The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications

The chemical biology of native nucleic acid modifications has seen an intense upswing, first concerning DNA modifications in the field of epigenetics and then concerning RNA modifications in a field that was correspondingly rebaptized epitranscriptomics by analogy. The German Research Foundation (DFG) has funded several consortia with a scientific focus in these fields, strengthening the traditionally well-developed nucleic acid chemistry community and inciting it to team up with colleagues from the life sciences and data science to tackle interdisciplinary challenges. This Perspective focuses on the genesis, scientific outcome, and downstream impact of the DFG priority program SPP1784 and offers insight into how it fecundated further consortia in the field. Pertinent research was funded from mid-2015 to 2022, including an extension related to the coronavirus pandemic. Despite being a detriment to research activity in general, the pandemic has resulted in tremendously boosted interest in the field of RNA and RNA modifications as a consequence of their widespread and successful use in vaccination campaigns against SARS-CoV-2. Funded principal investigators published over 250 pertinent papers with a very substantial impact on the field. The program also helped to redirect numerous laboratories toward this dynamic field. Finally, SPP1784 spawned initiatives for several funded consortia that continue to drive the fields of nucleic acid modification.

Genome streamlining and clonal erosion in nutrient-limited environments: a test using genome-size variable populations

Some selection-based theories propose that genome streamlining, favoring smaller genome sizes, is advantageous in nutritionally limited environments, particularly under P-limitation. To test this prediction, we conducted several experimental evolution trials on clonal populations of a facultatively asexual rotifer that exhibits intraspecific variation in genome size. Most trials showed a rapid decline in clonal diversity, which was accelerated in populations that were initially nonadapted. Populations consisting of three rotifer clones often became monoclonal within a few weeks, while populations starting with 120 clones eroded to 10 multilocus genotypes, of which only five were abundant in higher numbers. While P-limitation affected population growth during the experiments, it did not affect the outcome of clonal competition or the speed at which clonal diversity was lost. Common garden transplant experiments revealed that the evolved populations were better adapted to the experimental conditions than the ancestral controls. However, contrary to expectations, the evolved populations did not show an overrepresentation of small genomes. Intermediate genomes were also frequently abundant, although very large genomes were rare. Our findings suggest that fitness is more influenced by genotypic differences among clones than by differences in GS, and indicate that such differences might hinder genome streamlining during early adaptation to a new environment.

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed using computational tools. Numerous such tools have been developed, but a systematic comparison with orthogonal validation is missing. Here, we set up a circRNA detection tool benchmarking study, in which 16 tools detected more than 315,000 unique circRNAs in three deeply sequenced human cell types. Next, 1,516 predicted circRNAs were validated using three orthogonal methods. Generally, tool-specific precision is high and similar (median of 98.8%, 96.3% and 95.5% for qPCR, RNase R and amplicon sequencing, respectively) whereas the sensitivity and number of predicted circRNAs (ranging from 1,372 to 58,032) are the most significant differentiators. Of note, precision values are lower when evaluating low-abundance circRNAs. We also show that the tools can be used complementarily to increase detection sensitivity. Finally, we offer recommendations for future circRNA detection and validation.

Functional ecology of planktonic ciliates: Measuring mortality rates in response to starvation

Population dynamics of aquatic ciliates are controlled "bottom-up" via food supply and "top-down" by grazing and parasitism. While intrinsic growth rates of ciliates under saturating food conditions have been studied in some detail, mortality rates induced by starvation have received little attention thus far. To this end, we examined the response of three algivorous freshwater ciliate species to starvation using three different optical methods. Two of these methods, i.e. ciliate mortality rates (δ) estimated from (i) numerical response experiments and (ii) the rate of decline (ROD) in cell numbers, investigated the response of the ciliate population using conventional light microscopy. The third method, imaging cytometry using a FlowCAM instrument, monitored single cells during the starvation experiment. Like light microscopy, the FlowCAM approach estimated δ based on ROD in the experimental containers. However, imaging cytometry also measured the relative cellular chlorophyll a content in the ciliates' food vacuoles as a proxy for the nutritional status of the cells. The linear decline of the cellular chl. a yielded an independent estimate of δ that was similar to δ calculated from ROD. Additionally, the FlowCAM measurements revealed a high degree of phenotypic plasticity of the ciliates when exposed to starvation.

Dairying, diseases and the evolution of lactase persistence in Europe

In European and many African, Middle Eastern and southern Asian populations, lactase persistence (LP) is the most strongly selected monogenic trait to have evolved over the past 10,000 years1. Although the selection of LP and the consumption of prehistoric milk must be linked, considerable uncertainty remains concerning their spatiotemporal configuration and specific interactions2,3. Here we provide detailed distributions of milk exploitation across Europe over the past 9,000 years using around 7,000 pottery fat residues from more than 550 archaeological sites. European milk use was widespread from the Neolithic period onwards but varied spatially and temporally in intensity. Notably, LP selection varying with levels of prehistoric milk exploitation is no better at explaining LP allele frequency trajectories than uniform selection since the Neolithic period. In the UK Biobank4,5 cohort of 500,000 contemporary Europeans, LP genotype was only weakly associated with milk consumption and did not show consistent associations with improved fitness or health indicators. This suggests that other reasons for the beneficial effects of LP should be considered for its rapid frequency increase. We propose that lactase non-persistent individuals consumed milk when it became available but, under conditions of famine and/or increased pathogen exposure, this was disadvantageous, driving LP selection in prehistoric Europe. Comparison of model likelihoods indicates that population fluctuations, settlement density and wild animal exploitation-proxies for these drivers-provide better explanations of LP selection than the extent of milk exploitation. These findings offer new perspectives on prehistoric milk exploitation and LP evolution.

OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes

OrtSuite predicts synergistic species interactions using the genomic potential of microbial communities

The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96% of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. We evaluated the identification of putative synergistic species interactions using the sequenced genomes of an independent study that had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy-to-use workflow that allows for rapid functional annotation based on a user-curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known. OrtSuite is an open-source software available at https://github.com/mdsufz/OrtSuite.

Different ways to play it cool: Transcriptomic analysis sheds light on different activity patterns of three amphipod species under long-term cold exposure

Species of littoral freshwater environments in regions with continental climate experience pronounced seasonal temperature changes. Coping with long cold winters and hot summers requires specific physiological and behavioural adaptations. Endemic amphipods of Lake Baikal, Eulimnogammarus verrucosus and Eulimnogammarus cyaneus, show high metabolic activity throughout the year; E. verrucosus even reproduces in winter. In contrast, the widespread Holarctic amphipod Gammarus lacustris overwinters in torpor. This study investigated the transcriptomic hallmarks of E. verrucosus, E. cyaneus and G. lacustris exposed to low water temperatures. Amphipods were exposed to 1.5°C and 12°C (corresponding to the mean winter and summer water temperatures, respectively, in the Baikal littoral) for one month. At 1.5°C, G. lacustris showed upregulation of ribosome biogenesis and mRNA processing genes, as well as downregulation of genes related to growth, reproduction and locomotor activity, indicating enhanced energy allocation to somatic maintenance. Our results suggest that the mitogen-activated protein kinase (MAPK) signalling pathway is involved in the preparation for hibernation; downregulation of the actin cytoskeleton pathway genes could relate to the observed low locomotor activity of G. lacustris at 1.5°C. The differences between the transcriptomes of E. verrucosus and E. cyaneus from the 1.5°C and 12°C exposures were considerably smaller than for G. lacustris. In E. verrucosus, cold-exposure triggered reproductive activity was indicated by upregulation of respective genes, whereas in E. cyaneus, genes related to mitochondria functioning were upregulated, indicating cold compensation in this species. Our data elucidate the molecular characteristics behind the different adaptations of amphipod species from the Lake Baikal area to winter conditions.

Effects of lifestyle interventions on epigenetic signatures of liver fat: Central randomized controlled trial

BACKGROUND AND AIMS

In the CENTRAL trial context, we found diverse liver fat dynamics in response to different dietary interventions. Epigenetic mechanisms may contribute to the intraindividual variation. Moreover, genetic factors are involved in developing nonalcoholic fatty-liver disease (NAFLD), a disease reflected by an increase in intrahepatic fat (IHF). In this exploratory analysis, we primarily aimed to examine the effect of lifestyle interventions on DNA-methylation of NAFLD related genes associated with IHF.

METHODS

For 120 participants from the CENTRAL trial, an 18-month regimen of either low-fat (LF) or Mediterranean-low carbohydrate (MED/LC) diets, with or without physical activity (PA+/PA-), was instructed. Magnetic resonance imaging was used to measure IHF%, which was analysed for association with CpG specific DNA-methylation levels of 41 selected candidate genes. Single-nucleotide polymorphisms known to be associated with NAFLD within the studied genes were genotyped by TaqMan assays.

RESULTS

At baseline, participants (92% men; body mass index = 30.2 kg/m² ) had mean IHF of 10.7% (59% NAFLD). Baseline-IHF% was inversely correlated with DNA-methylation at individual CpGs within AC074286.1, CRACR2A, A2MP1, FARP1 (P < .05 for all multivariate models). FARP1 rs9584805 showed association with IHF, with the prevalence of NAFLD and baseline methylation level of the CpG site (cg00071727) associated with IHF%. Following 18-month lifestyle intervention, differential DNA-methylation patterns were observed between diets at cg14335324 annotated to A2MP1 (P = .04, LF vs. MED/LC), and differential DNA-methylation between PA groups within AC074286.1, CRACR2A, and FARP1 CpGs (P < .05 for all, PA-vs. PA+).

CONCLUSIONS

This study suggests epigenetic markers for IHF and potential epigenetic remodeling after long-term lifestyle interventions.

Combining immunotherapy with an epidrug in squamous cell carcinomas of different locations: rationale and design of the PEVO basket trial

Squamous cell carcinomas (SCCs) are among the most frequent solid tumors in humans. SCCs, related or not to the human papillomavirus, share common molecular features. Immunotherapies, and specifically immune checkpoint inhibitors, have been shown to improve overall survival in multiple cancer types, including SCCs. However, only a minority of patients experience a durable response with immunotherapy. Epigenetic modulation plays a major role in escaping tumor immunosurveillance and confers resistance to immune checkpoint inhibitors. Preclinical evidence suggests that modulating the epigenome might improve the efficacy of immunotherapy. We herein review the preclinical and the clinical rationale for combining immunotherapy with an epidrug, and detail the design of PEVOsq, a basket clinical trial combining pembrolizumab with vorinostat, a histone deacetylase inhibitor, in patients with SCCs of different locations. Sequential blood and tumor sampling will be collected in order to identify predictive and pharmacodynamics biomarkers of efficacy of the combination. We also present how clinical and biological data will be managed with the aim to enable the development of a prospective integrative platform to allow secure and controlled access to the project data as well as further exploitations.

Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch

We describe a synthetic riboswitch element that implements a regulatory principle which directly addresses an essential tRNA maturation step. Constructed using a rational in silico design approach, this riboswitch regulates RNase P-catalyzed tRNA 5′-processing by either sequestering or exposing the single-stranded 5′-leader region of the tRNA precursor in response to a ligand. A single base pair in the 5′-leader defines the regulatory potential of the riboswitch both in vitro and in vivo. Our data provide proof for prior postulates on the importance of the structure of the leader region for tRNA maturation. We demonstrate that computational predictions of ligand-dependent structural rearrangements can address individual maturation steps of stable non-coding RNAs, thus making them amenable as promising target for regulatory devices that can be used as functional building blocks in synthetic biology.

High-field (3 Tesla) MRI of the navicular apparatus of sound horses shows good agreement to histopathology

Magnetic resonance imaging and the correlation to histopathological findings of the equine palmar foot of lame horses have been described previously, using 0.27 and 1.5 T systems. Compared to these, 3 T systems provide superior spatial resolution and imaging contrast. The aim of our prospective anatomic study was to characterize the imaging anatomy of the navicular region on 3 T MRI in comparison to histopathological findings. We hypothesized that 3 T MRI allows a good visualization of the entire navicular apparatus and reliable measurements of navicular cartilage and cortical bone thickness. Twenty front feet of sound horses were examined using a 3 T MRI system. For histopathological examination, sagittal tissue sections of the navicular bones and adjacent ligaments were prepared. Alterations in magnetic resonance signal were graded for each region and compared to corresponding histological slices. Overall, there was good visualization of the anatomical detail and a very good agreement between MRI and histology for compact bone and spongiosa, good agreement for the fibrocartilage and the distal sesamoidean impar ligament, but only moderate agreement for the hyaline cartilage and the collateral sesamoidean ligament. A comparative measurement of cartilage and cortical bone thickness on magnetic resonance images and histological sections was performed. In MRI, the hyaline cartilage of the articular surface appeared significantly thinner and the fibrocartilage of the flexor surface appeared significantly thicker compared to histology. Findings indicated that MRI at a field strength of 3 T allows reliable depiction of anatomic details of the navicular apparatus.

Within-Population Genome Size Variation is Mediated by Multiple Genomic Elements That Segregate Independently during Meiosis

Within-species variation in genome size has been documented in many animals and plants. Despite its importance for understanding eukaryotic genome diversity, there is only sparse knowledge about how individual-level processes mediate genome size variation in populations. Here, we study a natural population of the rotifer Brachionus asplanchnoidis whose members differ up to 1.9-fold in diploid genome size, but were still able to interbreed and produce viable offspring. We show that genome size is highly heritable and can be artificially selected up or down, but not below a certain basal diploid genome size for this species. Analyses of segregation patterns in haploid males reveal that large genomic elements (several megabases in size) provide the substrate of genome size variation. These elements, and their segregation patterns, explain the generation of new genome size variants, the short-term evolutionary potential of genome size change in populations, and some seemingly paradoxical patterns, like an increase in genome size variation among highly inbred lines. Our study suggests that a conceptual model involving only two variables, 1) a basal genome size of the population, and 2) a vector containing information on additional elements that may increase genome size in this population (size, number, and meiotic segregation behavior), can effectively address most scenarios of short-term evolutionary change of genome size in a population.

Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750)

The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.

Abdominal aortic aneurysm as an IgG4-related disease

The objectives of this study were to evaluate patients with aortic abdominal aneurysm (AAA) with regard to immunoglobulin (Ig)G4‐related disease (IgG4‐RD). IgG4‐RD represents a recently defined condition comprised of a collection of disorders characterized by IgG4 hypergammaglobulinemia, the presence of IgG4‐positive plasma cells in organs affected with fibrotic or sclerotizing changes and typical histopathological features. It was identified as a possible cause of vasculitis in large vessels. Studies have been published on a possible association between inflammatory aortic or cardiovascular disease and IgG4‐RD. We examined 114 patients with AAA requiring surgery in order to identify findings which are characteristic of IgG4‐RD. Aneurysm samples from seven patients showed histopathological features consistent with IgG4‐RD and the presence of IgG4⁺ plasma cells. Only two of these seven patients showed elevated IgG4 serum levels higher 1·35 g/l. In five of the patients, the concentration of serum IgG4 was lower than 1·20 g/l, with the number of IgG4⁺ plasma cells being higher than 50/high‐power field. These findings were consistent with AAA being a heterogeneous group of inflammatory diseases with different pathogenesis.

Clinical Evidence for Correlation of Insufficient Tissue Oxygen Supply (Hypoxia) and Tumor-Associated Proteolysis in Squamous Cell Carcinoma of the Head and Neck

Hypoxic tumors of patients with squamous cell carcinoma of the head and neck show a consistent trend towards poor treatment outcome. We now report that tumor hypoxia in these patients is correlated with elevated antigen content of the tumor-associated serine protease uPA (urokinase-type plasminogen activator), a marker of tumor cell invasion and metastasis.

Regenerative Therapie von Sehnen- und Banderkrankungen bei Pferden

Herkömmliche Therapieansätze führen bei Pferden zu einer unbefriedigenden Sehnenheilung mit einer relativ hohen Rezidivrate. Deshalb werden seit einigen Jahren unter anderem in vitro und an Labortieren so genannte regenerative Therapieformen wissenschaftlich untersucht. Darunter wird der Einsatz von Substanzen verstanden, die idealerweise die Bildung eines Ersatzgewebes bewirken, das vergleichbare funktionelle Eigenschaften hat wie das Ursprungsgewebe und sich somit von minderwertigerem Narbengewebe abhebt. Derzeit ist eine Fülle verschiedener Substrate entweder kommerziell verfügbar oder mithilfe von „Kits“ unter Praxisbedingungen herstellbar. Es werden die wesentlichen Erkenntnisse zur Herstellung und zum regenerativen Potenzial von kernhaltigen Zellen bzw. Stammzellen aus Knochenmark und Fettgewebe sowie der Blutprodukte PRP (thrombozytenreiches Plasma), ACP (autologes konditioniertes Plasma), ACS (autologes konditioniertes Serum) und der Gerüstsubstanz UBM (urinary bladder matrix) vorgestellt. Zuletzt wird das Potenzial einzelner Wachstumsfaktoren und der Gentherapie beleuchtet. Bisher wird angenommen, dass die Regeneration von Sehnengewebe durch ein komplexes Zusammenspiel aus Gerüstsubstanzen, Wachstumsfaktoren und Zellen begünstigt wird. Es sind bislang nur wenige Untersuchungen verfügbar, die einen Vergleich zwischen den genannten Substanzen erlauben. Untersuchungen zur Wirkung der Substrate an lebenden Pferden werden an anderer Stelle vorgestellt.

Do genome size differences within Brachionus asplanchnoidis (Rotifera, Monogononta) cause reproductive barriers among geographic populations?

Genome size in the rotifer Brachionus asplanchnoidis, which belongs to the B. plicatilis species complex, is greatly enlarged and extremely variable (205-407 Mbp). Such variation raises the question whether large genome size differences among individuals might cause reproductive barriers, which could trigger speciation within this group by restricting gene flow across populations. To test this hypothesis, we used B. asplanchnoidis clones from three geographic populations and conducted assays to quantify reproductive isolation among clones differing in genome size, and we examined the population structure of all three populations using amplified fragment length polymorphisms (AFLPs). AFLPs indicated that these populations were genetically separated, but we also found hints of natural gene flow. Clones from different populations with genome size differences of up to 1.7-fold could interbred successfully in the laboratory and give rise to viable, fertile 'hybrid' offspring. Genome sizes of these 'hybrids' were intermediate between those of their parents, and fitness in terms of male production, population growth, and egg development time was not negatively affected. Thus, we found no evidence for reproductive isolation or nascent speciation within B. asplanchnoidis. Instead, our results suggest that gene flow within this species can occur despite a remarkably large range of genome sizes.

Ground-State Cooling of a Mechanical Oscillator by Interference in Andreev Reflection

We study the ground-state cooling of a mechanical oscillator linearly coupled to the charge of a quantum dot inserted between a normal metal and a superconducting contact. Such a system can be realized, e.g., by a suspended carbon nanotube quantum dot with a capacitive coupling to a gate contact. Focusing on the subgap transport regime, we analyze the inelastic Andreev reflections which drive the resonator to a nonequilibrium state. For small coupling, we obtain that vibration-assisted reflections can occur through two distinct interference paths. The interference determines the ratio between the rates of absorption and emission of vibrational energy quanta. We show that ground-state cooling of the mechanical oscillator can be achieved for many of the oscillator's modes simultaneously or for single modes selectively, depending on the experimentally tunable coupling to the superconductor.

Widespread exploitation of the honeybee by early Neolithic farmers

The pressures on honeybee (Apis mellifera) populations, resulting from threats by modern pesticides, parasites, predators and diseases, have raised awareness of the economic importance and critical role this insect plays in agricultural societies across the globe. However, the association of humans with A. mellifera predates post-industrial-revolution agriculture, as evidenced by the widespread presence of ancient Egyptian bee iconography dating to the Old Kingdom (approximately 2400 BC). There are also indications of Stone Age people harvesting bee products; for example, honey hunting is interpreted from rock art in a prehistoric Holocene context and a beeswax find in a pre-agriculturalist site. However, when and where the regular association of A. mellifera with agriculturalists emerged is unknown. One of the major products of A. mellifera is beeswax, which is composed of a complex suite of lipids including n-alkanes, n-alkanoic acids and fatty acyl wax esters. The composition is highly constant as it is determined genetically through the insect's biochemistry. Thus, the chemical 'fingerprint' of beeswax provides a reliable basis for detecting this commodity in organic residues preserved at archaeological sites, which we now use to trace the exploitation by humans of A. mellifera temporally and spatially. Here we present secure identifications of beeswax in lipid residues preserved in pottery vessels of Neolithic Old World farmers. The geographical range of bee product exploitation is traced in Neolithic Europe, the Near East and North Africa, providing the palaeoecological range of honeybees during prehistory. Temporally, we demonstrate that bee products were exploited continuously, and probably extensively in some regions, at least from the seventh millennium cal BC, likely fulfilling a variety of technological and cultural functions. The close association of A. mellifera with Neolithic farming communities dates to the early onset of agriculture and may provide evidence for the beginnings of a domestication process.

Processed Small RNAs in Archaea and BHB Elements

Bulge-helix-bulge (BHB) elements guide the enzymatic splicing machinery that in Archaea excises introns from tRNAs, rRNAs from their primary precursor, and accounts for the assembly of piece-wise encoded tRNAs. This processing pathway renders the intronic sequences as circularized RNA species. Although archaeal transcriptomes harbor a large number of circular small RNAs, it remains unknown whether most or all of them are produced through BHB-dependent splicing. We therefore conduct a genome-wide survey of BHB elements of a phylogenetically diverse set of archaeal species and complement this approach by searching for BHB-like structures in the vicinity of circularized transcripts. We find that besides tRNA introns, the majority of box C/D snoRNAs is associated with BHB elements. Not all circularized sRNAs, however, can be explained by BHB elements, suggesting that there is at least one other mechanism of RNA circularization at work in Archaea. Pattern search methods were unable, however, to identify common sequence and/or secondary structure features that could be characteristic for such a mechanism.

Effect of autologous adipose tissue-derived mesenchymal stem cells on neovascularization of artificial equine tendon lesions

AIMS

To investigate whether autologous adipose tissue-derived mesenchymal stem cells (AT-MSCs) treatment of tendon lesions increases neovascularization during tendon healing.

MATERIALS & METHODS

A standardized surgical model was used to create lesions in both front limb superficial digital flexor tendons (SDFTs) of nine horses. Either AT-MSCs or control substance was injected intralesionally 2 weeks post-surgery. Color Doppler ultrasonography of SDFTs was performed at regular intervals. Horses were euthanized 22 weeks post-treatment and SDFTs were harvested for histology.

RESULTS

The color Doppler ultrasonography signal was significantly more extensive at 2 weeks post-treatment and the number of vessels counted on histologic slides was significantly higher at 22 weeks post-treatment in AT-MSC-treated SDFTs.

CONCLUSION

Our findings indicate that AT-MSC treatment has a beneficial effect on neovascularization of healing tendons.

The Early Mediaeval manorial estate of Gars/Thunau, Lower Austria: An enclave of endemic tuberculosis?

In recent decades, an increasing number of studies have aimed to shed light on the origin and spread of tuberculosis in past human populations. Here we present the results of a systematic palaeodemographic and palaeopathological survey of the Early Mediaeval population of Gars/Thunau (Lower Austria), which - at this stage - includes 373 individuals recovered at two archaeological sub-sites: a fortified settlement (including a necropolis) at the top of a hill - probably reserved for social and military elites; and a large riverine settlement at the foot of the hill, a so-called 'suburbium', where burials and an area of 'industrial' character were discovered. We recorded a great number of pathological alterations and a variety of 'classical' features of tuberculosis, such as vertebral destructions (Pott's disease) and joint destructions, and other pathological (unspecific) features probably linked with Mycobacterium tuberculosis infection (e.g. new bone formation at the inner surface of the ribs, endocranial alterations in the form of 'pits', and new bone formation at the cranial base). We hypothesize that the two contemporaneous (∼900-1000 AD) populations of Gars/Thunau differed not only in their social affiliation/condition, but also in the type and frequencies of their population-density-related infectious diseases (in particular tuberculosis). Moreover, we investigated the molecular genetic evidence of the causative organism in a few selected immatures exhibiting pathological changes at the inner wall of the cranium and discuss these findings in regard to the macroscopic features observed. Finally, we analysed carbon and nitrogen stable isotopes of both populations and strontium isotope ratios of the hill-top inhabitants in order to reconstruct certain aspects of diet and mobility to test our hypothesis concerning the specific social and/or military character of the site.

Ground-state cooling of a carbon nanomechanical resonator by spin-polarized current

We study the nonequilibrium steady state of a mechanical resonator in the quantum regime realized by a suspended carbon nanotube quantum dot in contact with two ferromagnets. Because of the spin-orbit interaction and/or an external magnetic field gradient, the spin on the dot couples directly to the flexural eigenmodes. Accordingly, the nanomechanical motion induces inelastic spin flips of the tunneling electrons. A spin-polarized current at finite bias voltage causes either heating or active cooling of the mechanical modes. We show that maximal cooling is achieved at resonant transport when the energy splitting between two dot levels of opposite spin equals the vibrational frequency. Even for weak electron-resonator coupling and moderate polarizations we can achieve ground-state cooling with a temperature of the leads, for instance, of T = 10 ω.

A sensitive and robust method for automated on-line monitoring of enzymatic activities in water and water resources

The realisation of a novel concept for automated on-line monitoring of enzymatic activities in water was successfully demonstrated by long-term field testing at two remote Austrian ground water resources. The β-D-glucuronidase (GLUC) activity was selected as a representative enzymatic model parameter for the on-line determination. But the device can be adapted for any enzymatic reaction with diagnostic relevance for microbial water quality monitoring, as demonstrated for the β-D-galactosidase activity. Automated filtration of volumes up to 5 litres supports sensitive quantification of enzymatic activities. Internet-based data transfer, using internal control parameters for verification and a dynamic determination of the limit of quantification, enabled robust enzymatic on-line monitoring during a 2-year period. A proportion of 5,313 out of 5,506 GLUC activity measurements (96.5%) could be positively verified. Hydrological (discharge, gauge, turbidity, temperature, pH, electric conductivity, spectral absorbance coefficient at 254 nm) as well as microbiological parameters (Escherichia coli, coliforms) were concurrently determined to characterise the investigated ground water resources. The enzymatic on-line measurements closely reflected the different hydrological conditions and contamination patterns of the test sites. Contrary to expectations, GLUC did not qualify as a proxy-parameter for the occurrence of cultivation-based E. coli contamination and warrants further detailed investigations on its indication capacity as a rapid means for microbial faecal pollution detection in such aquatic habitats. Microbial on-line monitoring is likely to become more important in the future, complementing existing surveillance strategies for water safety management. Further perspectives on the application of such analytical on-line technologies, such as their connection with event-triggered sampling and standardised diagnostics, are discussed.

Functional ecology of the ciliate Glaucomides bromelicola, and comparison with the sympatric species Bromeliothrix metopoides

We investigated the ecology and life strategy of Glaucomides bromelicola (family Bromeliophryidae), a very common ciliate in the reservoirs (tanks) of bromeliads, assessing its response to food quality and quantity and pH. Further, we conducted competition experiments with the frequently coexisting species Bromeliothrix metopoides (family Colpodidae). In contrast to B. metopoides and many other colpodean ciliates, G. bromelicola does not form resting cysts, which jeopardizes this ciliate when its small aquatic habitats dry out. Both species form bactivorous microstomes and flagellate-feeding macrostomes. However, only G. bromelicola has a low feeding threshold and is able to adapt to different protist food. The higher affinity to the local bacterial and flagellate food renders it the superior competitor relative to B. metopoides. Continuous encystment and excystment of the latter may enable stable coexistence of both species in their natural habitat. Both are tolerant to a wide range of pH (4–9). These ciliates appear to be limited to tank bromeliads because they either lack resting cysts and vectors for long distance dispersal (G. bromelicola) and/or have highly specific food requirements (primarily B. metopoides).

Systematics and species-specific response to pH of Oxytricha acidotolerans sp. nov. and Urosomoida sp. (Ciliophora, Hypotricha) from acid mining lakes

We investigated the morphology, phylogeny of the 18S rDNA, and pH response of Oxytricha acidotolerans sp. nov. and Urosomoida sp. (Ciliophora, Hypotricha) isolated from two chemically similar acid mining lakes (pH~2.6) located at Langau, Austria, and in Lusatia, Germany. Oxytricha acidotolerans sp. nov. from Langau has 18 frontal-ventral-transverse cirri but a very indistinct kinety 3 fragmentation so that the assignment to Oxytricha is uncertain. The somewhat smaller species from Lusatia has a highly variable cirral pattern and the dorsal kineties arranged in the Urosomoida pattern and is, therefore, preliminary designated as Urosomoida sp. The pH response was measured as ciliate growth rates in laboratory experiments at pH ranging from 2.5 to 7.0. Our hypothesis was that the shape of the pH reaction norm would not differ between these closely related (3% difference in their SSU rDNA) species. Results revealed a broad pH niche for O. acidotolerans, with growth rates peaking at moderately acidic conditions (pH 5.2). Cyst formation was positively and linearly related to pH. Urosomoida sp. was more sensitive to pH and did not survive at circumneutral pH. Accordingly, we reject our hypothesis that similar habitats would harbour ciliate species with virtually identical pH reaction norm.

Bromeliothrix metopoides, a boom and bust ciliate (Ciliophora, Colpodea) from tank bromeliads

We investigated the recently described colpodid ciliate Bromeliothrix metopoides in a series of laboratory experiments to reveal the environmental factors that constrain this species to its peculiar habitat, i.e. the tanks of bromeliads. Our results demonstrated that the various life stages of this ciliate (bacterivorous theronts and microstome trophonts, flagellate-feeding macrostomes) have specific demands in terms of food quality and quantity. Bromeliothrix required a high food threshold (>1.4 mg C L⁻¹) in order to thrive. Food quality also affected resting cyst formation of B. metopoides when the experimental containers dried out. Its maximum growth rates (μ_max = 4.71 d⁻¹, i.e. 6.8 doublings d⁻¹) belong to the highest ones recorded thus far for free-living ciliates. The pH niche of B. metopoides was relatively wide (pH ∼4 to >9) under optimal food conditions. However, its high sensitivity to unfavourable environmental conditions let the population collapse within several hours. We conclude that B. metopoides is a boom and bust ciliate that is specifically adapted to its peculiar habitat but virtually unviable in other environments.

[Comparison of different electrocardiographic techniques for the detection of arrhythmias in horses]

OBJECTIVE

The aim of the study was to extend the range of the electrocardiographic examination in horses, evaluating the practicability of special electrocardiographic techniques (exercise- and Holter-ECG) and comparing these with more common techniques (resting-ECG) in equine medicine.

MATERIAL AND METHODS

Electrocardiographic examination (resting-ECG for 1 minute, exercise-ECG and Holter-ECG) was performed in 20 horses without any clinical or echocardiographic findings and in 80 patients with abnormal findings (valvular regurgitation and/or atrial fibrillation).

RESULTS

In comparison with the resting-ECG, the exercise-ECG demonstrated more atrial and ventricular premature beats, while the Holter-ECG had a higher detection rate of 2nd degree atrioventricular or sinuatrial blocks, and of ventricular and atrial premature depolarisations (p < 0.001). In comparison to the exercise-ECG, the Holter-ECG registered more 2nd degree atrioventricular blocks (p < 0.001) and ventricular (p < 0.001) or atrial premature contractions (p < 0.01). Atrial fibrillation was detected in every recorded ECG-type, but Holter-ECG provided additional information. Three of 16 horses with atrial fibrillation had R-on-T-episodes during Holter-monitoring. In addition to more common findings in the ECG, Holter-monitoring detected a 2nd degree atrioventricular block associated with an adjacent ventricular escape beat in a horse without any clinical or echocardiographic findings. An accelerated idioventricular rhythm was identified in a horse without any clinical or echocardiographic findings and in a horse with mitral valve insufficiency.

CONCLUSION AND CLINICAL RELEVANCE

The Holter-ECG is a useful tool in the evaluation of heart disease and could supply additional information when compared to the usual diagnostic electrocardiographic procedures used in horses. Exercise-ECG should not be replaced by Holter-ECG, however, Holter-EGC can provide additional diagnostic value.

Vergleichende Untersuchung von elektrokardiographischen Techniken zur Diagnostik von Herzrhythmusstörungen beim Pferd

Das Ziel dieser Studie war, die Befunde des Langzeit-EKGs beim Pferd mit denen des Belastungs- und des Ruhe-EKGs zu vergleichen. Material und Methode: Zwanzig klinisch und echokardiographisch unauffällige Kontrolltiere und 80 Patienten mit Klappeninsuffizienzen und/oder Vorhofflimmern wurden elektrokardiographisch untersucht. Die elektrokardiographischen Aufzeichnungen umfassten ein einminütiges Ruhe-EKG, ein Belastungs-EKG an der Longe und ein Langzeit-EKG über 24 Stunden. Ergebnisse: Im Vergleich zum Ruhe-EKG wurden Vorhof- und ventrikuläre Extrasystolen mithilfe des Belastungs-EKGs signifikant (p < 0,001) häufiger erkannt. Anhand des Langzeit-EKGs konnten signifikant mehr AV-Blöcke 2. Grades, sinuatriale Blöcke sowie Vorhof- und ventrikuläre Extrasystolen festgestellt werden als mithilfe des Ruhe-EKGs (p < 0,001). Beim Vergleich zwischen Belastungs-EKG und Langzeit-EKG zeigten sich im Langzeit-EKG signifikant häufiger AV-Blöcke 2. Grades (p < 0,001) sowie Extrasystolen atrialen (p < 0,001) und ventrikulären Ursprungs (p < 0,01). Vorhofflimmern wurde mit allen drei EKG-Techniken erfasst. Mittels Langzeit-EKG ließen sich allerdings neben dem Vorhofflimmern weitere elektrokardiographische Befunde erheben. Drei Tiere mit Vorhofflimmern zeigten zusätzlich das R-auf-T-Phänomen. Bei einem Pferd ohne klinische und echokardiographische Befunde traten im Langzeit-EKG Phasen mit je einem ventrikulären Ersatzschlag direkt nach einem AV-Block 2. Grades auf. Außerdem zeigten ein Kontrolltier und ein Pferd mit Mitralklappeninsuffizienz einen akzelerierten idioventrikulären Rhythmus. Schlussfolgerung und klinische Relevanz: Insgesamt erscheint es sinnvoll, das Langzeit-EKG wegen seines zusätzlichen Informationsgehalts in der Diagnostik von Herzerkrankungen häufiger anzuwenden als bisher üblich. Dabei sollte jedoch das Belastungs-EKG nicht ersetzt, sondern durch die Informationen des Langzeit-EKGs ergänzt werden.

Analyses of pig genomes provide insight into porcine demography and evolution

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Current trends in the diagnosis of vascular prosthesis infection

Early diagnosis of an infected vascular prosthesis, a potentially life-threatening disease, is a precondition of adequate treatment. The most frequently used diagnostic imaging method is computer tomography. Non-acute infections caused by low grade agents may pose a challenge with ambiguous CT-images and other ancillary imaging methods are used for these cases, each offering different levels of diagnostic sensitivity. These methods come from the fields of radiology (magnetic resonance imaging - MRI) and nuclear medicine studies using labelled leukocytes (111In or 99mTc HMPAO), 99mTc labelled antigranulocyte antibodies, 67Ga-citrate or labelled antibiotics (99mTc-ciprofloxacin) or avidin in combination with 111In-biotin. Positron emission tomography (PET) or hybrid PET/CT using 18F-FDG are becoming increasingly popular. The authors of this review article point out the diagnostic potential of the different methods and current trends, including the possibilities of microbiological demonstration of the agent, as well as their potential position in the diagnostic algorithm.

High mobility, low voltage operating C(60) based n-type organic field effect transistors

We report on C(60) based organic field effect transistors (OFETs) that are well optimized for low voltage operation. By replacing commonly used dielectric layers by thin parylene films or by utilizing different organic materials like divinyltetramethyldisiloxane-bis(benzocyclo-butene) (BCB), low density polyethylene (PE) or adenine in combination with aluminum oxide (AlOx) to form a bilayer gate dielectric, it was possible to significantly increase the capacitance per unit area (up to two orders of magnitude). The assembly of metal-oxide and organic passivation layer combines the properties of the high dielectric constant of the metal oxide and the good organic-organic interface between semiconductor and insulator provided by a thin capping layer on top of the AlOx film. This results in OFETs that operate with voltages lower than 500 mV, while exhibiting field effect mobilities exceeding 3 cm(2) V(-1) s(-1).