Front Cover: Wide‐field monitoring and real‐time local recording of microvascular networks on small animals with a dual‐raster‐scanned photoacoustic microscope

A dual‐raster‐scanned photoacoustic microscope (DRS‐PAM) was reported, which integrates a two‐dimensional motorized translation stage for large field‐of‐view imaging and a two‐axis fast galvanometer scanner for real‐time imaging. The DRS‐PAM provides a flexible transition from wide‐field monitoring the vasculature of organs to real‐time imaging of local dynamics. Further details can be found in the article by Fei Yang, Zhiyang Wang, Wuyu Zhang, et al. ( e202000022 ).

     

Increasing eDNA capabilities with CRISPR technology for real‐time monitoring of ecosystem biodiversity

The accelerating pace of scientific discovery is being driven by the development of transformative technologies that are expanding traditional scientific boundaries. In ecology, the concept that ecosystem structure can be monitored through the stew of genetic material released into the environment by local organisms is now a highly active area of research. At the same time that the use of environmental DNA (eDNA) has gained popularity in ecology, CRISPR genome editing technology has been revolutionizing organismal biology and the biomedical sciences. In a From the Cover article in this issue of Molecular Ecology Resources, Williams et al. (2019) report about the fusion of CRISPR technology with molecular ecology to improve the in situ processing capabilities of eDNA applications. Piloting this new CRISPR technology on aquatic systems, the authors describe tools to accurately identify the presence of Atlantic salmon (Salmo salar) from eDNA, using conditions that are highly amenable to implementation in the field. This overcomes a major barrier restricting the use of eDNA, opening a door to expanded use of the technology in ecological research.     

Accounting for space and uncertainty in real‐time location system‐derived contact networks

1. Point data obtained from real‐time location systems (RTLSs) can be processed into animal contact networks, describing instances of interaction between tracked individuals. Proximity‐based definitions of interanimal “contact,” however, may be inadequate for describing epidemiologically and sociologically relevant interactions involving body parts or other physical spaces relatively far from tracking devices. This weakness can be overcome by using polygons, rather than points, to represent tracked individuals and defining “contact” as polygon intersections.
2. We present novel procedures for deriving polygons from RTLS point data while maintaining distances and orientations associated with individuals' relocation events. We demonstrate the versatility of this methodology for network modeling using two contact network creation examples, wherein we use this procedure to create (a) interanimal physical contact networks and (b) a visual contact network. Additionally, in creating our networks, we establish another procedure to adjust definitions of “contact” to account for RTLS positional accuracy, ensuring all true contacts are likely captured and represented in our networks.
3. Using the methods described herein and the associated R package we have developed, called contact, researchers can derive polygons from RTLS points. Furthermore, we show that these polygons are highly versatile for contact network creation and can be used to answer a wide variety of epidemiological, ethological, and sociological research questions.
4. By introducing these methodologies and providing the means to easily apply them through the contact R package, we hope to vastly improve network‐model realism and researchers' ability to draw inferences from RTLS data.

     

Engineering a sensitive visual‐tracking reporter system for real‐time monitoring phosphorus deficiency in tobacco

Plant phosphorus (P) diagnosis is widely used for monitoring P status and guiding P fertilizer application in field conditions. The common methods for predicting plant response to P are time‐ and labour‐consuming chemical measurements of the extractable soil P and plant P concentrations. In this study, we successfully generated a visual reporter system in tobacco (Nicotiana tabacum L.) to monitor plant P status by expressing of a Purple gene (Pr) isolated from cauliflower (Brassica oleracea var botrytis) driven by the promoter (Pro) of OsPT6, a P‐starvation‐induced rice gene. The leaves of OsPT6_pro::Pr (PT6_pro::Pr) transgenic tobacco continuously turned into dark purple with the increase of duration and severity of P deficiency, and recovered rapidly to basal green colour upon resupply of P. The expression of several anthocyanin biosynthesis involving genes was strongly activated in the transgenic tobacco in comparison to wild type under P‐deficient condition. Such additive purple colour was not detected by deficiencies of other major‐ and micronutrients or stresses of salt, drought and cold. There was an extremely high correlation between P concentration and anthocyanin accumulation in the transgenic tobacco leaves. Using a hyperspectral sensing technology, P concentration in the leaves of transgenic plants could be predicted by the reflectance spectra at 554 nm wavelength with approximately 0.16 as the threshold value of the P deficiency. Taken together, the colour‐based visual reporter system could be specifically and readily used for monitoring the plant P status by naked eyes and accurately assessed by spectral reflectance.     

Generic Raman‐based calibration models enabling real‐time monitoring of cell culture bioreactors

Raman‐based multivariate calibration models have been developed for real‐time in situ monitoring of multiple process parameters within cell culture bioreactors. Developed models are generic, in the sense that they are applicable to various products, media, and cell lines based on Chinese Hamster Ovarian (CHO) host cells, and are scalable to large pilot and manufacturing scales. Several batches using different CHO‐based cell lines and corresponding proprietary media and process conditions have been used to generate calibration datasets, and models have been validated using independent datasets from separate batch runs. All models have been validated to be generic and capable of predicting process parameters with acceptable accuracy. The developed models allow monitoring multiple key bioprocess metabolic variables, and hence can be utilized as an important enabling tool for Quality by Design approaches which are strongly supported by the U.S. Food and Drug Administration. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1004–1013, 2015     

Feasibility of photoacoustic evaluations on dual‐thermal treatment of ex vivo bladder tumors

A variety of thermal therapeutic methods have been investigated to treat bladder tumors but often cause bowel injury and bladder wall perforation due to high treatment dosage and limited clinical margins. The objective of the current study is to develop a dual‐thermal modality to deeply coagulate the bladder tumors at low thermal dosage and to evaluate therapeutic outcomes with high contrast photoacoustic imaging (PAI). High intensity focused ultrasound (HIFU) is combined with 532 nm laser light to enhance therapeutic depth during thermal treatments on artificial tumor‐injected bladder tissue ex vivo. PAI is employed to identify the margins of the tumors pre‐ and post‐treatments. The dual‐thermal modality achieves 3‐ and 1.8‐fold higher transient temperature changes and 2.2‐ and 1.5‐fold deeper tissue denaturation than laser and HIFU, respectively. PAI vividly identifies the position of the injected tumor and entails approximately 7.9 times higher image contrast from the coagulated tumor as that from the untreated tumor. Spectroscopic analysis exhibits that both 740 nm and 760 nm attains the maximum photoacoustic amplitudes from the treated areas. The proposed PAI‐guided dual‐thermal treatments (laser and HIFU) treatments can be a feasible therapeutic modality to treat bladder tumors in a controlled and efficient manner.

     

Validation of a real‐time PCR for Haemophilus parasuis

Aims: To validate a real‐time PCR test for the diagnosis of Glässer’s disease, a major pig disease caused by Haemophilus parasuis. Methods and Results: The specificity of a real‐time PCR amplifying the inf B gene was validated with 68 H. parasuis isolates and 36 strains of closely related species. As well, 239 samples of DNA from tissues and fluids of 16 experimentally challenged animals were tested with the real‐time PCR, and the results were compared with culture and a conventional PCR. The real‐time PCR produced significantly more positive results than the conventional PCR (165 vs 86). Conclusions: The sensitivity of the real‐time PCR combined with high specificity makes it a very valuable tool for the diagnosis of Glässer’s disease. Significance and Impact of Study: This new method will improve the ability of laboratories to diagnose Glässer’s disease, especially in laboratories where the culture method for H. parasuis is not optimal.     

Stable carbon isotopes of methane for real‐time process monitoring in anaerobic digesters

Efficient operation and stability of biogas plants requires continuous monitoring of the digester content. Traditional laboratory analysis of digester sludge is often complex and time‐consuming and shows a delayed response to disruptions within the fermentation process. As a new approach, we applied an online measurement technique (laser absorption spectroscopy) for real‐time monitoring of stable carbon isotopes of methane () in a pilot‐scale biogas digester (3500 L) regularly fed with maize silage. Generally, isotopic composition of methane gives information about specific substrate degradation, that is, methanogenic pathways that reflect the actual digester state. First results of a 2‐wk monitoring experiment show that stable carbon isotopes of methane respond promptly and highly dynamic to changes in the process state of the digester. In combination with other monitoring parameters (methane production rate, concentration of volatile fatty acids, and pH) the fluctuations in can be interpreted as a change in methanogenic pathways due to a high organic loading rate. In this context, might be used as a new parameter tool for monitoring and characterization of the process state of the digester.     

Structure,interaction and real‐time monitoring of the enzymatic reaction of wild‐type APOBEC3G

Human APOBEC3G exhibits anti‐human immunodeficiency virus‐1 (HIV‐1) activity by deaminating cytidines of the minus strand of HIV‐1. Here, we report a solution structure of the C‐terminal deaminase domain of wild‐type APOBEC3G. The interaction with DNA was examined. Many differences in the interaction were found between the wild type and recently studied mutant APOBEC3Gs. The position of the substrate cytidine, together with that of a DNA chain, in the complex, was deduced. Interestingly, the deamination reaction of APOBEC3G was successfully monitored using NMR signals in real time. Real‐time monitoring has revealed that the third cytidine of the d(CCCA) segment is deaminated at an early stage and that then the second one is deaminated at a late stage, the first one not being deaminated at all. This indicates that the deamination is carried out in a strict 3′ → 5′ order. Virus infectivity factor (Vif) of HIV‐1 counteracts the anti‐HIV‐1 activity of APOBEC3G. The structure of the N‐terminal domain of APOBEC3G, with which Vif interacts, was constructed with homology modelling. The structure implies the mechanism of species‐specific sensitivity of APOBEC3G to Vif action.     

In vivo study of rat cortical hemodynamics using a stereotaxic‐apparatus‐compatible photoacoustic microscope

Brain imaging is an important technique in cognitive neuroscience. In this article, we designed a stereotaxic‐apparatus‐compatible photoacoustic microscope for the studies of rat cortical hemodynamics. Compared with existing optical resolution photoacoustic microscopy (ORPAM) systems, the probe owns feature of fast, light and miniature. In this microscope, we integrated a miniaturized ultrasound transducer with a center frequency of 10 MHz to detect photoacoustic signals and a 2‐dimensional (2D) microelectromechanical system (MEMS) scanner to achieve raster scanning of the optical focus. Based on phantom evaluation, this imaging probe has a high lateral resolution of 3.8 μm and an effective imaging domain of 2 × 2 mm². Different from conventional ORPAMs, combining with standard stereotaxic apparatus enables broad studies of rodent brains without any motion artifact. To show its capability, we successfully captured red blood cell flow in the capillary, monitored the vascular changes during bleeding and blood infusion and visualized cortical hemodynamics induced by middle cerebral artery occlusion.      

The real‐time quantification of autofluorescence spectrum shape for the monitoring of mitochondrial metabolism

The cellular proportion of free and protein‐bound NADH complexes is increasingly recognized as a metabolic indicator and biomarker. Because free and bound forms exhibit different fluorescence spectra, we consider whether autofluorescence shape sufficiently correlates with mitochondrial metabolism to be useful for monitoring in cellular suspensions. Several computational approaches for rapidly quantifying spectrum shape are used to detect Saccharomyces cereviseae response to oxygenation, and to the addition of mitochondrial functional modifiers and metabolic substrates. Observed changes appear consistent with previous studies probing free/protein‐bound proportions, making this a potentially useful approach for the real‐time monitoring of metabolism. (© 2015 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

Fluorescently labeled adrenomedullin allows real‐time monitoring of adrenomedullin receptor trafficking in living cells

The human adrenomedullin (ADM) is a 52 amino acid peptide hormone belonging to the calcitonin family of peptides, which plays a major role in the development and regulation of cardiovascular and lymphatic systems. For potential use in clinical applications, we aimed to investigate the fate of the peptide ligand after binding and activation of the adrenomedullin receptor (AM₁), a heterodimer consisting of the calcitonin receptor‐like receptor (CLR), a G protein‐coupled receptor, associated with the receptor activity‐modifying protein 2 (RAMP2). Full length and N‐terminally shortened ADM peptides were synthesized using Fmoc/tBu solid phase peptide synthesis and site‐specifically labeled with the fluorophore carboxytetramethylrhodamine (Tam) either by amide bond formation or copper(I)‐catalyzed azide alkyne cycloaddition. For the first time, Tam‐labeled ligands allowed the observation of co‐internalization of the whole ligand‐receptor complex in living cells co‐transfected with fluorescent fusion proteins of CLR and RAMP2. Application of a fluorescent probe to track lysosomal compartments revealed that ADM together with the CLR/RAMP2‐complex is routed to the degradative pathway. Moreover, we found that the N‐terminus of ADM is not a crucial component of the peptide sequence in terms of AM₁ internalization behavior. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.     

Effects of predation on real‐time host–parasite coevolutionary dynamics

The impact of community complexity on pairwise coevolutionary dynamics is theoretically dependent on the extent to which species evolve generalised or specialised adaptations to the multiple species they interact with. Here, we show that the bacteria Pseudomonas fluorescens diversifies into defence specialists, when coevolved simultaneously with a virus and a predatory protist, as a result of fitness trade‐offs between defences against the two enemies. Strong bacteria–virus pairwise coevolution persisted, despite strong protist‐imposed selection. However, the arms race dynamic (escalation of host resistance and parasite infectivity ranges) associated with bacteria–virus coevolution broke down to a greater extent in the presence of the protist, presumably through the elevated genetic and demographic costs of increased bacteria resistance ranges. These findings suggest that strong pairwise coevolution can persist even in complex communities, when conflicting selection leads to evolutionary diversification of different defence strategies.     

Integrated photoacoustic and hyperspectral dual‐modality microscopy for co‐imaging of melanoma and cutaneous squamous cell carcinoma in vivo

Skin carcinoma such as melanoma (MM) and cutaneous squamous cell carcinoma (cSCC) are considered as the highest mortality and the most aggressive skin cancers in dermatology. In view that early diagnosis and treatment can greatly improve the survival rate and life quality of the patients, developing noninvasive and effective evaluation methods is of great significance for the detection and identification of early stage cutaneous cancers. In this article, we propose a hybrid photoacoustic and hyperspectral dual‐modality microscopy to evaluate and differentiate skin carcinoma by structural and multiphysiological parameters. The proposed system's imaging abilities are verified by mimic phantoms and normal mice experiments. Furthermore, in vivo characterization and evaluation results of MM and cSCC mice are obtained successfully, which prove this novel method could be used as a reliable and useful method for skin cancer detection in early stages.     

Real‐time monitoring of herbivore induced volatile emissions in the field

When plants are damaged by herbivorous insects they emit a blend of volatile organic compounds (VOCs) which include a range or terpenoids and green leaf volatiles (GLVs) formed via different metabolic pathways. The precise timing of these emissions upon the onset of herbivore feeding has not been fully elucidated, and the information that is available has been mainly obtained through laboratory based studies. We investigated emissions of VOCs from Populus tremula L. ×P. tremuloides Michx. during the first 20 h of feeding by Epirrita autumnata (autumnal moth) larvae in a field site. The study was conducted using Proton Transfer Reaction‐Mass Spectrometry (PTR‐MS) to measure emissions online, with samples collected for subsequent analysis by complementary gas chromatography‐mass spectrometry for purposes of compound identification. GLV emission peaks occurred sporadically from the outset, indicating herbivore activity, while terpene emissions were induced within 16 h. We present data detailing the patterns of monoterpene (MT), GLV and sesquiterpene (SQT) emissions during the early stages of herbivore feeding showing diurnal MT and SQT emission that is correlated more with temperature than light. Peculiarities in the timing of SQT emissions prompted us to conduct a thorough characterization of the equipment used to collect VOCs and thus corroborate the accuracy of results. A laboratory based analysis of the throughput of known GLV, MT and SQT standards at different temperatures was made with PTR‐MS. Enclosure temperatures of 12, 20 and 25°C had little influence on the response time for dynamic measurements of a GLV or MT. However, there was a clear effect on SQT measurements. Elucidation of emission patterns in real‐time is dependent upon the dynamics of cuvettes at different temperatures.     

Volumetric hand‐held optoacoustic angiography as a tool for real‐time screening of dense breast

Existing mammographic screening solutions are generally associated with several major drawbacks, such as exposure to ionizing radiation or insufficient sensitivity in younger populations with radiographically‐dense breast. Even when combined with ultrasound or magnetic resonance imaging, X‐Ray mammography may still attain unspecific or false positive results. Thus, development of new breast imaging tools represents a timely medical challenge. We report on a new approach to high‐resolution functional and anatomical breast angiography using volumetric hand‐held optoacoustic tomography, which employs light intensities safe for human use. Experiments in young healthy volunteers with fibroglandular‐dominated dense breasts revealed the feasibility of rendering three‐dimensional images representing vascular anatomy and functional blood oxygenation parameters at video rate. Sufficient contrast was achieved at depths beyond 2 cm within dense breasts without compromising the real‐time imaging performance. The suggested solution may thus find applicability as a standalone or supplemental screening tool for early detection and follow‐up of carcinomas in radiographically‐dense breasts.

Volumetric handheld optoacoustic tomography scanner uses safe pulses of near‐infrared light to render three‐dimensional images of deep vascular anatomy, blood oxygenation and breast parenchyma at video rate.     

Wide‐field optical property mapping and structured light imaging of the esophagus with spatial frequency domain imaging

As the incidence of esophageal adenocarcinoma continues to rise, there is a need for improved imaging technologies with contrast to abnormal esophageal tissues. To inform the design of optical technologies that meet this need, we characterize the spatial distribution of the scattering and absorption properties from 471 to 851 nm of eight resected human esophagi tissues using Spatial Frequency Domain Imaging. Histopathology was used to categorize tissue types, including normal, inflammation, fibrotic, ulceration, Barrett's Esophagus and squamous cell carcinoma. Average absorption and reduced scattering coefficients of normal tissues were 0.211 ± 0.051 and 1.20 ± 0.18 mm^?1, respectively at 471 nm, and both values decreased monotonically with increasing wavelength. Fibrotic tissue exhibited at least 68% larger scattering signal across all wavelengths, while squamous cell carcinoma exhibited a 36% decrease in scattering at 471 nm. We additionally image the esophagus with high spatial frequencies up to 0.5 mm^?1 and show strong reflectance contrast to tissue treated with radiation. Lastly, we observe that esophageal absorption and scattering values change by an average of 9.4% and 2.7% respectively over a 30 minute duration post‐resection. These results may guide system design for the diagnosis, prevention and monitoring of esophageal pathologies.      

Preparation of extracellular domain 3 of human VEGF receptor‐2 and the monitoring of its real‐time binding to VEGF by biosensors

Vascular endothelial growth factor receptor‐2 (VEGFR‐2) plays an important role in stimulating the proliferation of endothelial cells and improving the permeability of blood vessels, which is involved in tumor angiogenesis, a process that is essential for tumor growth and metastasis. In this study, we describe a method for high yield of recombinant extracellular domain 3 (KDR3) of human VEGFR‐2 in an Escherichia coli system with further purification by cation exchange chromatography and immobilized metal affinity chromatography (IMAC). The biological activity of recombinant KDR3 was performed by sequestering VEGF in HUVEC proliferation assay. The real‐time binding of human VEGF to immobilized KDR3 was monitored by a label‐free biosensor, Optical waveguide lightmode spectroscopy (OWLS). Under the given experimental conditions, the association rate constant k_a was 4.2 × 10³ M^?1 s^?1 and the dissociation rate k_d was 5.1 × 10^?3 s^?1. The dissociation constant K_D was then calculated to be 1.2 × 10^?6 M. The obtained values will serve as baseline parameters for the design of improved versions of recombinant soluble VEGF receptors and the evaluation of developed anti‐KDR antibodies. In addition, such a scenario established by the use of OWLS will potentiate the kinetic study of ligand/receptor and antigen/antibody. The receptor discussed here, which block VEGF binding to cell membrane KDR, have potential clinical application in the treatment of cancer and other diseases where pathological angiogenesis is involved. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009