Monitoring Ammonium Polyphosphate (APP) Biodegradation by Acinetobacter nosocomialis D-3 Using DAPI.

Ammonium polyphosphate (APP), a pivotal constituent within environmentally friendly flame retardants, exhibits notable decomposition susceptibility and potentially engenders ecological peril. Consequently, monitoring the APP concentration to ensure product integrity and facilitate the efficacious management of wastewater from production processes is of great significance. A fluorescent assay was devised to swiftly discern APP utilizing 4',6'-diamino-2-phenylindole (DAPI). With increasing APP concentrations, DAPI undergoes intercalation within its structure, emitting pronounced fluorescence. Notably, the flame retardant JLS-PNA220-A, predominantly comprising APP, was employed as the test substrate. Establishing a linear relationship between fluorescence intensity (F-F0) and JLS-PNA220-A concentration yielded the equation y = 76.08x + 463.2 (R2 = 0.9992), with a LOD determined to be 0.853 mg/L. The method was used to assess the degradation capacity of APP-degrading bacteria. Strain D-3 was isolated, and subsequent analysis of its 16S DNA sequence classified it as belonging to the Acinetobacter genus. Acinetobacter nosocomialis D-3 demonstrated superior APP degradation capabilities under pH 7 at 37 °C, with degradation rates exceeding 85% over a four-day cultivation period. It underscores the sensitivity and efficacy of the proposed method for APP detection. Furthermore, Acinetobacter nosocomialis D-3 exhibits promising potential for remediation of residual APP through environmental biodegradation processes.

Function of Graphene Oxide as the "Nanoquencher" for Hg2+ Detection Using an Exonuclease I-Assisted Biosensor.

Graphene oxide is well known for its excellent fluorescence quenching ability. In this study, positively charged graphene oxide (pGO25000) was developed as a fluorescence quencher that is water-soluble and synthesized by grafting polyetherimide onto graphene oxide nanosheets by a carbodiimide reaction. Compared to graphene oxide, the fluorescence quenching ability of pGO25000 is significantly improved by the increase in the affinity between pGO25000 and the DNA strand, which is introduced by the additional electrostatic interaction. The FAM-labeled single-stranded DNA probe can be almost completely quenched at concentrations of pGO25000 as low as 0.1 µg/mL. A simple and novel FAM-labeled single-stranded DNA sensor was designed for Hg2+ detection to take advantage of exonuclease I-triggered single-stranded DNA hydrolysis, and pGO25000 acted as a fluorescence quencher. The FAM-labeled single-stranded DNA probe is present as a hairpin structure by the formation of T-Hg2+-T when Hg2+ is present, and no fluorescence is observed. It is digested by exonuclease I without Hg2+, and fluorescence is recovered. The fluorescence intensity of the proposed biosensor was positively correlated with the Hg2+ concentration in the range of 0-250 nM (R2 = 0.9955), with a seasonable limit of detection (3σ) cal. 3.93 nM. It was successfully applied to real samples of pond water for Hg2+ detection, obtaining a recovery rate from 99.6% to 101.1%.

Effect of NaOH molarities to the microstructure and sodium storage performance of the Sn-MOF derived SnO2microporous rod.

In this study, we demonstrated a facile method to prepare a novel SnO2microporous rod with various microstructures by controlling NaOH molarities in precursor synthesis processes. Four different molarities of NaOH solution (0.005 M, 0.048 M, 0.12 M and 0.5 M) were used together with o-phthalic acid in Sn-MOF synthesis to determine the effect of ligand [o-C6H4CO222-] concentration on microstructure evolution. It was found that increasing NaOH molarity can effectively decrease the size of Sn-MOF rods. Then, the SnO2microporous rods were obtained by calcinating the as-prepared Sn-MOF as microstructures. Under an optimized experimental condition (NaOH molarity of 0.12 M), the SnO2rods shows a modest initial coulombic efficiency of 61.3% with a high reversible sodium storage capacity of 503 mAh g-1after 150 cycles at 50 mA g-1. Moreover, an impressive reversible sodium storage capacity of 206 mAh g-1can be obtained at long-term cycling performance (800 cycles at current density of 2 A g-1). Effects of morphologies to electrochemical performances have been further discussed in aspects of intrinsic resistance, pseudocapacitive contribution, surface area and porous structure and microstructural stability, and the enhanced electrochemical performance could be attributed to factors of enhanced pseudocapacitive charge contribution, optimized microstructures, and structural stability, which ensure the SnO2-0.12 M to have a good rate performance and cyclability. This nanoscale-engineering method adopted here could be a promising path to fabricate SnO2-based anodes with novel microstructures for sodium storage applications.

WITHDRAWN: Effects of cancer-associated point mutations on the structure, function, and stability of succinate dehydrogenase A.

This article has been withdrawn by the authors. Some of the SDHA enzyme activity data were flawed and were not performed and analyzed correctly. The withdrawing authors are in the process of correcting the data and re-evaluating them for resubmission.

Combination probes with intercalating anchors and proximal fluorophores for DNA and RNA detection.

A new class of modified oligonucleotides (combination probes) has been designed and synthesised for use in genetic analysis and RNA detection. Their chemical structure combines an intercalating anchor with a reporter fluorophore on the same thymine nucleobase. The intercalator (thiazole orange or benzothiazole orange) provides an anchor, which upon hybridisation of the probe to its target becomes fluorescent and simultaneously stabilizes the duplex. The anchor is able to communicate via FRET to a proximal reporter dye (e.g. ROX, HEX, ATTO647N, FAM) whose fluorescence signal can be monitored on a range of analytical devices. Direct excitation of the reporter dye provides an alternative signalling mechanism. In both signalling modes, fluorescence in the unhybridised probe is switched off by collisional quenching between adjacent intercalator and reporter dyes. Single nucleotide polymorphisms in DNA and RNA targets are identified by differences in the duplex melting temperature, and the use of short hybridization probes, made possible by the stabilisation provided by the intercalator, enhances mismatch discrimination. Unlike other fluorogenic probe systems, placing the fluorophore and quencher on the same nucleobase facilitates the design of short probes containing multiple modifications. The ability to detect both DNA and RNA sequences suggests applications in cellular imaging and diagnostics.

Development of a fluorescent DNA sensor for dual detection of heavy metal ions utilising DAPI in distinct buffers.

The DNA-based biosensor utilises a thymine/guanine(T/G)-rich ODN-4 scaffold with 4',6-diamidino-2-phenylindole(DAPI) as a fluorescent emissary to monitor mercury/lead(Hg(II)/Pb(II)) ions simultaneously. Key to its bifocal detection capability is the twin unbound cytosine(C) bases strategically bridging the G-quadruplex and T-rich sequences, enabling their synergistic interplay. It facilitates the recognition of Hg(II)/Pb(II) ions, characterised by high specificity, and effectively mitigates interference from silver(Ag(I)). The G-quadruplex, guided by the C bases, induces a conformational transition in T-Hg(II)-T complexes, resulting in intense fluorescence. Pb(II) causes a spatial shift in the G-quadruplex, relaxing the T-Hg(II)-T base pairs and attenuating the fluorescence signal. The ODN-4 exhibits a robust, linear correlation with Hg(II) concentration (4.09 nmol/L to 1000 nmol/L) and Pb(II) concentration (3.22 nmol/L to 5 µmol/L). Recovery rates in milk, tap water, and rice water specimens with both ions validate method accuracy (Hg(II): 95.19% to 104.68%, Pb(II): 98.20% to 103.46%). It holds promising prospects for practical food analysis.

Aptamer-Based fluorescent DNA biosensor in antibiotics detection.

The inappropriate employment of antibiotics across diverse industries has engendered profound apprehensions concerning their cumulative presence within human bodies and food commodities. Consequently, many nations have instituted stringent measures limiting the admissible quantities of antibiotics in food items. Nonetheless, conventional techniques employed for antibiotic detection prove protracted and laborious, prompting a dire necessity for facile, expeditious, and uncomplicated detection methodologies. In this regard, aptamer-based fluorescent DNA biosensors (AFBs) have emerged as a sanguine panacea to surmount the limitations of traditional detection modalities. These ingenious biosensors harness the binding prowess of aptamers, singular strands of DNA/RNA, to selectively adhere to specific target antibiotics. Notably, the AFBs demonstrate unparalleled selectivity, affinity, and sensitivity in detecting antibiotics. This comprehensive review meticulously expounds upon the strides achieved in AFBs for antibiotic detection, particularly emphasizing the labeling modality and the innovative free-label approach. It also elucidates the design principles behind a diverse array of AFBs. Additionally, a succinct survey of signal amplification strategies deployed within these biosensors is provided. The central objective of this review is to apprise researchers from diverse disciplines of the contemporary trends in AFBs for antibiotic detection. By doing so, it aspires to instigate a concerted endeavor toward the development of heightened sensitivity and pioneering AFBs, thereby contributing to the perpetual advancement of antibiotic detection methodologies.

Recent Aptamer-Based Biosensors for Cd2+ Detection.

Cd2+, a major environmental pollutant, is heavily toxic to human health. Many traditional techniques are high-cost and complicated; thus, developing a simple, sensitive, convenient, and cheap monitoring approach is necessary. The aptamer can be obtained from a novel method called SELEX, which is widely used as a DNA biosensor for its easy acquisition and high affinity of the target, especially for heavy metal ions detection, such as Cd2+. In recent years, highly stable Cd2+ aptamer oligonucleotides (CAOs) were observed, and electrochemical, fluorescent, and colorimetric biosensors based on aptamers have been designed to monitor Cd2+. In addition, the monitoring sensitivity of aptamer-based biosensors is improved with signal amplification mechanisms such as hybridization chain reactions and enzyme-free methods. This paper reviews approaches to building biosensors for inspecting Cd2+ by electrochemical, fluorescent, and colorimetric methods. Finally, many practical applications of sensors and their implications for humans and the environment are discussed.

Development of a split G-quadruplex and DAPI-based fluorescent probe for Hg(II) and Pb(II) ions detection.

A novel thymine- and guanine-rich oligonucleotide (ODN-7) was engineered explicitly for the detection of Hg(II) and Pb(II) by a single intercalated dye 4',6-diamidinyl-2-phenylindole (DAPI). Upon the introduction of Hg(II), a rapid formation of T-Hg(II)-T base pairs takes place, triggering the assembly of a split G-quadruplex structure, resulting in a strong fluorescence signal due to DAPI intercalating into the T-Hg(II)-T mismatch. The introduction of Pb(II) initiates an interaction with the split G-quadruplex, causing a significant conformational change in its structure. Consequently, the altered split G-quadruplex structure fails to facilitate the insertion of DAPI into the T-Hg(II)-T complexes, leading to fluorescence quenching. This strategy offers a straightforward means of detecting Hg(II) and Pb(II). Leveraging the split G-quadruplex, the ODN-7 sensor enables the detection limits (3σ) for Hg(II) and Pb(II) to reach an impressive low of 0.39 nM and 4.98 nM, respectively. It exhibited a favorable linear range of 0.39-900 nM for Hg(II) detection (R2 = 0.9993) and 4.98 nM-5 µM for Pb(II) determination (R2 = 0.9953), respectively. Furthermore, the proposed sensor had excellent selectivity for detecting Hg(II) and Pb(II). It was used in milk samples containing mixed Hg(II) and Pb(II) solutions, yielding recovery rates of 99.3-103.8% for Hg(II) detection and 100.1-104.1% for Pb(II) detection.

Label-free hairpin probe for the rapid detection of Hg(II) based on T-Hg(II)-T.

A simple thymine-rich mercury-specific oligonucleotide (G9T24C9) was designed to quickly detect Hg(Ⅱ) via thymine-Hg(II)-thymine (T-Hg(Ⅱ)-T) coordination chemistry by using 4',6-diamidinyl-2-phenylindole (DAPI). When the stable GC-paired stem of the DNA hairpin occurred, DPAI could intercalate into the T-Hg(Ⅱ)-T base pairs as a fluorescent recognizer. As a result, the hairpin structure was able to promote the rapid formation of T-Hg(Ⅱ)-T mismatches in the presence of Hg(Ⅱ), trigger DAPI to recognize T-Hg(Ⅱ)-T as well as TA/AT base pairs and restore fluorescence; moreover, fluorescence increases were not observed when Hg(Ⅱ) was not introduced. This method represents a simple strategy to detect Hg(Ⅱ). Taking advantage of the hairpin structure, the fluorescence intensity of the G9T24C9 hairpin probe was positively correlated with the concentration of Hg(Ⅱ) from 2.87 to 1400 nM (R2 = 0.9968), and the limit of detection (3σ) was as low as 2.87 nM. Furthermore, this probe had high selectivity for Hg(Ⅱ) detection. The probe was applied to real samples of pond water for the detection of Hg(Ⅱ), and a recovery rate from 95.9% to 104.4% was obtained.

AXL Inactivation Inhibits Mesothelioma Growth and Migration via Regulation of p53 Expression.

Malignant mesothelioma is a locally aggressive and highly lethal neoplasm. Dysregulation and activation of Gas6/AXL tyrosine kinase signaling are associated with mesothelioma progression, but the mechanisms of these AXL tumorigenic roles are poorly understood. p53 mutants in lung carcinoma upregulate AXL expression by binding and acetylating the AXL promoter. Although TP53 mutations are uncommon in mesothelioma, we hypothesized that these tumors might have alternative feedback mechanisms between AXL and p53. In the current report, we investigated AXL regulation of TP53 transcription, expression, and biological function in mesothelioma. AXL expression was stronger in mesothelioma than most of the other tumor types from the TCGA gene expression profile dataset. AXL knockdown by shRNA induced wild-type and mutant p53 expression in mesothelioma cell lines, suggesting that AXL pro-tumorigenic roles result in part from the suppression of p53 function. Likewise, induced AXL inhibited expression of wild type p53 in COS-7 cells and 293T cells. Immunofluorescence staining showed nuclear colocalization of AXL and p53; however, association of AXL and p53 was not demonstrated in immunoprecipitation complexes. The AXL effects on p53 expression resulted from the inhibition of TP53 transcription, as demonstrated by qRT-PCR after AXL silencing and TP53 promotor dual luciferase activity assays. Chromatin immunoprecipitation-qPCR and sequencing showed that AXL bound to the initial 600 bp sequence at the 5' end of the TP53 promoter. AXL inhibition (shRNA or R428) reduced mesothelioma cell viability, migration, and invasion, whereas TP53 shRNA knockdown attenuated antiproliferative, migration, and invasive effects of AXL silencing or AXL inactivation in these cells. These studies demonstrate a novel feedback regulation loop between AXL and p53, and provide a rationale for mesothelioma therapies targeting AXL/p53 signaling.

Solid phase click ligation for the synthesis of very long oligonucleotides.

Oligonucleotides have been ligated efficiently on solid-phase using CuAAC and SPAAC chemistry to produce up to 186-mer triazole linked DNA products. Multiple sequential ligation reactions can be carried out by using a masked azide approach. This work suggests a novel modular approach to the synthesis of large complex oligonucleotide analogues.