Freie Universität Berlin

Sessilids (Oligohymenophorea, Peritrichia, Sessilida) reportedly colonize the gut of certain “higher termites” (family Termitidae), but only a single species, Termitophrya africana from Jugositermes tuberculatus (subfamily Apicotermitinae), has been described based on a drawing. Similar ciliates were observed in other Apicotermitinae but remained unspecified. Our SSU rDNA-based survey of peritrich ciliates in a broad range of Termitidae recovered distinct phylotypes from several Apicotermitinae (Astalotermes, Jugositermes, and Phoxotermes), albeit only from samples collected in Cameroon and not from all species of these genera. They form a monophyletic group in the family Epistylididae (Sessilida), with Orborhabdostyla bromelicola as the closest relative. Light, scanning, and transmission electron microscopy of the sessilid ciliates in J. tuberculatus revealed two morphotypes, which were assigned to their corresponding phylotypes by sequence analysis of capillary-picked single cells. One morphotype, which is highly contractile and broadens continuously towards the posterior end, matches the description of Termitophrya africana. The cells are attached by a posterior scopula with short cilia and are often covered with rod-shaped ectobionts. The other morphotype has a stockier, barrel-shaped body and a short, clearly demarcated anterior end and is always free of ectobionts. We designate it as Doliophrys denislynni gen. Nov., sp. nov.

Glycans are vital in biological processes, but their nontemplated, heterogeneous structures complicate structure‐function analyses. Glycosylation, the key reaction in synthetic glycochemistry, remains not entirely predictable due to its complex mechanism and the need for protecting groups that impact reaction outcomes. This concept highlights recent advancements in glycochemistry and emphasizes the integration of digital tools, including automation, computational modelling, and data management, to improve carbohydrate synthesis and support further progress in the field.

The air‐ and water‐stable perfluorinated Cp* [C5(CF3)5]⁻ is presented as a candidate for the vastly underexplored group of weakly coordinating carbanions (WCCAs). Its extreme electron deficiency, combined with the stabilization of the negative charge within an aromatic system, results in a low basicity, yielding a very weak coordination ability. As Cp anions usually possess a strongly pronounced carbanionic character, the perfluorinated Cp* resembles an extraordinary exception for both the WCA and Cp chemistry. However, the coordination ability remains ambivalent due to the substitution lability of many of its complexes, allowing for the formation of unique ligand‐WCA switches. Due to the low reactivity, there is a need for new transfer reagents containing the perfluorinated Cp* in combination with reactive cations. Thus, we report the synthesis and complete characterization of [C5(CF3)5]⁻ salts with hydride‐accepting [(C6H5)3C]⁺, valuable Ag(I) reagents, oxidizing [Fe(C5H5)2]⁺ or [N(p‐C6H4Br)3]⁺ and Brønsted acidic [H(m,m‐NC5H3F2)2]⁺. Notably, these unprecedented ion pairs are exclusively accessible and stabilized by the low coordination affinity and pronounced oxidative resistance of the perfluorinated Cp*.

Due to factors such as lower biosecurity, greater wildlife/farm animal interfaces, and environmental challenges, cattle in sub‐Saharan Africa are exposed to more diverse and intensive bacterial, viral and protozoan pathogen challenges than cattle in Europe and other high‐income regions of the world. Classical class I genes of the major histocompatibility complex (MHC) contribute to protection from diseases caused by these pathogens by refining a huge pool of potential pathogen‐derived peptide ligands into a smaller ensemble for presentation to CD8+ T cells. Knowledge of population‐prevalent MHC alleles is therefore critical for evidence‐based approaches to vaccine design and improved understanding of pathogen resistance. Whereas variation in MHC molecules is understood in most detail for European Bos taurus, the alleles expressed by Africa's cattle remain poorly defined. We have leveraged recent improvements in the accuracy of PacBio high‐fidelity (HiFi) circular consensus sequencing (CCS) and adapted stringent sequence filtering algorithms to identify hundreds of as yet uncharacterised fully phased BoLA‐I alleles from multiple populations of African taurine (Ankole) and indicine (Zebu) cattle in East Africa. The analysis highlights a convergence of population‐prevalent class I MHC allelic repertoires in taurine and indicine cattle, likely due to the similar pathogen‐driven selective pressures. Our analysis of the anchor residue accommodating pockets of these prevalent alleles revealed extremely high levels of polymorphism, which contrast with Holstein alleles that exhibit a more limited repertoire of MHC specificity‐determining pocket residues, potentially constraining the breadth of peptide presentation. However, in the context of considerable sequence and physicochemical variation in the pocket‐forming residues, it was possible to discern overlaps in the predicted peptide binding spectrum. Interrogation of potential differences in peptide binding specificities with European B. taurus alleles revealed that the fully phased African cattle class I MHC alleles represent five novel specificities. We envisage that this novel finding will find broad application in assessing potentially achievable vaccination coverages of future pathogen‐encoded vaccine candidates against important intracellular pathogens. One aim of future research should be to leverage recent improvements in the sensitivity of mass spectrometry combined with immunoprecipitation of peptides bound to African cattle MHC to search directly for T‐cell epitopes in the context of the inferred ‘supertype’ diversity.

Replicative senescence presents a significant challenge in mesenchymal stem cell (MSC) expansion due to high reactive oxygen species (ROS) levels generated during culture. Elevated ROS levels lead to oxidative stress, cellular damage, and senescence, limiting the biomedical applications of MSCs. In this study, a supramolecular thermo‐reversible hydrogel composed of the natural polyphenolic compound gallic acid (GA) and polyvinyl alcohol (PVA) was designed to scavenge ROS and mitigate MSC senescence. The PVA‐GA hydrogel, stabilized by strong hydrogen bonding forces, exhibited an elastic modulus comparable to that of human soft tissue and facilitated the sustained release of GA over 14 days. It enhanced MSC survival, protected against oxidative stress, reduced intracellular ROS levels, diminished mitochondrial damage, and decreased cellular senescence. The hydrogel maintained the multilineage differentiation potential and typical phenotype of MSCs. Additionally, it preserved vascular endothelial growth factor (VEGF) secretion from MSCs under oxidative stress and enhanced their pro‐angiogenic effect. The conditioned medium derived from MSCs in the hydrogel group promoted migration and tube formation of human umbilical vein endothelial cells (HUVECs). These findings suggest that the PVA‐GA hydrogel holds significant promise for the biomedical applications of MSCs, potentially addressing the challenges posed by oxidative stress and cellular senescence.

Global biodiversity hotspots, including Mediterranean‐type ecosystems worldwide, are highly threatened by global change that alters biodiversity, ecosystem functions, and services. Some restoration activities enhance ecosystem functions by reintroducing plant species based on known relationships between plant traits and ecosystem processes. Achieving multiple functions across different site conditions, however, requires understanding how abiotic factors like climate and soil, along with plant assemblages, influence ecosystem functions, including their trade‐offs and synergies. We used the ModEST ecosystem simulation model, which integrates carbon, water, and nutrient processes with plant traits, to assess the relationships between restored plant assemblages and ecosystem functions in Mediterranean‐type climates and soils. We investigated whether maximised carbon increment, water use efficiency, and nitrogen use efficiency, along with their trade‐offs and synergies, varied across different abiotic contexts. Further, we asked whether assemblages that maximised functions varied across environments and among these functions. We found that maximised ecosystem carbon increment and nitrogen use efficiency occurred under moist, warm conditions, while water use efficiency peaked under drier conditions. Generally, the assemblage that maximised one function differed from those for other maximised functions. Synergies were rare, except between water and nitrogen use efficiencies in loam soils across most climates. Trade‐offs among maximised functions were common, varying in strength with abiotic context and plant assemblages, and were more pronounced in sandy loam soils compared to clay‐rich soils. Our findings suggest that due to variation in abiotic conditions within and across Mediterranean‐type regions at the global scale, site‐specific plant assemblages are required to maximise ecosystem functions. Thus, lessons from a single site cannot be transferred to another site, even where the same plant functional types are available for restoration. Our simulation results offer valuable insights into potential ecosystem performance under specific abiotic conditions following restoration with particular plant functional types, thereby informing local restoration efforts.

Background Cerebellar disease may result in Cerebellar Cognitive Affective Syndrome (CCAS). The CCAS-Scale, designed to screen for CCAS, has been validated in English Hoche (Brain 141:248–270, 2018) and adapted to other languages. Methods Here, the German CCAS-Scale Thieme (Neurol Res Pract 2:39, 2020) was validated in 209 patients with cerebellar disorders and 232 healthy controls. Correction formulas for the outcome parameters [failed test items (range: 1–10) and sum raw score (range: 0–120)] were developed, controlling for age, education, and sex effects. Diagnostic accuracy and reliability were assessed. Results Correction formulas improved selectivity in controls, reducing false positives (failed items: 40%; sum score: 13% vs. original method Hoche (Brain 141:248–270, 2018): 67%), while maintaining moderate sensitivity (failed items: 69%; sum score: 48% vs. original method Hoche (Brain 141:248–270, 2018): 87%). Word fluency tests differentiated best between patients and controls, while other items did not. Internal consistency (α = 0.71) was acceptable. Removal of word fluency tests worsened it. Retest and interrater reliability were high [intraclass correlation coefficients (ICC): 0.77–0.95]. However, these ICCs yielded a large minimal detectable change (MDC; 2.2–2.4 failed items, 9.5–11.4 raw score points) in patients, limiting the use of the CCAS-Scale in follow-up examinations. Conclusion The correction formulas improved diagnostic accuracy of the CCAS-Scale, particularly for the sum raw score. Therefore, we recommend using the corrected sum raw score for evaluation instead of the uncorrected number of failed items, proposed originally Hoche (Brain 141:248–270, 2018). Some test items, however, did not differentiate well between patients and controls and MDCs were large, highlighting the need for refined CCAS assessment instruments as progression or treatment outcomes.

The scale of modern datasets has necessitated innovations to solve even the most traditional and fundamental of computational problems. Set membership and set cardinality are both examples of simple queries that, for large enough datasets, quickly become challenging using traditional approaches. Interestingly, we find a need for these innovations within the field of biology. Despite the vast differences among living organisms, there exist functions so critical to life that they are conserved in the genomes and proteomes across seemingly unrelated species. Regular expressions (regexes) can serve as a convenient way to represent these conserved sequences compactly. However, despite the strong theoretical foundation and maturity of tools available, the state-of-the-art regex search falls short of what is necessary to quickly scan an enormous database of biological sequences. In this work, we describe a novel algorithm for regex search that reduces the search space by leveraging a recently developed compact data structure for set membership, the hierarchical interleaved bloom filter. We show that the runtime of our method combined with a traditional search outperforms state-of-the-art tools.

Iridoviruses are a family of large DNA viruses that infect insects and poikilotherm vertebrates, including amphibians, reptiles, and fish. Notably, members of the genus Ranavirus cause mass mortality in fish and amphibians, threatening aquaculture and contributing to global amphibian decline. Despite their omnipresence and impact, key aspects of iridovirus biology remain unknown, largely due to the absence of reverse genetics systems. In this study, we developed, characterized, and utilized a reverse genetics system for frog virus 3 (FV3, Ranavirus rana1 ), one of the most widely studied iridoviruses. The rescued virus exhibits growth and phenotypic properties identical to those of the parental virus isolate. Furthermore, we established an alternative approach of virus reconstitution from genomic DNA, utilizing a heterologous iridovirus as a helper. This novel approach enables rapid and facile rescue of modified viruses from naked DNA. The reverse genetics and rescue systems described in this study will advance iridovirus research by facilitating efficient genetic modification of the virus genome in yeast or bacteria. This could clear the path to elucidating functions of virus genes and allow a much more detailed understanding of iridovirus biology. Moreover, owing to the promiscuous nature of FV3 with its ability to infect hosts from different classes of animals, the FV3 system has the potential to serve as a platform for the development of modified live vaccines for a variety of fish and amphibian species. IMPORTANCE Iridoviruses pose a substantial threat to aquaculture and global amphibian populations, yet research has been hindered by the lack of a reverse genetics system. In this study, we describe the development of the first such system for this virus family. We constructed a synthetic clone of frog virus 3 (FV3) that can be propagated and genetically manipulated in both yeast and bacteria, yielding a virus that has biological properties identical to the parental virus isolate. Furthermore, we developed a novel helper virus-based system for the rescue of FV3 from purified DNA. This system provides an essential tool for advancing our understanding of iridovirus biology and serves as a platform for the development of modified live virus vaccines.

Microplastics pollution has become an emerging concern globally, affecting all ecosystems. Microplastics contamination in terrestrial ecosystems has drawn less attention than in aquatic ecosystems, resulting in comparatively fewer studies. When considering studies on terrestrial ecosystems, very little has been reported from African countries, revealing a lack of data on microplastics contamination and its effect on the terrestrial ecosystems of Africa. Here, we position microplastics research in Africa within the global research landscape on terrestrial ecosystems, identify gaps in knowledge, and suggest a framework for research networks among African scientists within and outside Africa and institutional collaborations with well-established research groups outside the continent.

Mangroves are a critical habitat that provide a suite of ecosystem services and support livelihoods. Here we undertook a global analysis to model the density and abundance of 37 commercially important juvenile fish and juvenile and resident invertebrates that are known to extensively use mangroves, by fitting expert-identified drivers of density to fish and invertebrate density data from published field studies. The numerical model predicted high densities throughout parts of Southeast and South Asia, the northern coast of South America, the Red Sea, and the Caribbean and Central America. Application of our model globally estimates that mangroves support an annual abundance of over 700 billion juvenile fish and invertebrates. While abundance at the early life-history stage does not directly equate to potential economic or biomass gains, this estimate indicates the critical role of mangroves globally in supporting fish and fisheries, and further builds the case for their conservation and restoration.

Fraudulent published papers were once thought to be rare, but in recent years, there has been growing awareness of coordinated activities by for‐profit organizations that charge authors a fee to sell articles and submit them to reputable journals. These are known as paper mills. We reflect here on how Mind, Brain and Education suffered from such an attack in 2022 and 2023, discussing what we have learnt from this experience about how paper mills might operate in biomedical and social sciences, how to identify red flags that an article might be fraudulent, and what steps might be taken to prevent such attacks in future.

The high mountains of Taiwan provide a unique location for Quaternary palaeoclimate research in East Asia and the north‐western Pacific. This study applies geomorphological field mapping and rock surface exposure dating with paired ( ¹⁰ Be/ ²⁶ Al) in situ‐produced terrestrial cosmogenic nuclides to identify and date glacial landforms and boulders in a relatively low‐elevated (<3300 m) section of the Taiwanese Central Mountain Range, the southern Nenggao Shan. We propose two major glacial phases during the last glacial cycle: 1) During the Marine Isotope Stage 3 to the early Marine Isotope Stage 2, a small plateau glacier covered the main crest with a glacier equilibrium line altitude at 2800 m. This is the lowest ever reported equilibrium line altitude in Taiwan. The ice retreated during or just before the global Last Glacial Maximum. This is consistent with scenarios from other East Asian mountain ranges. 2) During the late glacial until the early Holocene, six cirque glaciers formed exclusively in east‐facing topographically favorable downwind positions. Their cirque floor elevations indicate an orographic equilibrium line altitude between 2700 m and 2800 m. These cirque positions confirm the dominant influence of the mid‐latitude westerlies above the shallow winter monsoon on the high‐altitude precipitation regime in East Asia.

CrSBr, a van der Waals material, stands out as an air-stable magnetic semiconductor with appealing intrinsic properties such as crystalline anisotropy, quasi-1D electronic characteristics, layer-dependent antiferromagnetism, and non-linear optical effects....

In recent years, there has been a notable increase in research projects aimed at understanding the ecology of cities. How and to what extent urbanization is responsible for species’ evolution is historically a much less understood topic, because urban evolutionary biology is a nascent science. Most of the empirical and theoretical investigation of this new branch of evolution has been published recently, that is within the last 15 years. Studies on urban evolutionary biology have relevant implications for the environmental design of cities and for conserving the evolutionary potential and ecological success of urban biota. There is a strong bias towards studies conducted in North America and Europe, and the literature lacks empirical studies that investigate how the greater biodiversity observed in the tropics responds evolutionarily to urbanization processes. Expanding urban evolutionary biology in tropical cities is a priority for urban evolutionary biologists. This perspective chapter explores how the Global Urban Evolution Project, the world’s largest scale study of urban evolutionary ecology, is contributing to understanding how urbanization is affecting the ecology and evolution of life, and how this knowledge can be applied to the conservation of the biological diversity of tropical cities.

Producing high‐purity oxygen (O2) has a wide range of applications across diverse sectors, such as medicine, tunnel construction, the chemical industry, and fermentation. However, current O2 production methods are burdened by complexity, heavy equipment, high energy consumption, and limited adaptability to harsh environments. Here, to address this grand challenge, the de novo design of Ru‐doped metal hydroxide is proposed to serve as bioinspired O2‐evolution catalysts with proton‐coupled electron transfer (PCET) pathway for low‐energy, environmentally friendly, cost‐effective, and portable O2 generation. The comprehensive studies confirm that the lattice H species in Ru‐Co(OH)x‐based O2‐evolution catalyst can trigger a PCET pathway to optimize Ru‐oxygen intermediates interactions, thus ultimately reducing reaction energy barriers and improving the activities and durabilities. Consequently, the prepared Ru‐Co(OH)x‐loaded membrane catalysts exhibit rapid and long‐term stable O2 production capabilities. Furthermore, the proposed material design strategy of lattice H‐species shows remarkable universality and adaptability to broad Ru‐doped metal hydroxides. This efficient, portable, and cost‐effective O2 generation technique is suggested to ensure an uninterrupted O2 supply during emergencies and in regions with limited O2 availability or air pollution, thus offering significant societal benefits in broad applications.

Logical Analysis of Data (LAD) is a powerful technique for data classification based on partially defined Boolean functions. The decision rules for class prediction in LAD are formed out of patterns. According to different preferences in the classification problem, various pattern types have been defined. The generation of these patterns plays a key role in the LAD methodology and represents a computationally hard problem. In this article, we introduce a new approach to pattern generation in LAD based on Answer Set Programming (ASP), which can be applied to all common LAD pattern types.

This article proposes a research heuristic to analyse practices of contradicting in networked publics. This heuristic is based on the thesis of the polarization of society, as witnessed in the media discourse, and the approach of a political sociology of conflict. Such an approach requires developing theories in communication and media studies to document social conflict dynamics in changing public dynamics, explain dominant communicative practices, and to interpret subsequent developments. The research heuristic presented here prefers an approach rooted in praxeology and as such makes it possible to analyse practices of contradiction in networked publics, leading to observations informed by theories of public sphere. This approach is particularly relevant in ongoing debates on gender relations, sexualized harassment, and violence, all of which have once again become ‘trigger points’ that are challenging individuals and institutions of modern societies on different levels. The debate about the accusations against Till Lindemann as the lead singer of the internationally renowned German band Rammstein, a debate that has garnered attention beyond the German-speaking contexts, illustrates how this proposed research heuristic can become a tool for an informed analysis.

Digital innovations can offer solutions to various food, water, and land systems challenges globally. However, there are concerns on the ethical and social inclusivity aspects of these innovations, particularly for marginalized groups of people in less industrialised countries. In this article, we describe the design and development of a digital inclusivity framework, which builds from a detailed synthesis of inclusivity in digital literature. Key insights from the review were collated into five dimensions: risk mitigation, accessibility, usability, benefits, and participation. These dimensions can be assessed by means of twenty-one concrete and measurable sub indicators. Our focus was to enable a more holistic approach to the usually technocentric design of digital innovations. The framework, including the associated indicators, lays the groundwork for the development of a digital inclusivity index, a tool for assessing and fostering the inclusivity of digital innovations in food, water, and land systems.