Friedrich Schiller University Jena

The functions of soils are intimately linked to their three-dimensional pore space and the associated biogeochemical interfaces, mirrored in the complex structure that developed during pedogenesis. Under stress overload, soil disintegrates into smaller compound structures, conventionally named aggregates. Microaggregates (<250 μm) are recognized as the most stable soil structural units. They are built of mineral, organic, and biotic materials, provide habitats for a vast diversity of microorganisms, and are closely involved in the cycling of matter and energy. However, exploring the architecture of soil microaggregates and their linkage to soil functions remains a challenging but demanding scientific endeavor. With the advent of complementary spectromicroscopic and tomographic techniques, we can now assess and visualize the size, composition, and porosity of microaggregates and the spatial arrangement of their interior building units. Their combinations with advanced experimental pedology, multi-isotope labeling experiments, and computational approaches pave the way to investigate microaggregate turnover and stability, explore their role in element cycling, and unravel the intricate linkage between structure and function. However, spectromicroscopic techniques operate at different scales and resolutions, and have specific requirements for sample preparation and microaggregate isolation; hence, special attention must be paid to both the separation of microaggregates in a reproducible manner and the synopsis of the geography of information that originates from the diverse complementary instrumental techniques. The latter calls for further development of strategies for synlocation and synscaling beyond the present state of correlative analysis. Here, we present examples of recent scientific progress and review both options and challenges of the joint application of cutting-edge techniques to achieve a sophisticated picture of the properties and functions of soil microaggregates.

Understanding and predicting how densities of interacting species change over time has been one of the main goals of community ecology, which has become a pressing challenge in the context of global change. We present the R package ATNr , which provides an implementation of different versions of Allometric Trophic Network models that simulate the biomass dynamics of trophically interacting species. Relying on C++ routines, the ATNr proposes an efficient and standardised implementation of the different ATNs models. By proposing a set of built in functions ready to use in a language widely used in the community of ecologists, the ATNr package offers an easy access to ATN models focusing on trophic interactions.

Bats (order Chiroptera ) are a major reservoir for emerging and re-emerging zoonotic viruses. Their tolerance toward highly pathogenic human viruses led to the hypothesis that bats may possess an especially active antiviral interferon (IFN) system. Here, we cloned and functionally characterized the virus RNA sensor, retinoic acid-inducible gene-I (RIG-I), from the “microbat” Myotis daubentonii (suborder Yangochiroptera ) and the “megabat” Rousettus aegyptiacus (suborder Yinpterochiroptera) and compared them to the human ortholog. Our data show that the overall sequence and domain organization are highly conserved and that all three RIG-I orthologs can mediate a similar IFN induction in response to viral RNA at 37° and 39°C but not at 30°C. Like human RIG-I, bat RIG-Is were optimally activated by double stranded RNA containing a 5’-triphosphate end and required mitochondrial antiviral-signaling protein (MAVS) for antiviral signaling. Moreover, the RIG-I orthologs of humans and of R. aegyptiacus , but not of M. daubentonii , enable innate immune sensing of SARS-CoV-2 infection. Our results thus show that microbats and megabats express a RIG-I that is not substantially different from the human counterpart with respect to function, temperature dependency, antiviral signaling, and RNA ligand properties, and that human and megabat RIG-I are able to sense SARS-CoV-2 infection. IMPORTANCE A common hypothesis holds that bats (order Chiroptera ) are outstanding reservoirs for zoonotic viruses because of a special antiviral interferon (IFN) system. However, functional studies about key components of the bat IFN system are rare. RIG-I is a cellular sensor for viral RNA signatures that activates the antiviral signaling chain to induce IFN. We cloned and functionally characterized RIG-I genes from two species of the suborders Yangochiroptera and Yinpterochiroptera . The bat RIG-Is were conserved in their sequence and domain organization, and similar to human RIG-I in (i) mediating virus- and IFN-activated gene expression, (ii) antiviral signaling, (iii) temperature dependence, and (iv) recognition of RNA ligands. Moreover, RIG-I of Rousettus aegyptiacus (suborder Yinpterochiroptera ) and of humans were found to recognize SARS-CoV-2 infection. Thus, members of both bat suborders encode RIG-Is that are comparable to their human counterpart. The ability of bats to harbor zoonotic viruses therefore seems due to other features.

Protein quality control pathways ensure a functional proteome and rely on a complex proteostasis network (PN) that is composed of molecular chaperones and proteases. Failures in the PN can lead to a broad spectrum of diseases, including neurodegenerative disorders like Alzheimer’s, Parkinson’s, and a range of motor neuron diseases. The EMBO workshop “Protein quality control: from molecular mechanisms to therapeutic intervention” covered all aspects of protein quality control from underlying molecular mechanisms of chaperones and proteases to stress signaling pathways and medical implications. This report summarizes the workshop and highlights selected presentations.

Marine macroalgae (seaweeds) are important primary producers and foundation species in coastal ecosystems around the world. Seaweeds currently contribute to an estimated 51% of the global mariculture production, with a long-term growth rate of 6% per year, and an estimated market value of more than US$11.3 billion. Viral infections could have a substantial impact on the ecology and aquaculture of seaweeds, but surprisingly little is known about virus diversity in macroalgal hosts. Using metagenomic sequencing, we characterized viral communities associated with healthy and bleached specimens of the commercially important green seaweed Ulva . We identified 20 putative new and divergent viruses, of which the majority belonged to the Circular Rep-Encoding Single-Stranded (CRESS) DNA viruses [single-stranded (ss)DNA genomes], Durnavirales [double-stranded (ds)RNA], and Picornavirales (ssRNA). Other newly identified RNA viruses were related to the Ghabrivirales , the Mitoviridae , and the Tombusviridae . Bleached Ulva samples contained particularly high viral read numbers. While reads matching assembled CRESS DNA viruses and picorna-like viruses were nearly absent from the healthy Ulva samples (confirmed by qPCR), they were very abundant in the bleached specimens. Therefore, bleaching in Ulva could be caused by one or a combination of the identified viruses but may also be the result of another causative agent or abiotic stress, with the viruses simply proliferating in already unhealthy seaweed tissue. This study highlights how little we know about the diversity and ecology of seaweed viruses, especially in relation to the health and diseases of the algal host, and emphasizes the need to better characterize the algal virosphere. IMPORTANCE Green seaweeds of the genus Ulva are considered a model system to study microbial interactions with the algal host. Remarkably little is known, however, about viral communities associated with green seaweeds, especially in relation to the health of the host. In this study, we characterized the viral communities associated with healthy and bleached Ulva . Our findings revealed the presence of 20 putative novel viruses associated with Ulva , encompassing both DNA and RNA viruses. The majority of these viruses were found to be especially abundant in bleached Ulva specimens. This is the first step toward understanding the role of viruses in the ecology and aquaculture of this green seaweed.

In this article, we present a general theorem and proof for the global identification of composed CFA models. They consist of identified submodels that are related only through covariances between their respective latent factors. Composed CFA models are frequently used in the analysis of multimethod data, longitudinal data, or multidimensional psychometric data. Firstly, our theorem enables researchers to reduce the problem of identifying the composed model to the problem of identifying the submodels and verifying the conditions given by our theorem. Secondly, we show that composed CFA models are globally identified if the primary models are reduced models such as the CT-C $$(M-1)$$ ( M - 1 ) model or similar types of models. In contrast, composed CFA models that include non-reduced primary models can be globally underidentified for certain types of cross-model covariance assumptions. We discuss necessary and sufficient conditions for the global identification of arbitrary composed CFA models and provide a Python code to check the identification status for an illustrative example. The code we provide can be easily adapted to more complex models.

Subjective tinnitus (hereafter tinnitus) is often considered and studied as a perceptual phenomenon. Accordingly, various abnormalities in the area of cognitive processing have been reported in patients with tinnitus. At the same time, the disorder is characterized by considerable emotional distress, which is associated with a high comorbidity of affective disorders. Here, we aim to outline the close link between cognition and emotion, and how current research from the field of cognitive neuroscience examines the processing and acquisition of emotional stimuli. The emotional valence of stimuli can be acquired after brief exposure to learning, leading from neutral to appetitive or aversive evaluation. In contrast to neutral stimuli, emotional stimuli attract attention very early (about 100 ms) during processing, leading to deeper processing and corresponding memory effects. The involved subcortical and cortical network encompasses limbic and sensory areas. In particular, prefrontal regions are involved in the acquisition and evaluation of emotional stimuli as also shown in studies of patients with affect disorders. The interplay of cognitive and emotional processes seems to be central to the development, maintenance, and treatment of tinnitus.

Purpose Protein-rich foods show heterogeneous associations with the risk of type 2 diabetes (T2D) and it remains unclear whether habitual protein intake is related to T2D risk. We carried out an umbrella review of systematic reviews (SR) of randomised trials and/or cohort studies on protein intake in relation to risks of T2D. Methods Following a pre-specified protocol (PROSPERO: CRD42018082395), we retrieved SRs on protein intake and T2D risk published between July 1st 2009 and May 22nd 2022, and assessed the methodological quality and outcome-specific certainty of the evidence using a modified version of AMSTAR 2 and NutriGrade, respectively. The overall certainty of evidence was rated according to predefined criteria. Results Eight SRs were identified of which six contained meta-analyses. The majority of SRs on total protein intake had moderate or high methodological quality and moderate outcome-specific certainty of evidence according to NutriGrade, however, the latter was low for the majority of SRs on animal and plant protein. Six of the eight SRs reported risk increases with both total and animal protein. According to one SR, total protein intake in studies was ~ 21 energy percentage (%E) in the highest intake category and 15%E in the lowest intake category. Relative Risks comparing high versus low intake in most recent SRs ranged from 1.09 (two SRs, 95% CIs 1.02–1.15 and 1.06–1.13) to 1.11 (1.05–1.16) for total protein (between 8 and 12 cohort studies included) and from 1.13 (1.08–1.19) to 1.19 (two SRs, 1.11–1.28 and 1.11–1.28) (8–9 cohort studies) for animal protein. However, SRs on RCTs examining major glycaemic traits (HbA1c, fasting glucose, fasting insulin) do not support a clear biological link with T2D risk. For plant protein, some recent SRs pointed towards risk decreases and non-linear associations, however, the majority did not support an association with T2D risk. Conclusion Higher total protein intake was possibly associated with higher T2D risk, while there is insufficient evidence for a risk increase with higher intakes of animal protein and a risk decrease with plant protein intake. Given that most SRs on plant protein did not indicate an association, there is possibly a lack of an effect.

Mycoplasmopsis (M.) bovis, the agent of mastitis, pneumonia, and arthritis in cattle, harbors a small genome of approximately 1 Mbp. Combining data from Illumina and Nanopore technologies, we sequenced and assembled the genomes of 35 European strains and isolate DL422_88 from Cuba. While the high proportion of repetitive structures in M. bovis genomes represent a particular challenge, implementation of our own pipeline Mycovista (available on GitHub www.github.com/sandraTriebel/mycovista) in a hybrid approach enabled contiguous assembly of the genomes and, consequently, improved annotation rates considerably. To put our European strain panel in a global context, we analyzed the new genome sequences together with 175 genome assemblies from public databases. Construction of a phylogenetic tree based on core genes of these 219 strains revealed a clustering pattern according to geographical origin, with European isolates positioned on clades 4 and 5. Genomic data allowing assignment of strains to tissue specificity or certain disease manifestations could not be identified. Seven strains isolated from cattle with systemic circular condition (SCC), still a largely unknown manifestation of M. bovis disease, were located on both clades 4 and 5. Pairwise association analysis revealed 108 genomic elements associated with a particular clade of the phylogenetic tree. Further analyzing these hits, 25 genes are functionally annotated and could be linked to a M. bovis protein, e.g. various proteases and nucleases, as well as ten variable surface lipoproteins (Vsps) and other surface proteins. These clade-specific genes could serve as useful markers in epidemiological and clinical surveys.

Background The number of complications in patients admitted for cirrhosis has increased over time. Portal hypertension is the driver of many complications of cirrhosis. TIPS placement is the most effective treatment of portal hypertension. The aim of this study was to analyze the use and impact of TIPS placement in the last decade in a nationwide study in Germany. Methods We analyzed 14,598 admissions of patients for TIPS insertions in Germany from 2007 to 2018 using the DRG system, 12,877 out of 2,000,765 total admissions of patients with cirrhosis. All diagnoses and procedures were coded according to ICD-10-CM and OPS codes. The data were analyzed, focusing on the number of admissions and in-hospital mortality. Results The number of TIPS placements increased over the last decade. In-hospital mortality of cirrhotic patients with TIPS decreased when it was placed for severe bleeding (15.2% [TIPS] vs. 19.5% [endoscopy treatment]), ascites (8.7% [TIPS] vs. 14.4% [paracentesis]), and hepatorenal syndrome (HRS) (17.1% [TIPS] vs. 43.3% [no-TIPS]). In the case of bleeding, TIPS significantly decreased in-hospital mortality and also in ascites and HRS. During hospitalization, 22.6% admissions of patients with TIPS insertion showed HE. However, in-hospital mortality in patients admitted with HE grades 1 or 2 and TIPS was lower than in patients without TIPS. In the logistic regression, a higher HE grade(3 and 4), infection, and circulatory disease were found to be independently associated with in-hospital mortality in patients with TIPS insertion. Conclusion Our nationwide study demonstrates that TIPS insertion is increasingly used in Germany. TIPS improves outcomes, especially in patients with ascites and HRS, regardless of lower HE grades, while higher HE grades, infection, and circulatory diseases seem to be associated with risk of in-hospital mortality.

Patients with potential or proven cardiovascular diseases represent a relevant proportion of the total spectrum in the emergency department. Their monitoring for cardiovascular surveillance until the diagnostics and acute treatment are initiated, often poses an interdisciplinary and interprofessional challenge, because resources are limited, nevertheless a high level of patient safety has to be ensured and the correct procedure has a major prognostic significance. This consensus paper provides an overview of the practical implementation, the modalities of monitoring and the application in a selection of cardiovascular diagnoses. The article provides specific comments on the clinical presentations of acute coronary syndrome, acute heart failure, cardiogenic shock, hypertensive emergency events, syncope, acute pulmonary embolism and cardiac arrhythmia. The level of evidence is generally low as no randomized trials are available on this topic. The recommendations are intended to supplement or establish local standards and to assist all physicians, nursing personnel and the patients to be treated in making decisions about monitoring in the emergency department.

Patients with potential or proven cardiovascular diseases represent a relevant proportion of the total spectrum in the emergency department. Their monitoring for cardiovascular surveillance until the diagnostics and acute treatment are initiated, often poses an interdisciplinary and interprofessional challenge, because resources are limited, nevertheless a high level of patient safety has to be ensured and the correct procedure has a major prognostic significance. This consensus paper provides an overview of the practical implementation, the modalities of monitoring and the application in a selection of cardiovascular diagnoses. The article provides specific comments on the clinical presentations of acute coronary syndrome, acute heart failure, cardiogenic shock, hypertensive emergency events, syncope, acute pulmonary embolism and cardiac arrhythmia. The level of evidence is generally low as no randomized trials are available on this topic. The recommendations are intended to supplement or establish local standards and to assist all physicians, nursing personnel and the patients to be treated in making decisions about monitoring in the emergency department.

Patients with potential or proven cardiovascular diseases represent a relevant proportion of the total spectrum in the emergency department. Their monitoring for cardiovascular surveillance until the diagnostics and acute treatment are initiated, often poses an interdisciplinary and interprofessional challenge, because resources are limited, nevertheless a high level of patient safety has to be ensured and the correct procedure has a major prognostic significance. This consensus paper provides an overview of the practical implementation, the modalities of monitoring and the application in a selection of cardiovascular diagnoses. The article provides specific comments on the clinical presentations of acute coronary syndrome, acute heart failure, cardiogenic shock, hypertensive emergency events, syncope, acute pulmonary embolism and cardiac arrhythmia. The level of evidence is generally low as no randomized trials are available on this topic. The recommendations are intended to supplement or establish local standards and to assist all physicians, nursing personnel and the patients to be treated in making decisions about monitoring in the emergency department.