Biology subjects

Schneider, A.

Publications and source records attributed to Schneider, A..

90 records · Page 5Linked to original sources

bioRxiv2021

Multichannel optogenetics combined with laminar recordings for ultra-controlled neuronal interrogation

Simultaneous large-scale recordings and optogenetic interventions hold the promise to decipher the fast-paced and multifaceted dialogue between neurons that sustains brain function. Here we developed unprecedentedly thin, cell-sized Lambertian side-emitting optical fibers and combined them with silicon probes to achieve high quality recordings and ultrafast multichannel optogenetic inhibition in freely moving animals. Our new framework paves the way for large-scale photo tagging and controlled interrogation of rapid neuronal communication in any combination of brain areas. HighlightsTo combine large-scale recordings with optical perturbation we have developed a number of new techniques such as thin optical side-emitting fibers, a fiber matrix connector for thin fibers, an electro-optical commutator for multiple thin fibers, an active patch cord, a flexible fiber bundle ribbon cable, and a modular multi-optrode implantation holder.

neuroscience↗

bioRxiv2020

Role of bradykinin type 2 receptors in human sweat secretion: translational evidence does not support a functional relationship

Bradykinin increases skin blood flow via a cGMP mechanism but its role in sweating in vivo is unclear. There is a current need to translate cell culture and non-human paw pad studies into in vivo human preparations to test for therapeutic viability for disorders affecting sweat glands. Protocol 1: physiological sweating was induced in 10 healthy subjects via perfusing warm (46-48{degrees}C) water through a tube-lined suit while bradykinin type 2 receptor (B2R) antagonist (HOE-140; 40 M) and only the vehicle (lactated Ringers) were perfused intradermally via microdialysis. Heat stress increased sweat rate (HOE-140 = +0.79{+/-}0.12 and vehicle = +0.64{+/-}0.10 mg/cm2/min), but no differences were noted with B2R antagonism. Protocol 2: pharmacological sweating was induced in 6 healthy subjects via intradermally perfusing pilocarpine (1.67 mg/ml) followed by the same B2R antagonist approach. Pilocarpine increased sweating (HOE-140 = +0.38{+/-}0.16 and vehicle = +0.32{+/-}0.12 mg/cm2/min); again no differences were observed with B2R antagonism. Lastly, 5 additional subjects were recruited for various control experiments which identified that a functional dose of HOE-140 was utilized and it was not sudorific during normothermic conditions. These data indicate B2R antagonists do not modulate physiologically-or pharmacologically-induced eccrine secretion volumes. Thus, B2R agonist/antagonist development as a potential therapeutic target for hypo- and hyperhidrosis appears unwarranted.

physiology↗

bioRxiv2020

Deep-learning based denoising and reconstruction of super-resolution structured illumination microscopy images

Super-resolution structured illumination microscopy (SR-SIM) provides an up to two-fold enhanced spatial resolution of fluorescently labeled samples. The reconstruction of high quality SR-SIM images critically depends on patterned illumination with high modulation contrast. Noisy raw image data, e.g. as a result of low excitation power or low exposure times, result in reconstruction artifacts. Here, we demonstrate deep-learning based SR-SIM image denoising that results in high quality reconstructed images. A residual encoding-decoding convolution neural network (RED-Net) was used to successfully denoise computationally reconstructed noisy SR-SIM images. We also demonstrate the entirely deep-learning based denoising and reconstruction of raw SIM images into high-resolution SR-SIM images. Both image reconstruction methods prove to be very robust against image reconstruction artifacts and generalize very well over various noise levels. The combination of computational reconstruction and subsequent denoising via RED-Net shows very robust performance during inference after training even if the microscope settings change.

biophysics↗

bioRxiv2020

Identification of Interleukin1β as an Amplifier of Interferon alpha-induced Antiviral Responses

The induction of an interferon-mediated response is the first line of defense against pathogens such as viruses. Yet, the dynamics and extent of interferon alpha (IFN)-induced antiviral genes vary remarkably and comprise three expression clusters: early, intermediate and late. By mathematical modeling based on time-resolved quantitative data, we identified mRNA stability as well as a negative regulatory loop as key mechanisms endogenously controlling the expression dynamics of IFN-induced antiviral genes in hepatocytes. Guided by the mathematical model, we uncovered that this regulatory loop is mediated by the transcription factor IRF2 and showed that knock-down of IRF2 results in enhanced expression of early, intermediate and late IFN-induced antiviral genes. Co-stimulation experiments with different pro-inflammatory cytokines revealed that this amplified expression dynamics of the early, intermediate and late IFN-induced antiviral genes can be mimicked by co-application of IFN and interleukin1 beta (IL1{beta}). Consistently, we found that IL1{beta} enhances IFN-mediated repression of viral replication. Conversely, we observed that in IL1{beta} receptor knock-out mice replication of viruses sensitive to IFN is increased. Thus, IL1{beta} is capable to potentiate IFN-induced antiviral responses and could be exploited to improve antiviral therapies. Author SummaryInnate immune responses contribute to the control of viral infections and the induction of interferon alpha (IFN)-mediated antiviral responses is an important component. However, IFN induces a multitude of antiviral response genes and the expression dynamics of these genes can be classified as early, intermediate and late. Here we show, based on a mathematical modeling approach, that mRNA stability as well as the negative regulator IRF2 control the expression dynamics of IFN-induced antiviral genes. Knock-down of IRF2 resulted in the amplified IFN-mediated induction of the antiviral genes and this amplified expression of antiviral genes could be mimicked by co-stimulation with IFN and IL1{beta}. We observed that co-stimulation with IFN and IL1{beta} enhanced the repression of virus replication and that knock-out of the IL1 receptor in mice resulted in increased replication of a virus sensitive to IFN. In sum, our studies identified IL1{beta} as an important amplifier of IFN-induced antiviral responses.

systems biology↗

bioRxiv2020

Optimization of data-independent acquisition using predicted libraries for deep and accurate proteome profiling

In silico spectral library prediction of all possible peptides from whole organisms has a great potential for improving proteome profiling by data-independent acquisition (DIA) and extending its scope of application. In combination with other recent improvements in the field of mass spectrometry (MS)-based proteomics, including sample preparation, peptide separation and data analysis, we aimed to uncover the full potential of such an advanced DIA strategy by optimization of the data acquisition. The results demonstrate that the combination of high-quality in silico libraries, reproducible and high-resolution peptide separation using micro-pillar array columns as well as neural network supported data analysis enables the use of long MS scan cycles without impairing the quantification performance. The study demonstrates that mean coefficient of variations of 4 % were obtained even at only 1.5 data points per peak (full width at half maximum) across different gradient lengths, which in turn improved proteome coverage up to more than 8000 proteins from HeLa cells using empirically-corrected libraries and more than 7000 proteins using a whole human in silico predicted library. These data were obtained using a Q Exactive orbitrap mass spectrometer with moderate scanning speed (12 Hz) and perform very well in comparison to recent studies using more advanced MS instruments, which underline the high potential of this optimization strategy for various applications in clinical proteomics, microbiology and molecular biology.

systems biology↗

bioRxiv2020

FreiPose: A Deep Learning Framework for Precise Animal Motion Capture in 3D Spaces

The increasing awareness of the impact of spontaneous movements on neuronal activity has raised the need to track behavior. We present FreiPose, a versatile learning-based framework to directly capture 3D motion of freely definable points with high precision (median error < 3.5% body length, 41.9% improvement compared to state-of-the-art) and high reliability (82.8% keypoints within < 5% body length error boundary, 72.0% improvement). The versatility of FreiPose is demonstrated in two experiments: (1) By tracking freely moving rats with simultaneous electrophysiological recordings in motor cortex, we identified neuronal tuning to behavioral states and individual paw trajectories. (2) We inferred time points of optogenetic stimulation in rat motor cortex from the measured pose across individuals and attributed the stimulation effect automatically to body parts. The versatility and accuracy of FreiPose open up new possibilities for quantifying behavior of freely moving animals and may lead to new ways of setting up experiments.

neuroscience↗

bioRxiv2020

DNA damage and macrophage infiltration in the ovaries of the long-lived GH deficient Ames Dwarf and the short-lived bGH transgenic mice

ObjectiveThe aim of the study was to evaluate the role of growth hormone (GH) in DNA damage, macrophage infiltration and the granulosa cells number of primordial and primary follicles. MethodsFor these experiments six groups of female mice were used. Four groups consisted of Ames dwarf (Prop-1df, df/df, n=12) and their normal littermates (N/df, n=12) mice, between sixteen and eighteen month-old, receiving GH (n=6 for df/df, and n=6 for N/df mice) or saline injections (n=6 for df/df, and n=6 for N/df mice). The other two groups consisted of ten to twelve-month-old bGH (n=6) and normal mice (N, n=6). Immunofluorescence for DNA damage (anti-{gamma}H2AX) and macrophage counting (anti-CD68) were performed. Granulosa cells of primordial and primary follicles were counted. ResultsFemale df/df mice had lower {gamma}H2AX foci intensity in in both oocytes and granulosa cells of primordial and primary follicles (p<0.05), indicating less DNA double strand breaks (DSBs). In addition, GH treatment increased DSBs in both df/df and N/df mice. Inversely, bGH mice had higher quantity of DSBs in both oocytes and granulosa cells of primordial and primary follicles (p<0.05). Df/df mice showed ovarian tissue with less macrophage infiltration than N/df mice (p<0.05) and GH treatment increased macrophage infiltration (p<0.05). On the other hand, bGH mice had ovarian tissue with more macrophage infiltration compared to normal mice (p<0.05). Df/df mice had less granulosa cells on primordial and primary follicles than N/df mice (p<0.05). GH treatment did not affect the granulosa cells number (p>0.05). However, bGH mice had an increased number of granulosa cells on primordial and primary follicles compared to normal mice (p<0.05). ConclusionThe current study points to the role of the GH/IGF-I axis in maintenance of oocyte DNA integrity and macrophage ovarian infiltration in mice.

physiology↗

bioRxiv2019

Evaluation of MALDI-ToF Mass Spectrometry for Rapid Detection of Cereulide from Bacillus cereus Cultures

1.Bacillus cereus plays an often unrecognized role in food borne diseases. Food poisoning caused by this pathogen is manifested by either diarrhea or emesis. While different enterotoxins have been linked to the diarrheal type of B. cereus infections, the emetic toxin cereulide is responsible for the second type. Due to the relatively high prevalence of cereulide associated food poisoning, methods for simple and reliable detection of cereulide producing strains are of utmost importance. Currently, liquid-chromatography coupled to mass spectrometry (LC-MS) is used for sensitive, specific and quantitative cereulide detection, but this technique requires specialized LC-MS equipment, which is often not available in microbiology routine diagnostic laboratories. The last decade has witnessed the advent of matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-ToF MS) as a simple, rapid and cost-efficient technique for identification of microbial pathogens in routine diagnostics. Just recently, two different studies reported on the application of MALDI-ToF MS for either the differentiation of emetic and non-emetic strains of B. cereus or for direct detection of cereulide from bacterial colony smears. However, no method evaluation and optimization was performed in frame of these studies. Thus, additional investigations on the selectivity and sensitivity of MALDI-TOF MS for cereulide detection are needed before implementation of this method in routine diagnostics can be considered. These aspects prompted us to investigate open or controversial issues and to systematically test sample preparation methods, commonly used for microbial identification for their suitability to detect the emetic toxin directly from bacteria. Based on our experimental findings we propose a MALDI-ToF MS workflow that allows identification of B. cereus and sensitive detection of cereulide in parallel, using standard, linear-mode MALDI-ToF MS equipment. The experimental protocol is based on the well-established ethanol/formic acid extraction method and offers, if required, possibilities for further characterization by more sophisticated LC-MS-based methods. In summary, the ease of use and the achieved level of analytical sensitivity as well as the wide-spread availability of standard MALDI-ToF MS equipment in clinical microbiological laboratories provides a promising tool to improve and to facilitate routine diagnostics of B. cereus associated food intoxications.

microbiology↗

bioRxiv2019

Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in silico Peptide Mass Data

1.Over the past decade, modern methods of mass spectrometry (MS) have emerged that allow reliable, fast and cost-effective identification of pathogenic microorganisms. While MALDI-TOF MS has already revolutionized the way microorganisms are identified, recent years have witnessed also substantial progress in the development of liquid chromatography (LC)-MS based proteomics for microbiological applications. For example, LC-tandem mass spectrometry (LC-MS2) has been proposed for microbial characterization by means of multiple discriminative peptides that enable identification at the species, or sometimes at the strain level. However, such investigations can be very time-consuming, especially if the experimental LC-MS2 data are tested against sequence databases covering a broad panel of different microbiological taxa. In this proof of concept study, we present an alternative bottom-up proteomics method for microbial identification. The proposed approach involves efficient extraction of proteins from cultivated microbial cells, digestion by trypsin and LC-MS measurements. MS1 data are then extracted and systematically tested against an in silico library of peptide mass data compiled in house. The library has been computed from the UniProt Knowledgebase Swiss-Prot and TrEMBL databases and comprises more than 12,000 strain-specific in silico profiles, each containing tens of thousands of peptide mass entries. Identification analysis involves computation of score values derived from spectral distances between experimental and in silico peptide mass data and compilation of score ranking lists. The taxonomic positions of the microbial samples are then determined by using the best-matching database entries. The suggested method is computationally efficient - less than two minutes per sample - and has been successfully tested by a set of 19 different microbial pathogens. The approach is rapid, accurate and automatable and holds great potential for future microbiological applications.

microbiology↗

bioRxiv2019

Slow and fast cortical dynamics distinguish motor planning and execution

The smooth conduction of movements requires simultaneous motor planning and execution according to internal goals. So far it is not known how such movement plans can be modified without being distorted by ongoing movements. Previous studies have isolated planning and execution related neuronal activity by separating behavioral planning and movement periods in time by sensory cues1-7. Here, we introduced two novel tasks in which motor planning developed intrinsically. We separated this continuous self-paced motor planning statistically from motor execution by experimentally minimizing the repetitiveness of the movements. Thereby, we found that in the rat sensorimotor cortex, neuronal motor planning processes evolved with slower dynamics than movement related responses both on a sorted unit and population level. The fast evolving neuronal activity preceded skilled forelimb movements while it coincided with movements in a locomotor task. We captured this fast evolving movement related activity via a high-pass filter approach and confirmed the results with optogenetic stimulations. As biological mechanism underlying such a high pass filtering we suggest neuronal adaption. The differences in dynamics combined with a high pass filtering mechanism represents a simple principle for concurrent motor planning and execution in which planning will result in relatively slow dynamics that will not produce movements.

neuroscience↗

bioRxiv2019

Dasatinib Plus Quercetin on Uterine Age-Related Dysfunction and Fibrosis in Mice

Female reproductive function is negatively impacted by age. Animal and human studies show that fibrosis of the uterus contributes to gestational outcomes. Collagen deposition in the myometrial and endometrial layers is the main change related to uterine aging. Senolytic therapies are a potential option for reducing diseases and health complications related to aging. We investigated effects of aging and the senolytic drug combination of dasatinib plus quercetin (D+Q) on uterine fibrosis. A total of 40 mice, 20 young females (03-months) and 20 old females (18-months), were analyzed. Young (Y) and old (O) animals were divided into groups of 10 mice, with one treatment (T) group (YT and OT) and another control (C) group (YC and OC). Comparative analysis of Pi3k/Akt1/mTor and p53 gene expression among the 4 groups was performed to test effects of age and treatment on collagen deposition in uterine tissue. Uterine levels of microRNAs (miR34a, miR34b, miR34c, miR146a, miR449a, miR21a, miR126a, and miR181b) were evaluated. Aging promoted downregulation of genes of the Pi3k/Akt1/mTor signaling pathway (p=0.005, p=0.031, and p=0.028, respectively) as well as a reduction in expression of miR34c (p=0.029), miR126a (p=0.009), and miR181b (p=0.007). D+Q treatment increased p53 gene expression (p=0.041) and decreased levels of miR34a (p=0.016). Our results demonstrate a role for the Pi3k/Akt1/mTor signaling pathway in uterine aging and suggest for the first time a possible anti-fibrotic effect in the uterus of D+Q senolytic therapy.

molecular biology↗

bioRxiv2019

Surface LSP1 is a phenotypic marker distinguishing human classical versus monocyte-derived dendritic cells

Human mononuclear phagocytes comprise several subsets of dendritic cells (DCs), monocytes and macrophages. Distinguishing one population from another is challenging, especially in inflammed tissues, due to the promiscuous expression of phenotypic markers. Using a synthetic library of humanized llama single domain antibodies, we identified a novel surface marker for human naturally-occuring monocyte-derived DCs. Our antibody targets an extra-cellular domain of LSP-1, specifically on monocyte-derived DCs, but not on monocytes, macrophages or classical DCs. Using this antibody, we provide evidence that the recently described blood DC3 population does not correspond to circulating monocyte-derived DCs. Our findings will pave the way for a better characterization of human mononuclear phagocytes in pathological settings.

immunology↗

bioRxiv2019

Large-scale dissection suggests that ultraconserved elements are dispensable for mouse embryonic stem cell survival and fitness

Withdrawal statementThe authors have withdrawn their manuscript from bioRxiv regretfully. During additional experiments for the revision we noticed inconsistencies in some results, which may affect the main conclusion of the manuscript. In particular, we noticed that using different primer pairs, some clones that were classified as homozygous knockouts, are actually not knockouts. These were unexpected findings, but might reflect the recently described larger rearrangements observed using CRISPR technology1,2,3,4. Follow up experiments are ongoing, but we would like to withdraw the manuscript at this point in time to avoid misunderstandings. Therefore, the manuscript should currently not be cited. Any questions regarding the manuscript should be addressed to the corresponding author.

genetics↗

bioRxiv2019

Real-time detection of neural oscillation bursts allows behaviourally relevant neurofeedback

Neural oscillations are increasingly interpreted as transient bursts, yet a method to measure these short-lived events in real-time is missing. Here we present a real-time data analysis system, capable to detect short and narrowband bursts, and demonstrate its usefulness for volitional increase of beta-band burst-rate in rats. This neurofeedback-training induced changes in overall oscillatory power, and bursts could be decoded from the movement of the rats, thus enabling future investigation of the role of oscillatory bursts.

neuroscience↗

bioRxiv2019

Memorability of photographs in subjective cognitive decline and mild cognitive impairment: implications for cognitive assessment

INTRODUCTIONImpaired long-term memory is a defining feature of Mild Cognitive Impairment (MCI). We tested whether this impairment is item-specific, limited to some memoranda whereas some remain consistently memorable.\n\nMETHODSWe conducted item-based analyses of long-term visual recognition memory. 394 participants (healthy controls (HC), Subjective Cognitive Decline (SCD), and MCI) in the multicentric DZNE-Longitudinal Cognitive Impairment and Dementia Study (DELCODE) were tested with images from a pool of 835 photographs.\n\nRESULTSWe observed consistent memorability for images in HCs, SCDs, and MCI, predictable by a neural network trained on another healthy sample. Looking at memorability differences between groups, we identified images that could successfully categorize group membership with higher success and a substantial image reduction than the original image set.\n\nDISCUSSIONIndividuals with SCD and MCI show consistent memorability for specific items, while other items show significant diagnosticity. Certain stimulus features could optimize diagnostic assessment, while others could support memory.

neuroscience↗

bioRxiv2018

Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics based on Acid Extraction

Mass spectrometry is the method of choice for deep and comprehensive analysis of proteomes and has become a key technology to support the progress in life science and biomedicine. However, sample preparation in proteomics is not standardized and contributes to a lack of reproducibility. The main challenge is to extract all proteins in a manner that enables efficient digestion into peptides and is compatible with subsequent mass spectrometric analysis. Current methods are based on the idea of removing detergents or chaotropic agents during sample processing, which are essential for protein extraction but interfere with digestion and LC-MS. These multi-step preparations are prone to losses, biases and contaminations, while being time-consuming and labor-intensive.\n\nWe report a universal detergent-free method, named Sample Preparation by Easy Extraction and Digestion (SPEED), which is based on a simple three-step procedure, acidification, neutralization and digestion. SPEED is a one-pot method for peptide generation from various sources and is easily applicable even for lysis-resistant sample types as pure trifluoroacetic acid (TFA) is used for highly efficient protein extraction. SPEED-based sample processing is highly reproducible, provides exceptional peptide yields and enables preparation even of tissue samples with less than 15 min hands-on time and without any special equipment. Evaluation of SPEED performance revealed, that the number of quantified proteins and the quantitative reproducibility are superior compared to the well-established sample processing protocols FASP, ISD-Urea and SP3 for various sample types, including human cells, bacteria and tissue, even at low protein starting amounts.

systems biology↗

bioRxiv2017

A molecular model of the mitochondrial genome segregation machinery in Trypanosoma brucei

In almost all eukaryotes mitochondria maintain their own genome. Despite the discovery more than 50 years ago still very little is known about how the genome is properly segregated during cell division. The protozoan parasite Trypanosoma brucei contains a single mitochondrion with a singular genome the kinetoplast DNA (kDNA). Electron microscopy studies revealed the tripartite attachment complex (TAC) to physically connect the kDNA to the basal body of the flagellum and to ensure proper segregation of the mitochondrial genome via the basal bodies movement, during cell cycle. Using super-resolution microscopy we precisely localize each of the currently known unique TAC components. We demonstrate that the TAC is assembled in a hierarchical order from the base of the flagellum towards the mitochondrial genome and that the assembly is not dependent on the kDNA itself. Based on biochemical analysis the TAC consists of several non-overlapping subcomplexes suggesting an overall size of the TAC exceeding 2.8 mDa. We furthermore demonstrate that the TAC has an impact on mitochondrial organelle positioning however is not required for proper organelle biogenesis or segregation.\n\nSignificance StatementMitochondrial genome replication and segregation are essential processes in most eukaryotic cells. While replication has been studied in some detail much less is known about the molecular machinery required distribute the replicated genomes. Using super-resolution microscopy in combination with molecular biology and biochemistry we show for the first time in which order the segregation machinery is assembled and that it is assembled de novo rather than in a semi conservative fashion in the single celled parasite Trypanosoma brucei. Furthermore, we demonstrate that the mitochondrial genome itself is not required for assembly to occur. It seems that the physical connection of the mitochondrial genome to cytoskeletal elements is a conserved feature in most eukaryotes, however the molecular components are highly diverse.\n\nAbbreviation

cell biology↗

bioRxiv2017

Biogenesis of a mitochondrial DNA inheritance machinery in the mitochondrial outer membrane

Mitochondria cannot form de novo but require mechanisms that mediate their inheritance to daughter cells. The parasitic protozoan Trypanosoma brucei has a single mitochondrion with a single-unit genome that is physically connected across the mitochondrial membranes to the basal body of the flagellum. This connection, termed tripartite attachment complex (TAC), is essential for the segregation of the replicated mitochondrial genomes prior to cytokinesis. Here we identify a protein complex consisting of three integral mitochondrial outer membrane proteins - TAC60, TAC42 and TAC40 - which are essential subunits of the TAC. TAC60 contains separable mitochondrial import and TAC-sorting signals and its biogenesis depends on the main outer membrane protein translocase. TAC40 is a member of the mitochondrial porin family, whereas TAC42 represents a novel class of mitochondrial outer membrane {beta}-barrel proteins. Consequently TAC40 and TAC42 contain C-terminal {beta}-signals. Thus in trypanosomes the highly conserved {beta}-barrel protein assembly machinery plays a major role in the biogenesis of its unique mitochondrial genome segregation system.

biochemistry↗