Facilitated endospore detection for Bacillus spp. through automated algorithm-based image processing.

Bacillus spp. endospores are important dormant cell forms and are distributed widely in environmental samples. While these endospores can have important industrial value (e.g. use in animal feed as probiotics), they can also be pathogenic for humans and animals, emphasizing the need for effective endospore detection. Standard spore detection by colony forming units (CFU) is time-consuming, elaborate and prone to error. Manual spore detection by spore count in cell counting chambers via phase-contrast microscopy is less time-consuming. However, it requires a trained person to conduct. Thus, the development of a facilitated spore detection tool is necessary. This work presents two alternative quantification methods: first, a colorimetric assay for detecting the biomarker dipicolinic acid (DPA) adapted to modern needs and applied for Bacillus spp. and second, a model-based automated spore detection algorithm for spore count in phase-contrast microscopic pictures. This automated spore count tool advances manual spore detection in cell counting chambers, and does not require human overview after sample preparation. In conclusion, this developed model detected various Bacillus spp. endospores with a correctness of 85-89%, and allows an automation and time-saving of Bacillus endospore detection. In the laboratory routine, endospore detection and counting was achieved within 5-10 min, compared to up to 48 h with conventional methods. The DPA-assay on the other hand enabled very accurate spore detection by simple colorimetric measurement and can thus be applied as a reference method.

An Antibody-Aptamer-Hybrid Lateral Flow Assay for Detection of CXCL9 in Antibody-Mediated Rejection after Kidney Transplantation.

Chronic antibody-mediated rejection (AMR) is a key limiting factor for the clinical outcome of a kidney transplantation (Ktx), where early diagnosis and therapeutic intervention is needed. This study describes the identification of the biomarker CXC-motif chemokine ligand (CXCL) 9 as an indicator for AMR and presents a new aptamer-antibody-hybrid lateral flow assay (hybrid-LFA) for detection in urine. Biomarker evaluation included two independent cohorts of kidney transplant recipients (KTRs) from a protocol biopsy program and used subgroup comparisons according to BANFF-classifications. Plasma, urine and biopsy lysate samples were analyzed with a Luminex-based multiplex assay. The CXCL9-specific hybrid-LFA was developed based upon a specific rat antibody immobilized on a nitrocellulose-membrane and the coupling of a CXCL9-binding aptamer to gold nanoparticles. LFA performance was assessed according to receiver operating characteristic (ROC) analysis. Among 15 high-scored biomarkers according to a neural network analysis, significantly higher levels of CXCL9 were found in plasma and urine and biopsy lysates of KTRs with biopsy-proven AMR. The newly developed hybrid-LFA reached a sensitivity and specificity of 71% and an AUC of 0.79 for CXCL9. This point-of-care-test (POCT) improves early diagnosis-making in AMR after Ktx, especially in KTRs with undetermined status of donor-specific HLA-antibodies.

A new lateral flow assay to detect sIL-2R during T-cell mediated rejection after kidney transplantation.

Kidney is the most frequently transplanted among all solid organs worldwide. Kidney transplant recipients (KTRs) undergo regular follow-up examinations for the early detection of acute rejections. The gold standard for proving a T-cell mediated rejection (TCMR) is a biopsy of the renal graft often occurring as indication biopsy, in parallel to an increased serum creatinine that may indicate deterioration of renal transplant function. The goal of the current work was to establish a lateral flow assay (LFA) for diagnosing acute TCMR to avoid harmful, invasive biopsies. Soluble interleukin-2 (IL-2) receptor (sIl-2R) is a potential biomarker representing the α-subunit of the IL-2 receptor produced by activated T-cells, e.g., after allogen contact. To explore the diagnostic potential of sIL-2R as a biomarker for TCMR and borderline TCMR, plasma and urine samples were collected from three independent KTR cohorts with various distinct histopathological diagnostic findings according to BANFF (containing 112 rsp. 71 rsp. 61 KTRs). Samples were analyzed by a Luminex-based multiplex technique and cut off-ranges were determined. An LFA was established with two specific sIL-2R-antibodies immobilized on a nitrocellulose membrane. A significant association between TCMR, borderline TCMR and sIL-2R in plasma and between TCMR and sIL-2R in urine of KTRs was confirmed using the Mann-Whitney U test. The LFA was tested with sIL-2R-spiked buffer samples establishing a detection limit of 25 pM. The performance of the new LFA was confirmed by analyzing urine samples of the 2nd and 3rd patient cohort with 35 KTRs with biopsy proven TCMRs, 3 KTRs diagnosed with borderline TCMR, 1 mixed AMR/TCMR rsp. AMR/borderline TCMR and 13 control patients with a rejection-free kidney graft proven by protocol biopsies. The new point-of-care assay showed a specificity of 84.6% and sensitivity of 87.5%, and a superior estimated glomerular filtration rate (eGFR) at the time point of biopsy (specificity 30.8%, sensitivity 85%).

Implementing a digital infrastructure for the lab using a central laboratory server and the SiLA2 communication standard.

In this report, a fully integrated solution for laboratory digitization is presented. The approach presents a flexible and complete integration method for the digitally assisted workflow. The worker in the laboratory performs procedures in direct interaction with the digitized infrastructure that guides through the process and aids while performing tasks. The digital transformation of the laboratory starts with standardized integration of both new and "smart" lab devices, as well as legacy devices through a hardware gateway module. The open source Standardization in Lab Automation 2 standard is used for device communication. A central lab server channels all device communication and keeps a database record of every measurement, task and result generated or used in the lab. It acts as a central entry point for process management. This backbone enables a process control system to guide the worker through the lab process and provide additional assistance, like results of automated calculations or safety information. The description of the infrastructure and architecture is followed by a practical example on how to implement a digitized workflow. This approach is highly useful for - but not limited to - the biotechnological laboratory and has the potential to increase productivity in both industry and research for example by enabling automated documentation.

Lung Surfactant Accelerates Skin Wound Healing: A Translational Study with a Randomized Clinical Phase I Study.

Lung surfactants are used for reducing alveolar surface tension in preterm infants to ease breathing. Phospholipid films with surfactant proteins regulate the activity of alveolar macrophages and reduce inflammation. Aberrant skin wound healing is characterized by persistent inflammation. The aim of the study was to investigate if lung surfactant can promote wound healing. Preclinical wound models, e.g. cell scratch assays and full-thickness excisional wounds in mice, and a randomized, phase I clinical trial in healthy human volunteers using a suction blister model were used to study the effect of the commercially available bovine lung surfactant on skin wound repair. Lung surfactant increased migration of keratinocytes in a concentration-dependent manner with no effect on fibroblasts. Significantly reduced expression levels were found for pro-inflammatory and pro-fibrotic genes in murine wounds. Because of these beneficial effects in preclinical experiments, a clinical phase I study was initiated to monitor safety and tolerability of surfactant when applied topically onto human wounds and normal skin. No adverse effects were observed. Subepidermal wounds healed significantly faster with surfactant compared to control. Our study provides lung surfactant as a strong candidate for innovative treatment of chronic skin wounds and as additive for treatment of burn wounds to reduce inflammation and prevent excessive scarring.

A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells.

BACKGROUND: Despite the significant contribution of transcriptomics to the fields of biological and biomedical research, interpreting long lists of significantly differentially expressed genes remains a challenging step in the analysis process. Gene set enrichment analysis is a standard approach for summarizing differentially expressed genes into pathways or other gene groupings. Here, we explore an alternative approach to utilizing gene sets from curated databases. We examine the method of deriving custom gene sets which may be relevant to a given experiment using reference data sets from previous transcriptomics studies. We call these data-derived gene sets, "gene signatures" for the biological process tested in the previous study. We focus on the feasibility of this approach in analyzing immune-related processes, which are complicated in their nature but play an important role in the medical research. RESULTS: We evaluate several statistical approaches to detecting the activity of a gene signature in a target data set. We compare the performance of the data-derived gene signature approach with comparable GO term gene sets across all of the statistical tests. A total of 61 differential expression comparisons generated from 26 transcriptome experiments were included in the analysis. These experiments covered eight immunological processes in eight types of leukocytes. The data-derived signatures were used to detect the presence of immunological processes in the test data with modest accuracy (AUC = 0.67). The performance for GO and literature based gene sets was worse (AUC = 0.59). Both approaches were plagued by poor specificity. CONCLUSIONS: When investigators seek to test specific hypotheses, the data-derived signature approach can perform as well, if not better than standard gene-set based approaches for immunological signatures. Furthermore, the data-derived signatures can be generated in the cases that well-defined gene sets are lacking from pathway databases and also offer the opportunity for defining signatures in a cell-type specific manner. However, neither the data-derived signatures nor standard gene-sets can be demonstrated to reliably provide negative predictions for negative cases. We conclude that the data-derived signature approach is a useful and sometimes necessary tool, but analysts should be weary of false positives.

Bringing IoT to the Lab: SiLA2 and Open-Source-Powered Gateway Module for Integrating Legacy Devices into the Digital Laboratory.

In this article a gateway module to integrate legacy laboratory devices into the network of the digital laboratory in the 21st century is introduced. The device is based on ready to buy consumer hardware that is easy to get and inexpensive. Depending on the specific requirements of the desired application (bare embedded computer, RS232 serial port connector, IP65 certified casing and connectors) the needed investment ranges from about 95 € up to 200 €. The embedded computer runs an open source Linux operating system and can in principle be used to run any kind of software needed for communicating with the laboratory device. Here the open source SiLA2 standard is used for presenting the device's functions in the network. As an example the digital integration of a magnetic stirrer is shown and can be used as a template for other applications. A method for easy remote integration of the device to ensure an easy and consistent workflow in development, testing and usage is also presented. This incorporates a method for remote installation of SiLA2 servers on the box as well as a web frontend for administration, debugging and management of those.

Introducing a Virtual Assistant to the Lab: A Voice User Interface for the Intuitive Control of Laboratory Instruments.

The introduction of smart virtual assistants (VAs) and corresponding smart devices brought a new degree of freedom to our everyday lives. Voice-controlled and Internet-connected devices allow intuitive device controlling and monitoring from all around the globe and define a new era of human-machine interaction. Although VAs are especially successful in home automation, they also show great potential as artificial intelligence-driven laboratory assistants. Possible applications include stepwise reading of standard operating procedures (SOPs) and recipes, recitation of chemical substance or reaction parameters to a control, and readout of laboratory devices and sensors. In this study, we present a retrofitting approach to make standard laboratory instruments part of the Internet of Things (IoT). We established a voice user interface (VUI) for controlling those devices and reading out specific device data. A benchmark of the established infrastructure showed a high mean accuracy (95% ± 3.62) of speech command recognition and reveals high potential for future applications of a VUI within the laboratory. Our approach shows the general applicability of commercially available VAs as laboratory assistants and might be of special interest to researchers with physical impairments or low vision. The developed solution enables a hands-free device control, which is a crucial advantage within the daily laboratory routine.

Array Analysis Manager-An automated DNA microarray analysis tool simplifying microarray data filtering, bias recognition, normalization, and expression analysis.

Desoxyribonucleic acid (DNA) microarray experiments generate big datasets. To successfully harness the potential information within, multiple filtering, normalization, and analysis methods need to be applied. An in-depth knowledge of underlying physical, chemical, and statistical processes is crucial to the success of this analysis. However, due to the interdisciplinarity of DNA microarray applications and experimenter backgrounds, the published analyses differ greatly, for example, in methodology. This severely limits the comprehensibility and comparability among studies and research fields. In this work, we present a novel end-user software, developed to automatically filter, normalize, and analyze two-channel microarray experiment data. It enables the user to analyze single chip, dye-swap, and loop experiments with an extended dynamic intensity range using a multiscan approach. Furthermore, to our knowledge, this is the first analysis software solution, that can account for photobleaching, automatically detected by an artificial neural network. The user gets feedback on the effectiveness of each applied normalization regarding bias minimization. Standardized methods for expression analysis are included as well as the possibility to export the results in the Gene Expression Omnibus (GEO) format. This software was designed to simplify the microarray analysis process and help the experimenter to make educated decisions about the analysis process to contribute to reproducibility and comparability.

A smart device application for the automated determination of E. coli colonies on agar plates.

The manual counting of colonies on agar plates to estimate the number of viable organisms (so-called colony-forming units-CFUs) in a defined sample is a commonly used method in microbiological laboratories. The automation of this arduous and time-consuming process through benchtop devices with integrated image processing capability addresses the need for faster and higher sample throughput and more accuracy. While benchtop colony counter solutions are often bulky and expensive, we investigated a cost-effective way to automate the colony counting process with smart devices using their inbuilt camera features and a server-based image processing algorithm. The performance of the developed solution is compared to a commercially available smartphone colony counter app and the manual counts of two scientists trained in biological experiments. The comparisons show a high accuracy of the presented system and demonstrate the potential of smart devices to displace well-established laboratory equipment.

Optimization of Cyanine Dye Stability and Analysis of FRET Interaction on DNA Microarrays.

The application of DNA microarrays for high throughput analysis of genetic regulation is often limited by the fluorophores used as markers. The implementation of multi-scan techniques is limited by the fluorophores' susceptibility to photobleaching when exposed to the scanner laser light. This paper presents combined mechanical and chemical strategies which enhance the photostability of cyanine 3 and cyanine 5 as part of solid state DNA microarrays. These strategies are based on scanning the microarrays while the hybridized DNA is still in an aqueous solution with the presence of a reductive/oxidative system (ROXS). Furthermore, the experimental setup allows for the analysis and eventual normalization of Förster-resonance-energy-transfer (FRET) interaction of cyanine-3/cyanine-5 dye combinations on the microarray. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the comparability of microarray experiment results between labs.

C3-induced release of neurotrophic factors from Schwann cells - potential mechanism behind its regeneration promoting activity.

Previous studies revealed a peripheral nerve regeneration (PNR)(1) promoting activity of Clostridium botulinum C3(2) exoenzyme or a 26(mer) C-terminal peptide fragment covering amino acids 156-181 (C3(156-181)),(3) when delivered as one-time injection at the lesion site. The current study was performed to 1) investigate if prolonged availability of C3 and C3(156-181) at the lesion site can further enhance PNR in vivo and to 2) elucidate effects of C3 and C3(156-181) on Schwann cells (SCs)(4)in vitro. For in vivo studies, 10 mm adult rat sciatic nerve gaps were reconstructed with the epineurial pouch technique or autologous nerve grafts. Epineurial pouches were filled with a hydrogel containing i) vehicle, ii) 40 µM C3 or iii) 40 µM C3(156-181). Sensory and motor functional recovery was monitored over 12 weeks and the outcome of PNR further analyzed by nerve morphometry. In vitro, we compared gene expression profiles (microarray analysis) and neurotrophic factor expression (western blot analysis) of untreated rat neonatal SCs with those treated with C3 or C3(156-181) for 72 h. Effects on neurotrophic factor expression levels were proven in adult human SCs. Unexpectedly, prolonged delivery of C3 and C3(156-181) at the lesion site did not increase the outcome of PNR. Regarding the potential mechanism underlying their previously detected PNR promoting action, however, 6 genes were found to be commonly altered in SCs upon treatment with C3 or C3(156-181). We demonstrate significant down-regulation of genes involved in glutamate uptake (Eaac1,(5)Grin2a(6)) and changes in neurotrophic factor expression (increase of FGF-2(7) and decrease of NGF(8)). Our microarray-based expression profiling revealed novel C3-regulated genes in SCs possibly involved in the axonotrophic (regeneration promoting) effects of C3 and C3(156-181). Detection of altered neurotrophic factor expression by C3 or C3(156-181) treated primary neonatal rat SCs and primary adult human SCs supports this hypothesis.

The Impact of Photobleaching on Microarray Analysis.

DNA-Microarrays have become a potent technology for high-throughput analysis of genetic regulation. However, the wide dynamic range of signal intensities of fluorophore-based microarrays exceeds the dynamic range of a single array scan by far, thus limiting the key benefit of microarray technology: parallelization. The implementation of multi-scan techniques represents a promising approach to overcome these limitations. These techniques are, in turn, limited by the fluorophores' susceptibility to photobleaching when exposed to the scanner's laser light. In this paper the photobleaching characteristics of cyanine-3 and cyanine-5 as part of solid state DNA microarrays are studied. The effects of initial fluorophore intensity as well as laser scanner dependent variables such as the photomultiplier tube's voltage on bleaching and imaging are investigated. The resulting data is used to develop a model capable of simulating the expected degree of signal intensity reduction caused by photobleaching for each fluorophore individually, allowing for the removal of photobleaching-induced, systematic bias in multi-scan procedures. Single-scan applications also benefit as they rely on pre-scans to determine the optimal scanner settings. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the lab-to-lab comparability of microarray experiment results.

Silver nanoparticle-doped zirconia capillaries for enhanced bacterial filtration.

Membrane clogging and biofilm formation are the most serious problems during water filtration. Silver nanoparticle (Agnano) coatings on filtration membranes can prevent bacterial adhesion and the initiation of biofilm formation. In this study, Agnano are immobilized via direct reduction on porous zirconia capillary membranes to generate a nanocomposite material combining the advantages of ceramics being chemically, thermally and mechanically stable with nanosilver, an efficient broadband bactericide for water decontamination. The filtration of bacterial suspensions of the fecal contaminant Escherichia coli reveals highly efficient bacterial retention capacities of the capillaries of 8 log reduction values, fulfilling the requirements on safe drinking water according to the U.S. Environmental Protection Agency. Maximum bacterial loading capacities of the capillary membranes are determined to be 3×10(9)bacterialcells/750mm(2) capillary surface until back flushing is recommendable. The immobilized Agnano remain accessible and exhibit strong bactericidal properties by killing retained bacteria up to maximum bacterial loads of 6×10(8)bacterialcells/750mm(2) capillary surface and the regenerated membranes regain filtration efficiencies of 95-100%. Silver release is moderate as only 0.8% of the initial silver loading is leached during a three-day filtration experiment leading to average silver contaminant levels of 100µg/L.

Analysis of aging in lager brewing yeast during serial repitching.

Serial repitching of brewing yeast inoculates is an important economic factor in the brewing industry, as their propagation is time and resource intensive. Here, we investigated whether replicative aging and/or the population distribution status changed during serial repitching in three different breweries with the same brewing yeast strain but different abiotic backgrounds and repitching regimes with varying numbers of reuses. Next to bud scar numbers the DNA content of the Saccharomyces pastorianus HEBRU cells was analyzed. Gene expression patterns were investigated using low-density microarrays with genes for aging, stress, storage compound metabolism and cell cycle. Two breweries showed a stable rejuvenation rate during serial repitching. In a third brewery the fraction of virgin cells varied, which could be explained with differing wort aeration rates. Furthermore, the number of bud scars per cell and cell size correlated in all 3 breweries throughout all runs. Transcriptome analyses revealed that from the 6th run on, mainly for the cells positive gene expression could be seen, for example up-regulation of trehalose and glycogen metabolism genes. Additionally, the cells' settling in the cone was dependent on cell size, with the lowest and the uppermost cone layers showing the highest amount of dead cells. In general, cells do not progressively age during extended serial repitching.

Cell assessment by at-line microscopy.

This protocol regards a microscopic application and software for image-guided monitoring of mammalian cells which grow in suspension cultures. It has been developed in order to establish an automated microscopic application for in situ and at-line cell monitoring in bioreactors (Akin et al., Biosens Bioelectron 26:4532-4537, 2011; Babitzky et al., At-line microscopic analysis of suspension cell cultures. In: ECCE/ECAB, the first joint European Congress of chemical engineering and applied biotechnology, September 25-29, 2011, Berlin, Germany, 2011. http://www.tci.uni-hannover.de, Poster). The application aims to assess the analysis of an appropriated sample volume of mammalian cell cultivation medium. The sample is injected into a microfluidic slide which is suitable for transmitted light microscopy and is attached to an automated microscope device, the at-line microscope. The major attribute of microscope automation ascribes to the camera software, which enables sequential image capturing and storing. Image analysis and cell detection are performed by the software that is based on the edge detection algorithm developed by Canny (IEEE Trans Pattern Anal Mach Intell 8:679-698, 1986; Finding edges and lines in images.Technical Report 720, MIT Artificial Intelligence Laboratory, 1983). The analysis results are cell count, morphological characteristics, and grayscale values of the detected cells. The presented setup can be applied to low-volume cultivations and has been successfully tested for monitoring CHO-K1 cell cultivation processes.

Light intensity dependence of the kinetics of the photocatalytic oxidation of nitrogen(II) oxide at the surface of TiO2.

Air pollution by nitrogen oxides represents a serious environmental problem in urban areas where numerous sources of these pollutants are concentrated. One approach to reduce the concentration of these air pollutants is their light-induced oxidation in the presence of molecular oxygen and a photocatalytically active building material which uses titanium dioxide as the photocatalyst. Herein, results of an investigation concerning the influence of the photon flux and the pollutant concentration on the rate of the photocatalytic oxidation of nitrogen(ii) oxide in the presence of molecular oxygen and UV(A) irradiated titanium dioxide powder are presented. A Langmuir-Hinshelwood-type rate law for the photocatalytic NO oxidation inside the photoreactor comprising four kinetic parameters is derived being suitable to describe the influence of the pollutant concentration and the photon flux on the rate of the photocatalytic oxidation of nitrogen(ii) oxide.

In situ microscopy for in-line monitoring of the enzymatic hydrolysis of cellulose.

A new in-line method for the monitoring of enzymatic hydrolysis of cellulose is described. Using a new in situ microscope prototype, the noninvasive determination of particle size distributions was possible. For the automated analysis of the acquired images, a new processing algorithm called CelluloseAnalyzer was developed. It enabled tracking of the number of particles and moreover allowed monitoring of the proportions of particle size fractions during the course of enzymatic hydrolysis reactions. Using this technique, significant differences between hydrolysis with endoglucanases and cellulase mixtures were observed. Furthermore, the in situ microscopy results were compared with results from off-line measurements with laser diffraction spectroscopy and gel permeation chromatography.

On-line monitoring of large cultivations of microalgae and cyanobacteria.

Large cultivations of microalgae will benefit from on-line monitoring to achieve process control and improved productivity. This monitoring requires reliable sensors for on-line, in situ measurement of both physicochemical and biological process variables. Although standard industrial sensors can be used for many physicochemical variables, monitoring methods for most biological quantities rely on sensors that are currently suitable only for laboratory scale or off-line use. Here, we review these methods and discuss new approaches that could be adapted. We suggest that these new methods should be noninvasive and based on approaches that have already been applied to other bioprocesses; examples discussed here are in situ microscopy, flow cytometry (FC), IR spectroscopy, and software sensors.

Comparison of the photoelectrochemical oxidation of methanol on rutile TiO2 (001) and (100) single crystal faces studied by intensity modulated photocurrent spectroscopy.

The photooxidation of methanol as a model substance for pollutants on rutile TiO(2) (001) and (100) surfaces was investigated using intensity modulated photocurrent spectroscopy (IMPS). The results are analyzed in view of the influence of the surface structure, the methanol concentration and the electrode potential on the rate constants of charge transfer and recombination. The obtained results have been explained with a model combining the theory of IMPS for a bulk semiconductor surface and the nature of the surface-bound intermediates (alternatively mobile or immobile OH˙ radicals). The results indicate that water photooxidation proceeds via mobile OH˙ radicals on both surfaces, while methanol addition gives rise to the involvement of immobile OH˙ radicals on the (100) surface. Detailed analysis in view of the surface structures suggests that the latter observation is due to efficient electron transfer from bridging OH˙ radicals on the (100) surface to methanol, while coupling of two of these radicals occurs in the absence of methanol, making them appear as mobile OH˙ radicals. In the case of the (001) surface, the coupling reaction dominates even in the presence of methanol due to the smaller distance between the bridging OH˙ radicals, leading to more efficient water oxidation, but less efficient methanol photooxidation on this surface.