Identification of prognosis-related lncRNAs and cell validation in lung squamous cell carcinoma based on TCGA data.

Objective: To discern long non-coding RNAs (lncRNAs) with prognostic relevance in the context of lung squamous cell carcinoma (LUSC), we intend to predict target genes by leveraging The Cancer Genome Atlas (TCGA) repository. Subsequently, we aim to investigate the proliferative potential of critical lncRNAs within the LUSC milieu. Methods: DESeq2 was employed to identify differentially expressed genes within the TCGA database. Following this, we utilized both univariate and multivariate Cox regression analyses to identify lncRNAs with prognostic relevance. Noteworthy lncRNAs were selected for validation in cell lines. The intracellular localization of these lncRNAs was ascertained through nucleocytoplasmic isolation experiments. Additionally, the impact of these lncRNAs on cellular proliferation, invasion, and migration capabilities was investigated using an Antisense oligonucleotides (ASO) knockdown system. Results: Multivariate Cox regression identified a total of 12 candidate genes, consisting of seven downregulated lncRNAs (BRE-AS1, CCL15-CCL14, DNMBP-AS1, LINC00482, LOC100129034, MIR22HG, PRR26) and five upregulated lncRNAs (FAM83A-AS1, LINC00628, LINC00923, LINC01341, LOC100130691). The target genes associated with these lncRNAs exhibit significant enrichment within diverse biological pathways, including metabolic processes, cancer pathways, MAPK signaling, PI3K-Akt signaling, protein binding, cellular components, cellular transformation, and other functional categories. Furthermore, nucleocytoplasmic fractionation experiments demonstrated that LINC00923 and LINC01341 are predominantly localized within the cellular nucleus. Subsequent investigations utilizing CCK-8 assays and colony formation assays revealed that the knockdown of LINC00923 and LINC01341 effectively suppressed the proliferation of H226 and H1703 cells. Additionally, transwell assays showed that knockdown of LINC00923 and LINC01341 significantly attenuated the invasive and migratory capacities of H226 and H1703 cells. Conclusion: This study has identified 12 candidate lncRNA associated with prognostic implications, among which LINC00923 and LINC01341 exhibit potential as markers for the prediction of LUSC outcomes.

The possible molecular mechanism underlying the involvement of the variable shear factor QKI in the epithelial-mesenchymal transformation of oesophageal cancer.

OBJECTIVE: Based on the GEO, TCGA and GTEx databases, we reveal the possible molecular mechanism of the variable shear factor QKI in epithelial mesenchymal transformation (EMT) of oesophageal cancer. METHODS: Based on the TCGA and GTEx databases, the differential expression of the variable shear factor QKI in oesophageal cancer samples was analysed, and functional enrichment analysis of QKI was performed based on the TCGA-ESCA dataset. The percent-spliced in (PSI) data of oesophageal cancer samples were downloaded from the TCGASpliceSeq database, and the genes and variable splicing types that were significantly related to the expression of the variable splicing factor QKI were screened out. We further identified the significantly upregulated circRNAs and their corresponding coding genes in oesophageal cancer, screened the EMT-related genes that were significantly positively correlated with QKI expression, predicted the circRNA-miRNA binding relationship through the circBank database, predicted the miRNA-mRNA binding relationship through the TargetScan database, and finally obtained the circRNA-miRNA-mRNA network through which QKI promoted the EMT process. RESULTS: Compared with normal control tissue, QKI expression was significantly upregulated in tumour tissue samples of oesophageal cancer patients. High expression of QKI may promote the EMT process in oesophageal cancer. QKI promotes hsa_circ_0006646 and hsa_circ_0061395 generation by regulating the variable shear of BACH1 and PTK2. In oesophageal cancer, QKI may promote the production of the above two circRNAs by regulating variable splicing, and these circRNAs further competitively bind miRNAs to relieve the targeted inhibition of IL-11, MFAP2, MMP10, and MMP1 and finally promote the EMT process. CONCLUSION: Variable shear factor QKI promotes hsa_circ_0006646 and hsa_circ_0061395 generation, and downstream related miRNAs can relieve the targeted inhibition of EMT-related genes (IL11, MFAP2, MMP10, MMP1) and promote the occurrence and development of oesophageal cancer, providing a new theoretical basis for screening prognostic markers of oesophageal cancer patients.

Orientation of the NV centers are determined using the cylindrical vector beam array.

The determination of nitrogen-vacancy centers plays an important role in quantum information sensing. Efficiently and rapidly determining the orientation of multiple nitrogen-vacancy center s in a low-concentration diamond is challenging due to its size. Here, we solve this scientific problem by using an azimuthally polarized beam array as the incident beam. In this paper, the optical pen is used to modulate the position of beam array to excite distinctive fluorescence characterizing multiple and different orientations of nitrogen-vacancy centers. The important result is that in a low concentration diamond layer, the orientation of multiple NV centers can be judged except when they are too close within the diffraction limit. Hence, this efficient and rapid method has a good application prospect in quantum information sensing.

Impact of Growth Rate on the Protein-mRNA Ratio in Pseudomonas aeruginosa.

Our understanding of how bacterial pathogens colonize and persist during human infection has been hampered by the limited characterization of bacterial physiology during infection and a research bias toward in vitro, fast-growing bacteria. Recent research has begun to address these gaps in knowledge by directly quantifying bacterial mRNA levels during human infection, with the goal of assessing microbial community function at the infection site. However, mRNA levels are not always predictive of protein levels, which are the primary functional units of a cell. Here, we used carefully controlled chemostat experiments to examine the relationship between mRNA and protein levels across four growth rates in the bacterial pathogen Pseudomonas aeruginosa. We found a genome-wide positive correlation between mRNA and protein abundances across all growth rates, with genes required for P. aeruginosa viability having stronger correlations than nonessential genes. We developed a statistical method to identify genes whose mRNA abundances poorly predict protein abundances and calculated an RNA-to-protein (RTP) conversion factor to improve mRNA predictions of protein levels. The application of the RTP conversion factor to publicly available transcriptome data sets was highly robust, enabling the more accurate prediction of P. aeruginosa protein levels across strains and growth conditions. Finally, the RTP conversion factor was applied to P. aeruginosa human cystic fibrosis (CF) infection transcriptomes to provide greater insights into the functionality of this bacterium in the CF lung. This study addresses a critical problem in infection microbiology by providing a framework for enhancing the functional interpretation of bacterial human infection transcriptome data. IMPORTANCE Our understanding of bacterial physiology during human infection is limited by the difficulty in assessing bacterial function at the infection site. Recent studies have begun to address this question by quantifying bacterial mRNA levels in human-derived samples using transcriptomics. One challenge for these studies is the poor predictivity of mRNA for protein levels for some genes. Here, we addressed this challenge by measuring the transcriptomes and proteomes of P. aeruginosa grown at four growth rates. Our results revealed that the growth rate does not impact the genome-wide correlation of mRNA and protein levels. We used statistical methods to identify the genes for which mRNA and protein were poorly correlated and developed an RNA-to-protein (RTP) conversion factor that improved the predictivity of protein levels across strains and growth conditions. Our results provide new insights into mRNA-protein correlations and tools to enhance our understanding of bacterial physiology from transcriptome data.

Polymicrobial Interactions of Oral Microbiota: a Historical Review and Current Perspective.

The oral microbiota is enormously diverse, with over 700 microbial species identified across individuals that play a vital role in the health of our mouth and our overall well-being. In addition, as oral diseases such as caries (cavities) and periodontitis (gum disease) are mediated through interspecies microbial interactions, this community serves as an important model system to study the complexity and dynamics of polymicrobial interactions. Here, we review historical and recent progress in our understanding of the oral microbiome, highlighting how oral microbiome research has significantly contributed to our understanding of microbial communities, with broad implications in polymicrobial diseases and across microbial community ecology. Further, we explore innovations and challenges associated with analyzing polymicrobial systems and suggest future directions of study. Finally, we provide a conceptual framework to systematically study microbial interactions within complex communities, not limited to the oral microbiota.

Aluminium is essential for root growth and development of tea plants (Camellia sinensis).

On acid soils, the trivalent aluminium ion (Al3+ ) predominates and is very rhizotoxic to most plant species. For some native plant species adapted to acid soils including tea (Camellia sinensis), Al3+ has been regarded as a beneficial mineral element. In this study, we discovered that Al3+ is actually essential for tea root growth and development in all the tested varieties. Aluminum ion promoted new root growth in five representative tea varieties with dose-dependent responses to Al3+ availability. In the absence of Al3+ , the tea plants failed to generate new roots, and the root tips were damaged within 1 d of Al deprivation. Structural analysis of root tips demonstrated that Al was required for root meristem development and activity. In situ morin staining of Al3+ in roots revealed that Al mainly localized to nuclei in root meristem cells, but then gradually moved to the cytosol when Al3+ was subsequently withdrawn. This movement of Al3+ from nuclei to cytosols was accompanied by exacerbated DNA damage, which suggests that the nuclear-targeted Al primarily acts to maintain DNA integrity. Taken together, these results provide novel evidence that Al3+ is essential for root growth in tea plants through maintenance of DNA integrity in meristematic cells.

Multiple instruments motion trajectory tracking in optical surgical navigation.

Optical surgical navigation system has been a hot research topic because of its high accuracy. This paper focuses on identifying and tracking multiple surgical instruments to meet the requirements of applying multiple surgical instruments in clinical medicine. The methods of instrument identification based on the marker's geometrical arrangement and instrument tracking based on markers' motion vector were applied in the proposed algorithm. The experiments of multiple instruments' identification and tracking, the instruments' stability, the space distance and rotation of a pair of instruments at the same tracking time were performed to verify the proposed algorithm. The stereoscopic camera is applied to capture images, and two 850 nm filters are added in front of the binocular camera. The tracking experiment shows that ten instruments can be fully and accurately identified, and then all of them can be quickly and accurately tracked at the same time. A pair of instruments is simultaneously measured in the stability test, such as the typical surgical instrument (TSI) and the miniature surgical instrument (MSI). The ranges of standard deviations (SD) of the stability test for the TSI in the X-, Y-, and Z- axes are from 0.016 mm to 0.127 mm, from 0.011 mm to 0.090 mm, and from 0.124 mm to 0.901 mm, respectively. And the ranges of SDs for the MSI's stability test are from 0.011 mm to 0.133 mm in the X-axis, from 0.010 mm to 0.106 mm in the Y-axis, and from 0.093 mm to 0.932 mm in the Z-axis. The sub-millimeter SDs show that the proposed algorithm has a high stability. Moreover, the space distance test and the rotation test were performed for simultaneously tracking TSI and MSI. All experimental results indicate the proposed algorithm is able to meet the clinical accuracy requirements.

Melanocortin Receptor 4 Signaling Regulates Vertebrate Limb Regeneration.

Melanocortin 4 receptor (Mc4r) plays a crucial role in the central control of energy homeostasis, but its role in peripheral organs has not been fully explored. We have investigated the roles of hypothalamus-mediated energy metabolism during Xenopus limb regeneration. We report that hypothalamus injury inhibits Xenopus tadpole limb regeneration. By loss-of-function and gain-of-function studies, we show that Mc4r signaling is required for limb regeneration in regeneration-competent tadpoles and stimulates limb regeneration in later-stage regeneration-defective tadpoles. It regulates limb regeneration through modulating energy homeostasis and ROS production. Even more interestingly, our results demonstrate that Mc4r signaling is regulated by innervation and α-MSH substitutes for the effect of nerves in limb regeneration. Mc4r signaling is also required for mouse digit regeneration. Thus, our findings link vertebrate limb regeneration with Mc4r-mediated energy homeostasis and provide a new avenue for understanding Mc4r signaling in the peripheral organs.

Dicer inactivation stimulates limb regeneration ability in Xenopus laevis.

The ontogenetic decline of regeneration capacity in the anuran amphibian Xenopus makes it an excellent model for regeneration studies. However, the cause of the regeneration ability decline is not fully understood. MicroRNAs regulate animal development and have been indicated in various regeneration situations. However, little is known about the role of microRNAs during limb regeneration in Xenopus. This study investigates the effect of Dicer, an enzyme responsible for microRNA maturation, on limb development and regeneration in Xenopus. Dicer is expressed in the developing Xenopus limbs and is up-regulated after limb amputation during both regeneration-competent and regeneration-deficient stages of tadpole development. Inactivation of Dicer in early (NF stage 53) tadpole limb buds leads to shorter tibulare/fibulare formation but does not affect limb regeneration. However, in late-stage, regeneration-deficient tadpole limbs (NF stage 57), Dicer inactivation restores the regeneration blastema and stimulates limb regeneration. Thus, our results demonstrated that Xenopus limb regeneration can be stimulated by the inactivation of Dicer in nonregenerating tadpoles, indicating that microRNAs present in late-stage tadpole limbs may be involved in the ontogenetic decline of limb regeneration in Xenopus.

Detection of UVA/UVC-induced damage of p53 fragment by rolling circle amplification with AIEgens.

Absorption of ultraviolet (UV) light by nucleic acid could lead to mutations and skin cancers. Traditional damage detection methods based on fluorescence not only need dye/quencher groups but also display relatively high background interference, causing difficulty in synthesis and purification and thus low specificity of detection. Here, by combining rolling circle amplification (RCA) and aggregation-induced emission molecules (AIE), we made up for the defects of traditional methods to some extent and could also differentiate damaged and undamaged DNA. We also studied radiation damage of the p53 gene fragment both from UVA and UVC, although the mechanism of UVA in mutagenesis remains controversial. To amplify the signal-to-background ratio, we ligated the linear p53 (L p53) gene fragment to be a circular p53 (C p53) gene fragment, which is a key component for RCA. The combination of RCA products and positive TPE-Z (quaternized tetraphenylethene salt) molecules induced the aggregation of AIE molecules, and subsequently resulted in significant fluorescence enhancement (the signal for the undamaged DNA is 598% higher than that of the damaged). Compared with the traditional aggregation-caused quenching (ACQ) based fluorescent method, our assay was more sensitive and more specific.

Live Cell MicroRNA Imaging Using Exonuclease III-Aided Recycling Amplification Based on Aggregation-Induced Emission Luminogens.

Enzyme-assisted detection strategies of microRNAs (miRNAs) in vitro have accomplished both great sensitivity and specificity. However, low expression of miRNAs and a complex environment in cells induces big challenges for monitoring and tracking miRNAs in vivo. The work reports the attempt to carry miRNA imaging into live cells, by enzyme-aided recycling amplification. We utilize facile probes based yellow aggregation-induced emission luminogens (AIEgens) with super photostable property but without quencher, which are applied to monitor miRNAs not only from urine sample extracts (in vitro) but also in live cells (in vivo). The assay could distinguish the cancer patients' urine samples from the healthy urine due to the good specificity. Moreover, the probe showed much higher fluorescence intensity in breast cancer cells (MCF-7) (miR-21 in high expression) than that in cervical cancer cells (HeLa) and human lung fibroblast cells (HLF) (miR-21 in low expression) in more than 60 min, which showed the good performance and super photostability for the probe in vivo. As controls, another two probes with FAM/Cy3 and corresponding quenchers, respectively, could perform miRNAs detections in vitro and parts of in vivo tests but were not suitable for the long-term cell tracking due to the photobleach phenomena, which also demonstrates that the probe with AIEgens is a potential candidate for the accurate identification of cancer biomarkers.

Tunable ultrasensitivity: functional decoupling and biological insights.

Sensitivity has become a basic concept in biology, but much less is known about its tuning, probably because allosteric cooperativity, the best known mechanism of sensitivity, is determined by rigid conformations of interacting molecules and is thus difficult to tune. Reversible covalent modification (RCM), owing to its systems-level ingenuity, can generate concentration based, tunable sensitivity. Using a mathematical model of regulated RCM, we find sensitivity tuning can be decomposed into two orthogonal modes, which provide great insights into vital biological processes such as tissue development and cell cycle progression. We find that decoupling of the two modes of sensitivity tuning is critical to fidelity of cell fate decision; the decoupling is thus important in development. The decomposition also allows us to solve the 'wasteful degradation conundrum' in budding yeast cell cycle checkpoint, which further leads to discovery of a subtle but essential difference between positive feedback and double negative feedback. The latter guarantees revocability of stress-induced cell cycle arrest; while the former does not. By studying concentration conditions in the system, we extend applicability of ultrasensitivity and explain the ubiquity of reversible covalent modification.

Facile, Fast-Responsive, and Photostable Imaging of Telomerase Activity in Living Cells with a Fluorescence Turn-On Manner.

In situ detecting and monitoring intracellular telomerase activity is significant for cancer diagnosis. In this work, we report a facile and fast-responsive bioprobe for in situ detection and imaging of intracellular telomerase activity with superior photostability. After transfected into living cells, quencher group labeled TS primer (QP) can be extended in the presence of intracellular telomerase. Positive charged TPE-Py molecules (AIE dye) will bind to the primer as well as extension repeated units, producing a telomerase activity-related turn-on fluorescence signal. By incorporating positive charged AIE dye and substrate oligonucleotides, in situ light-up imaging and detection of intracellular telomerase activity were achieved. This strategy exhibits good performance for sensitive in situ tracking of telomerase activity in living cells. The practicality of this facile and fast-responsive telomerase detection method was demonstrated by using it to distinguish tumor cells from normal cells and to monitor the change of telomerase activity during treatment with antitumor drugs, which shows its potential in clinical diagnostic and therapeutic monitoring.

Rational design of asymmetric red fluorescent probes for live cell imaging with high AIE effects and large two-photon absorption cross sections using tunable terminal groups.

In this work, we report the synthesis of a family of donor-acceptor (D-A) π-conjugated aggregation-induced red emission materials (TPABT, DTPABT, TPEBT and DTPEBT) with the same core 2,2-(2,2-diphenylethene-1,1-diyl)dithiophene (DPDT) and different amounts and different strengths of electron-donating terminal moieties. Interestingly, TPABT and TPEBT, which have asymmetric structures, give obviously higher solid fluorescence quantum efficiencies in comparison with those of the corresponding symmetric structures, DTPABT and DTPEBT, respectively. In particular, the thin film of TPEBT exhibited the highest fluorescence quantum efficiency of ca. 38% with the highest αAIE. Moreover, TPEBT and DTPEBT with TPE groups showed two-photon absorption cross-sections of (δ) 1.75 × 103 GM and 1.94 × 103 GM at 780 nm, respectively, which are obviously higher than the other two red fluorescent materials with triphenylamine groups. Then, the one-photon and two-photon fluorescence imaging of MCF-7 breast cancer cells and Hela cells, and cytotoxicity experiments, were carried out with these red fluorescent materials. Intense intracellular red fluorescence was observed for all the molecules using one-photon excitation and for TPABT using two-photon excitation in the cell cytoplasm. Finally, TPEBT is biocompatible and functions well in mouse brain blood vascular visualization. It is indicated that these materials can be used as a specific stain fluorescent probe for live cell imaging.

A photostable AIE fluorogen for lysosome-targetable imaging of living cells.

Disruptive variation in intracellular pH and its fluctuations in lysosomes have a close relationship with the more acidic lysosome lumen of cancer cells (pH 4.5-5.5). Traditional lysosome-targeted probes, such as LysoTracker Green DND-26 (LTG) and LysoTracker Red DND-99 (LTR), can fluoresce when the weak base units in the probes are removed after donating protons under the photoinduced electron-transfer (PET) effect. However they can only be used at low concentration to avoid the aggregation-caused quenching (ACQ) effect and are also easily photobleached under continuous excitation irradiation, displaying low photostability. Herein, a tetraphenylethylene (TPE)-based lysosome-targetable fluorescence probe, TPE-CA, was synthesized, which could selectively monitor the pH change in subcellular organelles and exhibited a strong blue emission under an acidic condition with pH = 4. Using crystallographic, NMR and HRMS analyses, the mechanism regarding the pH dependent fluorescent performance of TPE-CA has been illustrated at the molecular level. In addition, experimental results show that TPE-CA is cell-permeable and biocompatible with HeLa, MCF-7 and HLF cells. The punctate fluorescent spots in the co-staining experiment of TPE-CA with LTG and LTR proves that the blue fluorescence spots of TPE-CA are indeed localized in the most acidic lysosome organelles. In particular, TPE-CA also inherits the aggregation-induced emission (AIE) feature of TPE, showing better photostability under continuous UV illumination compared with the commercial dyes (LTG and LTR). These results show that TPE-CA would be beneficial for understanding the acid environment of lysosomes in related cells and organs with potential biological significance.

Correction: A photostable AIE fluorogen for lysosome-targetable imaging of living cells.

Correction for 'A photostable AIE fluorogen for lysosome-targetable imaging of living cells' by Xiaoding Lou et al., J. Mater. Chem. B, 2016, 4, 5412-5417.

Quencher group induced high specificity detection of telomerase in clear and bloody urines by AIEgens.

Telomerase is a widely used tumor biomarker for early cancer diagnosis. On the basis of the combined use of aggregation-induced emission (AIE) fluorogens and quencher, a quencher group induced high specificity strategy for detection of telomerase activity from cell extracts and cancer patients' urine specimens was creatively developed. In the absence of telomerase, fluorescence background is extremely low due to the short distance between quencher and AIE dye. In the addition of telomerase, fluorescence enhances significantly. The telomerase activity in the E-J, MCF-7, and HeLa extracts equivalent to 5-10 000 cells can be detected by this method in ∼1 h. Furthermore, the distinguishing of telomerase extracted from 38 cancer and 15 normal urine specimens confirms the reliability and practicality of this protocol. In contrast to our previous results (Anal. Chem. 2015, 87, 6822-6827), these advanced experiments obtain more remarkable specificity.