (latent) correlations with related constructs within the nomological net, i.e., with qualitative arguing, economic literacy, mathematical competencies, reading competencies and analytical problem solving. Furthermore, person-abilities increase with level of education for both dimensions. The identified competence dimensions quantitative modelling and perspective taking were successfully modelled and shown to be distinct; the resulting measuring instrument is reliable and valid.
• Journal Article

#### Quantitative Modelling and Perspective Taking: Two Competencies of Decision Making for Sustainable Development ﻿

Sustainability 2020; 12(17) p.1-32: Art. 6980
Land use change, natural resource use and climate change are challenging Sustainable Development issues (SDGs 13–15). Fostering the competencies to deal with such issues is one core task for current educational endeavors. Among these competencies, decision-making competencies are central. In detail, we investigate how learners evaluate alternative decision-making options to improve existing competence models. We exemplify our competence modelling approach using the designation of a Marine Protected Area. The cross-sectional sample consists of secondary school students and student teachers (N = 760). Partial Credit modelling shows that quantitative modelling of decision-making options is a different competence dimension than perspective taking if contextualized for Sustainable Development. In quantitative modelling, mathematical modelling is used to evaluate and reflect on decision-making options. Perspective taking covers the ability to consider different normative perspectives on Sustainable Development issues. Both dimensions show plausible (latent) correlations with related constructs within the nomological net, i.e., with qualitative arguing, economic literacy, mathematical competencies, reading competencies and analytical problem solving. Furthermore, person-abilities increase with level of education for both dimensions. The identified competence dimensions quantitative modelling and perspective taking were successfully modelled and shown to be distinct; the resulting measuring instrument is reliable and valid.
• Journal Article

#### Assessing the Effect of Diesel Fuel on the Seed Viability and Germination of Medicago sativa Using the Event-Time Model ﻿

Plants 2020; 9(9) p.1-9: Art. 1062
The remediation of contaminated sites using plant-based techniques has gained increasing attention in recent decades. However, information on the effects of contaminant imbibition on seed viability and germination rates are often lacking in the literature. To this end, our research investigated, by means of an event-time model, the effect of diesel fuel imbibition on the seed viability and germination rate of Medicago sativa, a plant species with great potential for remediation of organic contaminants. The event-time model provided an accurate and biologically relevant method for analysing germination data. Our results reveal that the direct imbibition of diesel fuel by M. sativa seeds for ≤48 h, or their exposure to soil diesel fuel concentrations of 0–10 g/kg diesel fuel, affects their germination rates, as shown by increasing t50 values from 90.6 (±2.78) to 114.2 (±2.67) hours, without significantly affecting seed viability. On the other hand, diesel fuel imbibition of longer duration, or the exposure of M. sativa seeds to ≥20 g/kg diesel fuel-contaminated soils, leads to no further effect on time to seed emergence. Instead, these conditions compromise seed viability, resulting in a decrease in the proportion of germinated seeds from 0.91 (±0.03) in 10 g/kg diesel fuel contaminated soil to 0.84 (±0.04) and 0.70 (±0.05) in 20 and 30 g/kg diesel fuel-contaminated soils, respectively. The fact that low concentrations of diesel fuel and 0–48 h of direct imbibition delayed seed emergence without adversely affecting the percentage of viable seeds suggests that this inhibitory effect on germination at low diesel fuel exposure could be attributed more to physical constraints rather than biological damage on the seeds. The models used in this study provide an accurate and biologically relevant method for the analyses of germination data. This is vital since expensive germination experiments, be it in the field of toxicology or agriculture, deserve to be accurately analysed.
• Journal Article

#### Rainforest conversion to smallholder plantations of rubber or oil palm leads to species loss and community shifts in canopy ants (Hymenoptera: Formicidae) ﻿

Myrmecological News 2020; 30 p.175-186
Currently, our understanding of the responses of ant communities under rainforest conversion to cash crops in SE Asia is based on comparisons of primary rainforests to large company-owned oil palm estates in Malaysian Borneo and a few comparisons of natural forests to rubber plantations in Thailand and China. In Indonesia, second largest rubber producer and largest oil palm producer worldwide, the vast majority of its rubber economy and almost half its oil palm acreage relies on smallholder farmers. This study compares canopy ant communities among four land-use systems in Jambi Province, Sumatra, Indonesia: 1) lowland rainforest, 2) jungle rubber (i.e., extensive rubber cultivation), and monoculture plantations of 3) rubber or 4) oil palm. Smallholder plantations of rubber and oil palm support less than 25% of the abundance and less than 50% of the canopy ant species richness in lowland rainforest, with intermediate levels in jungle rubber. Canopy ant communities from rainforest and jungle rubber were similar and differed from those in monoculture rubber and oil palm plantations, which each hosted distinct communities. Nestedness and turnover also differed between rainforest and jungle rubber on the one hand and rubber and oil palm on the other. This pattern was in part due to significantly greater proportions of tramp ants in the monoculture plantations: While virtually absent in forest (< 1%), six tramp ant species accounted for 9.8% of the collected ant individuals in jungle rubber, 26.6% in rubber and 41.1% in oil palm plantations (up to 88.1% in one studied plantation). Overall, this study improves our understanding of the effects of rainforest conversion to cash crop plantations of rubber and oil palm on ant communities by incorporating smallholder systems in one of the most important regions for oil palm and rubber production worldwide.
• Journal Article

#### Trophic level and basal resource use of soil animals are hardly affected by local plant associations in abandoned arable land ﻿

Ecology and Evolution 2020; 10(15) p.8279-8288
Plants provide resources and shape the habitat of soil organisms thereby affecting the composition and functioning of soil communities. Effects of plants on soil communities are largely taxon‐dependent, but how different functional groups of herbaceous plants affect trophic niches of individual animal species in soil needs further investigation. Here, we studied the use of basal resources and trophic levels of dominating soil meso‐ and macrofauna using stable isotope ratios of carbon and nitrogen in arable fallow systems 3 and 14–16 years after abandonment. Animals were sampled from the rhizosphere of three plant species of different functional groups: a legume (Medicaco sativa), a nonlegume herb (Taraxacum officinale), and a grass (Bromus sterilis). We found virtually no consistent effects of plant identity on stable isotope composition of soil animals and on thirteen isotopic metrics that reflect general food‐web structure. However, in old fallows, the carbon isotope composition of some predatory macrofauna taxa had shifted closer to that of co‐occurring plants, which was particularly evident for Lasius, an aphid‐associated ant genus. Trophic levels and trophic‐chain lengths in food webs were similar across plant species and fallow ages. Overall, the results suggest that variations in local plant diversity of grassland communities may little affect the basal resources and the trophic level of prey consumed by individual species of meso‐ and macrofauna belowground. By contrast, successional changes in grassland communities are associated with shifts in the trophic niches of certain species, reflecting establishment of trophic interactions with time, which shapes the functioning and stability of soil food webs.
• Journal Article

#### Genotyping by Sequencing Reads of 20 Vicia faba Lines with High and Low Vicine and Convicine Content ﻿

Data 2020; 5(3) p.1-4: Art. 63
The grain faba bean (Vicia faba) which belongs to the family of the Leguminosae, is a crop that is grown worldwide for consumption by humans and livestock. Despite being a rich source of plant-based protein and various agro-ecological advantages its usage is limited due to its anti-nutrients in the form of the seed-compounds vicine and convicine (V+C). While markers for a low V+C content exist the underlying pathway and the responsible genes have remained unknown for a long time and only recently a possible pathway and enzyme were found. Genetic research into Vicia faba is difficult due to the lack of a reference genome and the near exclusivity of V+C to the species. Here, we present sequence reads obtained through genotyping-by-sequencing of 20 Vicia faba lines with varying V+C contents. For each line, ∼3 million 150 bp paired end reads are available. This data can be useful in the genomic research of Vicia faba in general and its V+C content in particular.
• Journal Article

#### Verticillium longisporum Elicits Media-Dependent Secretome Responses With Capacity to Distinguish Between Plant-Related Environments ﻿

Frontiers in Microbiology 2020; 11 p.1-21: Art. 1876
Verticillia cause a vascular wilt disease affecting a broad range of economically valuable crops. The fungus enters its host plants through the roots and colonizes the vascular system. It requires extracellular proteins for a successful plant colonization. The exoproteomes of the allodiploid Verticillium longisporum upon cultivation in different media or xylem sap extracted from its host plant Brassica napus were compared. Secreted fungal proteins were identified by label free liquid chromatography-tandem mass spectrometry screening. V. longisporum induced two main secretion patterns. One response pattern was elicited in various non-plant related environments. The second pattern includes the exoprotein responses to the plant-related media, pectin-rich simulated xylem medium and pure xylem sap, which exhibited similar but additional distinct features. These exoproteomes include a shared core set of 221 secreted and similarly enriched fungal proteins. The pectin-rich medium significantly induced the secretion of 143 proteins including a number of pectin degrading enzymes, whereas xylem sap triggered a smaller but unique fungal exoproteome pattern with 32 enriched proteins. The latter pattern included proteins with domains of known pathogenicity factors, metallopeptidases and carbohydrate-active enzymes. The most abundant proteins of these different groups are the necrosis and ethylene inducing-like proteins Nlp2 and Nlp3, the cerato-platanin proteins Cp1 and Cp2, the metallopeptidases Mep1 and Mep2 and the carbohydrate-active enzymes Gla1, Amy1 and Cbd1. Their pathogenicity contribution was analyzed in the haploid parental strain V. dahliae. Deletion of the majority of the corresponding genes caused no phenotypic changes during ex planta growth or invasion and colonization of tomato plants. However, we discovered that the MEP1, NLP2, and NLP3 deletion strains were compromised in plant infections. Overall, our exoproteome approach revealed that the fungus induces specific secretion responses in different environments. The fungus has a general response to non-plant related media whereas it is able to fine-tune its exoproteome in the presence of plant material. Importantly, the xylem sap-specific exoproteome pinpointed Nlp2 and Nlp3 as single effectors required for successful V. dahliae colonization.
• Journal Article

#### Land-Use and Health Issues in Malagasy Primary Education—A Delphi Study ﻿

Sustainability 2020; 12(15) p.1-31: Art. 6212
Education for Sustainable Development (ESD) plays a key role in Sustainable Development. In low-income countries like Madagascar, this key role is particularly relevant to primary education. However, the curricula lack a comprehensive ESD approach that incorporates regional issues. In Madagascar, sustainable land-use practices (Sustainable Development Goals 12, 15) and health prevention (SDGs 2, 3, 6) are educational challenges. Procedural knowledge allows problem-solving regarding unsustainable developments. We adapted and further developed a measure of ESD-relevant procedural knowledge. Considering curricula, sustainability standards, research, and a two-round Delphi study (n = 34 experts), we identified regionally relevant land-use practices and health-protective behavior. After the experts rated the effectiveness and possibility of implementation of courses of actions, we calculated an index of what to teach under given Malagasy (regional) conditions. Combined with qualitative expert comments, the study offers insights into expert views on land-use and health topics: For example, when teaching ESD in Northeast Madagascar, sustainable management of cultivation and soil is suitable, particularly when linked to vanilla production. Health-protective behavior is ultimately more difficult to implement in rural than in urban areas. These results are important for further curricula development, for ESD during primary education, and because they give insights into the topics teacher education should address.
• Journal Article

#### First Complete Genome Sequences of Janthinobacterium lividum EIF1 and EIF2 and their Comparative Genome Analysis ﻿

Genome Biology and Evolution p.1-21
We present the first two complete genomes of the Janthinobacterium lividum species, namely strains EIF1 and EIF2, which both possess the ability to synthesize violacein. The violet pigment violacein is a secondary metabolite with antibacterial, antifungal, antiviral, and antitumoral properties. Both strains were isolated from environmental oligotrophic water ponds in Göttingen. The strains were phylogenetically classified by ANI analysis and showed a species assignment to Janthinobacterium lividum with 97.72% (EIF1) and 97.66% (EIF2) identity. These are the first complete genome sequences of strains belonging to the species Janthinobacterium lividum. The genome of strain EIF1 consists of one circular chromosome (6,373,589 bp) with a GC-content of 61.98%. The genome contains 5,551 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA. The genome of EIF2 comprises one circular chromosome (6,399,352 bp) with a GC-content of 61.63% and a circular plasmid p356839 (356,839 bp) with a GC-content of 57.21%. The chromosome encodes 5,691 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA and the plasmid harbors 245 coding sequences. In addition to the highly conserved chromosomally encoded violacein operon, the plasmid comprises a non-ribosomal peptide synthetase cluster (NRPS) with similarity to xenoamicin, which is a bioactive compound effective against protozoan parasites.
• Journal Article

#### Reference Values of the QOLIBRI from General Population Samples in the United Kingdom and The Netherlands ﻿

Journal of Clinical Medicine 2020; 9(7) p.1-29: Art. 2100
The Quality of Life after Traumatic Brain Injury (QOLIBRI) instrument is an internationally validated patient-reported outcome measure for assessing disease-specific health-related quality of life (HRQoL) in individuals after traumatic brain injury (TBI). However, no reference values for general populations are available yet for use in clinical practice and research in the field of TBI. The aim of the present study was, therefore, to establish these reference values for the United Kingdom (UK) and the Netherlands (NL). For this purpose, an online survey with a reworded version of the QOLIBRI for general populations was used to collect data on 4403 individuals in the UK and 3399 in the NL. This QOLIBRI version was validated by inspecting descriptive statistics, psychometric criteria, and comparability of the translations to the original version. In particular, measurement invariance (MI) was tested to examine whether the items of the instrument were understood in the same way by different individuals in the general population samples and in the TBI sample across the two countries, which is necessary in order to establish reference values. In the general population samples, the reworded QOLIBRI displayed good psychometric properties, including MI across countries and in the non-TBI and TBI samples. Therefore, differences in the QOLIBRI scores can be attributed to real differences in HRQoL. Individuals with and without a chronic health condition did differ significantly, with the latter reporting lower HRQoL. In conclusion, we provided reference values for healthy individuals and individuals with at least one chronic condition from general population samples in the UK and the NL. These can be used in the interpretation of disease-specific HRQoL assessments after TBI applying the QOLIBRI on the individual level in clinical as well as research contexts.
• Journal Article

#### Globally Abundant “Candidatus Udaeobacter” Benefits from Release of Antibiotics in Soil and Potentially Performs Trace Gas Scavenging ﻿

mSphere 2020; 5(4) p.1-17: Art. e00186-20
Verrucomicrobia affiliated with “Candidatus Udaeobacter” belong to the most abundant soil bacteria worldwide. Although the synthesis of antibiotics presumably evolved in soil, and environmental pollution with antimicrobials increases, the impact of these complex molecules on “Ca. Udaeobacter” remains to be elucidated. In this study, we demonstrate that “Ca. Udaeobacter” representatives residing in grassland as well as forest soil ecosystems show multidrug resistance and even take advantage of antibiotics release. Soils treated with up to six different antibiotics exhibited a higher “Ca. Udaeobacter” abundance than corresponding controls after 3, 8, and 20 days of incubation. In this context, we provide evidence that “Ca. Udaeobacter” representatives may utilize nutrients which are released due to antibiotic-driven lysis of other soil microbes and thereby reduce energetically expensive synthesis of required biomolecules. Moreover, genomic analysis revealed the presence of genes conferring resistance to multiple classes of antibiotics and indicated that “Ca. Udaeobacter” representatives most likely oxidize the trace gas H$_2$ to generate energy. This energy might be required for long-term persistence in terrestrial habitats, as already suggested for other dominant soil bacteria. Our study illustrates, for the first time, that globally abundant “Ca. Udaeobacter” benefits from release of antibiotics, which confers advantages over other soil bacteria and represents a so-far overlooked fundamental lifestyle feature of this poorly characterized verrucomicrobial genus. Furthermore, our study suggests that “Ca. Udaeobacter” representatives can utilize H$_2$ as an alternative electron donor. IMPORTANCE Soil bacteria have been investigated for more than a century, but one of the most dominant terrestrial groups on Earth, “Candidatus Udaeobacter,” remains elusive and largely unexplored. Its natural habitat is considered a major reservoir of antibiotics, which directly or indirectly impact phylogenetically diverse microorganisms. Here, we found that “Ca. Udaeobacter” representatives exhibit multidrug resistance and not only evade harmful effects of antimicrobials but even benefit from antibiotic pressure in soil. Therefore, “Ca. Udaeobacter” evidently affects the composition of soil resistomes worldwide and might represent a winner of rising environmental pollution with antimicrobials. In addition, our study indicates that “Ca. Udaeobacter” representatives utilize H$_2$ and thereby contribute to global hydrogen cycling. The here-reported findings provide insights into elementary lifestyle features of “Ca. Udaeobacter,” potentially contributing to its successful global dissemination.
• Journal Article

#### Testate Amoeba Species- and Trait-Based Transfer Functions for Reconstruction of Hydrological Regime in Tropical Peatland of Central Sumatra, Indonesia ﻿

Frontiers in Ecology and Evolution 2020; 8 p.1-15: Art. 225
Tropical peatlands play an important role in carbon storage and in water regulation on a landscape level. However, our understanding of their ecology and long-term hydrological dynamics remains limited. Transfer functions, constructed on the basis of biological indicators (proxies) with known ecological preferences, allow us to infer past environmental conditions and serve as a basis for prediction of future changes in peatlands. Here, we use testate amoebae to develop the first species- and functional trait-based transfer functions for the Southeast Asia. This provides a valuable tool for future reconstructions of past hydrological changes in tropical peatlands, their development, and climatic changes. Surface samples for testate amoeba analysis were taken in various biotopes along two transects across the Sungai Buluh peatland in Central Sumatra. The following environmental characteristics were measured: water table depth (WTD), light intensity, pH, total C and N concentrations. The analysis of the surface samples revealed 145 morphotypes of testate amoebae belonging to 25 genera. A significant fraction of the variance in testate amoeba morphotypes and functional trait composition was explained by WTD and pH. The wide WTD range (0–120 cm) seems more valuable for reconstruction than the extremely short pH gradient (2.5–3.8). Thus, transfer functions were developed only for WTD, based on weighted averaging model for morphotypes and multiple linear regression for functional traits. Both species- and trait-based model have a predictive ability for WTD reconstruction. For traits, the best performance of the model was reached by including five morphological traits: shell width, aperture shape, aperture invagination, shell shape and shell compression. We discuss the ecology of several taxa and highlight the traits, which reflect hydrological changes in this system. Though the hydrological preferences of some species are similar to those in high and middle latitude peatlands, we argue that latitudinal differences in morphospecies composition and variations in environmental relationships of species require the development of region-specific transfer functions. Moreover, our results indicate that ecological preferences of morphotypes within morphospecies also need to be considered and included in future studies.
• Journal Article

#### Authigenic formation of Ca-Mg carbonates in the shallow alkaline Lake Neusiedl, Austria ﻿

Biogeosciences 2020; 17(7) p.2085-2106
Despite advances regarding the microbial and organic-molecular impact on nucleation, the formation of dolomite in sedimentary environments is still incompletely understood. Since 1960, apparent dolomite formation has been reported from mud sediments of the shallow, oligohaline and alkaline Lake Neusiedl, Austria. To trace potential dolomite formation or diagenetic alteration processes in its deposits, lake water samples and sediment cores were analyzed with respect to sediment composition, hydrochemistry and bacterial community composition. Sediments comprise 20 cm of homogenous mud with 60 wt % carbonate, which overlies dark-laminated consolidated mud containing 50 wt % carbonate and plant debris. Hydrochemical measurements reveal a shift from oxic lake water with pH 9.0 to anoxic sediment pore water with pH 7.5. A decrease in SO$_2^{−4}$ with a concomitant increase in ΣH$_2$S and NH$^+_4$ from 0 to 15 cm core depth indicates anaerobic heterotrophic decomposition, including sulfate reduction. The bacterial community composition reflects the zonation indicated by the pore water chemistry, with a distinct increase in fermentative taxa below 15 cm core depth. The water column is highly supersaturated with respect to (disordered) dolomite and calcite, whereas saturation indices of both minerals rapidly approach zero in the sediment. Notably, the relative proportions of different authigenic carbonate phases and their stoichiometric compositions remain constant with increasing core depth. Hence, evidence for Ca–Mg carbonate formation or ripening to dolomite is lacking within the sediment of Lake Neusiedl. As a consequence, precipitation of high-magnesium calcite (HMC) and protodolomite does not occur in association with anoxic sediment and sulfate-reducing conditions. Instead, analytical data for Lake Neusiedl suggest that authigenic HMC and protodolomite precipitate from the supersaturated, well-mixed aerobic water column. This observation supports an alternative concept to dolomite formation in anoxic sediments, comprising Ca–Mg carbonate precipitation in the water column under aerobic and alkaline conditions.
• Journal Article

#### Non-Human Primate iPSC Generation, Cultivation, and Cardiac Differentiation under Chemically Defined Conditions ﻿

Cells 2020; 9(6) p.1-24: Art. 1349
Non-human primates (NHP) are important surrogate models for late preclinical development of advanced therapy medicinal products (ATMPs), including induced pluripotent stem cell (iPSC)-based therapies, which are also under development for heart failure repair. For effective heart repair by remuscularization, large numbers of cardiomyocytes are required, which can be obtained by efficient differentiation of iPSCs. However, NHP-iPSC generation and long-term culture in an undifferentiated state under feeder cell-free conditions turned out to be problematic. Here we describe the reproducible development of rhesus macaque (Macaca mulatta) iPSC lines. Postnatal rhesus skin fibroblasts were reprogrammed under chemically defined conditions using non-integrating vectors. The robustness of the protocol was confirmed using another NHP species, the olive baboon (Papio anubis). Feeder-free maintenance of NHP-iPSCs was essentially dependent on concurrent Wnt-activation by GSK-inhibition (Gi) and Wnt-inhibition (Wi). Generated NHP-iPSCs were successfully differentiated into cardiomyocytes using a combined growth factor/GiWi protocol. The capacity of the iPSC-derived cardiomyocytes to self-organize into contractile engineered heart muscle (EHM) was demonstrated. Collectively, this study establishes a reproducible protocol for the robust generation and culture of NHP-iPSCs, which are useful for preclinical testing of strategies for cell replacement therapies in NHP.
• Journal Article

#### Plant intraspecific functional trait variation is related to within‐habitat heterogeneity and genetic diversity in Trifolium montanum L. ﻿

Ecology and Evolution 2020; 10(11) p.5015-5033
Intraspecific trait variation (ITV), based on available genetic diversity, is one of the major means plant populations can respond to environmental variability. The study of functional trait variation and diversity has become popular in ecological research, for example, as a proxy for plant performance influencing fitness. Up to now, it is unclear which aspects of intraspecific functional trait variation (iFD$_{CV}$) can be attributed to the environment or genetics under natural conditions. Here, we examined 260 individuals from 13 locations of the rare (semi‐)dry calcareous grassland species Trifolium montanum L. in terms of iFD$_{CV}$, within‐habitat heterogeneity, and genetic diversity. The iFD$_{CV}$ was assessed by measuring functional traits (releasing height, biomass, leaf area, specific leaf area, leaf dry matter content, F$_v$/F$_m$, performance index, stomatal pore surface, and stomatal pore area index). Abiotic within‐habitat heterogeneity was derived from altitude, slope exposure, slope, leaf area index, soil depth, and further soil factors. Based on microsatellites, we calculated expected heterozygosity (He) because it best‐explained, among other indices, iFD$_{CV}$. We performed multiple linear regression models quantifying relationships among iFD$_{CV}$, abiotic within‐habitat heterogeneity and genetic diversity, and also between separate functional traits and abiotic within‐habitat heterogeneity or genetic diversity. We found that abiotic within‐habitat heterogeneity influenced iFD$_{CV}$ twice as strong compared to genetic diversity. Both aspects together explained 77% of variation in iFD$_{CV}$ ($R^2_{adj}$=.77, $F_{2,10}$ = 21.66, p < .001). The majority of functional traits (releasing height, biomass, specific leaf area, leaf dry matter content, F$_v$/F$_m$, and performance index) were related to abiotic habitat conditions indicating responses to environmental heterogeneity. In contrast, only morphology‐related functional traits (releasing height, biomass, and leaf area) were related to genetics. Our results suggest that both within‐habitat heterogeneity and genetic diversity affect iFD$_{CV}$ and are thus crucial to consider when aiming to understand or predict changes of plant species performance under changing environmental conditions.
• Journal Article

#### First Report on the Plasmidome From a High-Altitude Lake of the Andean Puna ﻿

Frontiers in Microbiology 2020; 11 p.1-15: Art. 1343
Mobile genetic elements, including plasmids, drive the evolution of prokaryotic genomes through the horizontal transfer of genes allowing genetic exchange between bacteria. Moreover, plasmids carry accessory genes, which encode functions that may offer an advantage to the host. Thus, it is expected that in a certain ecological niche, plasmids are enriched in accessory functions, which are important for their hosts to proliferate in that niche. Puquio de Campo Naranja is a high-altitude lake from the Andean Puna exposed to multiple extreme conditions, including high UV radiation, alkalinity, high concentrations of arsenic, heavy metals, dissolved salts, high thermal amplitude and low O$_2$ pressure. Microorganisms living in this lake need to develop efficient mechanisms and strategies to cope under these conditions. The aim of this study was to characterize the plasmidome of microbialites from Puquio de Campo Naranja, and identify potential hosts and encoded functions using a deep-sequencing approach. The potential ecological impact of the plasmidome, including plasmids from cultivable and non-cultivable microorganisms, is described for the first time in a lake representing an extreme environment of the Puna. This study showed that the recovered genetic information for the plasmidome was novel in comparison to the metagenome derived from the same environment. The study of the total plasmid population allowed the identification of genetic features typically encoded by plasmids, such as resistance and virulence factors. The resistance genes comprised resistances to heavy metals, antibiotics and stress factors. These results highlight the key role of plasmids for their hosts and impact of extrachromosomal elements to thrive in a certain ecological niche.
• Journal Article

#### Interpretation bias modification to reduce body dissatisfaction – a randomized controlled pilot study in women with elevated weight and shape concerns ﻿

Journal of Eating Disorders. 2020 Jul 02;8(1):34
Abstract Background Recent research has identified several cognitive biases in patients with eating disorders, such as a tendency to interpret ambiguous information about one’s own body in a negative way. The so-called “negative interpretation bias” is considered to be a key factor in maintaining maladaptive cognitions and behaviors in eating disorders. Studies on modification of the negative interpretation bias in eating disorders have yielded mixed results. This randomized controlled pilot study examined whether a specially adapted, computerized version of the Scrambled Sentences Task modifies negative interpretation bias in women with elevated body dissatisfaction. Methods The sample consisted of 40 normal-weight women with elevated body dissatisfaction, randomly assigned either to an intervention or a no-intervention control group (each n = 20). The intervention group received six sessions (within two weeks) of a newly-developed interpretation bias modification training that involved unscrambling positively valenced, body image-related sentences. The control group received no intervention. In both groups, body image-related negative interpretation bias (main outcome), trait body dissatisfaction and thin-ideal cue reactivity were assessed at baseline and two weeks later. Additionally, in the intervention condition, the trajectory of expected reductions in the thin-ideal internalization was measured during each training session. Results In both conditions, body image-related negative interpretation bias and trait body dissatisfaction decreased significantly from pre- to post-assessment; however, a specific effect imparted by the interpretation bias modification training was not found. Groups did not differ in thin-ideal cue reactivity. In the intervention group, thin-ideal internalization decreased significantly over the training sessions. Conclusions The findings do not support use of body image-related interpretation bias modification in its current form in the treatment of body dissatisfaction. Further research involving different versions of the training and clinical samples is warranted.
• Journal Article

#### Regeneration Dynamics Following the Formation of Understory Gaps in a Slovakian Beech Virgin Forest ﻿

Forests 2020; 11(5) p.1-20: Art. 585
The frequency and size of canopy gaps largely determine light transmission to lower canopy strata, controlling structuring processes in the understory. However, quantitative data from temperate virgin forests on the structure of regeneration in gaps and its dynamics over time are scarce. We studied the structure and height growth of tree regeneration by means of sapling density, shoot length growth and cumulative biomass in 17 understory gaps (29 to 931 m2 in size) in a Slovakian beech (Fagus sylvatica L.) virgin forest, and compared the gaps with the regeneration under closed-canopy conditions. Spatial differences in regeneration structure and growth rate within a gap and in the gap periphery were analyzed for their dependence on the relative intensities of direct and diffuse radiation (high vs. low). We tested the hypotheses that (i) the density and cumulative biomass of saplings are higher in gaps than in closed-canopy patches, (ii) the position in a gap influences the density and height growth of saplings, and (iii) height growth of saplings increases with gap size. Sapling density and biomass were significantly higher in understory gaps than under closed canopy. Density of saplings was positively affected by comparatively high direct, but low diffuse radiation, resulting in pronounced spatial differences. In contrast, sapling shoot length growth was positively affected by higher levels of diffuse radiation and also depended on sapling size, while direct radiation intensity was not influential. Conclusively, in this forest, regeneration likely becomes suppressed after a short period by lateral canopy expansion in small gaps (<100 m2), resulting in a heterogeneous understory structure. In larger gaps (≥100 m2) saplings may be capable even at low plant densities to fill the gap, often forming a cohort-like regeneration layer. Thus, gaps of different sizes imprint on the resulting canopy structure in different ways, enhancing spatial heterogeneity.