Trans-nuclease activity of Cas9 activated by DNA or RNA target binding.

Type V and type VI CRISPR-Cas systems have been shown to cleave nonspecific single-stranded DNA (ssDNA) or single-stranded RNA (ssRNA) in trans, but this has not been observed in type II CRISPR-Cas systems using single guide RNA. We show here that the type II CRISPR-Cas9 systems directed by CRISPR RNA and trans-activating CRISPR RNA dual RNAs show RuvC domain-dependent trans-cleavage activity for both ssDNA and ssRNA substrates. Cas9 possesses sequence preferences for trans-cleavage substrates, preferring to cleave T- or C-rich ssDNA substrates. We find that the trans-cleavage activity of Cas9 can be activated by target ssDNA, double-stranded DNA and ssRNA. The crystal structure of Cas9 in complex with guide RNA and target RNA provides a structural basis for the binding of target RNA to activate Cas9. Based on the trans-cleavage activity of Cas9 and nucleic acid amplification technology, we develop the nucleic acid detection platforms DNA-activated Cas9 detection and RNA-activated Cas9 detection, which are capable of detecting DNA and RNA samples with high sensitivity and specificity.

Association of lipid accumulation product with all-cause and cardiovascular disease mortality: Result from NHANES database.

BACKGROUND AND AIM: At present, there are few studies on the relationship between lipid accumulation product (LAP) and mortality. This study aims to explore the relationship between adult LAP and all-cause and cardiovascular disease (CVD) mortality. METHODS AND RESULTS: The study people from the National Health and Nutrition Examination Survey (NHANES). Results of the mortality study were based on death data up to December 31, 2019. Cox proportional risk model was used to estimate the risk ratio (HR) and 95 % CI of all-cause and CVD mortality. A total of 50162 people were included in the study (the weighted average age and male proportion were 48.14 years and 48.64 % respectively). During the follow-up of 203460871 person-years, 6850 deaths were recorded, including 1757 CVD deaths. After multivariable adjustment, the increase of LAP was significantly correlated with all-cause and CVD mortality. Compared with the participants of Quartile 1 of LAP, the multivariable adjusted HRs and 95 % CI of the participants of Quartile 4 of LAP were 1.54 (1.32, 1.80) all-cause mortality (P for trend<0.001), and 1.55 (1.16, 2.09) CVD mortality (P for trend = 0.04). For every increase of natural log-transformed LAP, the all-cause mortality increased by 22 %, and the CVD mortality increased by 14 % (both P < 0.05). CONCLUSIONS: Our cohort study based on NHANES showed that higher LAP was significantly associated with higher all-cause and CVD mortality. Maintaining a low LAP status may reduce the risk of death.

Construction and validation of a nomogram model to predict symptomatic intracranial hemorrhage after intravenous thrombolysis in severe white matter lesions.

Cerebral white matter lesions (WMLs) increase the risk of bleeding after intravenous thrombolysis (IVT) but are also considered to require IVT. Its risk factors and predictive models are still poorly studied. The aim of this study is to develop a clinically applicable model for post-IVT haemorrhage. It offers the possibility to prevent symptomatic intracranial hemorrhage (sICH) in patients with IVT in severe WMLs. A large single-center observational study conducted a retrospective analysis of IVT in patients with severe WMLs from January 2018 to December 2022. Univariate and multi-factor logistic regression results were used to construct nomogram model, and a series of validations were performed on the model. More than 2,000 patients with IVT were screened for inclusion in this study after cranial magnetic resonance imaging evaluation of 180 patients with severe WMLs, 28 of whom developed sICH. In univariate analysis, history of hypertension (OR 3.505 CI 2.257-4.752, p = 0.049), hyperlipidemia (OR 4.622 CI 3.761- 5.483, p < 0.001), the NIHSS score before IVT (OR 41.250 CI 39.212-43.288, p < 0.001), low-density lipoprotein levels (OR 1.995 CI 1.448-2.543, p = 0.013), cholesterol levels (OR 1.668 CI 1.246-2.090, p = 0.017), platelet count (OR 0.992 CI 0.985-0.999, p = 0.028), systolic blood pressure (OR 1.044 CI 1.022-1.066, p < 0.001), diastolic blood pressure (OR 1.047 CI 1.024-1.070, p < 0.001) were significantly associated with sICH. In a multifactorial analysis, the NIHSS score before IVT (OR 94.743 CI 92.311-97.175, p < 0.001), and diastolic blood pressure (OR 1.051 CI 1.005-1.097, p = 0.033) were considered to be significantly associated with sICH after IVT as risk factors for the occurrence of sICH. The four most significant factors from logistic regression are subsequently fitted to create a predictive model. The accuracy was verified using ROC curves, calibration curves, decision curves, and clinical impact curves, and the model was considered to have high accuracy (AUC 0.932, 95% 0.888-0.976). The NHISS score before IVT and diastolic blood pressure are independent risk factors for sICH after IVT in patients with severe WMLs. The models based on hyperlipidemia, the NIHSS score before IVT, low-density lipoprotein and diastolic blood pressure are highly accurate and can be applied clinically to provide a reliable predictive basis for IVT in patients with severe WMLs.

Structural basis for MTA1c-mediated DNA N6-adenine methylation.

DNA N6-adenine methylation (6 mA) has recently been found to play a crucial role in epigenetic regulation in eukaryotes. MTA1c, a newly discovered 6 mA methyltransferase complex in ciliates, is composed of MTA1, MTA9, p1 and p2 subunits and specifically methylates ApT dinucleotides, yet its mechanism of action remains unknown. Here, we report the structures of Tetrahymena thermophila MTA1 (TthMTA1), Paramecium tetraurelia MTA9 (PteMTA9)-TthMTA1 binary complex, as well as the structures of TthMTA1-p1-p2 and TthMTA1-p2 complexes in apo, S-adenosyl methionine-bound and S-adenosyl homocysteine-bound states. We show that MTA1 is the catalytically active subunit, p1 and p2 are involved in the formation of substrate DNA-binding channel, and MTA9 plays a structural role in the stabilization of substrate binding. We identify that MTA1 is a cofactor-dependent catalytically active subunit, which exhibits stable SAM-binding activity only after assembly with p2. Our structures and corresponding functional studies provide a more detailed mechanistic understanding of 6 mA methylation.

Highly sensitive detection of carcinoembryonic antigen using copper-free click chemistry on the surface of azide cofunctionalized graphene oxide.

In this study, we reported a highly sensitive method for detecting carcinoembryonic antigen (CEA) based on an azide cofunctionalized graphene oxide (GO-N3) and carbon dot (CDs) biosensor system. Carbon dots-labeled DNA (CDs-DNA) combined with GO-N3 using copper-free click chemistry (CFCC), which quenched the fluorescence of the CDs via fluorescence resonance energy transfer (FRET). Upon the addition of CEA, fluorescence was recovered due to the combination of CEA and aptamer. Under optimal conditions, the relative fluorescence intensity was linear with CEA concentration in the range of 0.01-1 ng/mL (R2 = 0.9788), and the limit of detection (LOD) was 7.32 pg/mL (S/N = 3). This biosensor had a high sensitivity and good selectivity for CEA detection in serum samples, indicating that the novel sensor platform holds a great potential for CEA and other biomarkers in practical applications.

Aptamer-based biosensor for detecting carcinoembryonic antigen.

Carcinoembryonic antigen (CEA), as one of the common tumor markers, is a human glycoprotein involved in cell adhesion and is expressed during human fetal development. Since the birth of human, CEA expression is largely inhibited, with only low levels in the plasma of healthy adults. Generally, CEA will overexpressed in many cancers, including gastric, breast, ovarian, lung, and pancreatic cancers, especially colorectal cancer. As one of the important tumor markers, the detection of CEA has great significance in differential diagnosis, condition monitoring and therapeutic evaluation of diseases. Conventional CEA testing typically uses immunoassay methods. However, immunoassay methods require complex and expensive instruments and professional personnel to operate. Moreover, radioactive element may cause certain damage to the human body, which limits their wide application. In the past few years, biosensors, especially aptamer-based biosensors, have attracted extensive attention due to their high sensitivity, good selectivity, high accuracy, fast response and low cost. This review briefly classifies and describes the advance in optical and electrochemical aptamer biosensors for CEA detection, also explains and compares their advantages and disadvantages.

Cocaine detection using aptamer and molybdenum disulfide-gold nanoparticle-based sensors.

Aim: The current work highlighted a novel colorimetric sensor based on aptamer and molybdenum disulfide (MoS2)-gold nanoparticles (AuNPs) that was developed for cocaine detection with high sensitivity. Materials & methods: Due to the presence of the plasmon resonance band on the surface of AuNPs, AuNPs aggregated and the color was changed from red to blue after adding a certain concentration of NaCl. We used MoS2 to optimize the sensing system of AuNPs. The folded conformation of the aptamer in combination with cocaine enhanced the salt tolerance of the MoS2-AuNPs, effectively preventing their aggregation. Results & conclusion: The detection limit of cocaine was 7.49 nM with good selectivity. The method based on MoS2-AuNPs colorimetry sensor is simple, quick, label-free and low cost.

The detection of mercury ion using DNA as sensors based on fluorescence resonance energy transfer.

Mercury ion (Hg2+) is a heavy metal that can cause serious water pollution. With the accumulation of large quantities in lakes, rivers, freshwater and aquatic life, Hg2+ can pass through the food chain, entering the human body and endangering health. Hg2+ detection has therefore become important thereby attracting extensive interests. Currently, several DNA-based sensors have been used for Hg2+ detection because they are not easy to degrade and are very stable. This paper summarizes the application of some DNA-based sensors based on fluorescence resonance energy transfer (FRET), analyzes their characteristic, and compares their sensitivity. Future perspectives and possible challenges in this area are also outlined.

Comparative mapping in watermelon [Citrullus lanatus (Thunb.) Matsum. et Nakai].

The first single-nucleotide polymorphism (SNP) maps for watermelon [Citrullus lanatus (Thunb.) Matsum. et Nakai] were constructed and compared. Three populations were developed from crosses between two elite cultivars, Klondike Black Seeded × New Hampshire Midget (KBS × NHM), an elite cultivar and wild egusi accession, Strain II × PI 560023 (SII × Egusi) and an elite cultivar and a wild citron accession, ZWRM50 × PI 244019 (ZWRM × Citroides). The SII × Egusi and ZWRM × Citroides F(2) populations consisted of 187 and 182 individuals respectively while the KBS × NHM recombinant inbred line (RIL) population consisted of 164 lines. The length of the genetic maps were 1,438, 1,514 and 1,144 cM with average marker distances of 3.8, 4.2, and 3.4 cM for the KBS × NHM, SII × Egusi and ZWRM × Citroides populations, respectively. Shared markers were used to align the three maps so that the linkage groups (LGs) represented the 11 chromosomes of the species. Marker segregation distortion were observed in all three populations, but was highest (12.7 %) in the ZWRM × Citroides population, where Citroides alleles were favored. The three maps were used to construct a consensus map containing 378 SNP markers with an average distance of 5.1 cM between markers. Phenotypic data was collected for fruit weight (FWT), fruit length (FL), fruit width (FWD), fruit shape index (FSI), rind thickness (RTH) and Brix (BRX) and analyzed for quantitative trait loci (QTL) associated with these traits. A total of 40 QTL were identified in the three populations, including major QTL for fruit size and shape that were stable across genetic backgrounds and environments. The present study reports the first SNP maps for Citrullus and the first map constructed using two elite parents. We also report the first stable QTL associated with fruit size and shape in Citrullus lanatus. These maps, QTL and SNPs should be useful for the watermelon community and represent a significant step towards the potential use of molecular tools in watermelon breeding.

Presence of tannins in sorghum grains is conditioned by different natural alleles of Tannin1.

Sorghum, an ancient old-world cereal grass, is the dietary staple of over 500 million people in more than 30 countries in the tropics and semitropics. Its C4 photosynthesis, drought resistance, wide adaptation, and high nutritional value hold the promise to alleviate hunger in Africa. Not present in other major cereals, such as rice, wheat, and maize, condensed tannins (proanthocyanidins) in the pigmented testa of some sorghum cultivars have been implicated in reducing protein digestibility but recently have been shown to promote human health because of their high antioxidant capacity and ability to fight obesity through reduced digestion. Combining quantitative trait locus mapping, meta-quantitative trait locus fine-mapping, and association mapping, we showed that the nucleotide polymorphisms in the Tan1 gene, coding a WD40 protein, control the tannin biosynthesis in sorghum. A 1-bp G deletion in the coding region, causing a frame shift and a premature stop codon, led to a nonfunctional allele, tan1-a. Likewise, a different 10-bp insertion resulted in a second nonfunctional allele, tan1-b. Transforming the sorghum Tan1 ORF into a nontannin Arabidopsis mutant restored the tannin phenotype. In addition, reduction in nucleotide diversity from wild sorghum accessions to landraces and cultivars was found at the region that codes the highly conserved WD40 repeat domains and the C-terminal region of the protein. Genetic research in crops, coupled with nutritional and medical research, could open the possibility of producing different levels and combinations of phenolic compounds to promote human health.