Segmentation, tracking, and sub-cellular feature extraction in 3D time-lapse images.

This paper presents a method for time-lapse 3D cell analysis. Specifically, we consider the problem of accurately localizing and quantitatively analyzing sub-cellular features, and for tracking individual cells from time-lapse 3D confocal cell image stacks. The heterogeneity of cells and the volume of multi-dimensional images presents a major challenge for fully automated analysis of morphogenesis and development of cells. This paper is motivated by the pavement cell growth process, and building a quantitative morphogenesis model. We propose a deep feature based segmentation method to accurately detect and label each cell region. An adjacency graph based method is used to extract sub-cellular features of the segmented cells. Finally, the robust graph based tracking algorithm using multiple cell features is proposed for associating cells at different time instances. We also demonstrate the generality of our tracking method on C. elegans fluorescent nuclei imagery. Extensive experiment results are provided and demonstrate the robustness of the proposed method. The code is available on GitHub and the method is available as a service through the BisQue portal.

Simple adsorptive removal of crystal violet, a triarylmethane dye, from synthetic wastewater using Fe (III)-treated pine needle biochar.

Untreated and Fe (III)-treated pine needle biochar (PNB) were evaluated at different pH for the removal of toxic crystal violet (CV) dye from synthetic wastewaters. Adsorption kinetics followed the pseudo-first-order kinetics involving intra-particle diffusion process. The adsorption rate constant increased with Fe treatment of PNB especially at pH 7.0. Adsorption data of CV conformed well to Freundlich adsorption isotherms and both adsorption capacity (ln K) and order of adsorption (1/n) of CV were nearly doubled with Fe (III) treatment of PNB at pH 7.0. Desorption of adsorbed CV from both untreated and Fe (III)-treated PNB could be accounted satisfactorily by third-degree polynomial equations. An increase in ionic strength and temperature enhanced dye adsorption onto untreated and Fe (III)-treated PNB. Adsorption of CV was an endothermic and spontaneous reaction with an increase in entropy of the system. FTIR spectra revealed that C = O of carboxylic acid aryls and C = O and C-O-C in lignin residues of PNB reacted with Fe (III) besides the formation of some iron oxyhydroxide minerals. The changes in FTIR confirmed the possible bonding of positively charged moiety of CV with the untreated and Fe-treated PNB. Scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS) revealed the porous surfaces of PNB with clear accumulation of Fe (III) after treatment and deposition of CV dye on surfaces and pores of PNB. Iron (III)-treated PNB at pH 7.0 can serve as an ecofriendly and cost-effective adsorbent for the efficient removal of CV dye from wastewaters.

NLR immune receptor-nanobody fusions confer plant disease resistance.

Plant pathogens cause recurrent epidemics, threatening crop yield and global food security. Efforts to retool the plant immune system have been limited to modifying natural components and can be nullified by the emergence of new pathogen strains. Made-to-order synthetic plant immune receptors provide an opportunity to tailor resistance to pathogen genotypes present in the field. In this work, we show that plant nucleotide-binding, leucine-rich repeat immune receptors (NLRs) can be used as scaffolds for nanobody (single-domain antibody fragment) fusions that bind fluorescent proteins (FPs). These fusions trigger immune responses in the presence of the corresponding FP and confer resistance against plant viruses expressing FPs. Because nanobodies can be raised against most molecules, immune receptor-nanobody fusions have the potential to generate resistance against plant pathogens and pests delivering effectors inside host cells.

Low-cost, portable, on-site fluorescent detection of As(III) by a paper-based microfluidic device based on aptamer and smartphone imaging.

A turn-on fluorescent aptasensor based on a paper-based microfluidic chip was developed to detect arsenite via aptamer competition strategy and smartphone imaging. The chip was prepared by wax-printing hydrophilic channels on filter paper. It is portable, low-cost, and environmentally friendly. Double-stranded DNA consisting of aptamer and fluorescence-labeled complementary strands was immobilized on the reaction zone of the paper chip. Due to the specific strong binding between aptamer and arsenite, the fluorescent complementary strand was squeezed out and driven by capillary force to the detection area of the paper chip, so that the fluorescent signal arose in the detection area under the excitation wavelength of 488 nm. Arsenite can be quantified by using smartphone imaging and RGB image analysis. Under the optimal conditions, the paper-based microfluidic aptasensor exhibited excellent linear response over a wide range of 1 to 1000 nM, with a detection limit as low as 0.96 nM (3σ).

Photothermal enhanced fluorescence quenching of Tb-norfloxacin for ultrasensitive human epididymal 4 detection.

A fluorescence quenching enhanced immunoassay has been developed to achieve ultrasensitive recognition of human epididymal 4 (HE4) modifying the fluorescence quencher. The carboxymethyl cellulose sodium-functionalized Nb2C MXene nanocomposite (CMC@MXene) was firstly introduced to quench the fluorescence signal of the luminophore Tb-Norfloxacin coordination polymer nanoparticles (Tb-NFX CPNPs). The Nb2C MXene nanocomposite as fluorescent nanoquencher inhibits the electron transfer between Tb and NFX to quench the fluorescent signal by coordinating the strongly electronegative carboxyl group on CMC with Tb (III) of Tb-NFX complex. Simultaneously, due to the superior photothermal conversion capability of CMC@MXene, the fluorescence signal has been further weakened by the photothermal effect driven non-radiative decay of the excited state under near-infrared laser irradiation. The constructed fluorescent biosensor based on CMC@MXene probe finally realized the enhanced fluorescence quenching effect, and achieved ultra-high sensitivity and selective detection of HE4, exhibiting a wide linear relationship with HE4 concentration on the logarithmic axis in the range of 10-5 to 10 ng/mL and a low detection limit of 3.3 fg/mL (S/N = 3). This work not only provides an enhanced fluorescent signal quenching method for the detection of HE4, but also provides novel insights for the design of fluorescent sensor toward different biomolecules.

Combination of SPE and fluorescent detection of AQC-derivatives for the determination at sub-mg/L levels of biogenic amines in dairy products.

Biogenic amines (BAs) are compounds generated by decarboxylation of their amino acid precursors. Their intake, even at low concentrations, can lead to several types of health problems in sensitive individuals. As they can be easily formed in fermented dairy products, their quantitative determination is very relevant. In the present paper, a method for the quantitative determination of four biogenic amines in different dairy products has been developed, validated and applied to 37 samples of milk, 23 of yogurt, and 14 of kefir. Amines were selectively extracted using solid phase extraction, subsequently derivatizatized with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate and further determined by High Performance Liquid Chromatography with fluorescence detection. The method's sensitivity was highly satisfactory, with limits of detection lower than 0.2 mg/L. Optimal linearity and repeatability were also achieved. BAs were not detected in most of the milk samples, but they were found frequently at high levels in yogurt and kefir samples, reaching values of up to 79 mg/kg total BAs in kefir samples. Levels measured should not be a cause for concern for the population at large, but should be known by BAs-sensitive individuals.

Profiling Locally Translated mRNAs in Regenerating Axons.

Spatial and temporal regulation of protein expression plays important roles in many cellular functions, particularly for highly polarized cell types. While the subcellular proteome can be altered by relocalizing proteins from other domains of the cell, transporting mRNAs to subcellular domains provides a means to locally synthesize new proteins in response to different stimuli. Localized protein synthesis is a critical mechanism in neurons that extend dendrites and axons long distances from their cell bodies. Here, we discuss methodologies that have been developed to study localized protein synthesis using axonal protein synthesis as an example. We provide an in-depth method using dual fluorescence recovery after photobleaching to visualize sites of protein synthesis using reporter cDNAs that encode two different localizing mRNAs along with diffusion-limited fluorescent reporter proteins. We show how this method can be used to determine how extracellular stimuli and different physiological states can alter the specificity of local mRNA translation in real time.

A genetically encoded far-red fluorescent indicator for imaging synaptically released Zn2.

Synaptic zinc ion (Zn2+) has emerged as a key neuromodulator in the brain. However, the lack of research tools for directly tracking synaptic Zn2+ in the brain of awake animals hinders our rigorous understanding of the physiological and pathological roles of synaptic Zn2+. In this study, we developed a genetically encoded far-red fluorescent indicator for monitoring synaptic Zn2+ dynamics in the nervous system. Our engineered far-red fluorescent indicator for synaptic Zn2+ (FRISZ) displayed a substantial Zn2+-specific turn-on response and low-micromolar affinity. We genetically anchored FRISZ to the mammalian extracellular membrane via a transmembrane (TM) ⍺ helix and characterized the resultant FRISZ-TM construct at the mammalian cell surface. We used FRISZ-TM to image synaptic Zn2+ in the auditory cortex in acute brain slices and awake mice in response to electric and sound stimuli, respectively. Thus, this study establishes a technology for studying the roles of synaptic Zn2+ in the nervous system.

A Fluorescent Intravital Imaging Approach to Study Load-Induced Calcium Signaling Dynamics in Mouse Osteocytes.

Bone tissue is exquisitely sensitive to differences in mechanical load magnitude. Osteocytes, dendritic cells that form a syncytium throughout the bone, are responsible for the mechanosensory function of bone tissue. Studies employing histology, mathematical modeling, cell culture, and ex vivo bone organ cultures have greatly advanced the understanding of osteocyte mechanobiology. However, the fundamental question of how osteocytes respond to and encode mechanical information at the molecular level in vivo is not well understood. Intracellular calcium concentration fluctuations in osteocytes offer a useful target for learning more about acute bone mechanotransduction mechanisms. Here, we report a method for studying osteocyte mechanobiology in vivo, combining a mouse strain with a fluorescently genetically encoded calcium indicator expressed in osteocytes with an in vivo loading and imaging system to directly detect osteocyte calcium levels during loading. This is achieved with a three-point bending device that can deliver well-defined mechanical loads to the third metatarsal of living mice while simultaneously monitoring fluorescently indicated calcium responses of osteocytes using two-photon microscopy. This technique allows for direct in vivo observation of osteocyte calcium signaling events in response to whole bone loading and is useful in the endeavor to reveal mechanisms in osteocyte mechanobiology.

Pattern-recognizing-assisted detection of mildewed wheat by Dyes/Dyes-Cu-MOF paper-based colorimetric sensor array.

In order to timely discriminate wheat with different mildew rates, a Dyes/Dyes-Cu-MOF paper-based colorimetric sensor array was designed. Using array points to capture volatile gases of wheat with different mildew rates, and output RGB values. The correlation between ΔR/ΔG/ΔB values and odor components was established. The ΔG values of array points 2' and 3' showed the best correlation with mildew rate, with R2 of 0.9816 and 0.9642. The ΔR value of 3 and the ΔG value of 2 correlate well with the mildew rate, with R2 of 0.9625 and 0.9502, respectively. Then, the ΔRGB values are subjected to pattern recognition processing, and LDA achieves 100% correct discrimination for all samples, or divides high and low mildew areas. This method provides an odor-based monitoring tool for fast, visual and nondestructive evaluation of food safety and quality through visualization of odors produced by different mildew rates.

Single-Molecule Imaging of Lateral Mobility and Ion Channel Activity in Lipid Bilayers using Total Internal Reflection Fluorescence (TIRF) Microscopy.

High-resolution imaging techniques have shown that many ion channels are not static, but subject to highly dynamic processes, including the transient association of pore-forming and auxiliary subunits, lateral diffusion, and clustering with other proteins. However, the relationship between lateral diffusion and function is poorly understood. To approach this problem, we describe how lateral mobility and activity of individual channels in supported lipid membranes can be monitored and correlated using total internal reflection fluorescence (TIRF) microscopy. Membranes are fabricated on an ultrathin hydrogel substrate using the droplet interface bilayer (DIB) technique. Compared to other types of model membranes, these membranes have the advantage of being mechanically robust and suitable for highly sensitive analytical techniques. This protocol measures Ca2+ ion flux through single channels by observing the fluorescence emission of a Ca2+-sensitive dye in close proximity to the membrane. In contrast to classical single-molecule tracking approaches, no fluorescent fusion proteins or labels, which can interfere with lateral movement and function in the membrane, are required. Possible changes in ion flux associated with conformational changes of the protein are only due to protein lateral motion in the membrane. Representative results are shown using the mitochondrial protein translocation channel TOM-CC and the bacterial channel OmpF. In contrast to OmpF, the gating of TOM-CC is very sensitive to molecular confinement and the nature of lateral diffusion. Hence, supported droplet-interface bilayers are a powerful tool to characterize the link between lateral diffusion and the function of ion channels.

Hypergravity Increases Blood-Brain Barrier Permeability to Fluorescent Dextran and Antisense Oligonucleotide in Mice.

The earliest effect of spaceflight is an alteration in vestibular function due to microgravity. Hypergravity exposure induced by centrifugation is also able to provoke motion sickness. The blood-brain barrier (BBB) is the crucial interface between the vascular system and the brain to ensure efficient neuronal activity. We developed experimental protocols of hypergravity on C57Bl/6JRJ mice to induce motion sickness and reveal its effects on the BBB. Mice were centrifuged at 2× g for 24 h. Fluorescent dextrans with different sizes (40, 70 and 150 kDa) and fluorescent antisense oligonucleotides (AS) were injected into mice retro-orbitally. The presence of fluorescent molecules was revealed by epifluorescence and confocal microscopies in brain slices. Gene expression was evaluated by RT-qPCR from brain extracts. Only the 70 kDa dextran and AS were detected in the parenchyma of several brain regions, suggesting an alteration in the BBB. Moreover, Ctnnd1, Gja4 and Actn1 were upregulated, whereas Jup, Tjp2, Gja1, Actn2, Actn4, Cdh2 and Ocln genes were downregulated, specifically suggesting a dysregulation in the tight junctions of endothelial cells forming the BBB. Our results confirm the alteration in the BBB after a short period of hypergravity exposure.

Adsorptive Removal of Direct Azo Dyes from Textile Wastewaters Using Weakly Basic Anion Exchange Resin.

Direct dyes are still widely used for coloring a variety of materials due to their ease of use and the wide range of colors available at a moderate cost of production. In the aquatic environment, some direct dyes, especially the azo type and their biotransformation products, are toxic, carcinogenic and mutagenic. Hence the need for their careful removal from industrial effluents. It was proposed adsorptive retention of C.I. Direct Red 23 (DR23), C.I. Direct Orange 26 (DO26) and C.I. Direct Black 22 (DB22) from effluents using anion exchange resin of tertiary amine functionalities Amberlyst A21 (A21). Applying the Langmuir isotherm model, the monolayer capacities were calculated as 285.6 mg/g for DO26 and 271.1 mg/g for DO23. The Freundlich isotherm model seems to be the better one for the description of DB22 uptake by A21, and the isotherm constant was found to be 0.609 mg1-1/n L1/n/g. The kinetic parameters revealed that the pseudo-second-order model could be used for the description of experimental data rather than the pseudo-first-order model or intraparticle diffusion model. The dye adsorption decreased in the presence of anionic and non-ionic surfactants, while their uptake was enhanced in the presence of Na2SO4 and Na2CO3. Regeneration of the A21 resin was difficult; a slight increase in its efficiency was observed using 1M HCl, 1 M NaOH and 1 M NaCl solutions in 50% v/v methanol.

Label-free and sensitive fluorescent sensing of ten-eleven translocation enzyme via cascaded recycling signal amplifications.

The sensitive detection of ten-eleven translocation (TET) dioxygenase is of significance for understanding the demethylation mechanism of 5-methylocytosine (5mC), which is responsible for a wide range of biological functions that can affect gene expression in eukaryotic species. Here, a non-label and sensitive fluorescence biosensing method for TET assay using TET1 as the model target molecule is established on the basis of target-triggered Mg2+-dependent DNAzyme and catalytic hairpin assembly (CHA)-mediated multiple signal amplification cascades. 5mC sites in the hairpin DNA probe are first oxidized by TET1 into 5-carboxycytosine, which are further reduced by pyridine borane into dihydrouracil, followed by its recognition and cleavage by the USER enzyme to liberate active DNAzyme and G-quadruplex sequences from the probe. The DNAzyme further cyclically cleaves the substrate hairpins to trigger subsequent CHA reaction and DNAzyme cleavage cycles for yielding many G-quadruplex strands. Thioflavin T dye then intercalates into G-quadruplexes to cause a magnificent increase of fluorescence for high sensitivity assay of TET1 with 47 fM detection limit. And, application of this method for TET1 monitoring in diluted serum has also been confirmed.

Dual-Signal Triple-Mode Optical Sensing Platform for Assisting in the Diagnosis of Kidney Disorders.

As known biomarkers of kidney diseases, N-acetyl-ß-d-glucosaminidase (NAG) and ß-galactosidase (ß-GAL) are of great importance for the diagnosis and treatment of diseases. The feasibility of using multiplex sensing methods to simultaneously report the outcome of the two enzymes in the same sample is even more alluring. Herein, we establish a simple sensing platform for the concurrent detection of NAG and ß-GAL using silicon nanoparticles (SiNPs) as a fluorescent indicator synthesized by a one-pot hydrothermal route. p-Nitrophenol (PNP), as a common enzymatic hydrolysis product of the two enzymes, led to the attenuation of fluorometric signal caused by the inner filter effect on SiNPs, the enhancement of colorimetric signal due to the increase of intensity of the characteristic absorption peak at around 400 nm with increasing reaction time, and the changes of RGB values of images obtained through a color recognition application on a smartphone. The fluorometric/colorimetric approach combined with the smartphone-assisted RGB mode was able to detect NAG and ß-GAL with good linear response. Applying this optical sensing platform to clinical urine samples, we found that the two indicators in healthy individuals and patients (glomerulonephritis) with kidney diseases were significantly different. By expanding to other renal lesion-related specimens, this tool may show great potentials in clinical diagnosis and visual inspection.

Wastewater from textile digital printing as a substrate for microalgal growth and valorization.

This study aims at evaluating an innovative biotechnological process for the concomitant bioremediation and valorization of wastewater from textile digital printing technology based on a microalgae/bacteria consortium. Nutrient and colour removal were assessed in lab-scale batch and continuous experiments and the produced algae/bacteria biomass was characterized for pigment content and biomethane potential. Microbial community analysis provided insight of the complex community structure responsible for the bioremediation action. Specifically, a community dominated by Scenedesmus spp. and xenobiotic and dye degrading bacteria was naturally selected in continuous photobioreactors. Data confirm the ability of the microalgae/bacteria consortium to grow in textile wastewater while reducing the nutrient content and colour. Improvement strategies were eventually identified to foster biomass growth and process performances. The experimental findings pose the basis of the integration of a microalgal-based process into the textile sector in a circular economy perspective.

Overcoming the field-of-view to diameter trade-off in microendoscopy via computational optrode-array microscopy.

High-resolution microscopy of deep tissue with large field-of-view (FOV) is critical for elucidating organization of cellular structures in plant biology. Microscopy with an implanted probe offers an effective solution. However, there exists a fundamental trade-off between the FOV and probe diameter arising from aberrations inherent in conventional imaging optics (typically, FOV < 30% of diameter). Here, we demonstrate the use of microfabricated non-imaging probes (optrodes) that when combined with a trained machine-learning algorithm is able to achieve FOV of 1x to 5x the probe diameter. Further increase in FOV is achieved by using multiple optrodes in parallel. With a 1 × 2 optrode array, we demonstrate imaging of fluorescent beads (including 30 FPS video), stained plant stem sections and stained living stems. Our demonstration lays the foundation for fast, high-resolution microscopy with large FOV in deep tissue via microfabricated non-imaging probes and advanced machine learning.

Novel Design and Application of High-NA Fiber Imaging Bundles for In Vivo Brain Imaging with Two-Photon Scanning Fluorescence Microscopy.

Here, we provide experimental verification supporting the use of short-section imaging bundles for two-photon microscopy imaging of the mouse brain. The 8 mm long bundle is made of a pair of heavy-metal oxide glasses with a refractive index contrast of 0.38 to ensure a high numerical aperture NA = 1.15. The bundle is composed of 825 multimode cores, ordered in a hexagonal lattice with a pixel size of 14 µm and a total diameter of 914 µm. We demonstrate successful imaging through custom-made bundles with 14 µm resolution. As the input, we used a 910 nm Ti-sapphire laser with 140 fs pulse and a peak power of 9 × 104 W. The excitation beam and fluorescent image were transferred through the fiber imaging bundle. As test samples, we used 1 µm green fluorescent latex beads, ex vivo hippocampal neurons expressing green fluorescent protein and cortical neurons in vivo expressing the fluorescent reporter GCaMP6s or immediate early gene Fos fluorescent reporter. This system can be used for minimal-invasive in vivo imaging of the cerebral cortex, hippocampus, or deep brain areas as a part of a tabletop system or an implantable setup. It is a low-cost solution, easy to integrate and operate for high-throughput experiments.

CRISPR/Cas12a-based MUSCA-PEC strategy for HSV-1 assay.

In the photoelectrochemical sensing, constant potential excitation to get the photoelectrochemical signal is the main excitation signal mode. Novel method for photoelectrochemical signal obtaining is needed. Inspired by this ideal, a photoelectrochemical strategy for Herpes simplex virus (HSV-1) detection with multiple potential step chronoamperometry (MUSCA) pattern was fabricated using CRISPR/Cas12a cleavage coupled with entropy-driven target recycling. In the presence of target, HSV-1, the Cas12a was activated by the H1-H2 complex obtained by entropy-driven, then digesting the circular fragment of csRNA to expose single-stranded crRNA2 and alkaline phosphatase (ALP). The inactive Cas12a was self-assembled with crRNA2 and activated again with the help of assistant dsDNA. After multiple rounds of CRISPR/Cas12a cleavage and magnetic separation, MUSCA, as a signal amplifier, collected the enhanced photocurrent responses generated by catalyzed p-Aminophenol (p-AP). Different from the reported signal enhancement strategies based on photoactive nanomaterials and sensing mechanisms, MUSCA technique endowed the strategy with unique advantages of direct, fast and ultrasensitive. A superior detection limit of 3 aM toward HSV-1 was achieved. This strategy was successfully applied for HSV-1 detection in Human serum samples. The combination of MUSCA technique and CRISPR/Cas12a assay brings broader potential prospect for the detection of nucleic acids.

Partially oxidized MoS2 nanosheets with high water-solubility to enhance the peroxidase-mimic activity for sensitive detection of glutathione.

Surface oxidation engineering is an effective strategy to construct nanomaterials with enhanced biocatalytic activity. In this study, a facile one-pot oxidation strategy was proposed to synthesize partially oxidized molybdenum disulfide nanosheets (ox-MoS2 NSs), which exhibit good water solubility and can be used as an excellent peroxidase substitute. Under the oxidation process, Mo-S bonds are partially broke and S atoms are replaced by excess oxygen atoms, and the released abundant heat and gases efficiently expended the interlayer distance and weaken the van der Waals forces between adjacent layers. Porous ox-MoS2 NSs can be easily exfoliated by further sonication, and the nanosheets exhibits excellent water dispersibility and no obvious sediment appear even after store for months. Benefiting from the desirable affinity property with enzyme substrates, optimized electronic structure and prominent electron transfer efficiency, the ox-MoS2 NSs exhibit enhanced peroxidase-mimic activity. Furthermore, the ox-MoS2 NSs catalyzed 3,3',5,5'-tetramethylbenzidine (TMB) oxidation reaction could be inhibited by the redox reaction that take place between glutathione (GSH) as well as the direct interaction between GSH and ox-MoS2 NSs. Thus, a colorimetric sensing platform was constructed for GSH detection with good sensitivity and stability. This work provides a facile strategy for engineering structure of nanomaterials and improving enzyme-mimic performance.