Perspectives on label-free microscopy of heterogeneous and dynamic biological systems

Significance

Advancements in label-free microscopy could provide real-time, non-invasive imaging with unique sources of contrast and automated standardized analysis to characterize heterogeneous and dynamic biological processes. These tools would overcome challenges with widely used methods that are destructive (e.g., histology, flow cytometry) or lack cellular resolution (e.g., plate-based assays, whole animal bioluminescence imaging).

Aim

This perspective aims to (1) justify the need for label-free microscopy to track heterogeneous cellular functions over time and space within unperturbed systems and (2) recommend improvements regarding instrumentation, image analysis, and image interpretation to address these needs.

Approach

Three key research areas (cancer research, autoimmune disease, and tissue and cell engineering) are considered to support the need for label-free microscopy to characterize heterogeneity and dynamics within biological systems. Based on the strengths (e.g., multiple sources of molecular contrast, non-invasive monitoring) and weaknesses (e.g., imaging depth, image interpretation) of several label-free microscopy modalities, improvements for future imaging systems are recommended.

Conclusion

Improvements in instrumentation including strategies that increase resolution and imaging speed, standardization and centralization of image analysis tools, and robust data validation and interpretation will expand the applications of label-free microscopy to study heterogeneous and dynamic biological systems.

Autophagic degradation of CDK4 is responsible for G0/G1 cell cycle arrest in NVP-BEZ235-treated neuroblastoma

BACKGROUND

CDK4 is highly expressed and associated with poor prognosis and decreased survival in advanced neuroblastoma (NB). Targeting CDK4 degradation presents a potentially promising therapeutic strategy compared to conventional CDK4 inhibitors. However, the autophagic degradation of the CDK4 protein and its anti-proliferation effect in NB cells has not been mentioned.

RESULTS

We identified autophagy as a new pathway for the degradation of CDK4. Firstly, autophagic degradation of CDK4 is critical for NVP-BEZ235-induced G0/G1 arrest, as demonstrated by the overexpression of CDK4, autophagy inhibition, and blockade of autophagy-related genes. Secondly, we present the first evidence that p62 binds to CDK4 and then enters the autophagy-lysosome to degrade CDK4 in a CTSB-dependent manner in NVP-BEZ235 treated NB cells. Similar results regarding the interaction between p62 and CDK4 were observed in the NVP-BEZ235 treated NB xenograft mouse model.

CONCLUSIONS

Autophagic degradation of CDK4 plays a pivotal role in G0/G1 cell cycle arrest in NB cells treated with NVP-BEZ235.

Investigating the overlap of machine learning algorithms in the final results of RNA-seq analysis on gene expression estimation

Advances in computer science in combination with the next-generation sequencing have introduced a new era in biology, enabling advanced state-of-the-art analysis of complex biological data. Bioinformatics is evolving as a union field between computer Science and biology, enabling the representation, storage, management, analysis and exploration of many types of data with a plethora of machine learning algorithms and computing tools. In this study, we used machine learning algorithms to detect differentially expressed genes between different types of cancer and showing the existence overlap to final results from RNA-sequencing analysis. The datasets were obtained from the National Center for Biotechnology Information resource. Specifically, dataset GSE68086 which corresponds to PMID:200,068,086. This dataset consists of 171 blood platelet samples collected from patients with six different tumors and healthy individuals. All steps for RNA-sequencing analysis (preprocessing, read alignment, transcriptome reconstruction, expression quantification and differential expression analysis) were followed. Machine Learning- based Random Forest and Gradient Boosting algorithms were applied to predict significant genes. The Rstudio statistical tool was used for the analysis.

Retrospective review of treatment outcomes and costs in children with sleep disordered breathing assessed with multi-channel studies

Current UK guidance on OSA management recommends only selective use of sleep studies - when there is diagnostic uncertainty, in children with comorbidities or to evaluate perioperative risk in those with suspected severe OSA. Routine use of sleep studies to confirm a diagnosis of obstructive sleep apnoea (OSA) in children before adenotonsillectomy is not currently recommended. We report the findings of a novel paediatric sleep service based on routine use of multi-channel sleep studies (MCSS) before adenotonsillectomy and present the results of a service evaluation assessing the impact of our practise on treatment outcomes and cost. We conducted a retrospective study of 264 children with sleep disordered breathing seen in our centre between July 2018-June 2019, using medical records and a sleep study database to determine treatment outcomes and costs. Using responses from a questionnaire completed by otolaryngologists for a separate prospective study, we compare our costs with estimates of those associated with a standard UK model of care i.e. with selective use of sleep studies. We estimate that our routine use of MCSS reduced the number of adenotonsillectomies by 44 % but at higher monetary costs than those estimated for the standard model of care. We note however, that reconfiguring our service to arrange a sleep study before the initial appointment, rather than after, would result in the service being cost neutral compared with the standard model. We also estimate that use of home multi-channel studies in our service would bring a significant cost saving (∼£50,000 - £80,000 per annum) compared to standard care.

3D-printed airway model as a platform for SARS-CoV-2 infection and antiviral drug testing

We present a bioprinted three-layered airway model with a physiologically relevant microstructure for the study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection dynamics. This model exhibited clear cell-cell junctions and mucus secretion with an efficient expression of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). Having infected air-exposed epithelial cells in the upper layer with a minimum multiplicity of infection of 0.01, the airway model showed a marked susceptibility to SARS-CoV-2 within one-day post-infection (dpi). Furthermore, the unique longevity allowed the observation of cytopathic effects and barrier degradation for 21 dpi. The in-depth transcriptomic analysis revealed dramatic changes in gene expression affecting the infection pathway, viral proliferation, and host immune response which are consistent with COVID-19 patient data. Finally, the treatment of antiviral agents, such as remdesivir and molnupiravir, through the culture medium underlying the endothelium resulted in a marked inhibition of viral replication within the epithelium. The bioprinted airway model can be used as a manufacturable physiological platform to study disease pathogeneses and drug efficacy.

Gra-CRC-miRTar: The pre-trained nucleotide-to-graph neural networks to identify potential miRNA targets in colorectal cancer

Colorectal cancer (CRC) is the third most diagnosed cancer and the second deadliest cancer worldwide representing a major public health problem. In recent years, increasing evidence has shown that microRNA (miRNA) can control the expression of targeted human messenger RNA (mRNA) by reducing their abundance or translation, acting as oncogenes or tumor suppressors in various cancers, including CRC. Due to the significant up-regulation of oncogenic miRNAs in CRC, elucidating the underlying mechanism and identifying dysregulated miRNA targets may provide a basis for improving current therapeutic interventions. In this paper, we proposed Gra-CRC-miRTar, a pre-trained nucleotide-to-graph neural network framework, for identifying potential miRNA targets in CRC. Different from previous studies, we constructed two pre-trained models to encode RNA sequences and transformed them into de Bruijn graphs. We employed different graph neural networks to learn the latent representations. The embeddings generated from de Bruijn graphs were then fed into a Multilayer Perceptron (MLP) to perform the prediction tasks. Our extensive experiments show that Gra-CRC-miRTar achieves better performance than other deep learning algorithms and existing predictors. In addition, our analyses also successfully revealed 172 out of 201 functional interactions through experimentally validated miRNA-mRNA pairs in CRC. Collectively, our effort provides an accurate and efficient framework to identify potential miRNA targets in CRC, which can also be used to reveal miRNA target interactions in other malignancies, facilitating the development of novel therapeutics. The Gra-CRC-miRTar web server can be found at: http://gra-crc-mirtar.com/.

Design rules applied to silver nanoparticles synthesis: A practical example of machine learning application

The synthesis of silver nanoparticles with controlled physicochemical properties is essential for governing their intended functionalities and safety profiles. However, synthesis process involves multiple parameters that could influence the resulting properties. This challenge could be addressed with the development of predictive models that forecast endpoints based on key synthesis parameters. In this study, we manually extracted synthesis-related data from the literature and leveraged various machine learning algorithms. Data extraction included parameters such as reactant concentrations, experimental conditions, as well as physicochemical properties. The antibacterial efficiencies and toxicological profiles of the synthesized nanoparticles were also extracted. In a second step, based on data completeness, we employed regression algorithms to establish relationships between synthesis parameters and desired endpoints and to build predictive models. The models for core size and antibacterial efficiency were trained and validated using a cross-validation approach. Finally, the features' impact was evaluated via Shapley values to provide insights into the contribution of features to the predictions. Factors such as synthesis duration, scale of synthesis and the choice of capping agents emerged as the most significant predictors. This study demonstrated the potential of machine learning to aid in the rational design of synthesis process and paves the way for the safe-by-design principles development by providing insights into the optimization of the synthesis process to achieve the desired properties. Finally, this study provides a valuable dataset compiled from literature sources with significant time and effort from multiple researchers. Access to such datasets notably aids computational advances in the field of nanotechnology.

Surface display provides an efficient expression system for production of recombinant proteins and bacterial whole cell biosensor in E. coli

A novel bacterial display vector based on Escherichia coli has been engineered for recombinant protein production and purification. Accordingly, a construct harboring the enhanced green fluorescent protein (EGFP) and the ice nucleation protein (INP) was designed to produce EGFP via the surface display in E. coli cells. The fusion EGFP-expressed cells were then investigated using fluorescence measurement, SDS- and native-PAGE before and after TEV protease digestion. The displayed EGFP was obtained with a recovery of 57.7 % as a single band on SDS-PAGE. Next, the efficiency of the cell surface display for mutant EGFP (EGFP S202H/Q204H) was examined in sensing copper ions. Under optimal conditions, a satisfactorily linear range for copper ions concentrations up to 10 nM with a detection limit of 0.073 nM was obtained for cell-displayed mutant EGFP (mEGFP). In the presence of bacterial cell lysates and purified mEGFP, response to copper was linear in the 2-10 nM and 0.1-2 μM concentration range, respectively, with a 1.3 nM and 0.14 μM limit of detection. The sensitivity of bacterial cell lysates and surface-displayed mEGFP in the detection of copper ions is higher than the purified mEGFP.

Interactions between U and V sex chromosomes during the life cycle of Ectocarpus

In many animals and flowering plants, sex determination occurs in the diploid phase of the life cycle with XX/XY or ZW/ZZ sex chromosomes. However, in early diverging plants and most macroalgae, sex is determined by female (U) or male (V) sex chromosomes in a haploid phase called the gametophyte. Once the U and V chromosomes unite at fertilization to produce a diploid sporophyte, sex determination no longer occurs, raising key questions about the fate of the U and V sex chromosomes in the sporophyte phase. Here, we investigate genetic and molecular interactions of the UV sex chromosomes in both the haploid and diploid phases of the brown alga Ectocarpus. We reveal extensive developmental regulation of sex chromosome genes across its life cycle and implicate the TALE-HD transcription factor OUROBOROS in suppressing sex determination in the diploid phase. Small RNAs may also play a role in the repression of a female sex-linked gene, and transition to the diploid sporophyte coincides with major reconfiguration of histone H3K79me2, suggesting a more intricate role for this histone mark in Ectocarpus development than previously appreciated.

Development and validation of a green analytical method for simultaneously determining plasticizers residues in honeys from different botanical origins

A novel method has been proposed to determine nine plasticizers in honey samples by gas chromatography-mass spectrometry. An efficient sample treatment was proposed (average analyte recoveries between 77% and 118%) involving a double solvent extraction with ethyl acetate, followed by a clean-up step with florisil. Chromatographic analysis (< 21 min) was performed in an Agilent HP-5MS column under programmed temperature conditions. The greenness of the method was assessed with different tools that classified it as environmentally friendly. The method was validated in terms of selectivity, limits of detection (0.1-3.1 μg kg-1) and quantification (0.2-10.3 μg kg-1), linearity, matrix effect, trueness, and precision (relative standard deviation <9%). An analysis of thirty samples from different sources (commercial or experimental apiaries) revealed the presence of residues of five plasticizers in most of the samples. Finally, health risk assessment was evaluated, and the results indicated no associated health risks for consumers.

Advanced applications of Nanodiscs-based platforms for antibodies discovery

Due to their fundamental biological importance, membrane proteins (MPs) are attractive targets for drug discovery, with cell surface receptors, transporters, ion channels, and membrane-bound enzymes being of particular interest. However, due to numerous challenges, these proteins present underutilized opportunities for discovering biotherapeutics. Antibodies hold the promise of exquisite specificity and adaptability, making them the ideal candidates for targeting complex membrane proteins. They can target specific conformations of a particular membrane protein and can be engineered into various formats. Generating specific and effective antibodies targeting these proteins is no easy task due to several factors. The antigen's design, antibody-generation strategies, lead optimization technologies, and antibody modalities can be modified to tackle these challenges. The rational employment of cutting-edge lipid nanoparticle systems for retrieving the membrane antigen has been successfully implemented to simplify the mechanism-based therapeutic antibody discovery approach. Despite the highlighted MP production challenges, this review unequivocally underscores the advantages of targeting complex membrane proteins with antibodies and designing membrane protein antigens. Selected examples of lipid nanoparticle success have been illustrated, emphasizing the potential of therapeutic antibody discovery in this regard. With further research and development, we can overcome these challenges and unlock the full potential of therapeutic antibodies directed to target complex MPs.

Understanding bacteriocin heterologous expression: A review

Bacteriocins are a diverse group of ribosomally synthesised antimicrobial peptides/proteins that play an important role in self-defence. They are widely used as bio-preservatives and effective substitutes for disease eradication. They can be used in conjunction with or as an alternative to antibiotics to minimize the risk of resistance development. There are remarkably few reports indicating resistance to bacteriocins. Although there are many research reports that emphasise heterologous expression of bacteriocin, there are no convincing reports on the significant role that intrinsic and extrinsic factors play in overexpression. A coordinated and cooperative expression system works in concert with multiple genetic elements encoding native proteins, immunoproteins, exporters, transporters and enzymes involved in the post-translational modification of bacteriocins. The simplest way could be to utilise the existing E. coli expression system, which is conventional, widely used for heterologous expression and has been further extended for bacteriocin expression. In this article, we will review the intrinsic and extrinsic factors, advantages, disadvantages and major problems associated with bacteriocin overexpression in E. coli. Finally, we recommend the most effective strategies as well as numerous bacteriocin expression systems from E. coli, Lactococcus, Kluveromyces lactis, Saccharomyces cerevisiae and Pichia pastoris for their suitability for successful overexpression.

A comparative in vitro and in vivo analysis of the impact of copper substitution on the cytocompatibility, osteogenic, and angiogenic properties of a borosilicate bioactive glass

The 0106-B1-bioactive glass (BG) composition (in wt %: 37.5 SiO2, 22.6 CaO, 5.9 Na2O, 4.0 P2O5, 12.0 K2O, 5.5 MgO, and 12.5 B2O3) has demonstrated favorable processing properties and promising bone regeneration potential. The present study aimed to evaluate the biological effects of the incorporation of highly pro-angiogenic copper (Cu) in 0106-B1-BG in vitro using human bone marrow-derived mesenchymal stromal cells (BMSCs) as well as its in vivo potential for bone regeneration. CuO was added to 0106-B1-BG in exchange for CaO, resulting in Cu-doped BG compositions containing 1.0, 2.5 and 5.0 wt % CuO (composition in wt %: 37.5 SiO2, 21.6/ 20.1/17.6 CaO, 5.9 Na2O, 4.0 P2O5, 12.0 K2O, 5.5 MgO, 12.5 B2O3, and 1.0/ 2.5/ 5.0 CuO). In vitro, the BGs' impact on the viability, proliferation, and growth patterns of BMSCs was evaluated. Analyses of protein secretion, matrix formation, and gene expression were used for the assessment of the BGs' influence on BMSCs regarding osteogenic differentiation and angiogenic stimulation. The presence of Cu improved cytocompatibility, osteogenic differentiation, and angiogenic response when compared with unmodified 0106-B1-BG in vitro. In vivo, a critical-size femoral defect in rats was filled with scaffolds made from BGs. Bone regeneration was evaluated by micro-computed tomography. Histological analysis was performed to assess bone maturation and angiogenesis. In vivo effects regarding defect closure, presence of osteoclastic cells or vascular structures in the defect were not significantly changed by the addition of Cu compared with undoped 0106-B1-BG scaffolds. Hence, while the in vitro properties of the 0106-B1-BG were significantly improved by the incorporation of Cu, further evaluation of the BG composition is necessary to transfer these effects to an in vivo setting.

Preparation of pyridoxine-based polyurethane modified sensors and their use in simultaneous determination of Cu(II) - Co(II) ions

In this study, pyridoxine-based polyurethane-modified electrodes were prepared to simultaneously and sensitively measure copper (Cu(II)) and cobalt (Co(II)) ions in complex matrix samples. For the production of the electrodes, firstly, the synthesis of pyridoxine-based polyurethane structures was carried out. In these syntheses, the polymer structure was diversified by using different isocyanates. Polyethyleneglycol-200 (PEG), pyridoxine (B6), and β-cyclodextrin (β-CD) groups were used as the source of polyol. The synthesized polyurethane structures were characterized by different instrumental techniques and used in gold electrode surface modification. Modified sensor surfaces were examined by scanning electron microscopy and atomic force microscopy techniques. The prepared modified sensors were used for the simultaneous detection of Cu(II) and Co(II) ions using the differential pulse voltammetry technique. The limit of detection (LOD), limit of quantitation (LOQ), and R2 values for Cu(II) ions were calculated as 8.81 μM, 29.4 μM, and 0.993, respectively. LOD, LOQ, and R2 values for Co(II) ions were calculated as 9.84 μM, 32.8 μM, and 0.9935, respectively. For repeatability, the relative standard deviation (RSD %) of the prepared simultaneous sensors was determined as 1.54 and 1.71 for Cu(II) and Co(II), respectively. As a result, Cu(II) and Co(II) ions were measured independently and simultaneously with high sensitivity. According to these results, it is predicted that pyridoxine-based polyurethane-modified sensors may be suitable for the simultaneous detection of Cu(II) and Co(II) in medical, food, and agricultural samples.

Identification and functional prediction of miRNAs that regulate ROS levels in dielectric barrier discharge plasma-treated boar spermatozoa

Dielectric barrier discharge (DBD) plasma regulates the levels of reactive oxygen species (ROS), which are critical for sperm quality. MicroRNAs (miRNAs) are non-coding single-stranded RNA molecules encoded by endogenous genes, which regulate post-transcriptional gene expression in animals. At present, it is unknown whether DBD plasma can regulate sperm ROS levels through miRNAs. To further understand the regulatory mechanism of DBD plasma on sperm ROS levels, miRNAs in fresh boar spermatozoa were detected using Illumina deep sequencing technology. We found that 25 known miRNAs and 50 novel miRNAs were significantly upregulated, and 14 known miRNAs and 74 novel miRNAs were significantly downregulated in DBD plasma-treated spermatozoa. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that target genes of differentially expressed miRNAs were involved in many activities and pathways associated with antioxidants. We verified that DBD plasma significantly increased boar sperm quality and reduced ROS levels. These results suggest that DBD plasma can improve sperm quality by regulating ROS levels via miRNAs. Our findings provide a potential strategy to improve sperm quality through miRNA-targeted regulation of ROS, which helps to increase male reproduction and protect cryopreserved semen in clinical practice.

Nucleic acid-responsive smart systems for controlled cargo delivery

Stimulus-responsive delivery systems allow controlled, highly regulated, and efficient delivery of various cargos while minimizing side effects. Owing to the unique properties of nucleic acids, including the ability to adopt complex structures by base pairing, their easy synthesis, high specificity, shape memory, and configurability, they have been employed in autonomous molecular motors, logic circuits, reconfigurable nanoplatforms, and catalytic amplifiers. Moreover, the development of nucleic acid (NA)-responsive intelligent delivery vehicles is a rapidly growing field. These vehicles have attracted much attention in recent years due to their programmable, controllable, and reversible properties. In this work, we review several types of NA-responsive controlled delivery vehicles based on locks and keys, including DNA/RNA-responsive, aptamer-responsive, and CRISPR-responsive, and summarize their advantages and limitations.

Detection of Subclinical Rejection in Pediatric Kidney Transplantation: Current and Future Practices

INTRODUCTION

The successes in the field of pediatric kidney transplantation over the past 60 years have been extraordinary. Year over year, there have been significant improvements in short-term graft survival. However, improvements in longer-term outcomes have been much less apparent. One important contributor has been the phenomenon of low-level rejection in the absence of clinical manifestations-so-called subclinical rejection (SCR).

METHODS

Traditionally, rejection has been diagnosed by changes in clinical parameters, including but not limited to serum creatinine and proteinuria. This review examines the shortcomings of this approach, the effects of SCR on kidney allograft outcome, the benefits and drawbacks of surveillance biopsies to identify SCR, and new urine and blood biomarkers that define the presence or absence of SCR.

RESULTS

Serum creatinine is an unreliable index of SCR. Surveillance biopsies are the method most utilized to detect SCR. However, these have significant drawbacks. New biomarkers show promise. These biomarkers include blood gene expression profiles and donor derived-cell free DNA; urine gene expression profiles; urinary cytokines, chemokines, and metabolomics; and other promising blood and urine tests.

CONCLUSION

Specific emphasis is placed on studies carried out in pediatric kidney transplant recipients.

TRIAL REGISTRATION

ClinicalTrials.gov: NCT03719339.

Promoting the production of challenging proteins via induced expression in CHO cells and modified cell-free lysates harboring T7 RNA polymerase and mutant eIF2α

Chinese hamster ovary (CHO) cells are crucial in biopharmaceutical production due to their scalability and capacity for human-like post-translational modifications. However, toxic proteins and membrane proteins are often difficult-to-express in living cells. Alternatively, cell-free protein synthesis can be employed. This study explores innovative strategies for enhancing the production of challenging proteins through the modification of CHO cells by investigating both, cell-based and cell-free approaches. A major result in our study involves the integration of a mutant eIF2 translation initiation factor and T7 RNA polymerase into CHO cell lysates for cell-free protein synthesis. This resulted in elevated yields, while eliminating the necessity for exogenous additions during cell-free production, thereby substantially enhancing efficiency. Additionally, we explore the potential of the Rosa26 genomic site for the integration of T7 RNA polymerase and cell-based tetracycline-controlled protein expression. These findings provide promising advancements in bioproduction technologies, offering flexibility to switch between cell-free and cell-based protein production as needed.

Isolation, characterization, and immunomodulatory effects of extracellular vesicles isolated from fish pathogenic Aeromonas hydrophila

Bacterial extracellular vesicles (BEVs) are natural nanocarriers that have shown great potential for biomedical applications such as biomarkers, cancer therapy, immunomodulators, vaccines, wound healing, tissue engineering, and drug carriers. In the present study, BEVs were isolated from the gram-negative bacterium, Aeromonas hydrophila using the ultracentrifugation method and denoted as AhEVs. Using transmission electron microscopy imaging, we confirmed the ultrastructure and spherical shape morphology of AhEVs. Nanoparticle-tracking analysis results showed a mean particle size of 105.5 ± 2.0 nm for AhEVs. Moreover, the particle concentration of AhEVs was 2.34 ± 0.12 × 1011 particles/mL of bacterial supernatant. AhEV-treated fathead minnow (FHM) cells did not show cytotoxicity effects up to 50 μg/mL with no significant decrease in cells. Moreover, no mortality was observed in larval zebrafish up to 50 μg/mL which indicates that the AhEVs are biocompatible at this concentration. Furthermore, fluorescent-labeled AhEVs were internalized into FHM cells. Results of qRT-PCR analysis in FHM cells revealed that cellular pro-inflammatory cytokines such as nuclear factor (NF)-κB, interferon (Ifn), Irf7, interleukin (Il) 8, and Il11 were upregulated while downregulating the expression of anti-inflammatory Il10 in a concentration-dependent manner. AhEV-treated adult zebrafish (5 μg/fish) induced toll-like receptor (tlr) 2 and tlr4; tumor necrosis factor-alpha (tnfα); heat shock protein (hsp) 70; and il10, il6, and il1β in kidney. Protein expression of NF-κB p65 and Tnfα presented amplified levels in the spleen of AhEVs-treated zebrafish. Based on the collective findings, we conclude that AhEVs exhibited morphological and physicochemical characteristics to known EVs of gram (-)ve bacteria. At biocompatible concentrations, the immunomodulatory activity of AhEVs was demonstrated by inducing different immune response genes in FHM cells and zebrafish. Hence, we suggest that AhEVs could be a novel vaccine candidate in fish medicine due to their ability to elicit strong immune responses.

Fabrication of rGO-decorated hBNNS hybrid nanocomposite via organic-inorganic interfacial chemistry for enhanced electrocatalytic detection of carcinoembryonic antigen

Organic-inorganic hybrid nanocomposites (OIHN), with tailored surface chemistry, offer ultra-sensitive architecture capable of detecting ultra-low concentrations of target analytes with precision. In the present work, a novel nano-biosensor was fabricated, acquainting dynamic synergy of reduced graphene oxide (rGO) decorated hexagonal boron nitride nanosheets (hBNNS) for detection of carcinoembryonic antigen (CEA). Extensive spectroscopic and microscopic analyses confirmed the successful hydrothermal synthesis of cross-linked rGO-hBNNS nanocomposite. Uniform micro-electrodes of rGO-hBNNS onto pre-hydrolyzed ITO were obtained via electrophoretic deposition (EPD) technique at low DC potential (15 V). Optimization of antibody incubation time, pH of supporting electrolyte, and immunoelectrode preparation was thoroughly investigated to enhance nano-biosensing efficacy. rGO-modified hBNNS demonstrated 29% boost in electrochemical performance over bare hBNNS, signifying remarkable electro-catalytic activity of nano-biosensor. The presence of multifunctional groups on the interface facilitated stable crosslinking chemistry, increased immobilization density, and enabled site-specific anchoring of Anti-CEA, resulting in improved binding affinity. The nano-biosensor demonstrated a remarkably low limit of detection of 5.47 pg/mL (R2 = 0.99963), indicating exceptional sensitivity and accuracy in detecting CEA concentrations from 0 to 50 ng/mL. The clinical evaluation confirmed its exceptional shelf life, minimal cross-reactivity, and robust recovery rates in human serum samples, thereby unraveling the potential for early, highly sensitive, and reliable CEA detection.

Rapid determination of germanium in lignite coal and coal-related solid byproducts by graphite furnace digestion inductively coupled plasma emission spectroscopy

This study developed a rapid and efficient graphite furnace digestion combined with inductively coupled plasma emission spectrometry (ICP-OES) method, enabling precise quantification of germanium (Ge) in coal and various coal-derived metallurgical byproducts across a broad concentration level (∼ppm-n%). The graphite furnace digestion conditions were examined intensively as a function of the acid amounts of HNO3 and HF (5-10 mL), temperature (80-180 °C), time (1-5 h), and acid drive methods (H3BO3 neutralization versus heating). Coal references including SARM 19, SARM 20, NIST SRM 1632e, and fly ash standard NIST SRM 2689 were tested. The optimum recovery of germanium was obtained when the HNO3 dosage, HF dosage, solid sample mass, temperature, and duration time were 10 mL, 5 mL, 0.1 g, 80 °C and 1 h. Agreement of 95.15-96.54 % between the measured and certified value was obtained under the optimum conditions. The spiked recovery was 103.23-103.54 %, indicating the matrix-analytes interactions were negligible. Boric acid neutralization reduced the recovery rates to 47.2-49.3 % and was not be appropriate for driving HF. The optimal spectral line for determining Ge is at a wavelength of 265.117 nm, at which the limit of detect and the limit of quantification were 0.46 μg L-1 and 1.53 μg L-1, respectively. The applicability of the method was validated by quantifying Ge in Ge-rich lignite, fly ashes (FA), and chlorinated distillation residue (CR) samples. The concentration of Ge in coals was 44.75-225.41 μg g-1, the content in FA was 0.68%-2.3 %, and the content in CR was 0.18 %, with the uncertainty of the method obtained being less than 0.5 %. X-ray fluorescence spectrometer (XRF) was used to verify the results. The difference between XRF data and ICP-OES data was less than 5 %, confirming the accuracy and reproductivity of the analytical method.

Applications of cell free protein synthesis in protein design

In protein design, the ultimate test of success is that the designs function as desired. Here, we discuss the utility of cell free protein synthesis (CFPS) as a rapid, convenient and versatile method to screen for activity. We champion the use of CFPS in screening potential designs. Compared to in vivo protein screening, a wider range of different activities can be evaluated using CFPS, and the scale on which it can easily be used-screening tens to hundreds of designed proteins-is ideally suited to current needs. Protein design using physics-based strategies tended to have a relatively low success rate, compared with current machine-learning based methods. Screening steps (such as yeast display) were often used to identify proteins that displayed the desired activity from many designs that were highly ranked computationally. We also describe how CFPS is well-suited to identify the reasons designs fail, which may include problems with transcription, translation, and solubility, in addition to not achieving the desired structure and function.

Unveiling the role of microRNAs in metabolic dysregulation of Gestational Diabetes Mellitus

Gestational Diabetes Mellitus (GDM) presents a significant health concern globally, necessitating a comprehensive understanding of its metabolic intricacies for effective management. MicroRNAs (miRNAs) have emerged as pivotal regulators in GDM pathogenesis, influencing glucose metabolism, insulin signaling, and lipid homeostasis during pregnancy. Dysregulated miRNA expression, both upregulated and downregulated, contributes to GDM-associated metabolic abnormalities. Ethnic and temporal variations in miRNA expression underscore the multifaceted nature of GDM susceptibility. This review examines the dysregulation of miRNAs in GDM and their regulatory functions in metabolic disorders. We discuss the involvement of specific miRNAs in modulating key pathways implicated in GDM pathogenesis, such as glucose metabolism, insulin signaling, and lipid homeostasis. Furthermore, we explore the potential diagnostic and therapeutic implications of miRNAs in GDM management, highlighting the promise of miRNA-based interventions for mitigating the adverse consequences of GDM on maternal and offspring health.

Association of antibiotics with the outcomes in COVID-19 pneumonia patients with elevated PCT levels

OBJECTIVE

To assess antibiotics impact on outcomes in COVID-19 pneumonia patients with varying procalcitonin (PCT) levels.

METHODS

This retrospective cohort study included 3665 COVID-19 pneumonia patients hospitalized at five Mayo Clinic sites (March 2020 to June 2022). PCT levels were measured at admission. Patients' antibiotics use and outcomes were collected via the Society of Critical Care Medicine (SCCM) Viral Infection and Respiratory Illness Universal Study (VIRUS) registry. Patients were stratified into high and low PCT groups based on the first available PCT result. The distinction between high and low PCT was demarcated at both 0.25 ng/ml and 0.50 ng/ml.

RESULTS

Our cohort consisted of 3665 patients admitted with COVID-19 pneumonia. The population was predominantly male, Caucasian and non-Hispanic. With the PCT cut-off of 0.25 ng/ml, 2375 (64.8 %) patients had a PCT level <0.25 ng/mL, and 1290 (35.2 %) had PCT ≥0.25 ng/ml. While when the PCT cut off of 0.50 ng/ml was used we observed 2934 (80.05 %) patients with a PCT <0.50 ng/ml while 731(19.94 %) patients had a PCT ≥0.50 ng/ml. Patients with higher PCT levels exhibited significantly higher rates of bacterial infections (0.25 ng/ml cut-off: 4.2 % vs 7.9 %; 0.50 ng/ml cut-off: 4.6 % vs 9.2 %). Antibiotics were used in 66.0 % of the cohort. Regardless of the PCT cutoffs, the antibiotics group showed increased hospital length of stay (LOS), intensive care unit (ICU) admission rate, and mortality. However, early de-escalation (<24 h) of antibiotics correlated with reduced hospital LOS, ICU LOS, and mortality. These results were consistent even after adjusting for confounders.

CONCLUSION

Our study shows a substantial number of COVID-19 pneumonia patients received antibiotics despite a low incidence of bacterial infections. Therefore, antibiotics use in COVID pneumonia patients with PCT <0.5 in the absence of clinical evidence of bacterial infection has no beneficial effect.

Biomarkers of Parkinson's disease in perspective of early diagnosis and translation of neurotrophic therapies

Parkinson's disease (PD) is a common neurodegenerative disorder characterized by progressive loss of dopamine neurons and aberrant deposits of alpha-synuclein (α-syn) in the brain. The symptomatic treatment is started after the onset of motor manifestations in a late stage of the disease. Preclinical studies with neurotrophic factors (NTFs) show promising results of disease-modifying neuroprotective or even neurorestorative effects. Four NTFs have entered phase I-II clinical trials with inconclusive outcomes. This is not surprising because the preclinical evidence is from acute early-stage disease models, but the clinical trials included advanced PD patients. To conclude the value of NTF therapies, clinical studies should be performed in early-stage patients with prodromal symptoms, that is, before motor manifestations. In this review, we summarize currently available diagnostic and prognostic biomarkers that could help identify at-risk patients benefiting from NTF therapies. Focus is on biochemical and imaging biomarkers, but also other modalities are discussed. Neuroimaging is the most important diagnostic tool today, but α-syn imaging is not yet viable. Modern techniques allow measuring various forms of α-syn in cerebrospinal fluid, blood, saliva, and skin. Digital biomarkers and artificial intelligence offer new means for early diagnosis and longitudinal follow-up of degenerative brain diseases.

Unraveling the genetic landscape of pulmonary arterial hypertension in Indian patients: A transcriptome study

BACKGROUND

Pulmonary hypertension (PH) is the abnormal elevation of pressure in the pulmonary vascular system, with various underlying causes. A specific type of PH is pulmonary arterial hypertension (PAH), a severe condition characterized by high pulmonary arterial pressure resulting from structural changes in distal pulmonary vessels, altered arterial tone, and inflammation. This leads to right ventricular hypertrophy and heart failure. The molecular mechanisms behind PAH are not well understood. This manuscript aims to elucidate these mechanisms using the genetic tool, aiding in diagnosis and treatment selection.

METHOD

In our present study, we have obtained blood samples from both patients with pulmonary arterial hypertension (PAH) and healthy individuals. We conducted a comparative transcriptome analysis to identify genes that are either upregulated or downregulated in PAH patients when compared to the control group. Subsequently, we carried out a validation study focusing on the log2-fold downregulated genes in PAH, employing Quantitative Real-Time PCR for confirmation. Additionally, we quantified the proteins encoded by the validated genes using the ELISA technique.

RESULTS

The results of the transcriptome analysis revealed that 97 genes were significantly upregulated, and 6 genes were significantly downregulated. Among these, we chose to focus on and validate only four of the downregulated genes, as they were directly or indirectly associated with the hypertension pathway. We also conducted validation studies for the proteins encoded by these genes, and the results were consistent with those obtained in the transcriptome analysis.

CONCLUSION

In conclusion, the findings of this study indicate that the four validated genes identified in the context of PAH can be further explored as potential targets for both diagnostic and therapeutic applications.

Development and validation of an analytical methodology based on solvent microextraction and UHPLC-MS/MS for determining bisphenols in honeys from different botanical origins

A new analytical methodology was proposed to determine fourteen bisphenols in honeys from different botanical origins using ultra-high performance liquid chromatography-tandem mass spectrometry. A fast, efficient, environmentally-friendly and simple sample treatment (recoveries between 81% and 116%; matrix effect <20% for all studied compounds except for bisphenol E, F and S) was proposed, which involved a solvent microextraction with acetone and a small volume/amount of 1-hexanol. Chromatographic analysis (< 15 min) was performed in a Kinetex EVO C18 column under gradient elution mode. The method was validated in terms of selectivity, limits of detection (0.2-1.5 μg/kg) and quantification (0.5-4.7 μg/kg), linearity, matrix effect, trueness, and precision (relative standard deviation <17%). Finally, thirty honey samples were analyzed, revealing the presence of residues of nine bisphenols in some of them. However, quantification was possible only in two cases for bisphenol A, with a concentration of approximately 13 μg/kg.

Probing cognitive flexibility in Shank2-deficient mice: Effects of D-cycloserine and NMDAR signaling hub dynamics

Neurodevelopmental disorders such as autism spectrum disorder (ASD) have a heterogeneous etiology but are largely associated with genetic factors. Robust evidence from recent human genetic studies has linked mutations in the Shank2 gene to idiopathic ASD. Modeling these Shank2 mutations in animal models recapitulates behavioral changes, e.g. impaired social interaction and repetitive behavior of ASD patients. Shank2-deficient mice exhibit NMDA receptor (NMDAR) hypofunction and associated behavioral deficits. Of note, NMDARs are strongly implicated in cognitive flexibility. Their hypofunction, e.g. observed in schizophrenia, or their pharmacological inhibition leads to impaired cognitive flexibility. However, the association between Shank2 mutations and cognitive flexibility is poorly understood. Using Shank2-deficient mice, we explored the role of Shank2 in cognitive flexibility measured by the attentional set shifting task (ASST) and whether ASST performance in Shank2-deficient mice can be modulated by treatment with the partial NMDAR agonist D-cycloserine (DCS). Furthermore, we investigated the effects of Shank2 deficiency, ASST training, and DCS treatment on the expression level of NMDAR signaling hub components in the orbitofrontal cortex (OFC), including NMDAR subunits (GluN2A, GluN2B, GluN2C), phosphoglycerate dehydrogenase and serine racemase. Surprisingly, Shank2 deficiency did not affect ASST performance or alter the expression of the investigated NMDAR signaling hub components. Importantly, however, DCS significantly improved ASST performance, demonstrating that positive NMDAR modulation facilitates cognitive flexibility. Furthermore, DCS increased the expression of GluN2A in the OFC, but not that of other NMDAR signaling hub components. Our findings highlight the potential of DCS as a pharmacological intervention to improve cognitive flexibility impairments downstream of NMDAR modulation and substantiate the key role of NMDAR in cognitive flexibility.

Differential microRNA expression in adolescent anxiety proneness

Biological mechanisms underlying anxiety proneness (AP), the tendency to react fearfully to stressors due to the belief that experiencing anxiety has harmful consequences, remain unclear. Epigenetic mechanisms, such as microRNAs (small, non-coding RNAs 19-20 nucleotides long), may be contributory. This study investigated AP-associated differences in microRNA expression among South African adolescents with variable exposure to childhood trauma (CT). AP was assessed using a composite score reflecting trait anxiety and anxiety sensitivity, while CT exposure was assessed with the Childhood Trauma Questionnaire. High-quality total RNA (n = 88) extracted from whole blood underwent microRNA-sequencing. Differential microRNA expression analysis was conducted with DESeq2 in R, messenger RNA target prediction analysis was performed using TargetScan and DIANA-microT, and the DIANA mirPATH tool was used for KEGG pathway analysis. The majority of participants were female (75.86%) with an average age of 15 (±1.19) years. MicroRNA expression analysis identified upregulation of hsa-miR-28-5p and downregulation of hsa-miR-502-3p and hsa-miR-500a-3p in high-AP individuals, irrespective of CT. Four KEGG pathways, each with ≥10% of their constituent genes predicted to be targets of the differentially expressed microRNAs, were identified and were enriched for genes involved in calcineurin and glutamate signalling. These findings suggest that epigenetically mediated effects on neuronal function contribute to the molecular aetiology of AP.

Dual color optogenetic tool enables heart arrest, bradycardic, and tachycardic pacing in Drosophila melanogaster

In order to facilitate cardiovascular research to develop non-invasive optical heart pacing methods, we have generated a double-transgenic Drosophila melanogaster (fruit fly) model suitable for optogenetic pacing. We created a fly stock with both excitatory H134R-ChR2 and inhibitory eNpHR2.0 opsin transgenes. Opsins were expressed in the fly heart using the Hand-GAL4 driver. Here we describe Hand > H134R-ChR2; eNpHR2.0 model characterization including bi-directional heart control (activation and inhibition) upon illumination of light with distinct wavelengths. Optical control and real-time visualization of the heart function were achieved non-invasively using an integrated light stimulation and optical coherence microscopy (OCM) system. OCM produced high-speed and high-resolution imaging; simultaneously, the heart function was modulated by blue (470 nm) or red (617 nm) light pulses causing tachycardia, bradycardia and restorable cardiac arrest episodes in the same animal. The irradiance power levels and illumination schedules were optimized to achieve successful non-invasive bi-directional heart pacing in Drosophila larvae and pupae.

Health promotion for dementia risk reduction in Indigenous populations of Canada, Aotearoa New Zealand, United States of America, and Australia: Scoping review protocol

Health promotion programs and strategies have the potential to support people to live healthier lives. Dementia, a collective name for brain disorders that impact thinking and memory, affects over 55 million people worldwide. Currently, there is no cure for dementia, so prevention is critical. Health promotion has the potential to reduce dementia by targeting the twelve potentially modifiable risk factors. A project currently being undertaken by the research team aims to strengthen the quality of clinical care and health services that specifically address dementia risk for Australian Aboriginal and Torres Strait Islander peoples. One of the intended strategies supporting the project's aim is the need for appropriate and safe health promotion programs and resources that support dementia risk reduction. Consequently, the aim of this scoping review is to identify and determine the quality and appropriateness of existing health promotion programs and resources aimed at dementia risk reduction developed or modified for Indigenous populations of Canada, the USA, Aotearoa New Zealand, and Australia that could be incorporated into the broader project. The Joanna Briggs Institute method for scoping reviews will be used to identify programs and resources focussed on dementia risk reduction for Indigenous peoples. Searches will be limited to the English language and literature published since January 2010. Databases to be searched include: CINAHL, Medline, PsychInfo, PubMed, Scopus and Google. Data that answers the research questions will be extracted from the literature and recorded on a data charting form. A combination of quantitative and qualitative methods will be used to analyse the findings of the scoping review. Dissemination of the findings through continuing community engagement, conference presentations and publications will be led by Aboriginal and Torres Strait Islander members of the research team.

Multi-marker DNA metabarcoding for precise species identification in ichthyoplankton samples

Ichthyoplankton monitoring is crucial for stock assessments, offering insights into spawning grounds, stock size, seasons, recruitment, and changes in regional ichthyofauna. This study evaluates the efficiency of multi-marker DNA metabarcoding using mitochondrial cytochrome c oxidase subunit I (COI), 12S rRNA and 16S rRNA gene markers, in comparison to morphology-based methods for fish species identification in ichthyoplankton samples. Two transects with four coastal distance categories were sampled along the southern coast of Portugal, being each sample divided for molecular and morphological analyses. A total of 76 fish species were identified by both approaches, with DNA metabarcoding overperforming morphology-75 versus 11 species-level identifications. Linking species-level DNA identifications with higher taxonomic morphological identifications resolved several uncertainties associated with traditional methods. Multi-marker DNA metabarcoding improved fish species detection by 20-36% compared to using a single marker/amplicon, and identified 38 species in common, reinforcing the validity of our results. PERMANOVA analysis revealed significant differences in species communities based on the primer set employed, transect location, and distance from the coast. Our findings underscore the potential of DNA metabarcoding to assess ichthyoplankton diversity and suggest that its integration into routine surveys could enhance the accuracy and comprehensiveness of fish stock assessments.

Two-month ketogenic diet alters systemic and brain metabolism in middle-aged female mice

The ketogenic diet (KD) is a very low-carbohydrate, high-fat diet that reduces glucose catabolism and enhances β-oxidation and ketogenesis. While research in female rodents is limited, research in male rodents suggests that ketogenic interventions initiated at midlife may slow age-related cognitive decline, as well as preserve muscle mass and physical function later in life. This study aimed to investigate the effects of a KD on global metabolic changes in middle-aged females to inform potential mechanisms behind the anti-aging effects of this diet in an understudied sex. Targeted 1H-NMR metabolomics was conducted on serum, the liver, the kidney, and the gastrocnemius muscle, as well as the cortex and the hippocampal brain regions in 16-month-old female mice after a 2-month KD. Analysis of the serum and liver metabolome revealed that the 2-month KD resulted in increased concentrations of fatty acid catabolism metabolites, as well as system-wide elevations in ketones, consistent with the ketogenic phenotype. Metabolites involved in the glucose-alanine cycle were altered in the gastrocnemius muscle, serum and the liver. Other tissue-specific alterations were detected, including distinct effects on hepatic and renal one-carbon metabolism, as well as region specific differences in metabolism across hippocampal and cortical parts of the brain. Alterations to hippocampal metabolites involved in myelinogenesis could relate to the potential beneficial effects of a KD on memory.

Multiplex Expression Cassette Assembly: A flexible and versatile method for building complex genetic circuits in conventional vectors

The manipulation of multiple transcription units for simultaneous and coordinated expression is not only key to building complex genetic circuits to accomplish diverse functions in synthetic biology, but is also important in crop breeding for significantly improved productivity and overall performance. However, building constructs with multiple independent transcription units for fine-tuned and coordinated regulation is complicated and time-consuming. Here, we introduce the Multiplex Expression Cassette Assembly (MECA) method, which modifies canonical vectors compatible with Golden Gate Assembly, and then uses them to produce multi-cassette constructs. By embedding the junction syntax in primers that are used to amplify functional elements, MECA is able to make complex constructs using only one intermediate vector and one destination vector via two rounds of one-pot Golden Gate assembly reactions, without the need for dedicated vectors and a coherent library of standardized modules. As a proof-of-concept, we modified eukaryotic and prokaryotic expression vectors to generate constructs for transient expression of green fluorescent protein and β-glucuronidase in Nicotiana benthamiana, genome editing to block monoterpene metabolism in tomato glandular trichomes, production of betanin in tobacco and synthesis of β-carotene in Escherichia coli. Additionally, we engineered the stable production of thymol and carvacrol, bioactive compounds from Lamiaceae family plants, in glandular trichomes of tobacco. These results demonstrate that MECA is a flexible, efficient and versatile method for building complex genetic circuits, which will not only play a critical role in plant synthetic biology, but also facilitate improving agronomic traits and pyramiding traits for the development of next-generation elite crops.

Applications of Lightsheet Fluorescence Microscopy by High Numerical Aperture Detection Lens

This Review explores the evolution, improvements, and recent applications of Light Sheet Fluorescence Microscopy (LSFM) in biological research using a high numerical aperture detection objective (lens) for imaging subcellular structures. The Review begins with an overview of the development of LSFM, tracing its evolution from its inception to its current state and emphasizing key milestones and technological advancements over the years. Subsequently, we will discuss various improvements of LSFM techniques, covering advancements in hardware such as illumination strategies, optical designs, and sample preparation methods that have enhanced imaging capabilities and resolution. The advancements in data acquisition and processing are also included, which provides a brief overview of the recent development of artificial intelligence. Fluorescence probes that were commonly used in LSFM will be highlighted, together with some insights regarding the selection of potential probe candidates for future LSFM development. Furthermore, we also discuss recent advances in the application of LSFM with a focus on high numerical aperture detection objectives for various biological studies. For sample preparation techniques, there are discussions regarding fluorescence probe selection, tissue clearing protocols, and some insights into expansion microscopy. Integrated setups such as adaptive optics, single objective modification, and microfluidics will also be some of the key discussion points in this Review. We hope that this comprehensive Review will provide a holistic perspective on the historical development, technical enhancements, and cutting-edge applications of LSFM, showcasing its pivotal role and future potential in advancing biological research.

Adeno-Associated Virus 5 Protein Particles Produced by E. coli Cell-Free Protein Synthesis

Recombinant adeno-associated viruses (rAAVs) have emerged as important tools for gene therapy and, more recently, vaccine development. Nonetheless, manufacturing can be costly and time-consuming, emphasizing the importance of alternative production platforms. We investigate the potential of E. coli-based cell-free protein synthesis (CFPS) to produce recombinant AAV5 virus-like particles (VLPs). AAV5 virus protein 3 (VP3) constructs, both with and without Strep-tag II, were expressed with CFPS. Lower reaction temperatures resulted in increased solubility, with the untagged variant containing nearly 90% more soluble VLP VP3 protein at 18 °C than at 37 °C. Affinity chromatography of N-terminally Strep(II)-tagged VP3 enabled successful isolation with minimal processing. DLS and TEM confirmed the presence of ∼20 nm particles. Furthermore, the N-terminally tagged AAV5 VP3 VLPs were biologically active, successfully internalizing into HeLa cells. This study describes an innovative approach to AAV VLP production using E. coli-based CFPS, demonstrating its potential for rapid and biologically active AAV VLP synthesis.

Loss of symmetric cell division of apical neural progenitors drives DENND5A-related developmental and epileptic encephalopathy

Developmental and epileptic encephalopathies (DEEs) feature altered brain development, developmental delay and seizures, with seizures exacerbating developmental delay. Here we identify a cohort with biallelic variants in DENND5A, encoding a membrane trafficking protein, and develop animal models with phenotypes like the human syndrome. We demonstrate that DENND5A interacts with Pals1/MUPP1, components of the Crumbs apical polarity complex required for symmetrical division of neural progenitor cells. Human induced pluripotent stem cells lacking DENND5A fail to undergo symmetric cell division with an inherent propensity to differentiate into neurons. These phenotypes result from misalignment of the mitotic spindle in apical neural progenitors. Cells lacking DENND5A orient away from the proliferative apical domain surrounding the ventricles, biasing daughter cells towards a more fate-committed state, ultimately shortening the period of neurogenesis. This study provides a mechanism for DENND5A-related DEE that may be generalizable to other developmental conditions and provides variant-specific clinical information for physicians and families.

Transferrin Receptor-Mediated Cellular Uptake of Fluorinated Chlorido[N,N'-bis(salicylidene)-1,2-phenylenediamine]iron(III) Complexes

Fluorinated chlorido[salophene]iron(III) complexes (salophene = N,N'-bis(salicylidene)-1,2-phenylenediamine) are promising anticancer agents. Apoptosis and necrosis induction have already been described as part of their mode of action. However, the involvement of ferroptosis in cell death induction, as confirmed for other chlorido[salophene]iron(III) complexes, has not yet been investigated. Furthermore, the mechanism of cellular uptake of these compounds is unknown. Therefore, the biological activity of the fluorescent chlorido[salophene]iron(III) complexes with a fluorine substituent at positions 3, 4, 5, or 6 at the salicylidene moieties (C1-C4) was evaluated in malignant and nonmalignant cell lines with focus on the involvement of the transferrin receptor-1 (TfR-1) in cellular uptake, the influence of the complexes on mitochondrial function, and the analysis of the molecular mechanism of cell death. All complexes significantly decreased the metabolic activity in the tested ovarian cancer (A2780, A2780cis), breast cancer (MDA-MB 231), and leukemia (HL-60) cell lines, while the nonmalignant human stroma cell line HS-5 at a concentration of 0.5 μM, which represents the IC50 of the complexes in most of the used tumorigenic cell lines, was not affected. The mitochondrial function was impaired, as evidenced by a reduced mitochondrial membrane potential ΔΨm and decreased mitochondrial activity. Besides apoptosis and necroptosis, ferroptosis was identified as part of the mode of action. It was further demonstrated for the first time that fluorinated chlorido[salophene]iron(III) complexes downregulate TfR-1 expression, comparable to ferristatin II, an iron transport inhibitor that acts via TfR-1 degradation. FerroOrange staining further indicated that the complexes strongly increased the intracellular iron(II) level as a driving force to induce ferroptosis. In conclusion, these fluorinated chlorido[salophene]iron(III) complexes are potent, tumor cell-specific chemotherapeutic agents, with the potential to treat various types of cancers.

Genomic regions influencing the hyperspectral phenome of deoxynivalenol infected wheat

The quantitative nature of fusarium head blight (FHB) resistance requires further exploration of the wheat genome to identify regions conferring resistance. In this study, we explored the application of hyperspectral imaging of Fusarium-infected wheat kernels and identified regions of the wheat genome contributing significantly to the accumulation of Deoxynivalenol (DON) mycotoxin. Strong correlations were identified between hyperspectral reflectance values for 204 wavebands in the 397-673 nm range and DON mycotoxin. Dimensionality reduction using principal components was performed for all 204 wavebands and 38 sliding windows across the range of wavebands. The first principal component (PC1) of all 204 wavebands explained 70% of the total variation in waveband reflectance values and was highly correlated with DON mycotoxin. PC1 was used as a phenotype in a genome wide association study and a large effect QTL on chromosome 2D was identified for PC1 of all wavebands as well as nearly all 38 sliding windows. The allele contributing variation in PC1 values also led to a substantial reduction in DON. The 2D polymorphism affecting DON levels localized to the exon of TraesCS2D02G524600 which is upregulated in wheat spike and rachis tissues during FHB infection. This work demonstrates the value of hyperspectral imaging as a correlated trait for investigating the genetic basis of resistance and developing wheat varieties with enhanced resistance to FHB.

Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins

Integral and interacting membrane proteins (IIMPs) constitute a vast family of biomolecules that perform essential functions in all forms of life. However, characterizing their interactions with lipid bilayers remains limited due to challenges in purifying and reconstituting IIMPs in vitro or labeling IIMPs without disrupting their function in vivo. Here, we report cell-free transcription-translation in a quartz crystal microbalance with dissipation (TXTL-QCMD) to dynamically characterize interactions between diverse IIMPs and membranes without protein purification or labeling. As part of TXTL-QCMD, IIMPs are synthesized using cell-free transcription-translation (TXTL), and their interactions with supported lipid bilayers are measured using a quartz crystal microbalance with dissipation (QCMD). TXTL-QCMD reconstitutes known IIMP-membrane dependencies, including specific association with prokaryotic or eukaryotic membranes, and the multiple-IIMP dynamical pattern-forming association of the E. coli division-coordinating proteins MinCDE. Applying TXTL-QCMD to the recently discovered Zorya anti-phage system that is unamenable to labeling, we discovered that ZorA and ZorB integrate within the lipids found at the poles of bacteria while ZorE diffuses freely on the non-pole membrane. These efforts establish the potential of TXTL-QCMD to broadly characterize the large diversity of IIMPs.

Biological characterization and genomic analysis of a novel bacteriophage, MopsHU1, infecting Morganella psychrotolerans

Morganella psychrotolerans is a histamine-producing bacterium that causes histamine poisoning. In this study, we isolated and characterized a novel phage, MopsHU1, that infects M. psychrotolerans. MopsHU1 is a podovirus with a limited host spectrum. Genomic analysis showed that MopsHU1 belongs to the family Autographiviridae, subfamily Studiervirinae, and genus Kayfunavirus. Comparative analysis revealed that the MopsHU1 genome is similar to those of Citrobacter phage SH3 and Cronobacter phage Dev2. Moreover, the Escherichia coli phage K1F genome is also similar, except for its tailspike gene sequence. These results expand our understanding of the Kayfunavirus phages that infect Morganella spp. Note: The nucleotide sequence data reported here are available in the DDBJ/EMBL/GenBank database under the accession number LC799501.

Acute lipopolysaccharide (LPS)-induced cell membrane hyperpolarization is independent of voltage gated and calcium activated potassium channels

The gram-negative toxin lipopolysaccharides (LPS) are known to trigger inflammatory cytokines in mammals, which can result in pathological responses. Upon treatment of bacterial sepsis with antibiotics, the lysing bacteria can present a surge in LPS, inducing a cytokine storm. However, LPS can also have direct cellular effects, including transient rapid hyperpolarizing of the membrane potential, blocking glutamate receptors and even promoting release of glutamate. The detailed mechanism of action for these immediate responses is still unresolved. In addressing the membrane hyperpolarization, voltage gated K+ channel blockers 4-aminopyridine (4-AP, 3 mM), quinidine hydrochloride monohydrate (0.1 mM) and tetraethylammonium (TEA, 20 mM) were examined along with RNAi knockdowns of potential calcium activated K+ channels. The immediate responses of LPS were not blocked. Even in the presence of glutamate, the membrane still hyperpolarizes with LPS. When the driving gradient for the ionotropic glutamate receptors is enhanced during hyperpolarization, spontaneous quantal responses are dampened in amplitude. Thus, glutamate receptors are blocked, and the mechanism of hyperpolarization remains unresolved. The larval Drosophila glutamatergic neuromuscular junction is used as a model synaptic preparation to address the direct rapid actions by LPS.

7p22.3 microdeletion: a case study of a patient with congenital heart defect, neurodevelopmental delay and epilepsy

BACKGROUND

Chromosome 7 has regions enriched with low copy repeats (LCRs), which increase the likelihood of chromosomal microdeletion disorders. Documented microdeletion disorders on chromosome 7 include both well-known Williams syndrome and more rare cases. It is noteworthy that most cases of various microdeletions are characterized by phenotypic signs of neuropsychological developmental disorders, which, however, have a different genetic origin. The localization of the microdeletions, the genes included in the region, as well as the structural features of the sequences of these genes have a cumulative influence on the phenotypic characteristics of the individuals for each specific case and the severity of the manifestations of disorders. The consideration of these features and their detailed analysis is important for a correct and comprehensive assessment of the disease.

RESULTS

The article describes a clinical case of 7p22.3 microdeletion in a patient with congenital heart defect and neurological abnormalities - epilepsy, combined with moderate mental and motor developmental delay.

CONCLUSIONS

Through detailed genetic analyses, we are improving the clinical description of the rare 7p22.3 microdeletion and thus creating a basis for future genetic counseling and research into targeted therapies.

Short Caco-2 model for evaluation of drug permeability: A sodium valerate-assisted approach

The human colorectal adenocarcinoma cell line Caco-2, widely used for studying intestinal drug permeability, is typically grown on permeable filter supports and matures in 21 days with frequent media changes. The process is labor-intensive, prone to contamination, and has low throughput, contributing to the overall high utilization cost. Efforts to establish a low-cost, high-throughput, and short-duration model have encountered obstacles, such as weaker tight junctions causing monolayer leaks, incomplete differentiation resulting in low transporter expression, intricate and challenging protocols, and cytotoxicity, limiting the usability. Hence, this study aimed to develop a low-cost, efficient, and short-duration model by addressing the aforementioned concerns by customizing the media and finding a safe differentiation inducer. We generated a new rapid model using sodium valerate, which demonstrated sufficient transporter activity, improved monolayer integrity, and higher levels of differentiation markers than the 21-day model. Furthermore, this model exhibited consistent and reliable results when used to evaluate drug permeability over multiple days of repeated use. This study demonstrates the potential of a sodium valerate-assisted abbreviated model for drug permeability assessment with economic and practical advantages.

Vagus nerve stimulation during training fails to improve learning in healthy rats

Learning new skills requires neuroplasticity. Vagus nerve stimulation (VNS) during sensory and motor events can increase neuroplasticity in networks related to these events and might therefore serve to facilitate learning on sensory and motor tasks. We tested if VNS could broadly improve learning on a wide variety of tasks across different skill domains in healthy, female adult rats. VNS was paired with presentation of stimuli or on successful trials during training, strategies known to facilitate plasticity and improve recovery in models of neurological disorders. VNS failed to improve either rate of learning or performance for any of the tested tasks, which included skilled forelimb motor control, speech sound discrimination, and paired-associates learning. These results contrast recent findings from multiple labs which found VNS pairing during training produced learning enhancements across motor, auditory, and cognitive domains. We speculate that these contrasting results may be explained by key differences in task designs, training timelines and animal handling approaches, and that while VNS may be able to facilitate rapid and early learning processes in healthy subjects, it does not broadly enhance learning for difficult tasks.

One-step detection of procollagen type III N-terminal peptide as a fibrosis biomarker using fluorescent immunosensor (quenchbody)

BACKGROUND

Procollagen type III N-terminal peptide (P-III-NP) is a fibrosis biomarker associated with liver and cardiac fibrosis. Despite the value of P-III-NP as a biomarker, its analysis currently relies on enzyme-linked immunosorbent assays (ELISA) and radioimmunoassays (RIA), which require more than 3 h. To facilitate early diagnosis and treatment through rapid biomarker testing, we developed a one-step immunoassay for P-III-NP using a quenchbody, which is a fluorescence-labeled immunosensor for immediate signal generation.

RESULTS

To create quenchbodies, the total mRNA of P-III-NP antibodies was extracted from early-developed hybridoma cells, and genes of variable regions were obtained through cDNA synthesis, inverse PCR, and sequencing. A single-chain variable fragment (scFv) with an N-terminal Cys-tag was expressed in E. coli Shuffle T7, resulting in a final yield of 9.8 mg L-1. The fluorescent dye was labeled on the Cys-tag of the anti-P-III-NP scFv using maleimide-thiol click chemistry, and the spacer arm lengths between the maleimide-fluorescent dyes were compared. Consequently, a TAMRA-C6-labeled quenchbody exhibited antigen-dependent fluorescence signals and demonstrated its ability to detect P-III-NP at concentrations as low as 0.46 ng mL-1 for buffer samples, 1.0 ng mL-1 for 2 % human serum samples.

SIGNIFICANCE

This one-step P-III-NP detection method provides both qualitative and quantitative outcomes within a concise 5-min timeframe. Furthermore, its application can be expanded using a 96-well platform and human serum, making it a high-throughput and sensitive method for testing fibrotic biomarkers.

Plant growth promoting activities of endophytic bacteria from Melia azedarach (Meliaceae) and their influence on plant growth under gnotobiotic conditions

Bacteria that live asymptomatically within plant tissues are known as endophytes. Because of the close relation with the plant host, they have been a matter of interest for application as plant growth promoters. Melia azedarach is a widely distributed medicinal tree with proven insecticidal, antimicrobial, and antiviral activity. The aim of this study was to isolate and characterize endophytic bacteria from M. azedarach and analyze their plant growth promoting activities for the potential application as biological products. Bacteria were isolated from roots and leaves of trees growing in two locations of Northeastern Argentina. The isolates were characterized by repetitive extragenic palindromic sequence PCR and 16S rDNA sequence analysis. The plant growth-promoting activities were assayed in vitro, improvement of plant growth of selected isolates was tested on M. azedarach plantlets, and the effect of selected ACC deaminase producing isolates was tested on tomato seedlings under salt-stress conditions. The highest endophytic bacterial abundance and diversity were obtained from the roots. All isolates had at least one of the assayed plant growth-promoting activities and 80 % of them had antagonistic activity. The most efficient bacteria were Pseudomonas monteilii, Pseudomonas farsensis, Burkholderia sp. and Cupriavidus sp. for phosphate solubilization (2064 μg P ml-1), IAA production (94.7 μg ml-1), siderophore production index (5.5) and ACC deaminase activity (1294 nmol α-ketobutyrate mg-1 h-1). M. azedarach inoculation assays revealed the bacterial growth promotion potential, with Pseudomonas monteilii, Pseudomonas farsensis and Cupriavidus sp. standing out for their effect on leaf area, leaf dry weight, specific leaf area, and total Chl, Mg and N content, with increases of up to 149 %, 58 %, 65 %, 178 %, 76 % and 97.7 %, respectively, compared to NI plants. Efficient ACC deaminase-producing isolates increased stress tolerance of tomato plants under saline condition. Overall, these findings indicate the potential of the endophytic isolates as biostimulant and biocontrol agents.

MicroRNA-135b mainly functions as an oncogene during tumor progression

Late diagnosis is considered one of the main reasons of high mortality rate among cancer patients that results in therapeutic failure and tumor relapse. Therefore, it is needed to evaluate the molecular mechanisms associated with tumor progression to introduce efficient markers for the early tumor detection among cancer patients. The remarkable stability of microRNAs (miRNAs) in body fluids makes them potential candidates to use as the non-invasive tumor biomarkers in cancer screening programs. MiR-135b has key roles in prognosis and survival of cancer patients by either stimulating or inhibiting cell proliferation, invasion, and angiogenesis. Therefore, in the present review we assessed the molecular biology of miR-135b during tumor progression to introduce that as a novel tumor marker in cancer patients. It has been reported that miR-135b mainly acts as an oncogene by regulation of transcription factors, signaling pathways, drug response, cellular metabolism, and autophagy. This review paves the way to suggest miR-135b as a tumor marker and therapeutic target in cancer patients following the further clinical trials and animal studies.

Engineered Proteins and Materials Utilizing Residue-Specific Noncanonical Amino Acid Incorporation

The incorporation of noncanonical amino acids into proteins and protein-based materials has significantly expanded the repertoire of available protein structures and chemistries. Through residue-specific incorporation, protein properties can be globally modified, resulting in the creation of novel proteins and materials with diverse and tailored characteristics. In this review, we highlight recent advancements in residue-specific incorporation techniques as well as the applications of the engineered proteins and materials. Specifically, we discuss their utility in bio-orthogonal noncanonical amino acid tagging (BONCAT), fluorescent noncanonical amino acid tagging (FUNCAT), threonine-derived noncanonical amino acid tagging (THRONCAT), cross-linking, fluorination, and enzyme engineering. This review underscores the importance of noncanonical amino acid incorporation as a tool for the development of tailored protein properties to meet diverse research and industrial needs.