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Background: Mutant analysis remains one of the main genetic tools for characterising unclarified gene functions in plants, especially in non-model plants. Daylily (Hemerocallis spp.) is a popular perennial ornamental plant grown worldwide. Analysis of daylily mutants can enhance understanding of genes regulating the albino phenotype and improve the cultivar quality of daylily. Methods: The natural albino mutant (Alb-⁣/-) was isolated by screening a self-pollinated progeny of daylily cultivar ‘black-eyed stella’. Transmission electron microscopy was used in analysing the structure of plastids between mutant and wild-type seedlings. The content of chlorophyll, carotenoids and chlorophyll precursors in plants was measured by ultraviolet spectrophotometry. RNA sequencing and physiological measurements were performed to explore the association between drought tolerance and mutation. Results: All the seedlings of the daylily albino mutants died spontaneously within fifteen days after germination when grown in soil. The carotenoid and chlorophyll content in the leaves of the mutant plants significantly decreased compared with those of the wild-type control. The mutant plants displayed stunted growth, and their leaves were white or light yellow in color. Abnormal plastids such as those showing endomembrane vesiculation and lacking stacking were discovered in the leaves of mutant plants. Furthermore, genetic analysis revealed that a single recessive nuclear gene mutation led to the albino trait, RNA sequencing and real-time quantitative PCR validation showed extensive differences in gene expression between the mutant plants and the wild-type control, and most of the genes related to chlorophyll metabolism were down-regulated, with foldchange ranging from 0.20–0.49. Additionally, the surviving homozygous plants (Alb+⁣/+), which do not contain this mutation, were also isolated by analysing the phenotype of their self-pollinated progeny. The net photosynthesis rate and light saturation point of Alb+⁣/+ were higher than those of heterozygous (Alb+⁣/-) plants. Additionally, the Alb+⁣/+ plants were more tolerant to drought conditions than the Alb+⁣/- plants, suggesting that a heterozygous Alb- mutation is sufficient to negatively affect photosynthetic efficiency and drought tolerance. Conclusions: The albino mutation negatively affects photosynthetic efficiency and drought tolerance, and homozygous mutation is required for the characteristic albino phenotype. This work highlights the link between albino mutation, photosynthetic pigment metabolism and drought sensitivity in daylily.

Her-2/neu-targeting therapy by passive application with trastuzumab is associated with acquired resistance and subsequent metastasis development, which is attributed to the upregulation of tumoral PD-L1 expression and the downregulation of Her-2/neu. We aimed to investigate this association, following active immunization with our recently constructed B-cell peptide-based Her-2/neu vaccines in both preclinical and clinical settings. Immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), and combined positive score (CPS) were applied to evaluate Her-2/neu and PD-L1 expression using a murine syngeneic tumor model for Her-2/neu lung metastases and tumor biopsies from a gastric cancer patient with disease progression. A significant and concomitant reduction in Her-2/neu and the upregulation of PD-L1 expression was observed in vaccinated mice after 45 days, but not after 30 days, of metastases development. A significant increase in tumor-infiltrating B lymphocytes was observed at both time points. The downregulation of Her-2/neu and the upregulation of PD-L1 were observed in a patient’s primary tumor at the disease progression time point but not prior to vaccination (Her-2/neu IHC: 3 to 0, FISH: 4.98 to 1.63; PD-L1 CPS: 0% to 5%). Our results further underline the need for combination therapy by targeting PD-L1 to prevent metastasis formation and immune evasion of Her-2/neu-positive and PD-L1-negative tumor cells.

Alave-Furrer et al adapted their recently-developed 3D bioprinting platform to allow microvalve-based drop-on-demand printing of cell-laden Matrigel containing primary human muscle precursor cells. Their bioprinting platform recapitulated aspects of exercise and pharmacological responses and thus could aid the engineering of more complex 3D microphysiological systems.

Subjective cognitive decline (SCD) and mild cognitive impairment (MCI) are early stages of Alzheimer’s disease (AD). Neurophysiological markers such as electroencephalography (EEG) and event-related potential (ERP) are emerging as alternatives to traditional molecular and imaging markers. This paper aimed to review the literature on EEG and ERP markers in individuals with SCD. We analysed 30 studies that met our criteria, with 17 focusing on resting-state or cognitive task EEG, 11 on ERPs, and two on both EEG and ERP parameters. Typical spectral changes were indicative of EEG rhythm slowing and were associated with faster clinical progression, lower education levels, and abnormal cerebrospinal fluid biomarkers profiles. Some studies found no difference in ERP components between SCD subjects, controls, or MCI, while others reported lower amplitudes in the SCD group compared to controls. Further research is needed to explore the prognostic value of EEG and ERP in relation to molecular markers in individuals with SCD.

Abstract Motivation Simultaneous alignment and folding (SA&F) of RNAs is the indispensable gold standard for inferring the structure of non-coding RNAs and their general analysis. The original algorithm, proposed by Sankoff, solves the theoretical problem exactly with a complexity of $$O(n^6)$$ O ( n 6 ) in the full energy model. Over the last two decades, several variants and improvements of the Sankoff algorithm have been proposed to reduce its extreme complexity by proposing simplified energy models or imposing restrictions on the predicted alignments. Results Here, we introduce a novel variant of Sankoff’s algorithm that reconciles the simplifications of PMcomp, namely moving from the full energy model to a simpler base pair-based model, with the accuracy of the loop-based full energy model. Instead of estimating pseudo-energies from unconditional base pair probabilities, our model calculates energies from conditional base pair probabilities that allow to accurately capture structure probabilities, which obey a conditional dependency. This model gives rise to the fast and highly accurate novel algorithm Pankov (Probabilistic Sankoff-like simultaneous alignment and folding of RNAs inspired by Markov chains). Conclusions Pankov benefits from the speed-up of excluding unreliable base-pairing without compromising the loop-based free energy model of the Sankoff’s algorithm. We show that Pankov outperforms its predecessors LocARNA and SPARSE in folding quality and is faster than LocARNA.

Background: The determination of kinetic parameters and the development of mathematical models are of great interest to predict the growth of microalgae, the consumption of substrate and the design of photobioreactors focused on CO2 capture. However, most of the models in the literature have been developed for CO2 concentrations below 10%. Results: A nonaxenic microalgal consortium was isolated from landfill leachate in order to study its kinetic behavior using a dynamic model. The model considered the CO2 mass transfer from the gas phase to the liquid phase and the effect of light intensity, assimilated nitrogen concentration, ammonium concentration and nitrate concentration. The proposed mathematical model was adjusted with 13 kinetic parameters and validated with a good fit obtained between experimental and simulated data. Conclusions: Good results were obtained, demonstrating the robustness of the proposed model. The assumption in the model of DIC inhibition in the ammonium and nitrate uptakes was correct, so this aspect should be considered when evaluating the kinetics with microalgae with high inlet CO2 concentrations. Keywords: Dynamic model, Nonaxenic consortium, Photon flux density, Mass transfer, Leachate, Landfill, Ammonium, Nitrate, Carbon dioxide

Abstract Background Seed and accessibility constraints are core features to enable highly accurate sRNA target screens based on RNA-RNA interaction prediction. Currently, available tools provide different (sets of) constraints and default parameter sets. Thus, it is hard to impossible for users to estimate the influence of individual restrictions on the prediction results. Results Here, we present a systematic assessment of the impact of established and new constraints on sRNA target prediction both on a qualitative as well as computational level. This is done exemplarily based on the performance of IntaRNA, one of the most exact sRNA target prediction tools. IntaRNA provides various ways to constrain considered seed interactions, e.g. based on seed length, its accessibility, minimal unpaired probabilities, or energy thresholds, beside analogous constraints for the overall interaction. Thus, our results reveal the impact of individual constraints and their combinations. Conclusions This provides both a guide for users what is important and recommendations for existing and upcoming sRNA target prediction approaches.We show on a large sRNA target screen benchmark data set that only by altering the parameter set, IntaRNA recovers 30% more verified interactions while becoming 5-times faster. This exemplifies the potential of seed, accessibility and interaction constraints for sRNA target prediction.

A pilot-scale biotrickling filter (BTF) was operated in counter-current flow mode under anoxic conditions, using diluted agricultural digestate as inoculum and as the recirculation medium for the nutrient source. The process was tested on-site at an agricultural fermentation plant, where real biogas was used. The pilot plant was therefore exposed to real process-related fluctuations. The purpose of this research was to attest the validity of the filtration process for use at an industrial-scale by operating the pilot plant under realistic conditions. Neither the use of agricultural digestate as trickling liquid and nor a BTF of this scale have previously been reported in the literature. The pilot plant was operated for 149 days. The highest inlet load was 8.5 gS-H2Sm−3h−1 with a corresponding removal efficiency of 99.2%. The pH remained between 7.5 and 4.6 without any regulation throughout the complete experimental phase. The analysis of the microbial community showed that both anaerobic and anoxic bacteria can adapt to the fluctuating operating conditions and coexist simultaneously, thus contributing to the robustness of the process. The operation of an anoxic BTF with agricultural digestate as the trickling liquid proved to be viable for industrial-scale use.

Con el objetivo de identificar las propiedades químicas y los antioxidantes de interés en la industria de los biopolímeros se realizó la caracterización química del jugo de cuatro variantes de cladodios de Opuntia megacantha; las variantes presentan dos grados de madurez (tiernos y maduros) y dos manejos diferentes durante su desarrollo (silvestres y cultivados). El grado de madurez de los cladodios fue estadísticamente significativo (p ≤ 0.05), el jugo de los cladodios maduros presentó mayor cantidad de fibra cruda y material libre de nitrógeno, el jugo de cladodios tiernos contiene mayor cantidad de proteína, extracto etéreo y cenizas. No existió diferencia estadística significativa (p = 0.6917), en el contenido de los fenoles en las cuatro variantes se obtuvieron concentraciones entre 165.6 y 176.6 mg GAE/mL; (2.18 y 3.61 mg GAE/g en peso seco). Los jugos de los cladodios maduros contienen mayor cantidad de los diferentes azúcares cuantificados (p ≤ 0.05). Se prepararon películas de biopolímero utilizando jugo clarificado de cladodios silvestres tiernos para determinar su resistencia a la tensión con un resultado de 1.42 MPa, módulo de Young de 1.77 MPa y elongación a la rotura de 124.16%; se concluye que los jugos caracterizados en este trabajo pueden ofrecer una alternativa viable a los polímeros derivados del petróleo.

A single-center study was conducted on 120 patients with inherited disorders of primary hemostasis followed at our hematological center. These patients presented a variety of bleeding symptoms; however, they had no definitive diagnosis. Establishing a diagnosis has consequences for the investigation of probands in families and for treatment management; therefore, we aimed to improve the diagnosis rate in these patients by implementing advanced diagnostic methods. According to the accepted international guidelines at the time of study, we investigated platelet morphology, platelet function assay, light-transmission aggregometry, and flow cytometry. Using only these methods, we were unable to make a definitive diagnosis for most of our patients. However, next-generation sequencing (NGS), which was applied in 31 patients, allowed us to establish definitive diagnoses in six cases (variants in ANKRD26, ITGA2B, and F8) and helped us to identify suspected variants (NBEAL2, F2, BLOC1S6, AP3D1, GP1BB, ANO6, CD36, and ITGB3) and new suspected variants (GFI1B, FGA, GP1BA, and ITGA2B) in 11 patients. The role of NGS in patients with suspicious bleeding symptoms is growing and it changes the diagnostic algorithm. The greatest disadvantage of NGS, aside from the cost, is the occurrence of gene variants of uncertain significance.

The intricate interplay between the immune system and microbes is an essential part of the physiological homeostasis in health and disease. Immunological recognition of commensal microbes, such as bacterial species resident in the gut or lung as well as dormant viral species, i.e., cytomegalovirus (CMV) or Epstein-Barr virus (EBV), in combination with a balanced immune regulation, is central to achieve immune-protection. Emerging evidence suggests that immune responses primed to guard against commensal microbes may cause unexpected pathological outcomes, e.g., chronic inflammation and/or malignant transformation. Furthermore, translocation of immune cells from one anatomical compartment to another, i.e., the gut-lung axis via the lymphatics or blood has been identified as an important factor in perpetrating systemic inflammation, tissue destruction, as well as modulating host-protective immune responses. We present in this review immune response patterns to pathogenic as well as non-pathogenic microbes and how these immune-recognition profiles affect local immune responses or malignant transformation. We discuss personalized immunological therapies which, directly or indirectly, target host biological pathways modulated by antimicrobial immune responses.

De novo shoot organogenesis (DNSO) is a procedure commonly used for the in vitro regeneration of shoots from a variety of plant tissues. Shoot regeneration occurs on nutrient media supplemented with the plant hormones cytokinin (CK) and auxin, which play essential roles in this process, and genes involved in their signaling cascades act as master regulators of the different phases of shoot regeneration. In the last 20 years, the genetic regulation of DNSO has been characterized in detail. However, as of today, the CK and auxin signaling events associated with shoot regeneration are often interpreted as a consequence of these hormones simply being present in the regeneration media, whereas the roles for their prior uptake and transport into the cultivated plant tissues are generally overlooked. Additionally, sucrose, commonly added to the regeneration media as a carbon source, plays a signaling role and has been recently shown to interact with CK and auxin and to affect the efficiency of shoot regeneration. In this review, we provide an integrative interpretation of the roles for CK and auxin in the process of DNSO, adding emphasis on their uptake from the regeneration media and their interaction with sucrose present in the media to their complex signaling outputs that mediate shoot regeneration.

The ecological value of abandoned quarries has gained increasing scientific attention in the last few decades, resulting in a paradigm shift in restoration programs regarding the use of natural processes. The linkages between biotic and abiotic diversity, such as landform and microclimatic diversity have been analyzed only slightly, however. In this paper, we use an interdisciplinary approach that includes vegetation mapping, geomorphological mapping, microclimatic measurements and modeling to reveal the specific two‑way linkages between abiotoc and biotic diversity. The present case study shows that in only 60 years landform diversity allowed the development of nine distinct biotopes with 134 identified species. At the same time, the vegetation diversity at these human‑induced biotopes is of high ecological value as it displays significant similarities with natural biotopes in the region (e.g., scree slope and rock cliff biotopes). Based on the results presented, the paper aims to contribute to current restoration programs involving processes of spontaneous succession and landforming.

Influenza viruses (IVs) tend to rapidly develop resistance to virus-directed vaccines and common antivirals targeting pathogen determinants, but novel host-directed approaches might preclude resistance development. To identify the most promising cellular targets for a host-directed approach against influenza, we performed a comparative small interfering RNA (siRNA) loss-of-function screen of IV replication in A549 cells. Analysis of four different IV strains including a highly pathogenic avian H5N1 strain, an influenza B virus (IBV) and two human influenza A viruses (IAVs) revealed 133 genes required by all four IV strains. According to gene enrichment analyses, these strain-independent host genes were particularly enriched for nucleocytoplasmic trafficking. In addition, 360 strain-specific genes were identified with distinct patterns of usage for IAVs versus IBV and human versus avian IVs. The strain-independent host genes served to define 43 experimental and otherwise clinically approved drugs, targeting reportedly fourteen of the encoded host factors. Amongst the approved drugs, the urea-based kinase inhibitors (UBKIs) regorafenib and sorafenib exhibited a superior therapeutic window of high IV antiviral activity and low cytotoxicity. Both UBKIs appeared to block a cell signaling pathway involved in IV replication after internalization, yet prior to vRNP uncoating. Interestingly, both compounds were active also against unrelated viruses including cowpox virus (CPXV), hantavirus (HTV), herpes simplex virus 1 (HSV1) and vesicular stomatitis virus (VSV) and showed antiviral efficacy in human primary respiratory cells. An in vitro resistance development analysis for regorafenib failed to detect IV resistance development against this drug. Taken together, the otherwise clinically approved UBKIs regorafenib and sorafenib possess high and broad-spectrum antiviral activity along with substantial robustness against resistance development and thus constitute attractive host-directed drug candidates against a range of viral infections including influenza.

Forensically trained facial reviewers are still considered as one of the most accurate approaches for person identification from video records. The human brain can utilize information, not just from a single image, but also from a sequence of images (i.e., videos), and even in the case of low-quality records or a long distance from a camera, it can accurately identify a given person. Unfortunately, in many cases, a single still image is needed. An example of such a case is a police search that is about to be announced in newspapers. This paper introduces a face database obtained from real environment counting in 17,426 sequences of images. The dataset includes persons of various races and ages and also different environments, different lighting conditions or camera device types. This paper also introduces a new multi-frame face super-resolution method and compares this method with the state-of-the-art single-frame and multi-frame super-resolution methods. We prove that the proposed method increases the quality of face images, even in cases of low-resolution low-quality input images, and provides better results than single-frame approaches that are still considered the best in this area. Quality of face images was evaluated using several objective mathematical methods, and also subjective ones, by several volunteers. The source code and the dataset were released and the experiment is fully reproducible.

In silico RNA-RNA interaction prediction is widely applied to identify putative interaction partners and to assess interaction details in base pair resolution. To verify specific interactions, in vitro evidence can be obtained via compensatory mutation experiments. Unfortunately, the selection of compensatory mutations is non-trivial and typically based on subjective ad hoc decisions. To support the decision process, we introduce our COmPensatOry MUtation Selector CopomuS. CopomuS evaluates the effects of mutations on RNA-RNA interaction formation using a set of objective criteria, and outputs a reliable ranking of compensatory mutation candidates. For RNA-RNA interaction assessment, the state-of-the-art IntaRNA prediction tool is applied. We investigate characteristics of successfully verified RNA-RNA interactions from the literature, which guided the design of CopomuS. Finally, we evaluate its performance based on experimentally validated compensatory mutations of prokaryotic sRNAs and their target mRNAs. CopomuS predictions highly agree with known results, making it a valuable tool to support the design of verification experiments for RNA-RNA interactions. It is part of the IntaRNA package and available as stand-alone webserver for ad hoc application.

The investigation of RNA-based regulation of cellular processes is becoming an increasingly important part of biological or medical research. For the analysis of this type of data, RNA-related prediction tools are integrated into many pipelines and workflows. In order to correctly apply and tune these programs, the user has to have a precise understanding of their limitations and concepts. Within this manuscript, we provide the mathematical foundations and extract the algorithmic ideas that are core to state-of-the-art RNA structure and RNA-RNA interaction prediction algorithms. To allow the reader to change and adapt the algorithms or to play with different inputs, we provide an open-source web interface to JavaScript implementations and visualizations of each algorithm. The conceptual, teaching-focused presentation enables a high-level survey of the approaches, while providing sufficient details for understanding important concepts. This is boosted by the simple generation and study of examples using the web interface available at http://rna.informatik.uni-freiburg.de/Teaching/. In combination, we provide a valuable resource for teaching, learning, and understanding the discussed prediction tools and thus enable a more informed analysis of RNA-related effects.

Biotrickling filters’ control for H2S removal has special challenges because of complexity of the systems. Feedback and feedforward control were implemented in an anoxic biotrickling filter, operated in co-current flow mode and using nitrite as an electron acceptor. The feedback controller was tuned by three methods—two based on Ziegler-Nichols’ rules (step-response and maintained oscillation) and the third using the Approximate M-constrained Integral Gain Optimization (AMIGO). Inlet H2S staircase step perturbations were studied using a feedforward control and the effect of EBRT considered by feedback control. The tuning method by maintained oscillation shows the lower errors. The selected controller was a PI, because unstable behavior at the lowest H2S inlet loading was found under a PID controller. The PI control was able to maintain an outlet H2S concentration of 14.7 ± 0.45 ppmV at three EBRT, studied at 117 s, 92 s and 67 s. Therefore, desulfurized biogas could be used to feed a fuel cell. Feedforward control enhances BTF performance compared to the system without control. The maximum outlet H2S concentration was reduced by 26.18%, although sulfur selectivity did not exceed 55%, as elemental sulfur was the main oxidation product.

Immune responses to human cytomegalovirus (CMV) can be used to assess immune fitness in an individual. Further to its clinical significance in posttransplantation settings, emerging clinical and translational studies provide examples of immune correlates of protection pertaining to anti-CMV immune responses in the context of cancer or infectious diseases, e.g., tuberculosis. In this viewpoint, we provide a brief overview about CMV-directed immune reactivity and immune fitness in a clinical context and incorporate some of our own findings obtained from peripheral blood or tumour-infiltrating lymphocytes (TIL) from patients with advanced cancer. Observations in patients with solid cancers whose lesions contain both CMV and tumour antigen-specific T-cell subsets are highlighted, due to a possible CMV-associated “bystander„ effect in amplifying local inflammation and subsequent tumour rejection. The role of tumour-associated antibodies recognising diverse CMV-derived epitopes is also discussed in light of anti-cancer immune responses. We discuss here the use of anti-CMV immune responses as a theranostic tool—combining immunodiagnostics with a personalised therapeutic potential—to improve treatment outcomes in oncological indications.

Expanding from remote areas of Mexico to a worldwide scale, the ten-striped insect, the Colorado potato beetle (CPB, Leptinotarsa decemlineata Say), has risen from being an innocuous beetle to a prominent global pest. A diverse life cycle, phenotypic plasticity, adaptation to adverse conditions, and capability to detoxify or tolerate toxins make this insect appear to be virtually “indestructible”. With increasing advances in molecular biology, tools of biotechnological warfare were deployed to combat CPB. In the last three decades, genetically modified potato has created a new challenge for the beetle. After reviewing hundreds of scientific papers dealing with CPB control, it became clear that even biotechnological means of control, if used alone, would not defeat the Colorado potato beetle. This control measure once again appears to be provoking the potato beetle to exhibit its remarkable adaptability. Nonetheless, the potential for adaptation to these techniques has increased our knowledge of this pest and thus opened possibilities for devising more sustainable CPB management programs.

Visualization and quantification of inflammatory processes is of high importance for early diagnosis of a multitude of diseases. Magnetic resonance imaging (MRI) using iron oxide (FeO) nanoparticles as contrast agents allows the study of macrophage infiltration during inflammation in a variety of tissues. Macrophages are effectors of the immune response, their appearance being orchestrated by activated T lymphocytes. Therefore, tracking of labeled T lymphocytes, which initiate the immune process, should enable earlier detection of tissue inflammation. In this study, we investigate the feasibility of specifically labeling harvested T cells by using dextran-coated FeO nanoparticles and commonly available transfection agents (TAs). Physicochemical properties of the newly formed FeO/TA vesicles were determined as well as their cell toxicity and their T cell activation potential. The labeling efficiency of each FeO/TA combination was evaluated by measuring the transverse MRI relaxation rate R 2 by X-ray spectroscopy and magnetic selection. Toxicity and labeling efficacy differed significantly among TAs. The best results were achieved by using polyamine TAs and in particular by using poly- l -lysine at a concentration of 1.5 µg/mL administered in combination with 22.5 µg iron/mL. By using this protocol, up to 60% of harvested T cells could be labeled. Microscopic investigation revealed FeO/TA nanoparticles not only localized within the cytoplasma of the cells but also sticking to the outer membrane surface.