Search

Mapping molecular deformation and forces in protein biomaterials is critical to understanding mechanochemistry. Here we use intramolecular Förster resonance energy transfer (FRET) of dual-labeled fibrin to distinguish molecular conformations of proteins in situ during mechanical loading. The FRET approach offers increased spatial resolution compared to our previous vibrational imaging. By using fluorescence lifetime microscopy (FLIM), we demonstrate that the combination of FRET and FLIM can probe the molecular changes in fibrin with high spatial (nanometer) and temporal (nanosecond) resolution. Our results map changes in fibrin monomer deformation during the macroscopic loading of the fibrin network, paving the way to directly visualizing the biomaterial mechanics and structure in cell-ECM scaffolds for the first time. [ABSTRACT FROM AUTHOR]

Understanding the stress distribution within fiber‐reinforced polymers (FRPs) is critical to extending their operational lifespan. The integration of mechanoresponsive molecular force probes, referred to as mechanophores, presents a potential solution by enabling direct monitoring of stress concentrations. In this study, spiropyran (SP) mechanophores (MPs) are embedded within a polydimethylsiloxane (PDMS) matrix to visualize stress localization during loading within a single fiber‐reinforced framework. The SP mechanophore undergoes a transition from a non‐fluorescent state to an active state (merocyanine) through isomerization in response to mechanical forces. Using a single fiber mounted axially within the matrix, the fundamental failure modes observed in conventional fiber‐reinforced composites are replicated. Samples are strained under uniaxial tensile loading along the fiber direction and the localization of stresses is observed via MP activation. Stresses are concentrated in the matrix near the fiber region that gradually decreases away from the fiber surface. Confocal microscopy is used to visualize mechanophore activation and quantitatively assess fluorescence intensity. Finite element modeling is used to develop a calibration to quantify the stresses based on the observed fluorescence intensity. These outcomes underscore the viability of employing these mechanoresponsive molecules as a potential means to visualize real‐time stress distribution, thereby facilitating the design of high‐performance composites. [ABSTRACT FROM AUTHOR]

The combination of low-temperature scanning tunnelling microscopy with a mass-selective electro-spray ion-beam deposition established the investigation of large biomolecules at nanometer and sub-nanometer scale. Due to complex architecture and conformational freedom, however, the chemical identification of building blocks of these biopolymers often relies on the presence of markers, extensive simulations, or is not possible at all. Here, we present a molecular probe-sensitisation approach addressing the identification of a specific amino acid within different peptides. A selective intermolecular interaction between the sensitiser attached at the tip-apex and the target amino acid on the surface induces an enhanced tunnelling conductance of one specific spectral feature, which can be mapped in spectroscopic imaging. Density functional theory calculations suggest a mechanism that relies on conformational changes of the sensitiser that are accompanied by local charge redistributions in the tunnelling junction, which, in turn, lower the tunnelling barrier at that specific part of the peptide. Chemical identification of the building blocks of biopolymers often considerably relies on the presence of markers, extensive simulations, or is not possible at all. Here, the authors report a molecular probe-sensitisation approach addressing the identification of a specific amino acid within different peptides. [ABSTRACT FROM AUTHOR]

Novel treatments for neurodegenerative disorders are in high demand. It is imperative that new protein targets be identified to address this need. Characterization and validation of nascent targets can be accomplished very effectively using highly specific and potent chemical probes. Human induced pluripotent stem cells (hiPSCs) provide a relevant platform for testing new compounds in disease relevant cell types. However, many recent studies utilizing this platform have focused on neuronal cells. In this study, we used hiPSC-derived microglia-like cells (MGLs) to perform side-by-side testing of a selective chemical probe, SGC-CK2-1, compared with an advanced clinical candidate, CX-4945, both targeting casein kinase 2 (CK2), one of the first kinases shown to be dysregulated in Alzheimer's disease (AD). CK2 can mediate neuroinflammation in AD, however, its role in microglia, the innate immune cells of the central nervous system (CNS), has not been defined. We analyzed available RNA-seq data to determine the microglial expression of kinases inhibited by SGC-CK2-1 and CX-4945 with a reported role in mediating inflammation in glial cells. As proof-of-concept for using hiPSCMGLs as a potential screening platform, we used both wild-type (WT) MGLs and MGLs harboring a mutation in presenilin-1 (PSEN1), which is causative for early-onset, familial AD (FAD). We stimulated these MGLs with pro-inflammatory lipopolysaccharides (LPS) derived from E. coli and observed strong inhibition of the expression and secretion of proinflammatory cytokines by simultaneous treatment with SGC-CK2-1. A direct comparison shows that SGC-CK2-1 was more effective at suppression of proinflammatory cytokines than CX-4945. Together, these results validate a selective chemical probe, SGC-CK2-1, in human microglia as a tool to reduce neuroinflammation. [ABSTRACT FROM AUTHOR]

The cannabinoid 2 receptor (CB2R) has high therapeutic potential for multiple pathogenic processes, such as neuroinflammation. Pathway‐selective ligands are needed to overcome the lack of clinical success and to elucidate correlations between pathways and their respective therapeutic effects. Herein, we report the design and synthesis of a photoswitchable scaffold based on the privileged structure of benzimidazole and its application as a functionally selective CB2R "efficacy‐switch". Benzimidazole azo‐arenes offer huge potential for the broad extension of photopharmacology to a wide range of optically addressable biological targets. We used this scaffold to develop compound 10 d, a "trans‐on" agonist, which serves as a molecular probe to study the β‐arrestin2 (βarr2) pathway at CB2R. βΑrr2 bias was observed in CB2R internalization and βarr2 recruitment, while no activation occurred when looking at Gα16 or mini‐Gαi. Overall, compound 10 d is the first light‐dependent functionally selective agonist to investigate the complex mechanisms of CB2R‐βarr2 dependent endocytosis. [ABSTRACT FROM AUTHOR]

Membrane rupture of lysosomes results in leakage of their contents, which is harmful to cells. Recent studies have reported that several systems contribute to the repair or elimination of damaged lysosomes. Lysophagy is a type of selective autophagy that plays a crucial role in the lysosomal damage response. Because multiple pathways are involved in this response, an assay that specifically evaluates lysophagy is needed. Here, we developed the TMEM192-mKeima probe to evaluate lysophagy. By comparing the use of this probe with the conventional galectin-3 assay, we showed that this probe is more specific to lysophagy. Using TMEM192-mKeima, we showed that TFEB and p62 are important for the lysosomal damage response but not for lysophagy, although they have previously been considered to be involved in lysophagy. We further investigated the initial steps in lysophagy and identified UBE2L3, UBE2N, TRIM10, 16, and 27 as factors involved in it. Our results demonstrate that the TMEM192-mKeima probe is a useful tool for investigating lysophagy. [ABSTRACT FROM AUTHOR]

Currently, there is great interest in the development of highly sensitive bioanalytical systems for diagnosing diseases at an early stage, when pathological biomarkers are present in biological fluids at low concentrations and there are no clinical manifestations. A promising direction is the use of molecular detectors―highly sensitive devices that detect signals from single biomacromolecules. A typical detector in this class is the atomic force microscope (AFM). The high sensitivity of an AFM-based bioanalysis system is determined by the size of the sensing element of an atomic force microscope―the cantilever―the radius of the curvature of which is comparable to that of a biomolecule. Biospecific molecular probe–target interactions are used to ensure detection system specificity. Antibodies, aptamers, synthetic antibodies, and peptides can be used as molecular probes. This study has demonstrated the possibility of using aptamers as molecular probes for AFM-based detection of the ovarian cancer biomarker CA125. Antigen detection in a nanomolar solution was carried out using AFM chips with immobilized aptamers, commercially available or synthesized based on sequences from open sources. Both aptamer types can be used for antigen detection, but the availability of sequence information enables additional modeling of the aptamer structure with allowance for modifications necessary for immobilization of the aptamer on an AFM chip surface. Information on the structure and oligomeric composition of aptamers in the solution was acquired by combining small-angle X-ray scattering and molecular modeling. Modeling enabled pre-selection, before the experimental stage, of aptamers for use as surface-immobilized molecular probes. [ABSTRACT FROM AUTHOR]

The complexity of space environment will lead to a series of health problems, especially the bone loss caused by weightlessness is one of the key medical problems limiting long-term manned space flight. However, the size and energy constraints of the aircraft make conventional bone loss detection methods impractical. Hence, it is necessary to establish on-orbit bone loss detection methods to ensure the health of astronauts. As one of NASA's recommended methods, the lateral flow assay (LFA) would be an ideal tool to solve this problem. Herein, a surface-enhanced Raman based molecular probe was designed and integrated with LFA to detect carboxy-terminal cross-linked telopeptides of type I collagen (CTX I) with high sensitivity and specificity, and the limit of detection was 232 pg/mL. This method was not interference by the serum matrix or other targets, and the storage life of LFA was up to 6 months at 4 °C. Compared with the method previously reported, SERS-based LFA was an ideal detection method with simple operation, convenient and time saving. It is also expected to be chosen as a potential analytical tool to detect bone loss for long-term on-orbit, and guarantee the health of astronauts. [Display omitted] • A new CTX I detection method using a surface-enhanced Raman scattering lateral flow assay was developed. • Rapid and sensitive quantification of CTX I at 480 pg/mL was achieved within 15 min. • SERS-based LFA is also expected to be chosen as a potential analytical tool to detect bone loss for long-term on-orbit, and guarantee the health of astronauts. [ABSTRACT FROM AUTHOR]

This study investigated the development of aptamer-based molecular probes to detect Methicillin-Resistant Staphylococcus aureus (MRSA) and evaluated the antibacterial activity. Early detection of MRSA infection will improve patients' recovery and reduce the cost for treating patients. S. aureus can become resistant to methicillin and other β-lactam antibiotics through the expression of PBP2A protein, which is resistant to the action of methicillin. We have developed two aptamer molecular probes against PBP2A protein and whole bacterial cell (MRSA) under optimized in vitro conditions using SELEX approach. Target aptamer sequences were identified, and chemically synthesized aptamer probes were evaluated using fluorescently-labelled aptamer probes using flow cytometry and confocal imaging. Antibacterial activities of those aptamers were also evaluated using a bacterial killing assay. The results showed that high specific aptamers were developed against purified PBP2A protein. However, these aptamers showed less specificity to detect MRSA under in vitro condition. These aptamers showed no cytotoxic effect on 3T3 cells and no antibacterial activity against MRSA. The results suggested that the specific aptamer development and the in vitro selection methodology require further refinement to improve the diagnostic and therapeutic utility of these aptamers. [ABSTRACT FROM AUTHOR]

Background: Active peptides play a vital role in the development of new drugs and the identification and discovery of drug targets. As the first reported native peptide homodimer with pro‐regenerative potency, OA‐GP11d could potentially be used as a novel molecular probe to help elucidate the molecular mechanism of skin wound repair and provide new drug targets. Methods: Bioinformatics analysis and luciferase assay were adopted to determine microRNAs (miRNAs) and its target. The prohealing potency of the miRNA was determined by MTS and a Transwell experiment against mouse macrophages. Enzyme‐linked immunosorbent assay, realtime polymerase chain reaction, and western blotting were performed to explore the molecular mechanisms. Results: In this study, OA‐GP11d was shown to induce Mus musculus microRNA‐186‐5p (mmu‐miR‐186‐5p) down‐regulation. Results showed that miR‐186‐5p had a negative effect on macrophage migration and proliferation as well as a targeted and negative effect on TGF‐β type II receptor (TGFβR2) expression and an inhibitory effect on activation of the downstream SMAD family member 2 (Smad2) and protein‐p38 kinase signaling pathways. Importantly, delivery of a miR‐186‐5p mimic delayed skin wound healing in mice. Conclusion: miR‐186‐5p regulated macrophage migration and proliferation to delay wound healing through the TGFβR2/Smad2/p38 molecular axes, thus providing a promising new pro‐repair drug target. [ABSTRACT FROM AUTHOR]

Although the extraordinary progress has been made in molecular biology, the prevention of cancer remains arduous. Most solid tumours exhibit both spatial and temporal heterogeneity, which is difficult to be mimicked in vitro. Additionally, the complex biochemical and immune features of tumour microenvironment significantly affect the tumour development. Molecular imaging aims at the exploitation of tumour‐associated molecules as specific targets of customized molecular probe, thereby generating image contrast of tumour markers, and offering opportunities to non‐invasively evaluate the pathological characteristics of tumours in vivo. Particularly, there are no "standard markers" as control in clinical imaging diagnosis of individuals, so the tumour pathological characteristics‐responsive nanoprobe‐based quantitative molecular imaging, which is able to visualize and determine the accurate content values of heterogeneous distribution of pathological molecules in solid tumours, can provide criteria for cancer diagnosis. In this context, a variety of "smart" quantitative molecular imaging nanoprobes have been designed, in order to provide feasible approaches to quantitatively visualize the tumour‐associated pathological molecules in vivo. This review summarizes the recent achievements in the designs of these nanoprobes, and highlights the state‐of‐the‐art technologies in quantitative imaging of tumour‐associated pathological molecules. [ABSTRACT FROM AUTHOR]

Plant polyphenols with a catechol structure can form covalent adducts with meat proteins, which affects the quality and processing of meat products. However, there is a lack of fast and effective methods of characterizing these adducts and understanding their mechanisms. This study aimed to investigate the covalent interaction between myofibrillar protein (MP) and caffeic acid (CA), a plant polyphenol with a catechol structure, using molecular probe technology. The CA-MP adducts were separated via sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) and detected via Western blot and LC-MS/MS analyses. The Western blot analysis revealed that various specific adducts were successfully enriched and identified as bands around 220 kDa, 45 kDa, and two distinct bands between 95 and 130 kDa. Combined with the LC-MS/MS analysis, a total of 51 peptides were identified to be CA-adducted, corresponding to 31 proteins. More than 80% of the adducted peptides carried one adducted site, and the rest carried two adducted sites. The adducted sites were located on cysteine (C/Cys), histidine (H/His), arginine (R/Arg), lysine (K/Lys), proline (P/Pro), and N-terminal (N-Term) residues. Results showed that the covalent interaction of CA and MP was highly selective for the R side chain of amino acids. Moreover, the adducts were more likely to form via C-N bonding than C-S bonding. This study provides new insights into the covalent interaction of plant polyphenols and meat proteins, which has important implications for the rational use of plant polyphenols in the meat processing industry. [ABSTRACT FROM AUTHOR]

Elevated macroautophagy/autophagy, typically characterized by increased autophagosome accumulation, occurs in a wide variety of physiological and pathophysiological processes, but the current methodology for studying autophagy aberration in native non-transfected cells is rather limited. Here we show that LKT, an engineered molecular probe composed of a cell-penetrating peptide, an LC3-interacting motif and the aggregation-inducedemission (AIE) luminogen tetraphenylethylene, achieved robust identification and isolation of viable autophagy-varying cell subpopulations without the need of foreign reporter gene expression. Non-fluorescent in water, LKT fluorescence is activated upon interaction with liposomes in an AIE-dependent fashion, and the presence of LC3 on the liposome membrane dramatically boosted LKT fluorescence enhancement. In LKT-treated GFP-LC3 HeLa cells, induction of autophagy with rapamycin or trehalose, and blockade of autophagy with chloroquine, both produced bright GFP-LC3-colocalizing LKT puncta, leading to an increase in LKT fluorescence that facilitated efficient separation of cells based on the level of autophagosome accumulation. Using fluorescence-activated cell sorting, we were able to isolate cell subpopulations varying in the level of basal autophagy from a variety of cultured cell lines and primary cells. In a proof-of-concept study, we isolated autophagy-high and autophagy-low subpopulations from differentiated THP-1 cells and revealed that the autophagy-high THP-1 cells, compared to their autophagy-low counterparts, exhibited a higher level of NLRP3 protein expression and a stronger NLRP3 inflammasome activation following nigericin challenge. Our work demonstrated the unique power of the AIE technology and LKT, filling a void, should prove valuable for autophagy research. 3-MA, 3-methyladenine; AIE, aggregation-induced emission; AIEgens, aggregation-induced emission luminogens; ATG5, autophagy related 5; BMDM, bone marrow-derived macrophage; CQ, chloroquine; DiD, 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbocyanine perchlorate; DiO, 3,3'-dioctadecyloxacarbocyanine perchlorate; DMSO, dimethyl sulfoxide; d-THP-1, differentiated THP-1; FACS, fluorescence activated cell sorting; FBS, fetal bovine serum; FCCP, carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone; GABARAP, GABA type A receptor-associated protein; GFP, green fluorescent protein; HBSS, Hanks' balanced salt solution; HPLC, high-performance liquid chromatography; HRP, horseradish peroxidase; IL1B, interleukin 1 beta; KT, an AIE probe composed of a cell-penetrating peptide and an AIEgen tetraphenyl ethylene; LC3-II, lipidated LC3; LDH, lactate dehydrogenase; LIR, LC3-interacting region; LKR, engineered molecular probe composed of an LC3-interacting peptide, a cell-penetrating peptide and a non-AIE fluorescent molecule rhodamine; LKT, engineered molecular probe composed of an LC3-interacting peptide, a cell-penetrating peptide and an AIEgen tetraphenyl ethylene; LPS, lipopolysaccharide; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MEF, mouse embryonic fibroblast; mRFP, monomeric red fluorescent protein; NHS, N-hydroxysuccinimide; NLRP3, NLR family pyrin domain containing 3; PBS, phosphate-buffered saline; PCC, pearson's correlation coefficient; PL, photoluminescence; PMA, phorbol 12-myristate 13-acetate; RAP, rapamycin; RIM, restriction of intramolecular motions; s.e.m., standard error of the mean; SPR, surface plasmon resonance; SQSTM1/p62, sequestosome 1; TAX1BP1, Tax1 binding protein 1; TPE, tetraphenylethylene; TPE-yne, 1-(4-ethynylphenyl)-1,2,2-triphenylethene; Tre, trehalose; u-THP-1: undifferentiated THP-1; UV-Vis, ultraviolet visible [ABSTRACT FROM AUTHOR]

Intermolecular interactions form the basis of the properties of solvents, such as their polarity, and are of central importance for chemistry; such interactions are widely discussed. Solvent effects were reported on the basis of various polarity probes with the ET(30) polarity scale of Dimroth and Reichardt being of special interest because of its sensitivity, precise measurability and other advantages, and has been used for the investigation of solvent interactions. A two-parameter equation for the concentration dependence of medium effects has been developed, providing insights into structural changes in liquid phases. Moving from condensed gases to binary solvent mixtures, where the property of one solvent can be continuously transformed to the other, it was shown how the polarity of a solvent can be composed from the effect of polar functional groups and other structural elements that form the matrix. Thermochromism was discussed as well as the effect of very long-range interactions. Practical applications were demonstrated. [ABSTRACT FROM AUTHOR]

Rapid, selective, and quantitative profiling of SO3 2- is a prerequisite for investigating its effect on different physiopathological processes. To address this challenge, our team prepared a ratiometric fluorescent probe HBTCS, based on 4-(benzothiazol-2-yl)-3-hydroxybenzaldehyde for specific detection of SO3 2- under a singlewavelength excitation. The solution of probe HBTC-S itself exhibited orange fluorescence (λem = 614 nm), and became green fluorescent (λem = 471 nm) after the addition of SO3 2-. The vitro experiments suggested that the probe displayed high sensitivity, excellent selectivity, and a low detection limit (0.15 µM). Moreover, probe HBTC-S was successfully applied for qualitative and quantitative monitoring of SO3 2° in realistic samples and living HeLa cells in a ratiometric manner. [ABSTRACT FROM AUTHOR]

Investigation on a competitive endogenous RNA (ceRNA) network attracted lots of attention due its function in cancer regulation. Here, we probed into the possible molecular mechanism of circSSPO/microRNA-6820-5p (miR-6820-5p)/kallikrein-related peptidase 8 (KLK8)/PKD1 network in the esophageal squamous cell carcinoma (ESCC). Following whole-transcriptome sequencing and differential analysis in collected ESCC tissue samples, circRNA-miRNA-mRNA regulatory network affecting ESCC was investigated. After interaction measurement among circSSPO/miR-6820-5p/KLK8/PKD1, their regulatory roles in ESCC cell functions in vitro and xenograft tumor growth and lung metastasis in vivo were analyzed. The bioinformatics prediction and sequencing results screened that circSSPO, miR-6820-5p, KLK8, and PKD1 were associated with ESCC development. In ESCC, miR-6820-5p was expressed at very low levels, while circSSPO, KLK8, and PKD1 were highly expressed. In vitro cell experiments further proved that circSSPO competitively inhibited miR-6820-5p to induce ESCC cell malignant properties. Moreover, knockdown of KLK8 or PKD1 inhibited ESCC cell malignant properties. circSSPO also promoted the tumorigenic and metastasis of ESCC through the upregulation of KLK8 and PKD1 expression in vivo. We found that circSSPO was an oncogenic circRNA that was significantly abundant in ESCC tissues and circSSPO exhibited an oncogenic activity in ESCC by elevating expression of KLK8 and PKD1 through suppressing miR-6820-5p expression. [ABSTRACT FROM AUTHOR]

DNA-binding transcription factors (TFs) remain challenging to target with molecular probes. Many TFs function in part through interaction with Mediator, a 26-subunit complex that controls RNA polymerase II activity genome-wide. We sought to block p53 function by disrupting the p53-Mediator interaction. Through rational design and activity-based screening, we characterize a stapled peptide, with functional mimics of both p53 activation domains, that blocks p53-Mediator binding and selectively inhibits p53-dependent transcription in human cells; importantly, this "bivalent" peptide has negligible impact, genome-wide, on non-p53 target genes. Our proof-of-concept strategy circumvents the TF entirely and targets the TF-Mediator interface instead, with desired functional outcomes (i.e., selective inhibition of p53 activation). Furthermore, these results demonstrate that TF activation domains represent viable starting points for Mediator-targeting molecular probes, as an alternative to large compound libraries. Different TFs bind Mediator through different subunits, suggesting this strategy could be broadly applied to selectively alter gene expression programs.

Nanofluids—dispersions of nanometer-sized particles in a liquid medium—have been proposed for a wide variety of thermal management applications. It is known that a solid-like nanolayer of liquid of typical thicknesses of 0.5–1 nm surrounding the colloidal nanoparticles can act as a thermal bridge between the nanoparticle and the bulk liquid. Yet, its effect on the nanofluid viscosity has not been elucidated so far. In this article, we compute the local viscosity of the nanolayer using equilibrium molecular dynamics based on the Green–Kubo formula. We first assess the validity of the method to predict the viscosity locally. We apply this methodology to the calculation of the local viscosity in the immediate vicinity of a metallic nanoparticle for a wide range of solid–liquid interaction strength, where a nanolayer of thickness 1 nm is observed as a result of the interaction with the nanoparticle. The viscosity of the nanolayer, which is found to be higher than its corresponding bulk value, is directly dependent on the solid–liquid interaction strength. We discuss the origin of this viscosity enhancement and show that the liquid density increment alone cannot explain the values of the viscosity observed. Rather, we suggest that the solid-like structure of the distribution of the liquid atoms in the vicinity of the nanoparticle contributes to the nanolayer viscosity enhancement. Finally, we observe a failure of the Stokes–Einstein relation between viscosity and diffusion close to the wall, depending on the liquid–solid interaction strength, which we rationalize in terms of the hydrodynamic slip. [ABSTRACT FROM AUTHOR]

We present a method to probe rare molecular dynamics trajectories directly using reinforcement learning. We consider trajectories that are conditioned to transition between regions of configuration space in finite time, such as those relevant in the study of reactive events, and trajectories exhibiting rare fluctuations of time-integrated quantities in the long time limit, such as those relevant in the calculation of large deviation functions. In both cases, reinforcement learning techniques are used to optimize an added force that minimizes the Kullback–Leibler divergence between the conditioned trajectory ensemble and a driven one. Under the optimized added force, the system evolves the rare fluctuation as a typical one, affording a variational estimate of its likelihood in the original trajectory ensemble. Low variance gradients employing value functions are proposed to increase the convergence of the optimal force. The method we develop employing these gradients leads to efficient and accurate estimates of both the optimal force and the likelihood of the rare event for a variety of model systems. [ABSTRACT FROM AUTHOR]

Breast cancer (BC) poses a significant threat to women’s health, with triple-negative breast cancer (TNBC) representing one of the most challenging and aggressive subtypes due to the lack of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) expression. Traditional TNBC treatments often encounter issues such as low drug efficiency, limited tumor enrichment, and substantial side effects. Therefore, it is crucial to explore novel diagnostic and treatment systems for TNBC. Multifunctional molecular probes (MMPs), which integrate target recognition as well as diagnostic and therapeutic functions, introduce advanced molecular tools for TNBC theranostics. Using an MMP system, molecular drugs can be precisely delivered to the tumor site through a targeted ligand. Real-time dynamic monitoring of drug release achieved using imaging technology allows for the evaluation of drug enrichment at the tumor site. This approach enables accurate drug release, thereby improving the therapeutic effect. Therefore, this review summarizes the recent advancements in MMPs for TNBC theranostics, encompassing the design and synthesis of MMPs as well as their applications in the field of TNBC theranostics.

The quantum control of ultrafast excited state dynamics remains an unachieved goal within the chemical physics community. In this study, we assess how strongly coupling to cavity photons affects the excited state dynamics of strongly coupled zinc (II) tetraphenyl porphyrin (ZnTPP) and copper (II) tetraphenyl porphyrin (CuTPP) molecules. By varying the concentration of each chromophore within different Fabry–Pérot (FP) structures, we control the collective vacuum Rabi splitting between the energies of cavity polariton states formed through the strong coupling of molecular electrons and cavity photons. Using ultrafast transient reflectivity and transmission measurements probing optical transitions of individual ZnTPP and CuTPP molecules, we find that the polaritonic states localize into uncoupled excited states of these chromophores through different mechanisms. For ZnTPP, we build a simple kinetic model including a direct channel of relaxation between the polaritonic states. We find that our models necessitate a small contribution from this interpolaritonic relaxation channel to explain both our steady-state and transient optical spectroscopic measurements adequately. In contrast, we propose that strong cavity coupling slows the internal conversion between electronic states of CuTPP not directly interacting with the photons of FP structures. These results suggest that researchers must consider the vibrational structure and excited state properties of the strongly coupled chromophores when attempting to use polariton formation as a tool to control the dynamics of molecules central to photo-sensitizing and light harvesting applications. [ABSTRACT FROM AUTHOR]

The theoretical framework for reorientation-induced spectral diffusion (RISD) describes the polarization dependence of spectral diffusion dynamics as measured with two-dimensional (2D) correlation spectroscopy and related techniques. Generally, RISD relates to the orientational dynamics of the molecular chromophore relative to local electric fields of the medium. The predictions of RISD have been shown to be very sensitive to both restricted orientational dynamics (generally arising from steric hindrance) and the distribution of local electric fields relative to the probe (electrostatic ordering). Here, a theory that combines the two effects is developed analytically and supported with numerical calculations. The combined effects can smoothly vary the polarization dependence of spectral diffusion from the purely steric case (least polarization dependence) to the purely electrostatic case (greatest polarization dependence). Analytic approximations of the modified RISD equations were also developed using the orientational dynamics of the molecular probe and two order parameters describing the degree of electrostatic ordering. It was found that frequency-dependent orientational dynamics are a possible consequence of the combined electrostatic and steric effects, providing a test for the applicability of this model to experimental systems. The modified RISD equations were then used to successfully describe the anomalous polarization-dependent spectral diffusion seen in 2D infrared spectroscopy in a polystyrene oligomer system that exhibits frequency-dependent orientational dynamics. The degree of polarization-dependent spectral diffusion enables the extent of electrostatic ordering in a chemical system to be quantified and distinguished from steric ordering. [ABSTRACT FROM AUTHOR]

Conventional methods for probing molecular changes in condensed matter systems, such as electronic and vibrational spectroscopy, are difficult to implement at the extreme conditions associated with dynamic compression experiments. This is particularly true for experiments in the multimegabar regime; to achieve the requisite energy density to produce such pressures, sample sizes are necessarily quite small and experimental timescales are, therefore, extremely short. Furthermore, these extreme pressure conditions also result in high temperatures and, therefore, significant thermal emission even in the visible to infrared regime and in some cases render the sample opaque or reflective, thereby precluding bulk spectroscopy techniques, such as Raman scattering. These experimental challenges require a different approach to evaluating shock-induced changes at the molecular or atomic level in the multimegabar or the so-called warm dense matter regime. The past few decades have seen significant advances in the use of first-principles methods to investigate materials under extreme conditions, enabling these methods to become a powerful tool for exploring molecular systems at extreme conditions. Here, we discuss the construct of combining high-precision shock wave experiments with first-principles theory to explore molecular systems at extreme conditions. The results from high-fidelity dynamic compression experiments are used to evaluate first-principles theoretical frameworks and identify the framework that best reproduces experimental results in the regime of interest. That validated framework is then used to perform detailed simulations of the system of interest, providing unique insight into the response of the system at the molecular level. [ABSTRACT FROM AUTHOR]

An accurate detection of lung metastasis is of great significance for making better treatment choices and improving cancer prognosis, but remains a big challenge in clinical practice. In this study, we propose a reinventing strategy to develop a pH‐activatable near‐infrared (NIR) fluorescent nanoprobe, pulmonary metastasis tracer (denoted as PMT), based on assembly of NIR dye IR780 and calcium phosphate (CaP). By delicately tuning the intermolecular interactions during the assembly process and dye doping content, as well as the synthetic condition of probe, the fluorescence of PMT could be finely adjusted via the tumor acidity‐triggered disassembly. Notably, the selected PMT9 could sharply convert subtle pH variations into a distinct fluorescence signal to generate high fluorescence ON/OFF contrast, dramatically reducing the background signals. Benefiting from such preferable features, PMT9 is able to precisely identify not only the tumor sites in orthotopic lung cancer models but also the pulmonary metastases in mice with remarkable signal‐to‐background ratio (SBR). This study provides a unique strategy to turn shortcomings of traditional dye IR780 during in vivo imaging into advantages and further expand the application of fluorescent probe to image lung associated tumor lesions. [ABSTRACT FROM AUTHOR]

Background: In the past few years, there has been an explosion in single-cell transcriptomics datasets, yet in vivo confirmation of these datasets is hampered in plants due to lack of robust validation methods. Likewise, modeling of plant development is hampered by paucity of spatial gene expression data. RNA fluorescence in situ hybridization (FISH) enables investigation of gene expression in the context of tissue type. Despite development of FISH methods for plants, easy and reliable whole mount FISH protocols have not yet been reported. Results: We adapt a 3-day whole mount RNA-FISH method for plant species based on a combination of prior protocols that employs hybridization chain reaction (HCR), which amplifies the probe signal in an antibody-free manner. Our whole mount HCR RNA-FISH method shows expected spatial signals with low background for gene transcripts with known spatial expression patterns in Arabidopsis inflorescences and monocot roots. It allows simultaneous detection of three transcripts in 3D. We also show that HCR RNA-FISH can be combined with endogenous fluorescent protein detection and with our improved immunohistochemistry (IHC) protocol. Conclusions: The whole mount HCR RNA-FISH and IHC methods allow easy investigation of 3D spatial gene expression patterns in entire plant tissues. [ABSTRACT FROM AUTHOR]

This study uses a rapid tandem mass‐spectrometry method to determine water content in complex organic solutions. Emphasis is placed on trace‐water analysis by a fast and accurate alternative to the Karl–Fischer method. In this new method, water is captured by a charge‐labeled molecular probe. Water binds strongly with high specificity to the strongly electrophilic aldehyde site in a charge‐labelled molecule (N‐methylpyridinium); competitive binding by other analytes is effectively discriminated against in the mass‐measurement step. Quantitative determinations are made over a wide concentration range, 0.001 % (10 ppm) to 99 %, with better than 10 % relative standard deviation, along with short (1 min) analysis times using small sample volumes (several μL). Applications include water measurement in simple organic solvents, for example, deuterated solvents, as well as in complex mixtures, for example, organic reaction mixtures. Additionally, this method allows for water monitoring in levitated droplets. Mechanistic investigations into the impact of water on important chemical processes in organic synthesis and environmental science are reported. [ABSTRACT FROM AUTHOR]

The purpose of this study is to clarify the metabolic dependence of ovarian clear cell carcinoma (CCC) by comparing normal tissues and to examine the applicability of fluorescence imaging probe to exploit these metabolic differences. Enhanced glutathione synthesis was supported by the increased uptake of related metabolites and elevated expression levels of genes. Accumulation of intracellular iron and lipid peroxide, induction of cell death by inhibition of the glutathione synthesis pathway indicated that ferroptosis was induced. The activation of γ-glutamyl hydroxymethyl rhodamine green (gGlu-HMRG), a fluorescent imaging probe that recognizes γ-glutamyl transferase, which is essential for the synthesis of glutathione, was investigated in fresh-frozen surgical specimens. gGlu-HMRG detected extremely strong fluorescent signals in the tumor lesions of CCC patients, compared to normal ovaries or endometrium. These results revealed that CCC occurs in the stressful and unique environment of free radical-rich endometrioma, and that glutathione metabolism is enhanced as an adaptation to oxidative stress. Furthermore, a modality that exploits these metabolic differences would be useful for distinguishing between CCC and normal tissues. [ABSTRACT FROM AUTHOR]

We present Atacama Large Millimeter/sub-millimeter Array neutral carbon, [ |${\rm C\, \small {\rm I}}$| ](1–0), line observations that probe molecular hydrogen gas (H2) within seven radio galaxies at z  = 2.9−4.5 surrounded by extended (≳100 kpc) Ly α nebulae. We extract [ |${\rm C\, \small {\rm I}}$| ](1–0) emission from the radio-active galactic nuclei (AGNs) host galaxies whose positions are set by near-infrared detections and radio detections of the cores. Additionally, we place constraints on the galaxies' systemic redshifts via |${\rm He\, \small {\rm II}}$| λ1640 lines seen with the Multi-Unit Spectroscopic Explorer. We detect faint [ |${\rm C\, \small {\rm I}}$| ] emission in four out of seven sources. In two of these galaxies, we discover narrow-line emission of full width at half-maximum ≲100 km s−1 that may trace emission from bright kpc-scale gas clouds within the interstellar medium (ISM). In the other two [ |${\rm C\, \small {\rm I}}$| ]-detected galaxies, line dispersions range from ∼100−600 km s−1 and may be tracing the rotational component of the cold gas. Overall, the [ |${\rm C\, \small {\rm I}}$| ] line luminosities correspond to H2 masses of |$M_{\rm H_2,[{\rm C\, \small {\rm I}}]} \simeq (0.5{\!-\!}3) \times 10^{10}$| M⊙ for the detections and |$M_{\rm H_2,[{\rm C\, \small {\rm I}}]}\lt 0.65\times 10^{10}$| M⊙ for the [ |${\rm C\, \small {\rm I}}$| ] non-detections in three out of seven galaxies within the sample. The molecular gas masses in our sample are relatively low in comparison to previously reported measures for similar galaxies that are |$M_{\rm H_2,[{\rm C\, \small {\rm I}}]} \simeq (3{\!-\!}4) \times 10^{10}$| M⊙. Our results imply that the observed faintness in carbon emission is representative of a decline in molecular gas supply from previous star formation epochs and/or a displacement of molecular gas from the ISM due to jet-powered outflows. [ABSTRACT FROM AUTHOR]

We report on single-molecule nanopore sensing combined with position-encoded DNA molecular probes, with chemistry tuned to simultaneously identify various antigen proteins and multiple RNA gene fragments of SARS-CoV-2 with high sensitivity and selectivity. We show that this sensing strategy can directly detect spike (S) and nucleocapsid (N) proteins in unprocessed human saliva. Moreover, our approach enables the identification of RNA fragments from patient samples using nasal/throat swabs, enabling the identification of critical mutations such as D614G, G446S, or Y144del among viral variants. In particular, it can detect and discriminate between SARS-CoV-2 lineages of wild-type B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.539 (Omicron) within a single measurement without the need for nucleic acid sequencing. The sensing strategy of the molecular probes is easily adaptable to other viral targets and diseases and can be expanded depending on the application required. Fast discrimination of SARS-CoV-2 variants in clinical samples remains a challenge. Here, authors report on single molecule nanopore sensing combined with DNA molecular probes to simultaneously detect various antigens and RNA mutations of SARS-CoV-2 variants in patient samples. [ABSTRACT FROM AUTHOR]

Objective: The global mortality rates have surged due to the ongoing coronavirus disease 2019 (COVID-19), leading to a worldwide catastrophe. Increasing incidents of patients suffering from cutaneous lupus erythematosus (CLE) exacerbations after either contracting COVID-19 or getting immunized against it, have been observed in recent research. However, the precise intricacies that prompt this unexpected complication are yet to be fully elucidated. This investigation seeks to probe into the molecular events inciting this adverse outcome. Method: Gene expression patterns from the Gene Expression Omnibus (GEO) database, specifically GSE171110 and GSE109248, were extracted. We then discovered common differentially expressed genes (DEGs) in both COVID-19 and CLE. This led to the creation of functional annotations, formation of a protein-protein interaction (PPI) network, and identification of key genes. Furthermore, regulatory networks relating to these shared DEGs and significant genes were constructed. Result: We identified 214 overlapping DEGs in both COVID-19 and CLE datasets. The following functional enrichment analysis of these DEGs highlighted a significant enrichment in pathways related to virus response and infectious disease in both conditions. Next, a PPI network was constructed using bioinformatics tools, resulting in the identification of 5 hub genes. Finally, essential regulatory networks including transcription factor-gene and miRNAgene interactions were determined. Conclusion: Our findings demonstrate shared pathogenesis between COVID-19 and CLE, offering potential insights for future mechanistic investigations. And the identification of common pathways and key genes in these conditions may provide novel avenues for research. [ABSTRACT FROM AUTHOR]

The outstanding acuity of the mammalian ear relies on cochlear amplification, an active mechanism based on the electromotility (eM) of outer hair cells. eM is a piezoelectric mechanism generated by little-understood, voltage-induced conformational changes of the anion transporter homolog prestin (SLC26A5). We used a combination of molecular dynamics (MD) simulations and biophysical approaches to identify the structural dynamics of prestin that mediate eM. MD simulations showed that prestin samples a vast conformational landscape with expanded (ES) and compact (CS) states beyond previously reported prestin structures. Transition from CS to ES is dominated by the translational-rotational movement of prestin's transport domain, akin to elevator-type substrate translocation by related solute carriers. Reversible transition between CS and ES states was supported experimentally by cysteine accessibility scanning, cysteine cross-linking between transport and scaffold domains, and voltage-clamp fluorometry (VCF). Our data demonstrate that prestin's piezoelectric dynamics recapitulate essential steps of a structurally conserved ion transport cycle. Probing the molecular dynamics of the membrane motor, prestin, with biophysical measures and MD simulations, Kuwabara et al. find that an elevator-like domain movement across the membrane produces the unique piezoelectric behavior. [ABSTRACT FROM AUTHOR]

Background: Interferon-γ (IFN-γ) is a key cytokine with diverse biological functions, including antiviral defense, antitumor activity, immune regulation, and modulation of cellular processes. Nonetheless, its role in pancreatic cancer (PC) therapy remains debated. Therefore, it is worthwhile to explore the role of Interferon-γ related genes (IFN-γGs) in the progression of PC development. Methodology: Transcriptomic data from 930 PC were sourced from TCGA, GEO, ICGC, and ArrayExpress, and 93 IFN-γGs were obtained from the MSigDB. We researched the characteristics of IFN-γGs in pan-cancer. Subsequently, the cohort of 930 PC was stratified into two distinct subgroups using the NMF algorithm. We then examined disparities in the activation of cancer-associated pathways within these subpopulations through GSVA analysis. We scrutinized immune infiltration in both subsets and probed classical molecular target drug sensitivity variations. Finally, we devised and validated a novel IFN-γ related prediction model using LASSO and Cox regression analyses. Furthermore, we conducted RT-qPCR and immunohistochemistry assays to validate the expression of seven target genes included in the prediction model. Results: We demonstrated the CNV, SNV, methylation, expression levels, and prognostic characteristics of IFN-γGs in pan-cancers. Notably, Cluster 2 demonstrated superior prognostic outcomes and heightened immune cell infiltration compared to Clusters 1. We also assessed the IC50 values of classical molecular targeted drugs to establish links between IFN-γGs expression levels and drug responsiveness. Additionally, by applying our prediction model, we segregated PC patients into high-risk and low-risk groups, identifying potential benefits of cisplatin, docetaxel, pazopanib, midostaurin, epothilone.B, thapsigargin, bryostatin.1, and AICAR for high-risk PC patients, and metformin, roscovitine, salubrinal, and cyclopamine for those in the low-risk group. The expression levels of these model genes were further verified through HPA website data and qRT-PCR assays in PC cell lines and tissues. Conclusion: This study unveils IFN-γGs related molecular subsets in pancreatic cancer for the first time, shedding light on the pivotal role of IFN-γGs in the progression of PC. Furthermore, we establish an IFN-γGs related prognostic model for predicting the survival of PC, offering a theoretical foundation for exploring the precise mechanisms of IFN-γGs in PC. [ABSTRACT FROM AUTHOR]

Background: Interferon-g (IFN-g) is a key cytokine with diverse biological functions, including antiviral defense, antitumor activity, immune regulation, and modulation of cellular processes. Nonetheless, its role in pancreatic cancer (PC) therapy remains debated. Therefore, it is worthwhile to explore the role of Interferon-g related genes (IFN-gGs) in the progression of PC development. Methodology: Transcriptomic data from 930 PC were sourced from TCGA, GEO, ICGC, and ArrayExpress, and 93 IFN-gGs were obtained from the MSigDB. We researched the characteristics of IFN-gGs in pan-cancer. Subsequently, the cohort of 930 PC was stratified into two distinct subgroups using the NMF algorithm. We then examined disparities in the activation of cancer-associated pathways within these subpopulations through GSVA analysis. We scrutinized immune infiltration in both subsets and probed classical molecular target drug sensitivity variations. Finally, we devised and validated a novel IFN-g related prediction model using LASSO and Cox regression analyses. Furthermore, we conducted RT-qPCR and immunohistochemistry assays to validate the expression of seven target genes included in the prediction model. Results: We demonstrated the CNV, SNV, methylation, expression levels, and prognostic characteristics of IFN-gGs in pan-cancers. Notably, Cluster 2 demonstrated superior prognostic outcomes and heightened immune cell infiltration compared to Clusters 1. We also assessed the IC50 values of classical molecular targeted drugs to establish links between IFN-gGs expression levels and drug responsiveness. Additionally, by applying our prediction model, we segregated PC patients into high-risk and low-risk groups, identifying potential benefits of cisplatin, docetaxel, pazopanib midostaurin, epothilone.B, thapsigargin, bryostatin.1, and AICAR for high-risk PC patients, and metformin, roscovitine, salubrinal, and cyclopamine for those in the low-risk group. The expression levels of these model genes were further verified through HPA website data and qRT-PCR assays in PC cell lines and tissues. Conclusion: This study unveils IFN-gGs related molecular subsets in pancreatic cancer for the first time, shedding light on the pivotal role of IFN-gGs in the progression of PC. Furthermore, we establish an IFN-gGs related prognostic model for predicting the survival of PC, offering a theoretical foundation for exploring the precise mechanisms of IFN-gGs in PC. [ABSTRACT FROM AUTHOR]

The cell interior is a highly crowded 'active material': ATP-consuming, non-equilibrium activities help fluidize the cell interior. Without metabolic energy, the crowded environment can become 'glassy' or solid like. Molecular crowding reduces particle diffusion, especially at the 'mesoscale' (10–1000 nm diameter) but can increase molecular assembly through 'depletion attraction'. We can probe molecular crowding and the active matter of the cell interior by observing the motion of tracer particles. This is called 'microrheology'. Both internal and external factors influence the biophysical properties of the cell interior: for example, decreased target of rapamycin complex 1 (TORC1) signaling reduces crowding, while mechanical compression increases crowding. Active control of these properties is crucial for normal physiology; we hypothesize that perturbed molecular crowding or decreased non-equilibrium motion could contribute to diseases like cancer and neurodegeneration. Life emerges from thousands of biochemical processes occurring within a shared intracellular environment. We have gained deep insights from in vitro reconstitution of isolated biochemical reactions. However, the reaction medium in test tubes is typically simple and diluted. The cell interior is far more complex: macromolecules occupy more than a third of the space, and energy-consuming processes agitate the cell interior. Here, we review how this crowded, active environment impacts the motion and assembly of macromolecules, with an emphasis on mesoscale particles (10–1000 nm diameter). We describe methods to probe and analyze the biophysical properties of cells and highlight how changes in these properties can impact physiology and signaling, and potentially contribute to aging, and diseases, including cancer and neurodegeneration. [ABSTRACT FROM AUTHOR]

Background: Feed efficiency is a research priority to support a sustainable meat production. It is recognized as a complex trait that integrates multiple biological pathways orchestrated in and by various tissues. This study aims to determine networks between biological entities to explain inter-individual variation of feed efficiency in growing pigs. Results: The feed conversion ratio (FCR), a measure of feed efficiency, and its two component traits, average daily gain and average daily feed intake, were obtained from 47 growing pigs from a divergent selection for residual feed intake and fed high-starch or high-fat high-fiber diets during 58 days. Datasets of transcriptomics (60 k porcine microarray) in the whole blood and metabolomics (1H-NMR analysis and target gas chromatography) in plasma were available for all pigs at the end of the trial. A weighted gene co-expression network was built from the transcriptomics dataset, resulting in 33 modules of co-expressed molecular probes. The eigengenes of eight of these modules were significantly ( P ≤ 0.05 ) or tended to be ( 0.05 < P ≤ 0.10 ) correlated to FCR. Great homogeneity in the enriched biological pathways was observed in these modules, suggesting co-expressed and co-regulated constitutive genes. They were mainly enriched in genes participating to immune and defense-related processes, and to a lesser extent, to translation, cell development or learning. They were also generally associated with growth rate and percentage of lean mass. In the whole network, only one module composed of genes participating to the response to substances, was significantly associated with daily feed intake and body adiposity. The plasma profiles in circulating metabolites and in fatty acids were summarized by weighted linear combinations using a dimensionality reduction method. Close association was thus found between a module composed of co-expressed genes participating to T cell receptor signaling and cell development process in the whole blood and related to FCR, and the circulating concentrations of polyunsaturated fatty acids in plasma. Conclusion: These systemic approaches have highlighted networks of entities driving key biological processes involved in the phenotypic difference in feed efficiency between animals. Connecting transcriptomics and metabolic levels together had some additional benefits. [ABSTRACT FROM AUTHOR]

Molecular recognition of complex isomeric biomolecules remains challenging in surface‐enhanced Raman scattering (SERS) spectroscopy due to their small Raman cross‐sections and/or poor surface affinities. To date, the use of molecular probes has achieved excellent molecular sensitivities but still suffers from poor spectral specificity. Here, we induce "charge and geometry complementarity" between probe and analyte as a key strategy to achieve high spectral specificity for effective SERS molecular recognition of structural analogues. We employ 4‐mercaptopyridine (MPY) as the probe, and chondroitin sulfate (CS) disaccharides with isomeric sulfation patterns as our proof‐of‐concept study. Our experimental and in silico studies reveal that "charge and geometry complementarity" between MPY's binding pocket and the CS sulfation patterns drives the formation of site‐specific, multidentate interactions at the respective CS isomerism sites, which "locks" each CS in its analogue‐specific complex geometry, akin to molecular docking events. Leveraging the resultant spectral fingerprints, we achieve > 97 % classification accuracy for 4 CSs and 5 potential structural interferences, as well as attain multiplex CS quantification with < 3 % prediction error. These insights could enable practical SERS differentiation of biologically important isomers to meet the burgeoning demand for fast‐responding applications across various fields such as biodiagnostics, food and environmental surveillance. [ABSTRACT FROM AUTHOR]

Antibiotic contamination is becoming a prominent global issue. Therefore, sensitive, specific and simple technology is desirable the demand for antibiotics detection. Biosensors based on split aptamer has gradually attracted extensive attention for antibiotic detection due to its higher sensitivity, lower cost, false positive/negative avoidance and flexibility in sensor design. Although many of the reported split aptamers are antibiotics aptamers, the acquisition and mechanism of splitting is still unknow. In this review, six reported split aptamers in antibiotics are outlined, including Enrofloxacin, Kanamycin, Tetracycline, Tobramycin, Neomycin, Streptomycin, which have contributed to promote interest, awareness and thoughts into this emerging research field. The study introduced the pros and cons of split aptamers, summarized the assembly principle of split aptamer and discussed the intermolecular binding of antibiotic-aptamer complexes. In addition, the recent application of split aptamers in antibiotic detection are introduced. Split aptamers have a promising future in the design and development of biosensors for antibiotic detection in food and other field. The development of the antibiotic split aptamer meets many challenges including mechanism discovery, stability improvement and new biosensor development. It is believed that split aptamer could be a powerful molecular probe and plays an important role in aptamer biosensor. [ABSTRACT FROM AUTHOR]

Chemical probes are essential tools for understanding biological systems and for credentialing potential biomedical targets. Programmed cell death 2 (PDCD2) is a member of the B‐cell lymphoma 2 (Bcl‐2) family of proteins, which are critical regulators of apoptosis. Here we report the discovery and characterization of 10 e, a first‐in‐class small molecule degrader of PDCD2. We discovered this PDCD2 degrader by serendipity using a chemical proteomics approach, in contrast to the conventional approach for making bivalent degraders starting from a known binding ligand targeting the protein of interest. Using 10 e as a pharmacological probe, we demonstrate that PDCD2 functions as a critical regulator of cell growth by modulating the progression of the cell cycle in T lymphoblasts. Our work provides a useful pharmacological probe for investigating PDCD2 function and highlights the use of chemical proteomics to discover selective small molecule degraders of unanticipated targets. [ABSTRACT FROM AUTHOR]

In a routine synthetic experiment, an elusive macrocyclic organic compound, namely cyclo-di-BADGE, was serendipitously acquired in a single crystalline form. This compound, widely known as a by-product from the co-polymerization reactions of bisphenol A (BPA) and bisphenol A diglycidyl ether (BADGE), has never been comprehensively characterized prior to this work. Herein, NMR and single crystal X-ray diffraction analyses have been conducted to investigate the molecular structural properties of cyclo-di-BADGE in the solution phase and solid state. Systematic conformational studies were carried out using the Conformer-Rotamer Ensemble Sampling Tool (CREST) in conjunction with density functional theory (DFT) calculations. Moreover, the aggregation behavior of cyclo-di-BADGE in organic and aqueous media was investigated through UV-Vis and dynamic light scattering (DLS) analyses. Detailed aggregation mechanisms were further probed by molecular dynamics (MD) simulations. Finally, we investigated the binding of cyclo-di-BADGE with a model protein, bovine serum albumin (BSA), through fluorescence and molecular docking analyses. Our studies provide valuable knowledge to facilitate the understanding of cyclo-di-BADGE in terms of its various physico-chemical properties and relevant effects on the environment and biological systems. [ABSTRACT FROM AUTHOR]

The microbiota that colonize the human gut and other tissues are dynamic, varying both in composition and functional state between individuals and over time. Gene expression measurements can provide insights into microbiome composition and function. However, efficient and unbiased removal of microbial ribosomal RNA (rRNA) presents a barrier to acquiring metatranscriptomic data. Here we describe a probe set that achieves efficient enzymatic rRNA removal of complex human-associated microbial communities. We demonstrate that the custom probe set can be further refined through an iterative design process to efficiently deplete rRNA from a range of human microbiome samples. Using synthetic nucleic acid spike-ins, we show that the rRNA depletion process does not introduce substantial quantitative error in gene expression profiles. Successful rRNA depletion allows for efficient characterization of taxonomic and functional profiles, including during the development of the human gut microbiome. The pan-human microbiome enzymatic rRNA depletion probes described here provide a powerful tool for studying the transcriptional dynamics and function of the human microbiome. [ABSTRACT FROM AUTHOR]

Cell fusion plays a critical role in cancer progression and metastasis. However, effective modulation of the cell fusion behavior and timely evaluation on the cell fusion to provide accurate information for personalized therapy are facing challenges. Here, it demonstrates that the cancer cell fusion behavior can be efficiently modulated and precisely detected through employing a multifunctional delivery vector to realize cancer targeting delivery of a genome editing plasmid and a molecular beacon-based AND logic gate. The multifunctional delivery vector decorated by AS1411 conjugated hyaluronic acid and NLS-GE11 peptide conjugated hyaluronic acid can specifically target circulating malignant cells (CMCs) of cancer patients to deliver the genome editing plasmid for epidermal growth factor receptor (EGFR) knockout. The cell fusion between CMCs and endothelial cells can be detected by the AND logic gate delivered by the multifunctional vector. After EGFR knockout, the edited CMCs exhibit dramatically inhibited cell fusion capability, while unedited CMCs can easily fuse with human umbilical vein endothelial cells (HUVEC) to form hybrid cells. This study provides a new therapeutic strategy for preventing cancer progression and a reliable tool for evaluating cancer cell fusion for precise personalized therapy. [ABSTRACT FROM AUTHOR]

The effective utilization of luminescent dyes often relies on a comprehensive understanding of their excitation and relaxation pathways. One such pathway, Excited‐State Proton Transfer (ESPT), involves the tautomerization of the dye in its excited state, resulting in a new structure that exhibits distinct emission properties, such as a very large Stokes′ shift or dual‐emission. Although the ESPT phenomenon is well‐explained theoretically, its experimental demonstration can be challenging due to the presence of numerous other phenomena that can yield similar experimental observations. In this review, we propose that an all‐encompassing methodology, integrating experimental findings, computational analyses, and a thorough evaluation of diverse mechanisms, is essential for verifying the occurrence of ESPT in luminescent dyes. Investigations have offered significant understanding of the elements impacting the ESPT process and the array of approaches that can be used to validate the existence of ESPT. These discoveries hold crucial ramifications for the advancement of molecular probes, sensors, and other applications that depend on ESPT as a detection mechanism. [ABSTRACT FROM AUTHOR]

Fundamental understanding of the supramolecular assemblies of organic chromophores and the development of design strategies have seen endless ripples of interest owing to their exciting photophysical properties and optoelectronic applications. The independent discovery of dye aggregates by Jelley and Scheibe was the commencement of the remarkable advancement in the field of aggregate photophysics. Subsequent research warranted an exceptional model for defining the exciton interactions in aggregates, proposed by Davydov, Kasha and co-workers, independently, based on the long-range Coulombic coupling. Fascinatingly, the orthogonally cross-stacked molecular transition dipole arrangement was foretold by Kasha to possess null exciton interaction leading to spectroscopically uncoupled molecular assembly, which lacked an experimental signature for decades. There have been several attempts to identify and probe atypical molecular aggregates for decoding their optical behaviour. Herein, we discuss the recent efforts in experimentally verifying the unusual exciton interactions supported with quantum chemical computations, primarily focusing on the less explored null exciton splitting. Exciton engineering can be realized through synthetic modifications that can additionally offer control over the assorted non-covalent interactions for orchestrating precise supramolecular assembly, along with molecular editing. The task of attaining a minimal excitonic coupling through an orthogonally cross-stacked crystalline architecture envisaged to offer a monomer-like optical behaviour was first reported in 1,7-dibromoperylene-3,4,9,10-tetracarboxylic tetrabutylester (PTE-Br2). The attempt to stitch molecules covalently in an orthogonal fashion to possess null excitonic character culminated in a spiro-conjugated perylenediimide dimer exhibiting a monomer-like spectroscopic signature. The computational and experimental efforts to map the emergent properties of the cross-stacked architecture are also discussed here. Using the null aggregates formed by the interference effects between CT-mediated and Coulombic couplings in the molecular array is another strategy for achieving monomer-like spectroscopic properties in molecular assemblies. Moreover, identifying supramolecular assemblies with precise angle-dependent properties can have implications in functional material design, and this review can provide insights into the uncharted realm of null exciton splitting. [ABSTRACT FROM AUTHOR]

Fluorine is becoming increasingly prevalent in medicinal chemistry, both in drug molecules and in molecular probes. The presence of fluorine allows convenient monitoring of such molecules in complex environments by NMR spectroscopy. However, sensitivity is a persistent limitation of NMR, especially when molecules are present at low concentrations. Here, sensitivity issues with 1H NMR are mitigated by sharing 19F photochemically-induced dynamic nuclear polarisation with 1H nuclei. Unlike direct 1H enhancement, this method enhances 1H signals without significantly distorting multiplet intensities, and has the potential to enable the use of suitable molecules as low-concentration probes. [ABSTRACT FROM AUTHOR]

The CCT/TRiC complex is a type II chaperonin that undergoes ATP-driven conformational changes during its functional cycle. Structural studies have provided valuable insights into the mechanism of this process, but real-time dynamics analyses of mammalian type II chaperonins are still scarce. We used diffracted X-ray tracking (DXT) to investigate the intramolecular dynamics of the CCT complex. We focused on three surface-exposed loop regions of the CCT1 subunit: the loop regions of the equatorial domain (E domain), the E and intermediate domain (I domain) juncture near the ATP-binding region, and the apical domain (A domain). Our results showed that the CCT1 subunit predominantly displayed rotational motion, with larger mean square displacement (MSD) values for twist (χ) angles compared with tilt (θ) angles. Nucleotide binding had a significant impact on the dynamics. In the absence of nucleotides, the region between the E and I domain juncture could act as a pivotal axis, allowing for greater motion of the E domain and A domain. In the presence of nucleotides, the nucleotides could wedge into the ATP-binding region, weakening the role of the region between the E and I domain juncture as the rotational axis and causing the CCT complex to adopt a more compact structure. This led to less expanded MSD curves for the E domain and A domain compared with nucleotide-absent conditions. This change may help to stabilize the functional conformation during substrate binding. This study is the first to use DXT to probe the real-time molecular dynamics of mammalian type II chaperonins at the millisecond level. Our findings provide new insights into the complex dynamics of chaperonins and their role in the functional folding cycle. [ABSTRACT FROM AUTHOR]

RNA-sequencing (RNA-seq) technology has led to a surge of neuroscience research using animal models to probe the complex molecular mechanisms underlying brain function and behavior, including substance use disorders. However, findings from rodent studies often fail to be translated into clinical treatments. Here, we developed a novel pipeline for narrowing candidate genes from preclinical studies by translational potential and demonstrated its utility in 2 RNA-seq studies of rodent self-administration. This pipeline uses evolutionary conservation and preferential expression of genes across brain tissues to prioritize candidate genes, increasing the translational utility of RNA-seq in model organisms. Initially, we demonstrate the utility of our prioritization pipeline using an uncorrected P-value. However, we found no differentially expressed genes in either dataset after correcting for multiple testing with false discovery rate (FDR < 0.05 or <0.1). This is likely due to low statistical power that is common across rodent behavioral studies, and, therefore, we additionally illustrate the use of our pipeline on a third dataset with differentially expressed genes corrected for multiple testing (FDR < 0.05). We also advocate for improved RNA-seq data collection, statistical testing, and metadata reporting that will bolster the field's ability to identify reliable candidate genes and improve the translational value of bioinformatics in rodent research. [ABSTRACT FROM AUTHOR]

Allophycocyanin (APC) is a key molecule of the light harvesting complex - phycobilisome of Cyanobacteria and Red Algae. Its bright color and fluorescent nature make it a suitable molecular for biomedical applications. Here, we report the dilution induced changes in the spectral and structural properties of APC, isolated from marine cyanobacterium, Phormidium sp. A09DM. We observe measurable blue shift in the light absorption and fluorescence emission properties of APC upon dilution. The blue shift in spectral properties is originated from the disruption of hydrophobic interactions and systematic dissociation of the APC into its building blocks. APC, a trimer of αβ-heterodimer, dissociates into monomer and further into individual subunits upon dilution. The observed dilution induced spectral and structural changes can be moderated in the presence of physiological osmolytes with the moderation strength in the order, Sucrose > Trehalose > Betaine = Potassium Phosphate buffer > Glycine. Our results conclude that the spectral properties of APC is a function of osmolytes concentrations, which makes it a potential candidate to be explored as the molecular probe for measuring the molecular crowding. [Display omitted] • Allophycocyanin (APC) exhibits spectral blue shift upon dilution. • APC dissociates into monomers upon dilution. • Structure and spectral properties of APC is a function of molecular crowding. [ABSTRACT FROM AUTHOR]