Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes

Bacteria are the most abundant and diverse organisms among the kingdoms of life. Due to this excessive variance, finding a unified, comprehensive, and safe workflow for quantitative bacterial proteomics is challenging. In this study, we have systematically evaluated and optimized sample preparation, mass spectrometric data acquisition, and data analysis strategies in bacterial proteomics. We investigated workflow performances on six representative species with highly different physiologic properties to mimic bacterial diversity. The best sample preparation strategy was a cell lysis protocol in 100% trifluoroacetic acid followed by an in-solution digest. Peptides were separated on a 30-min linear microflow liquid chromatography gradient and analyzed in data-independent acquisition mode. Data analysis was performed with DIA-NN using a predicted spectral library. Performance was evaluated according to the number of identified proteins, quantitative precision, throughput, costs, and biological safety. With this rapid workflow, over 40% of all encoded genes were detected per bacterial species. We demonstrated the general applicability of our workflow on a set of 23 taxonomically and physiologically diverse bacterial species. We could confidently identify over 45,000 proteins in the combined dataset, of which 30,000 have not been experimentally validated before. Our work thereby provides a valuable resource for the microbial scientific community. Finally, we grew Escherichia coli and Bacillus cereus in replicates under 12 different cultivation conditions to demonstrate the high-throughput suitability of the workflow. The proteomic workflow we present in this manuscript does not require any specialized equipment or commercial software and can be easily applied by other laboratories to support and accelerate the proteomic exploration of the bacterial kingdom.

Rapid Calibration of Nanoliter per Second Flow Rate by Image Processing Technology

The need for high-precision microflow control is increasingly evident across various fields. For instance, microsatellites employed in gravitational wave detection require flow supply systems with a high accuracy of up to 0.1 nL/s to achieve on-orbit attitude control and orbit control. However, conventional flow sensors are unable to provide the necessary precision in the nanoliter per second range, and thus, alternative methods are required. In this study, we propose the use of image processing technology for rapid microflow calibration. Our method involves capturing images of the droplets at the outlet of the flow supply system to rapidly obtain the flow rate, and we used the gravimetric method to verify the accuracy of our approach. We conducted several microflow calibration experiments within the 1.5 nL/s range and demonstrated that image processing technology can achieve the desired accuracy of 0.1 nL/s while saving more than two-thirds of the time required to obtain the flow rate within an acceptable margin of error compared to the gravimetric method. Our study presents an efficient and innovative approach to addressing the challenges of measuring microflows with high precision, particularly in the nanoliter per second range, and has the potential for widespread applications in various fields.

Automated Supramolecular Polymerization in a Microflow: A Versatile Platform for Multistep Supramolecular Reactions

This work reports a basic microflow system capable of performing multistep supramolecular polymerization. In this system, injection of the monomer, directional supramolecular copolymerization, removal of the unreacted monomer, and purification of the product supramolecular diblock copolymers are realized along a three-stream flow. When injecting a supramolecular polymer into the central stream of the three-stream flow, the supramolecular polymerization always occurs in the central flow, with the two lateral flows serving as supply and removal lines for the monomer. Employing two kinds of perylene bisimide derivatives as monomers, we confirmed that the reaction occurred selectively at the forward-facing terminus of the supramolecular polymer, along with recovery of the unreacted monomer, ultimately leading to a high-purity supramolecular diblock copolymer. Diblock copolymers are basic units for preparing multicomponent supramolecular block copolymers. Thus, connecting the present system in series would, in principle, result in a "microplant" capable of producing supramolecular polymers having desired inner complexity.

Assessment of drug delivery devices working at microflow rates

Almost every medical department in hospitals around the world uses infusion devices to administer fluids, nutrition, and medications to patients to treat many different diseases and ailments. There have been several reports on adverse incidents caused by medication errors associated with infusion equipment. Such errors can result from malfunction or improper use, or even inaccuracy of the equipment, and can cause harm to patients' health. Depending on the intended use of the equipment, e.g. if it is used for anaesthesia of adults or for medical treatment of premature infants, the accuracy of the equipment may be more or less important. A well-defined metrological infrastructure can help to ensure that infusion devices function properly and are as accurate as needed for their use. However, establishing a metrological infrastructure requires adequate knowledge of the performance of infusion devices in use. This paper presents the results of various tests conducted with two types of devices.

Measurement of internal diameters of capillaries and glass syringes using gravimetric and optical methods for microflow applications

OBJECTIVES

Microflow measurement devices are used in several science and health applications, mainly drug delivery. In the last decade, several new methods based on optical technology were developed, namely the front tracking and interferometric method, in which the knowledge of the inner diameter of the syringe or the capillary used is critical. Only a few National Metrology Institutes (NMIs) can perform inner diameter measurements below 1 mm, which requires expensive technology. Therefore, IPQ, in cooperation with CETIAT, CMI and UNIDEMI, under the EMPIR project 18HLT08 MeDDII - Metrology for Drug Delivery, developed new measurement methods for small inner diameter tubes based on the gravimetric principle and optical methods in order to simplify the apparatus used for this type of measurements without increasing uncertainty.

METHODS

The gravimetric experimental setup consists of measuring the liquid volume on a specific length of the glass tube. The optical method used is based on the front track principle that uses a high-resolution camera and ImageJ software, to determine the diameter at both ends of each capillary.

RESULTS

To validate the developed methods, a comparison was performed between CETIAT, CMI and IPQ and the results obtained were all consistent.

CONCLUSIONS

This work allowed the determination of inner diameter of syringes or capillaries using two different methods with relative expanded uncertainties from 0.1 to 0.5% (k=2), that can be applied for flow measurements using optical technology.

Application of a new approach methodology (NAM)-based strategy for genotoxicity assessment of data-poor compounds

The conventional battery for genotoxicity testing is not well suited to assessing the large number of chemicals needing evaluation. Traditional in vitro tests lack throughput, provide little mechanistic information, and have poor specificity in predicting in vivo genotoxicity. New Approach Methodologies (NAMs) aim to accelerate the pace of hazard assessment and reduce reliance on in vivo tests that are time-consuming and resource-intensive. As such, high-throughput transcriptomic and flow cytometry-based assays have been developed for modernized in vitro genotoxicity assessment. This includes: the TGx-DDI transcriptomic biomarker (i.e., 64-gene expression signature to identify DNA damage-inducing (DDI) substances), the MicroFlow^® assay (i.e., a flow cytometry-based micronucleus (MN) test), and the MultiFlow^® assay (i.e., a multiplexed flow cytometry-based reporter assay that yields mode of action (MoA) information). The objective of this study was to investigate the utility of the TGx-DDI transcriptomic biomarker, multiplexed with the MicroFlow^® and MultiFlow^® assays, as an integrated NAM-based testing strategy for screening data-poor compounds prioritized by Health Canada's New Substances Assessment and Control Bureau. Human lymphoblastoid TK6 cells were exposed to 3 control and 10 data-poor substances, using a 6-point concentration range. Gene expression profiling was conducted using the targeted TempO-Seq™ assay, and the TGx-DDI classifier was applied to the dataset. Classifications were compared with those based on the MicroFlow^® and MultiFlow^® assays. Benchmark Concentration (BMC) modeling was used for potency ranking. The results of the integrated hazard calls indicate that five of the data-poor compounds were genotoxic in vitro, causing DNA damage via a clastogenic MoA, and one via a pan-genotoxic MoA. Two compounds were likely irrelevant positives in the MN test; two are considered possibly genotoxic causing DNA damage via an ambiguous MoA. BMC modeling revealed nearly identical potency rankings for each assay. This ranking was maintained when all endpoint BMCs were converted into a single score using the Toxicological Prioritization (ToxPi) approach. Overall, this study contributes to the establishment of a modernized approach for effective genotoxicity assessment and chemical prioritization for further regulatory scrutiny. We conclude that the integration of TGx-DDI, MicroFlow^®, and MultiFlow^® endpoints is an effective NAM-based strategy for genotoxicity assessment of data-poor compounds.

Interstitial Fluid Flows along Perivascular and Adventitial Clearances around Neurovascular Bundles

This study reports new phenomena of the interstitial fluid (ISF) microflow along perivascular and adventitial clearances (PAC) around neurovascular bundles. The fluorescent tracing was used to observe the ISF flow along the PAC of neurovascular bundles in 8-10 week old BALB/c mice. The new results include: (1) the topologic structure of the PAC around the neurovascular bundles is revealed; (2) the heart-orientated ISF flow along the PAC is observed; (3) the double-belt ISF flow along the venous adventitial clearance of the PAC is recorded; (4) the waterfall-like ISF flow induced by the small branching vessel or torn fascia along the PAC is discovered. Based on the above new phenomena, this paper approached the following objectives: (1) the kinematic laws of the ISF flow along the PAC around neurovascular bundles are set up; (2) the applicability of the hypothesis on the PAC and its subspaces by numerical simulations are examined. The findings of this paper not only enriched the image of the ISF flow through the body but also explained the kernel structure of the ISF flow (i.e., the PAC). It helps to lay the foundation for the kinematics and dynamics of the ISF flow along the PAC around neurovascular bundles.

Improved Detection of Gallbladder Perforation Using Ultrasound Small Vessel Slow Flow "Perfusion" Imaging

Gallbladder (GB) perforation is a potentially fatal cause of acute abdomen. Higher morbidity and mortality are associated with this entity due to delayed diagnosis and treatment. Ultrasound with color/power Doppler and contrast sonography can detect wall discontinuity; however, sometimes it can be subtle or unavailable. Small vessel slow flow "perfusion" imaging allows improved microvascular perfusion detection using different filters, which result in increased spatial resolution and vessel visualization. Noncontrast perfusion imaging was of immense clinical value in the diagnosis of GB perforation in the six cases presented here. To the best of our knowledge, this is the first case report describing efficacy of noncontrast "perfusion" imaging in detection of GB perforation.

A quantitative model to understand the microflow-controlled sintering mechanism of metal particles at nanometer to micron scale

In this paper, the particle size effect on the sintering behaviors of Cu particles at nanometer to micron scale is explored. The results show that micron-sized particles could form obvious sintering necks at a low temperature of 260 °C, exhibiting a shear strength as high as 64 MPa. A power relation ofx ∝ a^0.8between sintering neck radius (x) and particle radius (a) is discovered, and a sintering model with a quantitative relational expression of (x/a)⁵ = 160γδDt/3akTis proposed by considering the surface tension driven microflow process between adjacent particles to predict the growth of sintering necks. It is concluded that the sintering process of particles at nanometer to micron scale is controlled by microflow mechanism instead of diffusion mechanism. Our proposed model provides a new theoretical basis for understanding the kinetic growth mechanism of sintering necks of metal particles.

Numerical Study of the Microflow Characteristics in a V-ball Valve

V-ball valves are widely applied in many process industries to regulate fluid flow, and they have advantages of good approximately equal percentage flow characteristics and easy maintenance. However, in some applications, the V-ball valve needs to have good performance under both large and extremely small flow coefficients. In this paper, the improvement of the original V-ball valve is made and the flow characteristics between the original and the improved V-ball valve are compared. Two types of small gaps are added to the original V-ball, namely the gap with an approximately rectangular port and the gap with an approximately triangular port. The effects of the structure and the dimension of the gap on flow characteristics are investigated. Results show that within the gap, the flow coefficient increases but the loss coefficient decreases as the valve opening increases, and the flow coefficient has an approximately linear relationship with the flow cross-area of the added gap. Results also show that under the same flow cross-area, the flow coefficient has a higher value if the distance between the gap and the ball center is greater or if the gap is an approximately rectangular port, while the loss coefficient has an opposite trend.

Report on the 17th Annual Land O'Lakes Bioanalytical Conference

17th Annual Land O'Lakes Bioanalytical Conference, Madison, WI, USA, 11-14 July 2016 The 17th Annual Land O'Lakes Bioanalytical Conference, titled 'Biomarker Validation, Stability, and Regulatory Concerns', was held on 11-14 July 2016 (Monday through Thursday) in Madison, WI, USA. The Land O'Lakes Conference is presented each year by the Division of Pharmacy Professional Development within the School of Pharmacy at the University of Wisconsin-Madison (USA). The purpose of this 3-day conference is to provide an educational forum to discuss issues and applications associated with the analysis of xenobiotics, metabolites, biologics and biomarkers in biological matrices. The conference is designed to include and encourage an open exchange of scientific and methodological applications for bioanalysis. To increase the interactive nature of the conference, the program is a mixture of lectures, interactive discussions and a poster session. This report summarizes the presentations at the 17th Annual Conference.

16th Annual Land O'Lakes Bioanalytical Conference

This Land O'Lakes Conference is presented each year by the Division of Pharmacy Professional Development within the School of Pharmacy at the University of Wisconsin-Madison (USA). The purpose of this 3-day conference is to provide an educational forum to discuss issues and applications associated with the analysis of xenobiotics, metabolites, biologics and biomarkers in biological matrices. The conference is designed to include and encourage an open exchange of scientific and methodological applications for bioanalysis. To increase the interactive nature of the conference, the program is a mixture of lectures, interactive discussions and a poster session. This report summarized the presentations at the 16th Annual Conference. 6th Annual Land O'Lakes Bioanalytical Conference, Fluno Center Madison, WI, USA, 13-16 July 2015.

Microphotochemistry: 4,4'-Dimethoxybenzophenone mediated photodecarboxylation reactions involving phthalimides

A series of 4,4'-dimethoxybenzophenone mediated intra- and intermolecular photodecarboxylation reactions involving phthalimides have been examined under microflow conditions. Conversion rates, isolated yields and chemoselectivities were compared to analogous reactions in a batch photoreactor. In all cases investigated, the microreactions gave superior results thus proving the superiority of microphotochemistry over conventional technologies.

An electric impedance based microelectromechanical system flow sensor for ionic solutions

Microfluidic devices with channel cross sections measuring 4 × 10 μm(2) instrumented with gold microelectrodes were used to sense flow rates of ionic solutions on the basis of electric impedance (EI) measured perpendicular to the flow. Negative pressures were applied to access ports of the microdevices to generate flow of saline solutions (physiologic concentrations 0.9%) through the micro-EI recording zone with flow rates between 2.4 and 4.8 μl min(-1). The EI spectra (100 Hz-20 MHz) recorded under flow conditions were compared with the no-flow condition. Changes in the magnitude of EI (at 350 Hz) for flow rates as low as 2.4 μl min(-1) were statistically significant compared with the no-flow condition. The observed dependence of EI on flow rate is attributed to the relative difference between the rate of migration of charge-balancing electrolyte ions to the electrode surface and the rate of removal of the same ions by forced convection. An electrochemical convection-diffusion model was used to study the observed dependence on flow. Simulations support the conceptual model that passing DC current from the gold electrodes into the ionic solution results in an increase in ionic concentration near the electrode surface (due to the inward migration of counter-balancing ions). When the fluid flow rates increase, these counter-balancing ions are replaced by the bulk solution, thereby lowering the average ionic concentration within the recording zone. This local concentration drop results in an increase in the real part of the impedance.