Uncertainty Quantification and Interpretability for Clinical Trial Approval Prediction

Background: Clinical trial is a crucial step in the development of a new therapy (e.g., medication) and is remarkably expensive and time-consuming. Forecasting the approval of clinical trials accurately would enable us to circumvent trials destined to fail, thereby allowing us to allocate more resources to therapies with better chances. However, existing approval prediction algorithms did not quantify the uncertainty and provide interpretability, limiting their usage in real-world clinical trial management. Methods: This paper quantifies uncertainty and improves interpretability in clinical trial approval predictions. We devised a selective classification approach and integrated it with the Hierarchical Interaction Network, the state-of-the-art clinical trial prediction model. Selective classification, encompassing a spectrum of methods for uncertainty quantification, empowers the model to withhold decision-making in the face of samples marked by ambiguity or low confidence. This approach not only amplifies the accuracy of predictions for the instances it chooses to classify but also notably enhances the model's interpretability. Results: Comprehensive experiments demonstrate that incorporating uncertainty markedly enhances the model's performance. Specifically, the proposed method achieved 32.37%, 21.43%, and 13.27% relative improvement on area under the precision-recall curve over the base model (Hierarchical Interaction Network) in phase I, II, and III trial approval predictions, respectively. For phase III trials, our method reaches 0.9022 area under the precision-recall curve scores. In addition, we show a case study of interpretability that helps domain experts to understand model's outcome. The code is publicly available at https://github.com/Vincent-1125/Uncertainty-Quantification-on-Clinical-Trial-Outcome-Prediction. Conclusion: Our approach not only measures model uncertainty but also greatly improves interpretability and performance for clinical trial approval prediction.

High Value-Added Application of Natural Products in Crop Protection: Discovery and Exploration of Caffeoyl and Flavonoid Derivatives from Clematis brevicaudata DC. as Novel Insecticide Candidates

Nine caffeoyl derivatives (1-9), including two new dicaffeoyl glycosides, brevicaudatosides A and B (1 and 2), and six flavonoids (10-15), were identified from overground Clematis brevicaudata DC. Compounds 1 and 13 exhibited significant oral toxicities against Acyrthosiphon pisum Harris with LC50 (half-lethal concentration) values of 0.12 and 0.28 mM, respectively. Meanwhile, compounds 1, 8, 10, 13, and 15 showed remarkable repellent effects against A. pisum with the repellent indexes valued at 1.00 under 50-200 μg/mL at 24 h. Compounds 1 and 8 also displayed moderate antifeedant activities against Plutella xylostella L. The shrunken bodies, especially for wizened cauda, and the ultrastructural damages of microvilli, mitochondrion, nucleus, and endoplasmic reticulum in midgut were toxic symptoms of A. pisum caused by 1 and 13. The inhibition of Chitinase was the main reason for their potent insecticidal activities. This study provided valuable pieces of evidence for the high value-added application of caffeoyl and flavonoid derivatives from C. brevicaudata as novel plant-origin biopesticides for crop protection.

Mesenchymal stem cell-derived extracellular vesicles: A novel promising neuroprotective agent for Alzheimer's disease

Alzheimer's disease (AD) is a neurodegenerative disease characterized by progressive loss of neurons in the brain. However, there are no effective drugs for AD. Mesenchymal stem cell-derived extracellular vesicles (MSCs-EVs), as a new mediator of intercellular communication, are associated with low immunogenicity, low risk of tumor formation, and good safety profile. Therefore, MSCs-EVs may be a safe and attractive cell-free nanotherapeutics, offering a new perspective for AD treatment. Although preclinical studies have demonstrated that MSCs-EVs have significant neuroprotective effects, the underlying mechanism is unclear. This study aimed to: outline the diagnostic and delivery roles of MSCs-EVs for AD treatment; summarize the optimal sources and delivery methods of MSCs-EVs; provide a comprehensive review on the neuroprotective mechanisms of MSCs-EVs; explore how to enhance the neuroprotective effects of MSCs-EVs; and discuss the limitations and potential of their translation to the clinic. Therefore, this study may provide a more precise theoretical reference and practical basis for clinical research of MSCs-EVs.

Discovery of New Botanical Insecticides: Identification and Insecticidal Activity of Saponins from Clematis obscura Maxim and Insights into the Stress Response of Acyrthosiphon pisum Harris

To discover new botanical products-based insecticide candidates, 14 triterpenoid saponins (1-14) including four new ones, obscurosides A-D (1-4), were isolated from Clematis obscura Maxim as potential agrochemicals against Acyrthosiphon pisum Harris and Plutella xylostella (L.). Compounds 1-3 were characterized by a rare ribose substitution at C-3, and 4 was a bidesmoside glycosylated at the rare C-23 and C-28 positions of the oleanane aglycone. Compounds 10 (median antifeeding concentration, AFC50 = 1.10 mg/mL; half-lethal concentration, LC50 = 1.21 mg/mL) and 13 (AFC50 = 1.09 mg/mL, LC50 = 1.37 mg/mL) showed significant insecticidal activities against third larvae of P. xylostella at 72 h. All saponins displayed antifeedant activities against A. pisum with the deterrence index of 0.20-1.00 at 400 μg/mL. Compound 8 showed optimal oral toxicity (LC50 = 50.09 μg/mL) against A. pisum, followed by compounds 1, 5-7, 9, and 14 (LC50 = 90.21-179.25 μg/mL) at 72 h. The shrinkage of the cuticle and the destruction of intestinal structures of microvilli, nucleus, endoplasmic reticulum, and mitochondria were toxic symptoms of 8-treated A. pisum. The significantly declined Chitinase activity in 8-treated A. pisum with an inhibition rate of 79.1% at LC70 (70% lethal concentration) could be the main reason for its significant oral toxicities. Molecular docking revealed favorable affinities of compounds 1 and 8 with group I Chitinase OfChtI (Group I Chitinase from Ostrinia furnacalis) through conventional hydrogen bonds and alkey/π-alkey interactions by different patterns. These results will provide valuable information for the development of novel botanical pesticides for the management of insect pests, especially against A. pisum.

A perovskite-based electrochemiluminescence aptasensor for tetracycline screening

Tetracyclines are currently the most commonly used class of antibiotics, and their residue issue significantly impacts public health safety. In this study, a surface modification of perovskite with cetyltrimethylammonium bromide led to the generation of stable electrochemiluminescence (ECL) emitters in aqueous systems and improved the biocompatibility of perovskite. A perovskite quantum dot-based ECL sensing strategy was developed. Utilizing the corresponding aptamer of the antibiotics, strain displacement reactions were triggered, disrupting the ECL quenching system composed of perovskite and Ag nanoclusters (Ag NCs) on the electrode surface, generating a signal to achieve quantitative detection of several common tetracycline antibiotics. The perovskite quantum dot provided a strong and stable initial signal, while the efficient catalytic activity of the silver cluster enhanced the recognition sensitivity. Tetracycline, chlortetracycline, and oxytetracycline were used as examples to demonstrate the differentiation and quantitative detection through this method. In addition, the aptasensor exhibited analytical performance with the linear range (0.1-10 μM OTC) and good recovery rates of 94.7% to 101.6% in real samples. This approach has the potential to become a sensitive and practical approach for assessing antibiotic residues.

Study of Impacts of Two Types of Cellular Aging on the Yeast Bud Morphogenesis

Understanding the mechanisms of cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying cellular aging. With their powerful genetics, relatively short lifespan and well-established signaling pathways also found in animals, yeast cells offer valuable insights into the aging process. Recent experiments suggested the existence of two aging modes in yeast characterized by nucleolar and mitochondrial declines, respectively. In this study, by analyzing experimental data it was shown that cells evolving into those two aging modes behave differently when they are young. While buds grow linearly in both modes, cells that consistently generate spherical buds throughout their lifespan demonstrate greater efficacy in controlling bud size and growth rate at young ages. A three-dimensional chemical-mechanical model was developed and used to suggest and test hypothesized mechanisms of bud morphogenesis during aging. Experimentally calibrated simulations showed that tubular bud shape in one aging mode could be generated by locally inserting new materials at the bud tip guided by the polarized Cdc42 signal during the early stage of budding. Furthermore, the aspect ratio of the tubular bud could be stabilized during the late stage, as observed in experiments, through a reduction on the new cell surface material insertion or an expansion of the polarization site. Thus model simulations suggest the maintenance of new cell surface material insertion or chemical signal polarization could be weakened due to cellular aging in yeast and other cell types.

A portable polymeric electrochromism-based visual biosensing device with distance readout

A distance-based visual electrochromic biosensing device is proposed. With this device, the naked eye is capable of discerning the distance of discoloration, which exhibits a positive correlation with the concentration of the detected substance.

Tumor-targeted nanodrug FSGG/siGal-9 for transdermal photothermal immunotherapy of melanoma

Photothermal therapy (PTT) is a cancer-targeted treatment approach.The occurrence of tumors may be related to microbial infections (Viruses, bacteria, fungi, etc.), which probably provokes anti-tumor immunity. However, T cells in the context of cancer become exhausted and dysfunctional. Galectin-9 (Gal-9) is highly expressed in normal tissues and associates with body immune tolerance, and was firstly evidenced with much higher expression on the primary solid tumors than CD80/86 (B7) and CD274 (PD-L1) here, which suggests that Gal-9 may be a key factor in inhibiting the anti-tumor immunity, and its receptor T cell immunoglobulin and mucin domain 3 (TIM-3) was discovered on the cytotoxic T lymphocytes (CTL) with high expression as well based on the single cell analysis. The immune checkpoint communications showed that the Gal-9/TIM-3 axis played the most vital role on negatively regulating the anti-tumor immunity of CTL for melanoma. Then, we used a novel transdermal photothermal nanosensitizer (FSGG) loading Gal-9 siRNA (FSGG/siGal-9) for knocking the tumor cells down Gal-9 to block the Gal-9/TIM-3 axis and prohibit CTL exhaustion synergizing PTT against melanoma, which evidenced good effects on inhibiting tumor growth and enhancing anti-tumor immunity, named "photothermal immunotherapy". This paper provides a new perspective for tumor prevention and treatment.

First report of Botrytis cinerea causing gray mold on Alternanthera philoxeroides in China

Alternanthera philoxeroides is a perennial herbaceous plant used as a forage crop (Wang et al. 2005) and is known to have medicinal properties. One of notable active components is flavonoids, which have been found to exhibit anti-Hepatitis B Virus activity (Li et al. 2016). In 2021, a leaf spot on A. philoxeroides was observed in the science and education experimental park of Hebei Agricultural University (38°49'38″ N, 115°26'39″ E). Initial symptoms included leaf tissue water loss, chloro-sis and elliptical lesions scattered across the leaf margin with further development leading to ellipse-shaped disease spots and leaf wilting (Fig. 1A). In the field, 50 plants of A. philoxeroides were randomly selected to investigate and quantify dis-ease. Incidence of leaf disease was approximately 25%, and the infected leaves ex-hibited an average affected area of about 20%. In order to identify the pathogen, three diseased plants were randomly selected from different areas. Stems and leaves of diseased plants were cut into pieces (2 to 3 mm × 5 mm) and disinfested with 1% sodium hypochlorite for 1 minute. After rinsing with sterile water three times, each lesion sample was isolated and purified on PDA at 25°C. Eventually, all samples pro-duced morphologically consistent colonies of pure strains. From the 9 isolates ob-tained, ZLQ-1 was selected as a representative isolate for further study. Colonies were initially white, turning gray from the centre, then gray-brown with cottony aerial hyphae, and finally growing black, stiff, round or irregular sclerotia (0.6 to 4.0 mm × 1.1 to 4.2 mm, n=50) (Fig1. B, C). ZLQ-1 exhibited branched conidia with en-larged apical cells. The conidia of this isolate were unicellular, ovoid or ellipsoid in shape, with dimensions ranging from 5.8 to 16.9 μm × 6.3 to 11.2 μm (n=50) (Fig. 1D). These morphological characteristics were consistent with Botrytis cinerea (Ellis, 1971). The genes of internal transcribed spacer (ITS), heat shock protein (HSP60), DNA-dependent RNA polymerase subunit II (RPB2), and glyceraldehyde-3-phosphate dehydrogenase (G3PDH) were amplified with specific primers ITS1/ITS4, HSP60-F/HSP60-R, RPB2-F/RPB2-R and G3PDH-F/G3PDH-R (Aktaruzzaman et al., 2022). Sequences were deposited into GenBank with accession numbers ON479490 for ITS, ON572246 for G3PDH, ON572248 for HSP60, ON572247 for RPB2. BLASTn analysis showed that the ITS sequence shared 99.62% similarity to B. cinerea (CP009808), and the sequences of the other three nuclear protein-encoding genes (G3PDH, HSP60, and RPB2) showed at least 99.9% identity with the genome of B. ci-nerea (B05.10) (Staats et al. 2005). We have inoculated 10 healthy A. philoxeroides leaves with a suspension of 1x105 spores/mL, and used sterile water treatment as control (Aktaruzzaman et al., 2022). Each leaf was inoculated with 10 μL spore sus-pension. After 7 days in a controlled incubation environment (25℃, 40%RH), the plants inoculated with conidial suspensions displayed lesions covered in a gray-white mycelial layer, resembling those observed in the field (Fig. 1E-G). In con-trast, the plants inoculated with sterile water remained unaffected. Morphological and PCR analysis confirmed that the pathogen responsible for the observed symp-toms was B. cinerea. Koch's postulates were fulfilled as the same pathogen was con-sistently re-isolated from the inoculated leaves and confirmed to be B. cinerea through morphological and molecular methods. This is the first reported case of B. cinerea causing gray mold on A. philoxeroides in China. It is important to monitor and prevent B. cinerea infection during cultivation to ensure the production of healthy Chinese medicine and feed.

A Standardized Set of MoClo-Compatible Inducible Promoter Systems for Tunable Gene Expression in Yeast

Small-molecule control of gene expression underlies the function of numerous engineered gene circuits that are capable of environmental sensing, computation, and memory. While many recently developed inducible promoters have been tailor-made for bacteria or mammalian cells, relatively few new systems have been built for Saccharomyces cerevisiae, limiting the scale of synthetic biology work that can be done in yeast. To address this, we created the yeast Tunable Expression Systems Toolkit (yTEST), which contains a set of five extensively characterized inducible promoter systems regulated by the small-molecules doxycycline (Dox), abscisic acid (ABA), danoprevir (DNV), 1-naphthaleneacetic acid (NAA), and 5-phenyl-indole-3-acetic acid (5-Ph-IAA). Assembly was made to be compatible with the modular cloning yeast toolkit (MoClo-YTK) to enhance the ease of use and provide a framework to benchmark and standardize each system. Using this approach, we built multiple systems with maximal expression levels greater than those of the strong constitutive TDH3 promoter. Furthermore, each of the five classes of systems could be induced at least 60-fold after a 6 h induction and the highest fold change observed was approximately 300. Thus, yTEST provides a reliable, diverse, and customizable set of inducible promoters to modulate gene expression in yeast for applications in synthetic biology, metabolic engineering, and basic research.

Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair

Transcription-coupled nucleotide excision repair (TC-NER) is a highly conserved DNA repair pathway that removes bulky lesions in the transcribed genome. Cockayne syndrome B protein (CSB), or its yeast ortholog Rad26, has been known for decades to play important roles in the lesion-recognition steps of TC-NER. Another conserved protein ELOF1, or its yeast ortholog Elf1, was recently identified as a core transcription-coupled repair factor. How Rad26 distinguishes between RNA polymerase II (Pol II) stalled at a DNA lesion or other obstacles and what role Elf1 plays in this process remains unknown. Here, we present cryo-EM structures of Pol II-Rad26 complexes stalled at different obstacles that show that Rad26 uses a common mechanism to recognize a stalled Pol II, with additional interactions when Pol II is arrested at a lesion. A cryo-EM structure of lesion-arrested Pol II-Rad26 bound to Elf1 revealed that Elf1 induces further interactions between Rad26 and a lesion-arrested Pol II. Biochemical and genetic data support the importance of the interplay between Elf1 and Rad26 in TC-NER initiation. Together, our results provide important mechanistic insights into how two conserved transcription-coupled repair factors, Rad26/CSB and Elf1/ELOF1, work together at the initial lesion recognition steps of transcription-coupled repair.

Active ingredients of Chinese medicine with immunomodulatory properties: NF-κB pathway and Parkinson's disease

Parkinson's disease (PD) is a neurodegenerative disease with a complex pathogenesis and no cure. Persistent neuroinflammation plays an important role in the development of PD, and activation of microglia and astrocytes within the central nervous system leads to an inflammatory response and production of pro-inflammatory factors, and activation of NF-κB is key to neuroglial activation in chronic inflammation in PD and a hallmark of the onset of neuroinflammatory disease. Therefore, inhibiting NF-κB activation to prevent further loss of dopaminergic nerves is a more effective means of treating PD. It has been found that an increasing number of active ingredients in Chinese medicines, such as flavonoids, alkaloids, saponins, terpenoids, phenols and phenylpropanoids, have anti-inflammatory properties that can regulate neuroglia cell activation and ameliorate neuroinflammation through the NF-κB pathway, and increase dopamine release or protect dopaminergic neurons for neuroprotection to improve behavioural dysfunction in PD. The active ingredients of traditional Chinese medicine are expected to be good candidates for the treatment of PD, as they provide holistic regulation through multi-targeting and multi-level effects, and are safe, inexpensive and readily available. Therefore, this paper summarises that the active ingredients of some relevant Chinese medicines ameliorate the symptoms of PD and delay the development of PD by inhibiting glial cell-mediated neuroinflammation through the NF-κB pathway, which may provide new ideas for exploring the molecular mechanism of PD pathogenesis and developing new anti-PD drugs.

A Microfluidic Platform for Screening Gene Expression Dynamics across Yeast Strain Libraries

The relative ease of genetic manipulation in S. cerevisiae is one of its greatest strengths as a model eukaryotic organism. Researchers have leveraged this quality of the budding yeast to study the effects of a variety of genetic perturbations, such as deletion or overexpression, in a high-throughput manner. This has been accomplished by producing a number of strain libraries that can contain hundreds or even thousands of distinct yeast strains with unique genetic alterations. While these strategies have led to enormous increases in our understanding of the functions and roles that genes play within cells, the techniques used to screen genetically modified libraries of yeast strains typically rely on plate or sequencing-based assays that make it difficult to analyze gene expression changes over time. Microfluidic devices, combined with fluorescence microscopy, can allow gene expression dynamics of different strains to be captured in a continuous culture environment; however, these approaches often have significantly lower throughput compared to traditional techniques. To address these limitations, we have developed a microfluidic platform that uses an array pinning robot to allow for up to 48 different yeast strains to be transferred onto a single device. Here, we detail a validated methodology for constructing and setting up this microfluidic device, starting with the photolithography steps for constructing the wafer, then the soft lithography steps for making polydimethylsiloxane (PDMS) microfluidic devices, and finally the robotic arraying of strains onto the device for experiments. We have applied this device for dynamic screens of a protein aggregation library; however, this methodology has the potential to enable complex and dynamic screens of yeast libraries for a wide range of applications. Key features • Major steps of this protocol require access to specialized equipment (i.e., microfabrication tools typically found in a cleanroom facility and an array pinning robot). • Construction of microfluidic devices with multiple different feature heights using photolithography and soft lithography with PDMS. • Robotic spotting of up to 48 different yeast strains onto microfluidic devices.

A double-quenching paperclip ECL biosensing platform for ultrasensitive detection of antibiotic resistance genes (mecA) based on Ti3C2 MXene-Au NPs as a coreactant accelerator

The global spread of environmental biological pollutants, such as antibiotic-resistant bacteria and their antibiotic resistance genes (ARGs), has emerged as a critical public health concern. It is imperative to address this pressing issue due to its potential implications for public health. Herein, a DNA paperclip probe with double-quenching function of target cyclic cleavage was proposed, and an electrochemiluminescence (ECL) biosensing platform was constructed using Ti3C2 MXene in-situ reduction growth of Au NPs (TCM-Au) as a coreactant accelerator, and applied to the sensitive detection of ARGs. Thanks to the excellent catalytic performance, large surface area and Au-S affinity of TCM-Au, the ECL performance of CdS QDs have been significantly improved. By cleverly utilizing the negative charge of the paperclip nucleic acid probe and its modification group, double-quenching of the ECL signal was achieved. This innovative approach, combined with target cyclic amplification, facilitated specific and sensitive detection of the mecA gene. This biosensing platform manifested highly selective and sensitive determination of mecA genes in the range of 10 fM to 100 nM and a low detection limit of 2.7 fM. The credible detectability and anti-interference were demonstrated in Yangtze river and Aeration tank outlet, indicating its promising application toward pollution monitoring of ARGs.

Dual-mode sensing chip for photoelectrochemical and electrochromic visual determination of deoxynivalenol mycotoxin

The successful development of a dual-mode sensing chip for deoxynivalenol (DON) detection using photoelectrochemical (PEC) and electrochromic visualization techniques is reported. By laser etching technology, different functional areas, including the photoanode, the cathode, and the electrochromic area, are fabricated on indium tin oxide (ITO) glass. Then, these three areas are further respectively modified with PEC active materials, platinum nanoparticles, and Prussian blue. Under light illumination, photocurrents generate between the photoanode and the cathode due to the separation of photo-induced electrons and holes in the TiO2/3DNGH material. Meanwhile, the photo-induced electrons are transferred to Prussian blue on the visualization area, which will be reduced to colorless Prussian white. The binding of DON molecules and aptamers can promote electron transfer and reduce the recombination of electrons and holes, allowing for simultaneous quantitative detection of DON using either the photocurrent or color change. The sensor chip has a broad detection range of DON concentrations of 1 fg⋅mL-1 to 100 pg⋅mL-1 in the PEC mode with the limit of detection of 0.37 fg⋅mL-1, and 1 to 250 ng⋅mL-1 in the visualization mode with the limit of detection of 0.51 ng⋅mL-1. This portable dual-mode sensor chip can be used in both laboratory and field settings without the need for specialized instruments, making it a powerful tool for ensuring food safety. At the same time, the analysis of the standard addition method of the actual sample by using the sensor chip shows that, in the PEC mode, the recoveries of the dual-mode aptasensor chip were 91.3 to 99.0% with RSD values of 1.73~2.55%, and in visualization mode, the recoveries of the dual-mode aptasensor chip were 99.2 to 102.0% with RSD values of 1.00~6.21%, which indicate good accuracy and reproducibility.

Whole-genome sequencing analysis in fetal structural anomalies: novel phenotype-genotype discoveries

OBJECTIVES

The identification of structural variants and single-nucleotide variants is essential in finding molecular etiologies of monogenic genetic disorders. Whole-genome sequencing (WGS) is becoming more widespread in genetic disease diagnosis. However, data on its clinical utility remain limited in prenatal practice. We aimed to expand our understanding of implementing WGS in the genetic diagnosis of fetal structural anomalies.

METHODS

We employed trio WGS with a minimum coverage of 40× on the MGI DNBSEQ-T7 platform in a cohort of 17 fetuses presenting with aberrations detected by ultrasound, but uninformative findings of standard chromosomal microarray analysis (CMA) and exome sequencing (ES).

RESULTS

Causative genetic variants were identified in two families, with an increased diagnostic yield of 11.8% (2/17). Both were exon-level copy-number variants of small size (3.03 kb and 5.16 kb) and beyond the detection thresholds of CMA and ES. Moreover, to the best of our knowledge, we have described the first prenatal instance of the association of FGF8 with holoprosencephaly and facial deformities.

CONCLUSIONS

Our analysis demonstrates the clinical value of WGS in the diagnosis of the underlying etiology of fetuses with structural abnormalities, where routine genetic tests have failed to diagnose. Additionally, the novel variants and new fetal manifestations have expanded the mutational and phenotypic spectrums of BBS9 and FGF8. © 2023 International Society of Ultrasound in Obstetrics and Gynecology.

Quantifying dynamic pro-inflammatory gene expression and heterogeneity in single macrophage cells

Macrophages must respond appropriately to pathogens and other pro-inflammatory stimuli in order to perform their roles in fighting infection. One way in which inflammatory stimuli can vary is in their dynamics-that is, the amplitude and duration of stimulus experienced by the cell. In this study, we performed long-term live cell imaging in a microfluidic device to investigate how the pro-inflammatory genes IRF1, CXCL10, and CXCL9 respond to dynamic interferon-gamma (IFNγ) stimulation. We found that IRF1 responds to low concentration or short duration IFNγ stimulation, whereas CXCL10 and CXCL9 require longer or higherconcentration stimulation to be expressed. We also investigated the heterogeneity in the expression of each gene and found that CXCL10 and CXCL9 have substantial cell-to-cell variability. In particular, the expression of CXCL10 appears to be largely stochastic with a subpopulation of nonresponding cells across all the stimulation conditions tested. We developed both deterministic and stochastic models for the expression of each gene. Our modeling analysis revealed that the heterogeneity in CXCL10 can be attributed to a slow chromatin-opening step that is on a similar timescale to that of adaptation of the upstream signal. In this way, CXCL10 expression in individual cells can remain stochastic in response to each pulse of repeated stimulation, which we also validated by experiments. Together, we conclude that pro-inflammatory genes in the same signaling pathway can respond to dynamic IFNγ stimulus with very different response features and that upstream signal adaptation can contribute to shaping heterogeneous gene expression.

Fabrication of Microfluidic Devices for Continuously Monitoring Yeast Aging

For several decades, aging in Saccharomyces cerevisiae has been studied in hopes of understanding its causes and identifying conserved pathways that also drive aging in multicellular eukaryotes. While the short lifespan and unicellular nature of budding yeast has allowed its aging process to be observed by dissecting mother cells away from daughter cells under a microscope, this technique does not allow continuous, high-resolution, and high-throughput studies to be performed. Here, we present a protocol for constructing microfluidic devices for studying yeast aging that are free from these limitations. Our approach uses multilayer photolithography and soft lithography with polydimethylsiloxane (PDMS) to construct microfluidic devices with distinct single-cell trapping regions as well as channels for supplying media and removing recently born daughter cells. By doing so, aging yeast cells can be imaged at scale for the entirety of their lifespans, and the dynamics of molecular processes within single cells can be simultaneously tracked using fluorescence microscopy. Key features This protocol requires access to a photolithography lab in a cleanroom facility. Photolithography process for patterning photoresist on silicon wafers with multiple different feature heights. Soft lithography process for making PDMS microfluidic devices from silicon wafer templates.

Enhanced cellular longevity arising from environmental fluctuations

Cellular longevity is regulated by both genetic and environmental factors. However, the interactions of these factors in the context of aging remain largely unclear. Here, we formulate a mathematical model for dynamic glucose modulation of a core gene circuit in yeast aging, which not only guided the design of pro-longevity interventions, but also revealed the theoretical principles underlying these interventions. We introduce the dynamical systems theory to capture two general means for promoting longevity - the creation of a stable fixed point in the "healthy" state of the cell and the dynamic stabilization of the system around this healthy state through environmental oscillations. Guided by the model, we investigate how both of these can be experimentally realized by dynamically modulating environmental glucose levels. The results establish a paradigm for theoretically analyzing the trajectories and perturbations of aging that can be generalized to aging processes in diverse cell types and organisms.

When push comes to shove - RNA polymerase and DNA-bound protein roadblocks

In recent years, transcriptional roadblocking has emerged as a crucial regulatory mechanism in gene expression, whereby other DNA-bound obstacles can block the progression of transcribing RNA polymerase (RNAP), leading to RNAP pausing and ultimately dissociation from the DNA template. In this review, we discuss the mechanisms by which transcriptional roadblocks can impede RNAP progression, as well as how RNAP can overcome these obstacles to continue transcription. We examine different DNA-binding proteins involved in transcriptional roadblocking and their biophysical properties that determine their effectiveness in blocking RNAP progression. The catalytically dead CRISPR-Cas (dCas) protein is used as an example of an engineered programmable roadblock, and the current literature in understanding the polarity of dCas roadblocking is also discussed. Finally, we delve into a stochastic model of transcriptional roadblocking and highlight the importance of transcription factor binding kinetics and its resistance to dislodgement by an elongating RNAP in determining the strength of a roadblock.

Incidence and Predictive Model of Medical Adhesive-Related Skin Injury in Cancer Patients Managed With Central Venous Access Devices: A Retrospective Study

PURPOSE

The purpose of this study was to determine the prevalence of medical adhesive-related skin injury (MARSI) at the site of central venous access device (CVAD) implantation in patients with cancer, identify risk factors associated with MARSI in patients with cancer, and create a nomogram for predicting risk of MARSI.

DESIGN

Retrospective, single-center study.

SUBJECTS AND SETTING

The sample comprised 1172 consecutive patients who underwent CVAD implantation between February 2018 and February 2019; their mean age was 55.7 years (SD: 13.9). Data were collected at the First Affiliated Hospital of Xi'an Jiaotong University, located in Xi'an, China.

METHODS

Demographic and pertinent clinical data were collected from patient records. Routine dressing changes were performed every 7 days for peripherally inserted central venous catheters (PICCs) or 28 days for ports except in patients with existing skin injuries. Skin injuries related to use of medical adhesives and persisting for more than for 30 minutes were classified MARSI. Data were used to develop a nomogram for predicting MARSI. The accuracy of the nomogram was verified by calculating the concordance index (C-index) and drawing a calibration curve.

RESULTS

Among the 1172 patients, 330 (28.2%) had undergone PICC implantation, and 282 (24.1%) experienced 1 or more MARSIs representing an incidence rate of 1.7 events per 1000 CVAD days. Statistical analysis identified previous MARSI history, the need for total parenteral nutrition support, other catheter-related complications, a history of allergy, and PICC implantation as associated with a higher likelihood of developing for MARSI. Based on these factors, we established a nomogram for predicting the risk of developing MARSI in patients with cancer who underwent CVAD implantation. The C-index of the nomogram was 0.96, and the calibration curve of the nomogram showed that the predictive ability of the nomogram was strong.

CONCLUSIONS

We evaluated patients with cancer who were undergoing CVAD and identified that previous MARSI history, patients needing total parenteral nutrition support, other catheter-related complications, allergic history, and PICC implantation (compared with ports) were associated with a higher likelihood for developing MARSI. The nomogram we developed showed a good ability for predicting the risk of developing MARSI and may assist nurses to predict MARSI in this population.

Engineering longevity-design of a synthetic gene oscillator to slow cellular aging

Synthetic biology enables the design of gene networks to confer specific biological functions, yet it remains a challenge to rationally engineer a biological trait as complex as longevity. A naturally occurring toggle switch underlies fate decisions toward either nucleolar or mitochondrial decline during the aging of yeast cells. We rewired this endogenous toggle to engineer an autonomous genetic clock that generates sustained oscillations between the nucleolar and mitochondrial aging processes in individual cells. These oscillations increased cellular life span through the delay of the commitment to aging that resulted from either the loss of chromatin silencing or the depletion of heme. Our results establish a connection between gene network architecture and cellular longevity that could lead to rationally designed gene circuits that slow aging.

Rapid quality assessment of Gentianae Macrophyllae Radix based on near infrared spectroscopy and capillary electrophoresis

The aim of this study was to establish a rapid quality assessment method for Gentianae Macrophyllae Radix (RGM) using near infrared (NIR) spectra combined with chemometric analysis. The NIR spectra were acquired using an integrating sphere diffuse reflectance module, using air as the reference. Capillary electrophoresis (CE) analyses were performed on a model P/ACE MDQ Plus system. Partial least squares-discriminant analysis qualitative model was developed to distinguish different species of RGM samples, and the prediction accuracy for all samples was 91%. The CE response values at each retention time were predicted by building a partial least squares regression (PLSR) calibration model with the CE data set as the Y matrix and the NIR spectra data set as the X matrix. The converted CE fingerprints basically match the real ones, and the six main peaks can be accurately predicted. Transforming NIR spectra fingerprints into the form of CE fingerprints increases its interpretability and more intuitively demonstrates the components that cause diversity among samples of different species and origins. Loganic acid, gentiopicroside and roburic acid were considered as quality indicators of RGM and calibration models were built using PLSR algorithm. The developed models gave root mean square error of prediction of 0.2592% for loganic acid, 0.5341% for gentiopicroside and 0.0846% for roburic acid. The overall results demonstrate that the rapid quality assessment system can be used for quality control of RGM. This article is protected by copyright. All rights reserved.

Immunomodulation: The next target of mesenchymal stem cell-derived exosomes in the context of ischemic stroke

Ischemic stroke (IS) is the most prevalent form of brain disease, characterized by high morbidity, disability, and mortality. However, there is still a lack of ideal prevention and treatment measures in clinical practice. Notably, the transplantation therapy of mesenchymal stem cells (MSCs) has been a hot research topic in stroke. Nevertheless, there are risks associated with this cell therapy, including tumor formation, coagulation dysfunction, and vascular occlusion. Also, a growing number of studies suggest that the therapeutic effect after transplantation of MSCs is mainly attributed to MSC-derived exosomes (MSC-Exos). And this cell-free mediated therapy appears to circumvent many risks and difficulties when compared to cell therapy, and it may be the most promising new strategy for treating stroke as stem cell replacement therapy. Studies suggest that suppressing inflammation via modulation of the immune response is an additional treatment option for IS. Intriguingly, MSC-Exos mediates the inflammatory immune response following IS by modulating the central nervous system, the peripheral immune system, and immunomodulatory molecules, thereby promoting neurofunctional recovery after stroke. Thus, this paper reviews the role, potential mechanisms, and therapeutic potential of MSC-Exos in post-IS inflammation in order to identify new research targets.

Laser-induced breakdown spectroscopy (LIBS) for the detection of exogenous contamination of metal elements in lily bulbs

Natural products with the underground edible part have the risk of excessive heavy metals due to the influence of the growing environment. In this study, the content of five metal elements in lily bulbs was detected by laser-induced breakdown spectroscopy (LIBS). In view of the mutual interference among elements, multivariable analysis models were established to effectively eliminate the interference. The partial least squares regression (PLSR) multivariate analysis model was evaluated by combining different data preprocessing with variable selection methods to achieve the best fit. The results show that the best regression model for Cu, Pb, Zn, Al, and Mg content achieved the coefficients determination of prediction (R_p²) values of 0.9920, 0.9737, 0.9835, 0.9723 and 0.9939, respectively, and root mean square error of prediction (RMSEP) values of 3.2386 mg/kg, 5.8559 mg/kg, 4.6334 mg/kg, 6.0073 mg/kg and 2.8103 mg/kg, respectively. Comprehensively comparing the accuracy, robustness, and number of variables of each model, it can be found that the PLSR model on the least absolute shrinkage and selection operator (LASSO) achieved good results in the quantitative prediction model of three kinds of metal elements. This indicates the superiority of the LASSO-PLSR algorithm framework and confirms the feasibility of LIBS technology for the detection of various metal elements in natural products.

Visual Electrochemiluminescence Biosensor Chip Based on Distance Readout for Deoxynivalenol Detection

Visual electrochemiluminescence (ECL) biosensors do not need complex instruments or well-trained operators, which is regarded as an ideal choice for portable and low-cost detection. But traditional visual ECL biosensors are based on the change in ECL intensity, which is easily affected by environmental factors and signal acquisition processes. In this work, a visual ECL biosensor chip based on distance readout has been developed for the first time. The chip is composed of a square detection region and a visual channel region, which are modified with graphene oxide (GO) and gold nanoparticles (AuNPs)@Ti₃C₂ nanocomposites, respectively. Target molecules can release aptamers adsorbed on the GO surface of the detection region and further change the electrode potential of the visual channel region, which can determine the length of the long channel that generates visible ECL signals. The application of AuNPs@Ti₃C₂ nanocomposites can effectively enhance ECL intensity by six times. Through the unique design of the sensor chip, quantification detection can be achieved based on the length change instead of the traditional intensity change. This visual ECL sensor is successfully applied for deoxynivalenol toxin detection in actual samples, demonstrating that the introduction of the distance readout strategy into ECL sensing has a good prospect in on-site testing.

XTP1 facilitates the growth and development of gastric cancer by activating CDK6

Background

Hepatitis B virus X protein (XTP1) is overexpressed in tumor tissues and regulates cancer progression. However, the molecular mechanism of XTP1 in gastric cancer (GC) is poorly understood. Hence, we aimed to dissect the underlying role of XTP1 in the development of GC.

Methods

Lentiviruses were constructed and transfected into GC cells to upregulate or downregulate gene expression. The expressions of proteins in GC cells or tumor tissues were assessed by quantitative reverse transcription polymerase chain reaction (RT-qPCR), Western blotting, immunohistochemistry (IHC) assay, or the Gene Expression Profiling Interactive Analysis (GEPIA) database. Cell proliferation was assessed via methylthiazolyldiphenyl-tetrazolium bromide (MTT) assay, Celigo cell counting assay, cell cycle analysis, and colony formation assay. Cell apoptosis was assessed by flow cytometry. The apoptosis-related proteins were evaluated using the human apoptosis antibody array. GC cell migration was detected by scratch wound-healing assays and Transwell migration assays. Potential downstream molecules were identified by the human GeneChip assay combined with bioinformatics analysis.

Results

We found that XTP1 is overexpressed in GC tissues and is positively related to its pathological grade. XTP1 knockdown restrained the growth and migration of GC cells, while XTP1 overexpression promoted cell proliferation and suppressed apoptosis. A mechanistic study indicated that XTP1 knockdown inhibited cyclin-dependent kinase 6 (CDK6) expression and that CDK6 might be a potential downstream molecule of XTP1. Further study confirmed that CDK6 depletion also suppressed GC cell proliferation and migration and increased GC cell apoptosis. Moreover, rescue experiments verified that CDK6 knockdown abated the promotion of XTP1 overexpression on GC progression.

Conclusions

XTP1 facilitated the development and progression of GC cells by activating CDK6. Therefore, the XTP1-CDK6 axis might be a potential therapeutic target for GC.

Identification of azukisapogenol triterpenoid saponins from Oxytropis hirta Bunge and their aphicidal activities against pea aphid Acyrthosiphon pisum Harris

BACKGROUND

Acyrthosiphon pisum Harris is the most destructive pest worldwide because of its ability to feed on plants directly and transmit plant viruses as a vector. This study aims to identify triterpenoid saponins from Oxytropis hirta Bunge as biopesticides to control aphids.

RESULTS

Three new azukisapogenol triterpenoid saponins (1-3), a new pinoresinol lignan glycoside (8), and four known saponins (4-7) were identified from the root of O. hirta. Compounds 4-7 displayed significant aphicidal activities against A. pisum with oral toxicities (LC₅₀  = 51.10-147.43 μg/mL, 72 h), deterrent effects (deterrence index = 1.00, 100-200 μg/mL, 24 h), and aphid reproduction inhibitory effects (inhibition rates = 75.91-86.73%, 400 μg/mL, 24 h), respectively. The carboxyl groups at C-3 GlcA and C-30 were functional groups for their aphicidal activities. The toxic symptoms caused by the optimal 5 involved insect body-color changes from light green to dark or gray-green, and then brown until death. The intestinal cavity, apical microvilli, nuclei, mitochondria, and electron dense granules in the midgut tissues of A. pisum were the target sites showing aphicidal activity. The suppression of pepsin and α-amylase, and the activation of lipase and trypsin could be the signs of organelle damage in the midgut tissues.

CONCLUSION

Azukisapogenol triterpenoid saponins from O. hirta could be used as biopesticides to control aphids for their multiple efficacies, including oral toxicity, deterrent activity, and reproduction inhibitory activity. The toxic symptoms involved insect body-color changes. Midgut tissues and their related enzymes were the targets for saponins showing aphicidal activities. © 2022 Society of Chemical Industry.

3D printing a biocompatible elastomer for modeling muscle regeneration after volumetric muscle loss

Volumetric muscle loss (VML) injuries due to trauma, tumor ablation, or other degenerative muscle diseases are debilitating and currently have limited options for self-repair. Advancements in 3D printing allow for the rapid fabrication of biocompatible scaffolds with designer patterns. However, the materials chosen are often stiff or brittle, which is not optimal for muscle tissue engineering. This study utilized a photopolymerizable biocompatible elastomer - poly (glycerol sebacate) acrylate (PGSA) - to develop an in vitro model of muscle regeneration and proliferation into an acellular scaffold after VML injury. Mechanical properties of the scaffold were tuned by controlling light intensity during the 3D printing process to match the specific tension of skeletal muscle. The effect of both geometric (channel sizes between 300 and 600 μm) and biologic (decellularized muscle extracellular matrix (dECM)) cues on muscle progenitor cell infiltration, proliferation, organization, and maturation was evaluated in vitro using a near-infrared fluorescent protein (iRFP) transfected cell line to assess cells in the 3D scaffold. Larger channel sizes and dECM coating were found to enhance cell proliferation and maturation, while no discernable effect on cell alignment was observed. In addition, a pilot experiment was carried out to evaluate the regenerative capacity of this scaffold in vivo after a VML injury. Overall, this platform demonstrates a simple model to study muscle progenitor recruitment and differentiation into acellular scaffolds after VML repair.

Quantitative cell imaging approaches to metastatic state profiling

Genetic heterogeneity of metastatic dissemination has proven challenging to identify exploitable markers of metastasis; this bottom-up approach has caused a stalemate between advances in metastasis and the late stage of the disease. Advancements in quantitative cellular imaging have allowed the detection of morphological phenotype changes specific to metastasis, the morphological changes connected to the underlying complex signaling pathways, and a robust readout of metastatic cell state. This review focuses on the recent machine and deep learning developments to gain detailed information about the metastatic cell state using light microscopy. We describe the latest studies using quantitative cell imaging approaches to identify cell appearance-based metastatic patterns. We discuss how quantitative cancer biologists can use these frameworks to work backward toward exploitable hidden drivers in the metastatic cascade and pioneering new Frontier drug discoveries specific for metastasis.

Age-dependent aggregation of ribosomal RNA-binding proteins links deterioration in chromatin stability with challenges to proteostasis

Chromatin instability and protein homeostasis (proteostasis) stress are two well-established hallmarks of aging, which have been considered largely independent of each other. Using microfluidics and single-cell imaging approaches, we observed that, during the replicative aging of Saccharomyces cerevisiae, a challenge to proteostasis occurs specifically in the fraction of cells with decreased stability within the ribosomal DNA (rDNA). A screen of 170 yeast RNA-binding proteins identified ribosomal RNA (rRNA)-binding proteins as the most enriched group that aggregate upon a decrease in rDNA stability induced by inhibition of a conserved lysine deacetylase Sir2. Further, loss of rDNA stability induces age-dependent aggregation of rRNA-binding proteins through aberrant overproduction of rRNAs. These aggregates contribute to age-induced proteostasis decline and limit cellular lifespan. Our findings reveal a mechanism underlying the interconnection between chromatin instability and proteostasis stress and highlight the importance of cell-to-cell variability in aging processes.

Effect of AKT silence on malignant biological behavior of renal cell carcinoma cells

BACKGROUND

As the most common malignant tumor of primary renal tumor, renal cell carcinoma (RCC) is the highly invasive disease with high mortality. AKT is a serine/threonine kinase that play a critical role in the phosphoinositide 3-kinase (PI3K) signaling pathway, and it is an attractive target for RCC treatment. The aim of present study was to investigate the effect of AKT silence on malignant behavior of renal cell carcinoma cells.

METHODS

AKT expression was quantified by immunohistochemistry in tumor tissues and normal tissues. The human RCC cell lines Caki-2 cell were chosen for this study. The optimal silencing siRNA was subsequently selected by RT-qPCR and western blot. The effect of AKT silence on RCC cells was investigated by CCK8 assay, transwell assay, scratch test and flow cytometry. The AKT1 expression in human renal cell carcinoma tissue was detected by immunohistochemical staining.

RESULTS

The AKT in Caki-2 cells was silenced successfully. The results shown AKT silence could inhibit cell proliferation, invasion, and, migration. In addition, AKT silence could promote Caki-2 cell apoptosis with prevention of RCC cells move from G1 phase to S phase. Immunohistochemical staining revealed significant difference of expression of AKT1 in RCC tissues and normal renal tissues. Taken together, AKT family members might involve in malignant growth of RCC, and might be a potential therapeutic target.

CONCLUSION

Our data show that AKT silence inhibited cell proliferation, invasion, and, migration of Caki-2 cell, and promoted Caki-2 cell apoptosis. Moreover, AKT silence prevented RCC cells move from G1 phase to S phase. Therefore, AKT may act as an effective therapeutic target for RCC.

Enhanced cathodic electrochemiluminescent microcystin-LR aptasensor based on surface plasmon resonance of Bi nanoparticles

Sensitive testing for Microcystins-LR (MC-LR) is needed because of its serious environmental and human health hazards. In this work, a new type of surface plasmon resonance (SPR) enhanced cathodic electrochemiluminescence (ECL) aptasensing platform was designed in which boron and nitrogen co-doped graphene quantum dots (BN-GQDs) were used as the luminary and bismuth nanoparticles (Bi NPs) were used as the SPR source. SPR effect of non-precious metal Bi NPs can induce and enhance ECL signal of BN-GQDs because the fluorescence spectrum of BN-GQDs overlaps well with the ultraviolet-visible absorption spectrum of Bi NPs. On this basis, a sensitive sensing system based on the Bi NPs and BN-GQDs was established for MC-LR detection. The results showed that the ECL sensing signal obtained was linear with the negative logarithm of the target MC-LR concentration in the range of 0.01-5000 pM, and the detection limit was 0.003 pM. In addition, the sensor had high stability and good reproducibility, which can be applied to the detection of MC-LR in actual samples. The method had good specificity and can not be disturbed by its homolog, which can be used for sensitive and reliable detection of complex samples.

A complex systems approach to aging biology

Having made substantial progress understanding molecules, cells, genes and pathways, aging biology research is now moving toward integration of these parts, attempting to understand how their joint dynamics may contribute to aging. Such a shift of perspective requires the adoption of a formal complex systems framework, a transition being facilitated by large-scale data collection and new analytical tools. Here, we provide a theoretical framework to orient researchers around key concepts for this transition, notably emergence, interaction networks and resilience. Drawing on evolutionary theory, network theory and principles of homeostasis, we propose that organismal function is accomplished by the integration of regulatory mechanisms at multiple hierarchical scales, and that the disruption of this ensemble causes the phenotypic and functional manifestations of aging. We present key examples at scales ranging from sub-organismal biology to clinical geriatrics, outlining how this approach can potentially enrich our understanding of aging.

[Corrigendum] Screening of hub genes and evaluation of the growth regulatory role of CD44 in metastatic prostate cancer

Subsequently to the publication of the above article, the authors have realized that they inadvertently included images of the same mice in Figs. 7A [the Negative Control (NC) experiment] and 8A [the 5B‑3CT + Docetaxel (10 mg/kg) experiment]. After having consulted their original data, the authors have realized that these mice were correctly shown in the paper for the experiments portrayed in Fig. 7A; therefore, the corrected version of Fig. 8 is shown on the next page, showing the mice pertaining to the 5B‑3CT + Docetaxel (10 mg/kg) experiment in Fig. 8A. The authors are grateful to the Editor of Oncology Reports for allowing them the opportunity to publish a Corrigendum, and all the authors agree to this Corrigendum. Furthermore, they apologize to the readership for any inconvenience caused. [Oncology Reports 46: 196, 2021; DOI: 10.3892/or.2021.8147].

Laminin-integrin a6b4 interaction activates notch signaling to facilitate bladder cancer development

Background

Laminins are high-molecular weight (400 ~ 900 kDa) proteins in extracellular matrix, which serve as major component of the basal lamina, and play a crucial role in promoting tumor cell migration. This study aimed at characterizing the role of laminin in promoting cancer development, and elucidating the mechanism of tumor progression driven by laminin-Notch signaling in bladder cancer.

Methods

2D collagen/laminin culture system was established and CCK-8/transwell assay was conducted to evaluate the proliferation/migration ability of Biu-87 and MB49 cells cultured on 2D gels. Activation of integrins-Notch1 signaling was determined by western blotting. Orthotopic bladder cancer mice model was established to assess the therapeutic effects of Notch inhibitor.

Results

Our study demonstrated that extracellular laminin can trigger tumor cell proliferation/migration through integrin α6β4/Notch1 signaling in bladder cancer. Inhibition of Telomere repeat-binding factor 3 (TRB3)/Jagged Canonical Notch Ligand 1 (JAG1) signaling suppressed Notch signals activation induced by laminin-integrin axis. In MB49 orthotopic bladder cancer mice model, Notch inhibitor SAHM1 efficiently improved tumor suppressive effects of chemotherapy and prolonged survival time of tumor-bearing mice.

Conclusion

In conclusion, we show that, in bladder cancer, extracellular laminin induced the activation of Notch pathway through integrin α6β4/TRB3/JAG3, and disclosed a novel role of laminin in bladder cancer cells proliferation or migration.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-022-09645-7.

Effect of Ultrasonic Induction on the Main Physiological and Biochemical Indicators and γ–Aminobutyric Acid Content of Maize during Germination

Research on the nutrient content of cereal grains during germination is becoming a hot topic; however, studies on germinated maize are still scarce. This study aimed to provide a technical reference and theoretical basis for the development of functional maize health foods and to expand the application of ultrasonic technology in the production of germinated grains. In this study, the germination rate of maize was used as the evaluation index, and the ultrasonic frequency, ultrasonic temperature, and induction time were selected as the influencing factors in orthogonal experiments to determine the optimal process parameters for ultrasonic induction of maize germination (ultrasonic frequency of 45 kHz, ultrasonic temperature of 30 °C, and ultrasonic induction time of 30 min). Based on this process, the effects of ultrasonic induction on the main physiological, biochemical, and γ–aminobutyric acid contents of maize during germination were investigated. The results showed that the respiration of the ultrasonic treated maize was significantly enhanced during germination, resulting in a 27% increase in sprout length, as well as a 4.03% higher dry matter consumption rate, and a 2.11% higher starch consumption rate. Furthermore, the reducing sugar content of germinated maize increased by 22.83%, soluble protein content increased by 22.52%, and γ–aminobutyric acid content increased by 30.55% after ultrasonic induction treatment. Throughout the germination process, the glutamate acid decarboxylase activity of the ultrasonically treated maize was higher than that of the control group, indicating that ultrasonication can promote maize germination, accelerate the germination process, and shorten the enrichment time of γ–aminobutyric acid in germinated maize. The results of this study can be applied to the production of γ–aminobutyric acid enrichment in germinated maize.

[Efficacy and initial clinical evaluation of optical genome mapping in the diagnosis of structural variations]

To investigate the efficacy and value of optical genome mapping (OGM) in detecting chromosomal structural variations. In a clinical study about high-precision analysis of genomic structural variation for complex genetic diseases, a retrospective study was performed on the cases with karyotyping at the department of Obstetrics and Gynecology, and Endocrinology of Peking Union Medical College Hospital from January to December 2021. Ten cases with abnormal karyotype was detected by OGM. Partial cases were verified by fluorescence in situ hybridization (FISH), SNP array or CNV-seq. Results of ten cases, nine were detected with abnormality by OGM, including unbalanced chromosomal rearrangements (n=3), translocation (n=5) and paracentric inversion (n=1), and the results were in concordance with other standard assays. However, one case with breakpoint and reconnected at centromere has not been detected. In conclusion, ten samples were comprehensively analyzed by karyotyping, FISH, SNP array or CNV-seq, and OGM, and results demonstrated that optical genome mapping as a new technology can not only detect unbalanced rearrangements such as copy number variants as well as balanced translocations and inversions, but more importantly, it can refine breakpoints and orientation of duplicated segments or insertions. So it can contribute to the diagnosis of genetic diseases and prevent birth defect. However, the current technology is not yet capable of detecting breakpoints of balanced structural variations lying within unmapped regions.

Hierarchical Regulation of LaMnO3 Dual-Pathway Strategy for Excellent Room-Temperature Organocatalytic Oxidation Performance

The performance-enhancing strategy of a single pathway for perovskite has been widely studied. In this work, the dual-pathway strategy of A-site Ce substitution and nitric acid selective dissolution was proposed. The catalytic oxidation performance of LaMnO₃ exhibits the characteristic of hierarchical regulation, that is, a steplike improvement, which avoids the limitation of performance improvement of the single pathway. The B-site Mn with catalytic activity was in situ reconstituted on the surface to build a Mn-rich surface. The obtained sdLa_0.7Ce_0.3MnO₃ has the advantages of good oxygen mobility, high Mn⁴⁺/Mn³⁺ molar ratio, and large specific surface area, and this material showed excellent catalytic oxidation performance for organics, which can realize colorimetric chemical oxygen demand detection at room temperature. Here, Ce substitution improved the oxidation capacity by improving the oxygen mobility and the ratio of Mn⁴⁺/Mn³⁺, and further nitric acid treatment not only accelerated the in situ reconstruction of B-site Mn but also increased the specific surface area.

Simulation design of natural enzyme binding pocket structure in MOFs for enhanced catalytic activity

This study confirms the activity gap between MOFs (Fe) and horseradish peroxidase can be bridged by simulating the binding pocket structure and adding active center. The customized structure promoted the...

TdIF1-LSD1 Axis Regulates Epithelial-Mesenchymal Transition and Metastasis via Histone Demethylation of E-Cadherin Promoter in Lung Cancer

We have previously found that TdT-interacting factor 1 (TdIF1) is a potential oncogene expressed in non-small cell lung cancer (NSCLC) and is associated with poor prognosis. However, its exact mechanism is still unclear. The lysine-specific demethylase 1 (LSD1) is a crucial mediator of the epithelial-mesenchymal transition (EMT), an important process triggered during cancer metastasis. Here, we confirm that TdIF1 is highly expressed in NSCLC and related to lymph node metastasis through The Cancer Genome Atlas (TCGA) analysis of clinical samples. Silencing TdIF1 can regulate the expression of EMT-related factors and impair the migration and invasion ability of cancer cells in vitro. An analysis of tumor xenografts in nude mice confirmed that silencing TdIF1 inhibits tumor growth. Furthermore, we determined the interaction between TdIF1 and LSD1 using immunoprecipitation. Chromatin immunoprecipitation (ChIP) revealed that TdIF1 was enriched in the E-cadherin promoter region. The knockdown of TdIF1 repressed the enrichment of LSD1 at the E-cadherin promoter region, thereby regulating the level of promoter histone methylation and modulating E-cadherin transcription activity, ultimately leading to changes in EMT factors and cancer cell migration and invasion ability. The LSD1 inhibitor and TdIF1 knockdown combination showed a synergistic effect in inhibiting the growth, migration, and invasion of NSCLC cells. Taken together, this is the first demonstration that TdIF1 regulates E-cadherin transcription by recruiting LSD1 to the promoter region, thereby promoting EMT and tumor metastasis and highlighting the potential of TdIF1 as a therapeutic target for NSCLC.

An upgraded 2D nanosheet-based FRET biosensor: insights into avoiding background and eliminating effects of background fluctuations

We demonstrated a new class of 2D nanosheet-based FRET biosensor utilizing vertically oriented MoS₂ nanosheets on a magnetic nanocarrier. Compared with the non-separated biosensor under identical conditions, this upgraded one can avoid the background signal of the system and eliminate the effects of background fluctuations, which produces more excellent detection methods.

High level of TXNDC9 predicts poor prognosis and contributes to the NF-κB-regulated metastatic potential in gastric cancer

Gastric cancer (GC) is the most frequent malignant tumor in the digestive system, with high metastasis potential and poor prognosis. This study aimed to investigate the prognostic value and biological function of thioredoxin domain-containing protein 9 (TXNDC9) in GC. The expression of TXNDC9 was analyzed based on The Cancer Genome Atlas (TCGA) database. The prognostic value of TXNDC9 was evaluated by Kaplan-Meier curves and Cox regression analysis. The mRNA and protein expression of TXNDC9 were analyzed using quantitative real-time PCR and western blot analysis. The effects of TXNDC9 on GC cell invasion and EMT were assessed in vitro, and its effects on tumorigenesis were confirmed using animal experiments. The activity of the NF-κB signaling pathway was examined by both in vitro and in vivo experiments. TXNDC9 was highly expressed in GC tissues and cell lines. A high level of TXNDC9 was associated with poor overall survival and served as an independent prognostic biomarker in GC patients. The knockdown of TXNDC9 led to restrained GC cell invasion, microtubule formation, and EMT in vitro, and suppressed tumorigenesis in vivo. In addition, the NF-κB signaling pathway was demonstrated to mediate the functional role of TXNDC9 in GC. In conclusion, this study found that high TXNDC9 predicted poor prognosis in GC, and served as an oncogene by enhancing tumor cell invasion and EMT through the NF-κB signaling pathway.

Terbutaline attenuates LPS-induced injury of pulmonary microvascular endothelial cells by cAMP/Epac signaling

Acute lung injury (ALI), characterized by an acute onset of severe hypoxemia, is a common and devastating syndrome usually triggered by lipopolysaccharide (LPS) infection from bacteria. This study is intended to explore whether terbutaline can alleviate LPS-induced human pulmonary microvascular endothelial cell (HPMVEC) injury through cAMP/Epac signaling. LPS was utilized to induce ALI in HPMVECs, and after exposure of LPS-induced HPMVECs to terbutaline, the cellular functions including cell viability and apoptosis were measured by cell counting kit-8 and terminal deoxynucleotidyl transferase dUTP nick-end labeling. The protein expression related to cAMP/Epac signaling, apoptosis, and that of tight junction and inflammatory factors were evaluated at the same time. The effects of terbutaline on cellular functions were confirmed again after the addition of antagonists of cAMP and Epac, respectively. The levels of both cAMP and Epac reduced by LPS was concentration-dependently increased by terbutaline. The apoptosis and endothelial cell permeability damage of LPS-induced HPMVECs were enhanced after the addition of KT-5720 and ESI-09. The beneficial effects of terbutaline on alleviating the inflammation and apoptosis in HPMVECs injured by LPS are mediated by cAMP/Epac signaling, and this evidence would demonstrate the potential of terbutaline in the treatment of ALI.

Identification of anti-TMV active flavonoid glycosides and their mode of action on virus particles from Clematis lasiandra Maxim

BACKGROUND

Tobacco mosaic virus (TMV) is a disreputable plant pathogen that causes a decline in the quality and yield of various economic crops. Natural products are important potential sources of biopesticides to control TMV. This study focuses on the discovery of anti-TMV active flavonoid glycosides and their mode of action on TMV particles from Clematis lasiandra Maxim.

RESULTS

A new benzoyl acylated flavonoid glycoside, kaempferol 3-O-(2''-benzoyl)-β-d-glucopyranosyl-7-O-α-l-rhamnopyranoside (1), and nine known flavonoids (2-10) were identified first from C. lasiandra. The hydroxyl group at C-7, E-p-coumarate at C-6'' in the Glc of C-6, and the glucuronic acid at C-3 were functional groups for the antiviral flavonoid glycosides. Flavonoids 2, 5, and 6 showed higher inactivation efficacies of 64.62% to 82.54% compared with ningnanmycin at 500 μg ml^-1 . The protective and curative efficacies for 2 and 5 were 57.44-59.00% and 41.17-43.92% at 500 μg ml^-1 , respectively. Compound 5 showed higher TMV systemic resistance with control efficacies of 41.64%, 36.56% and 27.62% at concentrations of 500, 250 and 125 μg ml^-1 compared with ningnanmycin in K326 tobaccos, respectively. Compound 5 can directly fracture TMV particles into small fragments combining with the fusion phenomena, and TMV-CP was an important target for 5 to break TMV particles.

CONCLUSION

Flavonoid glycosides from C. lasiandra showed potent antiviral activities against TMV with multiple modes of action including inactivation, protective and curative effects, and inducing systemic resistance. TMV-CP was an important target for active flavonoid glycosides to fracture TMV particles. The results provided evidence that flavonoid glycosides from C. lasiandra have the potential to control TMV.

High-Throughput Detection of Multiple Contaminants Based on Portable Photoelectrochromic Sensor Chip

With the increasing concerns about the environment and food safety, it is necessary to develop portable, low-cost, and high-throughput biosensors for the simultaneous detection of multiple contaminates. However, traditional photoelectrochemical (PEC) biosensors lack the ability of multiplexed assays due to the inherent mechanism limitation. Also, specialized instruments are necessary for most PEC biosensors. In this work, a portable high-throughput sensor chip has been successfully developed. By introducing electrochromic materials, the detection is based on color change instead of electric signals, which reduces the limitation of instruments. This designed sensor chip is composed of three parallel sensing channels fabricated by laser etching. Each channel is modified with TiO₂/3D-g-C₃N₄ composites with excellent PEC activity and electrochromic material Prussian blue (PB). Under light illumination, photoinduced electrons generated by TiO₂/3D-g-C₃N₄ are injected into PB, and blue PB is reduced to colorless Prussian white. Three organic contaminates, ochratoxin A, lincomycin, and edifenphos, can be simultaneously detected because the binding of these molecules with aptamers affects the electron transfer and the corresponding color changes. This portable and high-throughput sensor chip provides a convenient choice for multiplexed assays with good sensitivity and accuracy.

Prospective evaluation of first-trimester screening strategy for preterm pre-eclampsia and its clinical applicability in China

OBJECTIVES

To evaluate, in a Chinese population, the performance of a screening strategy for preterm pre-eclampsia (PE) using The Fetal Medicine Foundation (FMF)'s competing-risks model and to explore its clinical applicability in mainland China.

METHODS

This was a prospective, multicenter, observational cohort study including 10 899 women with singleton pregnancy who sought prenatal care at one of 13 hospitals, located in seven cities in mainland China, between 1 December 2017 and 30 December 2019. Mean arterial pressure (MAP), uterine artery pulsatility index (UtA-PI) and maternal serum levels of placental growth factor (PlGF) and pregnancy-associated plasma protein-A (PAPP-A) at 11 + 0 to 13 + 6 weeks' gestation were measured and converted into multiples of the median using Chinese reference ranges. Individualized risk for preterm PE was calculated using the FMF algorithm. Prior risk was calculated based on maternal demographic characteristics and obstetric history. We evaluated the efficiency of the screening strategy using various combinations of biomarkers and analyzed its predictive performance for a composite of placenta-associated adverse pregnancy outcomes, including PE, placental abruption, small-for-gestational age (SGA) and preterm birth, at fixed false-positive rates for preterm PE.

RESULTS

We identified 312 pregnancies that developed PE, of which 117 cases were diagnosed as preterm PE (< 37 weeks' gestation). There were 386 pregnancies complicated by severe composite placenta-associated adverse outcome, including preterm PE, 146 cases of severe SGA (birth weight < 3^rd percentile) neonate, 61 cases with placental abruption and 109 cases of early preterm birth < 34 gestational weeks. The triple-marker model containing biomarkers MAP, UtA-PI and PAPP-A achieved, at fixed false-positive rates of 10%, 15% and 20%, detection rates for preterm PE of 65.0%, 72.7% and 76.1%, respectively, and detection rates for severe composite placenta-associated adverse outcome of 34.7%, 41.7% and 46.4%, respectively. Replacing PAPP-A with PlGF or adding PlGF to the model did not improve the performance. Of women screening positive for preterm PE at a fixed 5% false-positive rate, an estimated 30% developed at least one placenta-associated adverse pregnancy outcome, including PE, placental abruption, SGA (birth weight < 10^th percentile) and preterm birth < 37 weeks.

CONCLUSIONS

The FMF competing-risks model for preterm PE was found to be effective in screening a mainland Chinese population. Women who screened positive for preterm PE had increased risk for other placenta-associated pregnancy complications. © 2021 International Society of Ultrasound in Obstetrics and Gynecology.

Analysis of Infection Time Courses Shows CII Levels Determine the Frequency of Lysogeny in Phage 186

Engineered phage with properties optimised for the treatment of bacterial infections hold great promise, but require careful characterisation by a number of approaches. Phage–bacteria infection time courses, where populations of bacteriophage and bacteria are mixed and followed over many infection cycles, can be used to deduce properties of phage infection at the individual cell level. Here, we apply this approach to analysis of infection of Escherichia coli by the temperate bacteriophage 186 and explore which properties of the infection process can be reliably inferred. By applying established modelling methods to such data, we extract the frequency at which phage 186 chooses the lysogenic pathway after infection, and show that lysogenisation increases in a graded manner with increased expression of the lysogenic establishment factor CII. The data also suggest that, like phage λ, the rate of lysogeny of phage 186 increases with multiple infections.

Novel Anti-Interference Strategy for a Self-Powered Sensor: Mediator-Free and Biospecific Photocathode Interface

As a new electrochemical sensing concept, a self-powered sensor shows a good application prospect in the field of analysis. However, it is still a great challenge to improve the anti-interference capability of sensors through reasonable design. In this study, we investigated the difference between the single photoanode and photocathode self-powered sensor and combined the advantages of these two aspects to fabricate a mediator-free self-powered aptasensor based on the dual-photoelectrode system, which combined the biological events from the photocathode. The biological events occurred at the photocathode could avoid the interference caused by the generated hole oxidation of reducing small molecules in the real sample on the photoanode surface, which was helpful to enhance the anti-interference capability of the sensor. Moreover, due to the sufficient Fermi level differentiation between two photoelectrodes, the redox mediator was not necessary. This could avoid the redox reaction caused by the introduction of extra electron donors or electron acceptors occurring before the photoelectrical behavior, thus improving the accuracy of the sensor. According to the influence of the generated biological conjugate on the external circuit, electron transmission between interfaces, and the obstruction of visible light irradiation, the sensitive and accurate detection of the analytical model was achieved. This work provided a proof-of-concept for the establishment of a mediator-free dual-photoelectrode self-powered sensing platform with high sensitivity and strong anti-interference performance.