Probe Design Research Articles

Accelerated Screening of Alternative DNA Base-Organic Molecule-Base Architectures via Integrated Theory and Experiment.

Organic molecule-mediated noncanonical DNA self-assembly expands the standard DNA base-pairing alphabets. However, only a very limited number of small molecules have been recognized as mediators because of the tedious and complicated experiments like crystallization and microscopy imaging. Here we present an integrative screening protocol incorporating molecular dynamics (MD) for fast theoretical simulation and native polyacrylamide gel electrophoresis for convenient experimental validation. Melamine, the molecule that was confirmed mediating noncanonical DNA base-pairing, and 38 other candidate molecules were applied to demonstrate the feasibility of this protocol. We successfully identified seven stable noncanonical DNA duplex structures, and another eight novel structures with sub-stability. In addition, we discovered that hairpins at both ends can significantly stabilize the noncanonical DNA structures, providing a guideline to design small organic molecule-incorporated DNA structures. Such an efficient screening protocol will accelerate the design of alternative DNA-molecule architectures beyond Watson-Crick pairs. Considering the wide range of potential mediators, it will also facilitate applications such as noncovalent, highly dense loading of drug molecules in DNA-based delivery system and probe design for sensitive detection of certain molecules.

Performance study of novel metal corrosion probes based on the adjust method of series and parallel connections

Abstract Rod-type metal corrosion probes based on electromechanical impedance (EMI) technique can quantitatively assess the amount of corrosion, which have a promising application in pipeline corrosion monitoring and have received more and more attention. In the design of piezoelectric smart devices, electrical series and parallel connections are very important and effective adjust method to improve the device performance, but it is yet to be used in the probe design. In this work, a kind of novel metal corrosion probe with two piezoelectric elements in series and parallel connections was proposed, and its performance was investigated comprehensively by combining theoretical analysis with experiment research. Theoretical models of the proposed probe in the longitudinal vibration mode for both series and parallel connections were established, and verified by the experimental results. Influences of the thicknesses of piezoelectric layer and ceramic layer on the probe performance were analyzed. Artificial quantitative corrosion tests and accelerated corrosion tests were designed to evaluate the quantitative corrosion monitoring capacity. Temperature sensitivity tests were conducted to study the temperature dependence. The wireless impedance measurement was performed to confirm the online monitoring ability. Comparisons for the probe performance between the series and parallel connections were also presented. This work provided a comprehensive understanding for this kind of novel probe, which is beneficial to develop low-cost, high-precision, high-stability pipeline corrosion real-time monitoring technology.

AnoPrimer: Primer Design in malaria vectors informed by range-wide genomic variation

The major malaria mosquitoes, Anopheles gambiae s.l and Anopheles funestus, are some of the most studied organisms in medical research and also some of the most genetically diverse. When designing polymerase chain reaction (PCR) or hybridisation-based molecular assays, reliable primer and probe design is crucial. However, single nucleotide polymorphisms (SNPs) in primer binding sites can prevent primer binding, leading to null alleles, or bind suboptimally, leading to preferential amplification of specific alleles. Given the extreme genetic diversity of Anopheles mosquitoes, researchers need to consider this genetic variation when designing primers and probes to avoid amplification problems. In this note, we present a Python package, AnoPrimer, which exploits the Ag1000G and Af1000 datasets and allows users to rapidly design primers in An. gambiae or An. funestus, whilst summarising genetic variation in the primer binding sites and visualising the position of primer pairs. AnoPrimer allows the design of both genomic DNA and cDNA primers and hybridisation probes. By coupling this Python package with Google Colaboratory, AnoPrimer is an open and accessible platform for primer and probe design, hosted in the cloud for free. AnoPrimer is available here https://github.com/sanjaynagi/AnoPrimer and we hope it will be a useful resource for the community to design probe and primer sets that can be reliably deployed across the An. gambiae and funestus species ranges.

Unlocking Creativity with Playful Probes

Acquiring data from potential users regarding their daily activities, especially young users or families, can present considerable challenges. Employing playful probes is a method for gathering data from young users; these probes are interactive, intuitive, and visually appealing. This approach allows users to express their thoughts in a non-traditional manner, producing rich qualitative data that can reveal the nuances of their perceptions and behaviors. Although only a few researchers have employed this technique in game design, it has shown great potential in gathering user information for the ideation process. However, there is a need for further exploration of this approach, especially when it comes to children as users. This study seeks to explore the potential of employing playful probes in game design and to identify any obstacles that may arise. Understanding the needs and characteristics of the target users is crucial to adapting the probes to effectively connect with them. By engaging participants in playful and immersive activities, design probes could provide deeper insights into the user and stimulate their creativity, leading to a more efficient final design that accommodates the wants and needs of the users. Keywords: design probes, playful probes, game design, human-centered design

Playing with persona: Highlighting older adults’ lived experience with the digital media

During the COVID-19 pandemic lockdowns (2020-2021), almost all facets of life were rendered digital – health, work, schooling, and logistics. In this phenomenon, not only did digital access become synonymous with social inclusion but inequalities were also amplified – particularly in the case of older adults (65 years and over). Contemporary older adults represent one of the most diverse spectrums of digital media users – spanning from technologically savvy to non-users. As the first generation of older adults to age in and through data in a data-saturated world, their understandings and experiences can teach us much about the possibilities and limitations of new media. Understanding these practices through cultural probes – like drawing, photos and writing prompts – can enable playful behaviours that not only elicit new thoughts and actions but also allow insight into some of the tacit lived experience that can support opportunities for technological use. In this paper, we ask: How can we playfully co-design through personas to enhance understandings of older adults’ lived experience of digital media? In this paper, we focus on the six co-design workshops in which we deployed personas as representations of digital experience to challenge, explore, provoke and help build nuanced tools for implementation. Through personas, speculative fiction and lived experience collide, offering some fascinating ways to rethink the digital-social dimension for older adults now and into the future.

Rational design of peptide-based fluorescent probe for sequential recognitions of Cu(II) ions and glyphosate: Smartphone, test strip, real sample and living cells applications

A new peptide-based fluorescent probe named DMDH with easy-to-synthesize, excellent stability, good water solubility and large Stokes shift (225 nm) was synthesized for highly selective sequential detections of copper ions (Cu2+) and glyphosate (Glyp). DMDH demonstrated great detection performance towards Cu2+via strong fluorescence quenching, and forming non-fluorescence DMDH-Cu2+ ensemble. As a new promising cascade probe, the fluorescence of DMDH-Cu2+ ensemble was significantly recovered based on displacement approach after glyphosate was added. Interestingly, the limit of detections (LODs) for Cu2+ and glyphosate were 40.6 nM and 10.6 nM, respectively, which were far lower than those recommended by the WHO guidelines for drinking water. More importantly, DMDH was utilized to evaluate Cu2+ and glyphosate content in three real water samples, demonstrating that its effectiveness in water quality monitoring. Additionally, it is worth noting that DMDH was also applied to analyze Cu2+ and glyphosate in living cells in view of significant cells permeability and low cytotoxicity. Moreover, DMDH soaked in filter paper was used to create qualitative test strips and visually identify Cu2+ and glyphosate through significant color changes. Furthermore, smartphone RGB color recognition provided a new method for semi-quantitative testing of Cu2+ and glyphosate in the absence of expensive instruments.

Design of ESIPT-Based Fluorescent Probes for Dual-Mode Sensing of Cyanide: Application to Rapid On-Location Detection and Screening of Natural Water Samples

Design of ESIPT-Based Fluorescent Probes for Dual-Mode Sensing of Cyanide: Application to Rapid On-Location Detection and Screening of Natural Water Samples

Gather ‘round and listen close: Increasing responding to voices in children with autism

ABSTRACT We investigated the effects of a response-contingent pairing (RCP) procedure on responses to voices for preschoolers with autism spectrum disorder (ASD). The participants were 4 preschool males who attended full-day special education classes utilizing a behavior-analytic system of schooling. The participants were chosen due to (a) their low numbers of observing responses to voices during initial probe screenings for observing responses to different forms of voice stimuli, and (b) their slow rates of mastery of educational objectives in their Individualized Education Programs (IEPs). We used an iPad-based RCP voice conditioning protocol during which we taught the participants to touch a correct stimulus on a screen (a red circle) that would activate 10 s of either sung or spoken song lyrics or spoken storylines. The conditioning component involved a response-contingent pairing procedure; contingent on a correct selection response, the investigators immediately paired the voice output with preferred edibles and/or light, preferred physical contact for the entire interval. We employed a multiple probe design across participants for five observing responses to voices (OV) following the intervention. The results showed increases for all four participants’ OV responses. We explore future implications of research involving increasing preferences for voices, and discuss other potential dependent variables.

A New Fluorene-Based Fluorescent Probe for Recognition of Hypochlorite Ions and its Applications.

Oxidative stress is a trigger for many diseases and occurs with the unstable hypochlorite (ClO-), known as one of the reactive oxygen species (ROS) in organisms. Then, HOCI is acknowledged as an oxidizing species that eliminates a variety of environmental pollutants. Hence, the development of novel methodologies for the selective and precise identification of HOCl/ ClO- is considered to be of utmost importance. In this study, the design, characterization, and applications of a fluorene-based fluorescent probe (FHBP) dependent on the ESIPT mechanism with a "turn-on" response for the sensitive/selective determination of ClO- against other competing samples were reported. The experimental results indicated that the detection limit for ClO-could be quantitatively determined by the probe to be 8.2 × 10-7M. The binding constant of the probe FHBP with ClO- was computed as 9.75 × 103M-1. In addition, the response time of FHBP was appointed to be 30s, indicating a rapid reaction with ClO-. It has also been demonstrated that this probe can be successfully used for the detection of ClO- on filter papers, TLC sheets, cotton swabs, and real samples.

From cell membrane to endoplasmic reticulum: Tunable lipid membrane imaging by regulating the lipophilicity and internalization of carbon dots

The interactions between various organelles play a crucial role on cellular activity, and the design and construction of multi-organelle fluorescent probes is of great challenges. Herein, fluorescent CDs with tunable cell plasma membrane and lipid-rich organelle-targeting ability were fabricated via exquisitely regulating the ratio of tridecanedioic acid and m-diethylaminophenol as the co-precursor, combining the structure–activity relationship to modulate the CDs structure and surficial property. Condensation of m-diethylaminophenol in the presence of different amount of tridecanedioic acid was exploited to construct MCDs and ECDs for targeted cell membrane and endoplasmic reticulum imaging respectively. The appropriately incorporated alkyl chains as membrane anchoring group and the suppressed internalization by carboxyl group led to the retention of MCDs in cell membrane, while the excessive introduction of alkyl chains offered ECDs with high lipophilicity, resulting in the rapid internalization and subsequential distribution in endoplasmic reticulum membrane. The favorable membrane retention capability and excellent photostability make MCDs an excellent probe for long-term targeted-imaging of cell membrane in vitro, with remarkable tracking duration long to five passages and effectively display cell membrane morphological dynamics during cell division and cell death. Moreover, real-time evaluation of cholesterol consumption of Lo phase in cell membrane via ratiometric fluorescence imaging was achieved, attributed to the sensitive response of CDs to polarity variations.

A compact single-ended optical sensor for temperature measurements via laser absorption spectroscopy

The tunable diode laser absorption spectroscopy (TDLAS) has been employed in various fields successfully. However, most current TDLAS sensors have low spatial resolution, which is the inherent disadvantage of TDLAS techniques. To address this issue, a compact single-ended optical sensor based on the laser absorption spectroscopy is developed in this manuscript. The laser is delivered to the region of interest by a quartz rod, providing the sensor with millimeter-level spatial resolution. And the design of probe makes the singled-end sensor convenient and capable for measurements in diverse situations. In order to validate the feasibility of this structure, temperature of the flame produced with a McKenna burner is measured via absorption of H2O 7185.59 cm−1 and 7444.35 cm−1 transitions. Applying the scanned-wavelength modulation spectroscopy with second-harmonic detection and first-harmonic normalization (WMS-2f/1f) strategy, an enhancement of the signal-to-noise ratio over the short absorption path can be obtained. The temperature obtained by the single-ended sensor agrees well with that measured by a B-type thermocouple across different radial positions and heights, regardless of variations in equivalence ratios, confirming the accuracy of the sensor. In addition, a CFD simulation is performed to investigate the nonuniformity in the measurement region and the results show that the nonuniformity can be negligible.

Magnetic susceptibility modeling of Magic-Angle spinning modules for part per billion scale field homogeneity

Magic-angle spinning (MAS) solid-state NMR methods are crucial in many areas of biology and materials science. Conventional probe designs have often been specified with 0.1 part per million (ppm) or 100 part per billion (ppb) magnetic field resolution, which is a limitation for many modern scientific applications. Here we describe a novel 5-mm MAS module design that significantly improves the linewidth and line shape for solid samples by an improved understanding of the magnetic susceptibility of probe materials and geometrical symmetry considerations, optimized to minimize the overall perturbation to the applied magnetic field (B0). The improved spinning module requires only first and second order shimming adjustments to achieve a sub-Hz resolution of 13C resonances of adamantane at 150 MHz Larmor frequency (14.1Tesla magnetic field). Minimal use of third and higher order shims improves experimental reproducibility upon sample changes and the exact placement within the magnet. Furthermore, the shimming procedure is faster, and the required gradients smaller, thus minimizing thermal drift of the room temperature (RT) shims. We demonstrate these results with direct polarization (Bloch decay) and cross polarization experiments on adamantane over a range of sample geometries and with multiple superconducting magnet systems. For a direct polarization experiment utilizing the entire active sample volume of a 5-mm rotor (90 µl), we achieved full width at half maximum (FWHM) of 0.76 Hz (5 ppb) and baseline resolved the 13C satellite peaks for adamantane as a consequent of the 7.31 Hz (59 ppb) width at 2 % intensity. We expect these approaches to be increasingly pivotal for high-resolution solid-state NMR spectroscopy at and above 1 GHz 1H frequencies.

The Effectiveness of Augmented Reality Offered with Constant Time Delay Procedure in Teaching the Functions of Organs to Students with Intellectual Disabilities

Introduction: Science course allows student to follow scientific developments, understand and interpret the events that occur around them, and develop scientific process skills. Different methods are employed in teaching science to student childeren with intellectual disabilities. There has been a recent increase in technology-supported methods. One of the technology-supported methods is Augmented Reality. For this reason, the effectiveness of the augmented reality provided with the constant time delay procedure in teaching the functions of the organs to childeren with intellectual disabilities was investigated in the present study. The study was conducted in the individual education setting of a private special education and rehabilitation center. Method: Three students who had intellectual disabilities participated in the study. The multiple probe design with probe conditions. Phases across behaviors, which is one of the single-case research designs, was used in the study. Findings: According to the study results, it was found that all participants acquired the target behaviors successfully and the participants retained the behaviors they acquired after the teaching of organs and their functions ended and they were able to generalize the behaviors they acquired to different materials. Discussion: Based on the results of the study, it can be argued that the Augmented Reality offered with the Constant Time Delay Procedure is effective in teaching science subjects to childeren with intellectual disabilities. It can also be argued that the permanence of the acquired behaviors is high when students who have mental disabilities are taught science subjects by using Augmented Reality along with the Constant Time Delay Procedure. To generalize the results obtained in the present study, it may be suggested that the same practice be performed with other experimenters and different age groups. For the social validity of the study, the teachers of the participants expressed positive opinions about the Augmented Reality offered with target behaviors and Constant Time Delay Procedure.

The EmotionProbe: an exploration of design students’ emotions when designing

AbstractThe emotional experiences significantly impact students' design processes. This research presents the EmotionProbe, a design probe tool for capturing design students' emotions while designing. The tool allows simple data collection, offering important insights into the students' design experiences, introducing the spectrum of emotions that design students go through, and showcasing various analysis approaches, allowing for a richer understanding of the design's emotional dimension. The research highlights the need for an emotional tool supporting students' emotional well-being while designing.

The Effects of an Instructional Package on Reading Skills for Multilingual Learners With Extensive Support Needs

In the current study, investigators examined the effects of an instructional reading package consisting of shared reading and systematic instruction (e.g., task analysis, system of least prompts, visual supports, and native language support) in a small group setting on percentage of correct consonant-vowel-consonant (CVC) words for three elementary participants with extensive support needs who also were multilingual learners. A multiple probe design across word sets with replication across participants resulted in a functional relation between the percentage of correct CVC words acquired and the instructional package. In addition, there were positive changes in exploratory (secondary) dependent variables that included components of reading (i.e., phonemic awareness, fluency, vocabulary, comprehension, and generalization) as demonstrated through pre-posttest assessments. Social validity measures for parents, students, and paraprofessionals also revealed positive pre-post changes. Limitations and future research are discussed.

Bienzyme-Locked Activatable Fluorescent Probes for Specific Imaging of Tumor-Associated Mast Cells.

Tumor-associated mast cells (TAMCs) have been recently revealed to play a multifaceted role in the tumor microenvironment. Noninvasive optical imaging of TAMCs is thus highly desired to gain insights into their functions in cancer immunotherapy. However, due to the lack of a single enzyme that is specific to mast cells, a common probe design approach based on single-enzyme activation is not applicable. Herein, we reported a bienzyme-locked molecular probe (THCMC) based on a photoinduced electron transfer-intramolecular charge-transfer hybrid strategy for in vivo imaging of TAMCs. The bienzyme-locked activation mechanism ensures that THCMC exclusively turns on near-infrared (NIR) fluorescence only in the presence of both tryptase and chymase specifically coexpressed by mast cells. Thus, THCMC effectively distinguishes mast cells from other leukocytes, including T cells, neutrophils, and macrophages, a capability lacking in single-locked probes. Such a high specificity of THCMC allows noninvasive tracking of the fluctuation of TAMCs in the tumor of living mice during cancer immunotherapy. The results reveal that the decreased intratumoral signal of THCMC after combination immunotherapy correlates well with the reduced population of TAMCs, accurately predicting the inhibition of tumor growth. Thus, this study not only presents the first NIR fluorescent probe specific for TAMCs but also proposes a generic bienzyme-locked probe design approach for in vivo cell imaging.

Design of an endoscopic OCT probe based on piezoelectric tube with quartered outside electrodes.

Introduction: Optical coherence tomography (OCT) is a pivotal imaging modality in ophthalmology for real-time, in vivo visualization of retinal structures. To enhance the capability and safety of OCT, this study focuses on the development of a micro intraocular OCT probe. The demand for minimal invasiveness and precise imaging drives the need for advanced probe designs that can access tight and sensitive areas, such as the ocular sclera. Methods: A novel OCT probe was engineered using a piezoelectric tube with quartered electrodes to drive Lissajous scanning movements at the end of a single-mode fiber. This design allows the probe to enter the eyeball through a scleral opening. Structural innovation enables the outer diameter of the endoscopic OCT probe to be adjusted from 13G (2.41mm) to 25G (0.51mm), accommodating various imaging field sizes and ensuring compatibility with different scleral incisions. Results: The fabricated micro intraocular OCT probe successfully performed preliminary imaging experiments on in vivo fingers. The Lissajous scanning facilitated comprehensive coverage of the target area, enhancing the imaging capabilities. Discussion: The integration of a piezoelectric tube with quartered outside electrodes into the OCT probe design proved effective for achieving precise control over scanning movements and adaptability to different surgical needs. The design characteristics and practical applications demonstrated the probe's potential in clinical settings.

Hydrogen-bond tuned conjugated architectures for nitric oxide sensing in single-benzene framework: Advances and mechanistic insights

In contrast to the conventional fluorescence enhancement resulting from the cessation of the photoinduced electron transfer effect upon capturing nitric oxide (NO) by o-phenylenediamine, we found an interesting fluorescence quench within small molecule fluorophores characterized by intramolecular hydrogen bonding. Herein, the integration of a push-pull electron system with intramolecular hydrogen bonding onto an ultra-small fluorophore was employed to fabricate a hydrogen bond-tuned single benzene core fluorescent probe with an exceptional fluorescence quantum yield of 26 %, denoted as HSC-1. By virtue of its small size and low molecular weight (mere 192 g/mol), it demonstrated superior solubility and biocompatibility. Given the optimized conditions, HSC-1 manifested extraordinary linearity in detecting NO concentrations ranging from 0.5 to 60 μM, with an outstanding detection limit of 23.8 nM. Theoretical calculations unraveled the photophysical properties of hydrogen bonding-related probe molecules and highlighted the NO sensing mechanism. This pioneering work offers an important platform for the design of small fluorescence probes only with a single benzene core applied to NO sensing, which will potentially emerge as a new frontier in the area.

Small-Molecule Fluorescent Probes for Binding- and Activity-Based Sensing of Redox-Active Biological Metals.

Although transition metals constitute less than 0.1% of the total mass within a human body, they have a substantial impact on fundamental biological processes across all kingdoms of life. Indeed, these nutrients play crucial roles in the physiological functions of enzymes, with the redox properties of many of these metals being essential to their activity. At the same time, imbalances in transition metal pools can be detrimental to health. Modern analytical techniques are helping to illuminate the workings of metal homeostasis at a molecular and atomic level, their spatial localization in real time, and the implications of metal dysregulation in disease pathogenesis. Fluorescence microscopy has proven to be one of the most promising non-invasive methods for studying metal pools in biological samples. The accuracy and sensitivity of bioimaging experiments are predominantly determined by the fluorescent metal-responsive sensor, highlighting the importance of rational probe design for such measurements. This review covers activity- and binding-based fluorescent metal sensors that have been applied to cellular studies. We focus on the essential redox-active metals: iron, copper, manganese, cobalt, chromium, and nickel. We aim to encourage further targeted efforts in developing innovative approaches to understanding the biological chemistry of redox-active metals.

Rational Design of NIR-II G-Quadruplex Fluorescent Probes for Accurate In Vivo Tumor Metastasis Imaging.

Accurate in vivo imaging of G-quadruplexes (G4) is critical for understanding the emergence and progression of G4-associated diseases like cancer. However, existing in vivo G4 fluorescent probes primarily operate within the near-infrared region (NIR-I), which limits their application accuracy due to the short emission wavelength. The transition to second near-infrared (NIR-II) fluorescent imaging has been of significant interest, as it offers reduced autofluorescence and deeper tissue penetration, thereby facilitating more accurate in vivo imaging. Nonetheless, the advancement of NIR-II G4 probes has been impeded by the absence of effective probe design strategies. Herein, through a "step-by-step" rational design approach, we have successfully developed NIRG-2, the first small-molecule fluorescent probe with NIR-II emission tailored for in vivo G4 detection. Molecular docking calculations reveal that NIRG-2 forms stable hydrogen bonds and strong π-π interactions with G4 structures, which effectively inhibit twisted intramolecular charge transfer (TICT) and, thereby, selectively illuminate G4 structures. Due to its NIR-II emission (940 nm), large Stokes shift (90 nm), and high selectivity, NIRG-2 offers up to 47-fold fluorescence enhancement and a tissue imaging depth of 5 mm for in vivo G4 detection, significantly outperforming existing G4 probes. Utilizing NIRG-2, we have, for the first time, achieved high-contrast visualization of tumor metastasis through lymph nodes and precise tumor resection. Furthermore, NIRG-2 proves to be highly effective and reliable in evaluating surgical and drug treatment efficacy in cancer lymphatic metastasis models. We are optimistic that this study not only provides a crucial molecular tool for an in-depth understanding of G4-related diseases in vivo but also marks a promising strategy for the development of clinical NIR-II G4-activated probes.