Mesoscale DNA feature in antibody-coding sequence facilitates somatic hypermutation.

Somatic hypermutation (SHM), initiated by activation-induced cytidine deaminase (AID), generates mutations in the antibody-coding sequence to allow affinity maturation. Why these mutations intrinsically focus on the three nonconsecutive complementarity-determining regions (CDRs) remains enigmatic. Here, we found that predisposition mutagenesis depends on the single-strand (ss) DNA substrate flexibility determined by the mesoscale sequence surrounding AID deaminase motifs. Mesoscale DNA sequences containing flexible pyrimidine-pyrimidine bases bind effectively to the positively charged surface patches of AID, resulting in preferential deamination activities. The CDR hypermutability is mimicable in in vitro deaminase assays and is evolutionarily conserved among species using SHM as a major diversification strategy. We demonstrated that mesoscale sequence alterations tune the in vivo mutability and promote mutations in an otherwise cold region in mice. Our results show a non-coding role of antibody-coding sequence in directing hypermutation, paving the way for the synthetic design of humanized animal models for optimal antibody discovery and explaining the AID mutagenesis pattern in lymphoma.

Sex differences orchestrated by androgens at single-cell resolution.

Sex differences in mammalian complex traits are prevalent and are intimately associated with androgens1-7. However, a molecular and cellular profile of sex differences and their modulation by androgens is still lacking. Here we constructed a high-dimensional single-cell transcriptomic atlas comprising over 2.3 million cells from 17 tissues in Mus musculus and explored the effects of sex and androgens on the molecular programs and cellular populations. In particular, we found that sex-biased immune gene expression and immune cell populations, such as group 2 innate lymphoid cells, were modulated by androgens. Integration with the UK Biobank dataset revealed potential cellular targets and risk gene enrichment in antigen presentation for sex-biased diseases. This study lays the groundwork for understanding the sex differences orchestrated by androgens and provides important evidence for targeting the androgen pathway as a broad therapeutic strategy for sex-biased diseases.

Examining the linkage between economic policy uncertainty, coal price, and carbon pricing in China: Evidence from pilot carbon markets.

Economic policies affect companies' production decisions. And the energy consumption volume is an intuitive reflection of the enterprise's production decisions. In China, coal is the main source of carbon emissions and the most important energy source. Therefore, the coal market and the uncertainty of economic policies are both directly tied to the carbon market. This study explores both the direct impact of economic policy uncertainty and coal price on carbon prices as well as the indirect impact of economic policy uncertainty on carbon prices through coal prices by utilizing the DCC-GARCH model and the NARDL model. The findings indicate that the dynamic correlations between coal prices and the CEPU are always negative and that those between the price of carbon and the CEPU vary by area. Meanwhile, the dynamic correlations between coal and carbon prices are only positive in Shenzhen and Beijing. Both coal prices and economic policy uncertainty produce asymmetrical impacts on carbon prices. Some policy implications are provided for developing the carbon markets in light of the results drawn from the study.

Associations of walking impairment with visual impairment, depression, and cognitive function in U.S. older adults: NHANES 2013-2014.

BACKGROUND: Walking impairment, a common health problem among older adults, has been linked to poor vision and mental health. This study aimed to investigate the associations of walking impairment with visual impairment, depression, and cognitive function in older adults. METHODS: A total of 1,489 adults aged 60 years and older who had participated in the National Health and Examination Survey (NHANES) 2013-2014 in the United States were included. Multivariate logistic regression models were used to examine the associations of walking impairment with visual impairment, depression, and four subdomains of cognitive function. Sample weights were used to ensure the generalizability of the results. RESULTS: Among all the participants (median age = 68 years; 53.7% women), 17.5% reported walking impairment. Walking impairment was significantly associated with visual impairment (adjusted odds ratio [aOR] = 2.76; 95% CI: 1.47-5.20) and depression (aOR = 4.66; 95% CI: 3.11-6.99). Walking impairment was only associated with the Digit Symbol Substitution (DSST) subdomain of cognitive function in total participants (aOR = 0.97; 95% CI: 0.95-0.99) and in non-Hispanic white adults (aOR = 0.96; 95% CI: 0.94-0.98). Participants with two or three impairment indicators had a higher OR of walking impairment (aOR = 3.64, 95% CI = 2.46-5.38) than those with 0-1 (reference group) impairment indicator. CONCLUSIONS: Walking impairment was associated with visual impairment, depression, and cognitive impairment in American older adults and also positively associated with the number of impairment indicators. The association between walking impairment and cognitive impairment varied according to race. Evaluations of vision, cognition, and depression should be conducted among older adults with walking impairment, and the needs of older adults should be provided in the evaluations alongside information on the biological aspects of their particular race.

Swc4 positively regulates telomere length independently of its roles in NuA4 and SWR1 complexes.

Telomeres at the ends of eukaryotic chromosomes are essential for genome integrality and stability. In order to identify genes that sustain telomere maintenance independently of telomerase recruitment, we have exploited the phenotype of over-long telomeres in the cells that express Cdc13-Est2 fusion protein, and examined 195 strains, in which individual non-essential gene deletion causes telomere shortening. We have identified 24 genes whose deletion results in dramatic failure of Cdc13-Est2 function, including those encoding components of telomerase, Yku, KEOPS and NMD complexes, as well as quite a few whose functions are not obvious in telomerase activity regulation. We have characterized Swc4, a shared subunit of histone acetyltransferase NuA4 and chromatin remodeling SWR1 (SWR1-C) complexes, in telomere length regulation. Deletion of SWC4, but not other non-essential subunits of either NuA4 or SWR1-C, causes significant telomere shortening. Consistently, simultaneous disassembly of NuA4 and SWR1-C does not affect telomere length. Interestingly, inactivation of Swc4 in telomerase null cells accelerates both telomere shortening and senescence rates. Swc4 associates with telomeric DNA in vivo, suggesting a direct role of Swc4 at telomeres. Taken together, our work reveals a distinct role of Swc4 in telomere length regulation, separable from its canonical roles in both NuA4 and SWR1-C.

Is the cross-correlation of EU carbon market price with policy uncertainty really being? A multiscale multifractal perspective.

This paper aims to examine the cross-correlation relationship between EU carbon market price and the economic policy uncertainty. The United Kingdom and the United State of America are chosen as the representative countries. We first conduct the linear analysis to explore the correlation of EU carbon market futures return with the economic policy uncertainty of the two countries. Our findings show that there is no linear correlation between EU carbon market return and economic policy uncertainty. Then, we apply the multifractal detrended cross-correlation analysis to examine the cross-correlation between the return of EU carbon market futures and economic policy uncertainty. The empirical results indicate that the cross-correlations really exist, and the cross-correlation behavior structure over different carbon trading phases are not the same. Moreover, the empirical results show that the anti-persistence between the EU carbon futures return and economic policy uncertainty changes from the UK and the USA are both relatively strong. The findings provide deeper insights and management implications for the carbon market from a new perspective.

Observation of double indirect interlayer exciton in WSe2/WS2 heterostructure.

Interlayer excitons (IX) are produced by the spatially separated electron-hole pairs due to the robust Coulomb interactions in van der Waals transition metal dichalcogenide (TMDC) heterostructures (HSS). IX is characterized by a larger binding energy, and its lifetime is orders of magnitude longer than that of the direct excitons, providing a significant platform for the manufacture of long-lived exciton devices and the exploration of exciton quantum gas. However, the studies are restricted to the single interlayer exciton, and the simultaneous capture and study of double IX remain challenging in the WSe2/WS2 HS. Here, we demonstrate the existence of double indirect IX in the WSe2/WS2 HS with the emission centers at 1.4585eV (∼25.9meV wide) and 1.4885 eV (∼14.4 meV wide) at cryogenic temperature. Interestingly, the intensities of the double IX emission peaks are almost equal, and the energy difference between them is in a good agreement with the cleavage value of the WS2 conduction band (CB). Additionally, diverse types of excitons in the individual materials were successfully observed in the PL spectra at 8 K. Such unique double IX features, in combination with excellent exciton identification, open up new opportunities for further investigations for new physical properties of TMDCs and explorations for the technological innovation of exciton devices.

Angelica polysaccharide alleviates oxidative response damage in HaCaT cells through up-regulation of miR-126.

BACKGROUND: Pressure ulcers (PUs) prevalence has been considered as an index for patient safety and cure quality of hospital and community. Skin cellular oxidative response damage is existed in the development of PUs. Angelica polysaccharide (AP) has the anti-oxidation function. Therefore, our goal was to investigate the mechanism of AP in relieving cellular oxidative damage. METHODS: Transfected HaCaT cells with miR-126 inhibitor, pre-treated by AP, and then treated by H2O2. CCK-8 assay and flow cytometry detection were set to test viability and apoptosis of cells respectively. qRT-PCR and western blot tested levels of miR-126 and oxidative damage relative factors. ROS assay tested the production of ROS in cells. RESULTS: Cellular oxidative response damage was induced by H2O2 at concentration of 300 µM. We found that AP could attenuate cellular oxidative response damage caused by H2O2 that it elevated cell viability, attenuated cell apoptosis and production of ROS and promoted activation of PI3K/AKT and mTOR signal pathways. Further, miR-126 was up-regulated by AP. The up-regulation of miR-126 could activate the PI3K/AKT and mTOR signal pathways. CONCLUSION: Our study demonstrated that AP attenuated cellular oxidative response damage in HaCaT cells by positively regulated miR-126.

Cleavage of C(aryl)-CH3 Bonds in the Absence of Directing Groups under Transition Metal Free Conditions.

Organic chemists now can construct carbon-carbon σ-bonds selectively and sequentially, whereas methods for the selective cleavage of carbon-carbon σ-bonds, especially for unreactive hydrocarbons, remain limited. Activation by ring strain, directing groups, or in the presence of a carbonyl or a cyano group is usually required. In this work, by using a sequential strategy site-selective cleavage and borylation of C(aryl)-CH3 bonds has been developed under directing group free and transition metal free conditions. Methyl groups of various arenes are selectively cleaved and replaced by boryl groups. Mechanistic analysis suggests that it proceeds by a sequential intermolecular oxidation and coupling of a transient aryl radical, generated by radical decarboxylation, involving a pyridine-stabilized persistent boryl radical.

Effects of macamides on endurance capacity and anti-fatigue property in prolonged swimming mice.

CONTEXT: Lepidium meyenii Walp. (Brassicaceae), most commonly known as "maca", has been used as a food or folk medicine to improve vitality in Peru. Previous research demonstrated that lipid-soluble extract from maca improved swimming endurance capacity. Macamides are considered the typical lipid-soluble markers for maca and proved to have several pharmacological properties, such as improving sexual performance and neuroprotective activies. OBJECTIVE: The present study investigates the effects of macamides on endurance capacity and anti-fatigue property in prolonged swimming mice. MATERIALS AND METHODS: The Balb/c mice were divided into seven groups: a control group, low-dose groups of N-benzyllinoleamide, N-benzyloleamide, and N-benzylpalmitamide, high-dose groups of these macamides. The macamides groups received the commercial products (12 and 40 mg/kg, ig), while the control group received vehicle for 21 d. On the 14th day, the mice were given the weight-loaded swimming test. On the 21st day, the mice were sacrificed immediately after 90 min swimming, and some biochemical parameters were measured. RESULTS AND DISCUSSION: Compared with the control group, exhaustive swimming time was significantly prolonged in high-dose group of N-benzyloleamide (p < 0.05); the levels of lactic acid (LD), blood ammonia (BA), and lactate dehydrogenase (LDH) were significantly decreased (p < 0.05), whereas the levels of liver glycogen (LG) and non-esterified fatty acid (NEFA) were significantly increased (p < 0.05) in high-dose group of N-benzyloleamide. The malondialdehyde (MDA) contents in the brain, muscle, and liver were significantly decreased (p < 0.05), whereas superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX) activities in the brain, muscle, and liver were significantly increased in high-dose group of N-benzyloleamide (p < 0.05). CONCLUSION: The results indicate that N-benzyloleamide has pharmaceutical property against exercise-induced fatigue, and this effect can be explained by the modulated energy metabolism and improved antioxidant status.

Ultrasensitive Detection of Dual Cancer Biomarkers with Integrated CMOS-Compatible Nanowire Arrays.

A direct, rapid, highly sensitive and specific biosensor for detection of cancer biomarkers is desirable in early diagnosis and prognosis of cancer. However, the existing methods of detecting cancer biomarkers suffer from poor sensitivity as well as the requirement of enzymatic labeling or nanoparticle conjugations. Here, we proposed a two-channel PDMS microfluidic integrated CMOS-compatible silicon nanowire (SiNW) field-effect transistor arrays with potentially single use for label-free and ultrasensitive electrical detection of cancer biomarkers. The integrated nanowire arrays showed not only ultrahigh sensitivity of cytokeratin 19 fragment (CYFRA21-1) and prostate specific antigen (PSA) with detection to at least 1 fg/mL in buffer solution but also highly selectivity of discrimination from other similar cancer biomarkers. In addition, this method was used to detect both CYFRA21-1 and PSA real samples as low as 10 fg/mL in undiluted human serums. With its excellent properties and miniaturization, the integrated SiNW-FET device opens up great opportunities for a point-of-care test (POCT) for quick screening and early diagnosis of cancer and other complex diseases.

CMOS-compatible silicon nanowire field-effect transistors for ultrasensitive and label-free microRNAs sensing.

MicroRNAs (miRNAs) have been regarded as promising biomarkers for the diagnosis and prognosis of early-stage cancer as their expression levels are associated with different types of human cancers. However, it is a challenge to produce low-cost miRNA sensors, as well as retain a high sensitivity, both of which are essential factors that must be considered in fabricating nanoscale biosensors and in future biomedical applications. To address such challenges, we develop a complementary metal oxide semiconductor (CMOS)-compatible SiNW-FET biosensor fabricated by an anisotropic wet etching technology with self-limitation which provides a much lower manufacturing cost and an ultrahigh sensitivity. This nanosensor shows a rapid (< 1 minute) detection of miR-21 and miR-205, with a low limit of detection (LOD) of 1 zeptomole (ca. 600 copies), as well as an excellent discrimination for single-nucleotide mismatched sequences of tumor-associated miRNAs. To investigate its applicability in real settings, we have detected miRNAs in total RNA extracted from lung cancer cells as well as human serum samples using the nanosensors, which demonstrates their potential use in identifying clinical samples for early diagnosis of cancer.

Ultra-sensitive nucleic acids detection with electrical nanosensors based on CMOS-compatible silicon nanowire field-effect transistors.

Silicon nanowire field-effect transistors (SiNW-FETs) have recently emerged as a type of powerful nanoelectronic biosensors due to their ultrahigh sensitivity, selectivity, label-free and real-time detection capabilities. Here, we present a protocol as well as guidelines for detecting DNA with complementary metal oxide semiconductor (CMOS) compatible SiNW-FET sensors. SiNWs with high surface-to-volume ratio and controllable sizes were fabricated with an anisotropic self-stop etching technique. Probe DNA molecules specific for the target DNA were covalently modified onto the surface of the SiNWs. The SiNW-FET nanosensors exhibited an ultrahigh sensitivity for detecting the target DNA as low as 1 fM and good selectivity for discrimination from one-base mismatched DNA.

Signal-to-noise ratio enhancement of silicon nanowires biosensor with rolling circle amplification.

Herein, we describe a novel approach for rapid, label-free and specific DNA detection by applying rolling circle amplification (RCA) based on silicon nanowire field-effect transistor (SiNW-FET) for the first time. Highly responsive SiNWs were fabricated with a complementary metal oxide semiconductor (CMOS) compatible anisotropic self-stop etching technique which eliminated the need for hybrid method. The probe DNA was immobilized on the surface of SiNW, followed by sandwich hybridization with the perfectly matched target DNA and RCA primer that acted as a primer to hybridize the RCA template. The RCA reaction created a long single-stranded DNA (ssDNA) product and thus enhanced the electronic responses of SiNW significantly. The signal-to-noise ratio (SNR) as a figure-of-merit was analyzed to estimate the signal enhancement and possible detection limit. The nanosensor showed highly sensitive concentration-dependent conductance change in response to specific target DNA sequences. Because of the binding of an abundance of repeated sequences of RCA products, the SNR of >20 for 1 fM DNA detection was achieved, implying a detection floor of 50 aM. This RCA-based SiNW biosensor also discriminated perfectly matched target DNA from one-base mismatched DNA with high selectivity due to the substantially reduced nonspecific binding onto the SiNW surface through RCA. The combination of SiNW FET sensor with RCA will increase diagnostic capacity and the ability of laboratories to detect unexpected viruses, making it a potential tool for early diagnosis of gene-related diseases.

Research on the Reliability of Threshold Voltage Based on GaN High-Electron-Mobility Transistors.

With the development of high-voltage and high-frequency switching circuits, GaN high-electron-mobility transistor (HEMT) devices with high bandwidth, high electron mobility, and high breakdown voltage have become an important research topic in this field. It has been found that GaN HEMT devices have a drift in threshold voltage under the conditions of temperature and gate stress changes. Under high-temperature conditions, the difference in gate contact also causes the threshold voltage to shift. The variation in the threshold voltage affects the stability of the device as well as the overall circuit performance. Therefore, in this paper, a review of previous work is presented. Temperature variation, gate stress variation, and gate contact variation are investigated to analyze the physical mechanisms that generate the threshold voltage (VTH) drift phenomenon in GaN HEMT devices. Finally, improvement methods suitable for GaN HEMT devices under high-temperature and high-voltage conditions are summarized.

Synthesis and Preclinical Evaluation of Novel 68Ga-DOTA-RBB as Potential PET Radiotracer for Imaging CDK4/6 in Tumors.

Many malignant tumors, including breast cancer, exhibit amplification and overexpression of cyclin-dependent kinase 4 and 6 (CDK4/6). Ribociclib, approved and used in clinical treatment, acts as a highly selective CDK4/6 inhibitor for ER+/HER2- breast cancer. By modifying ribociclib with the chelator DOTA, we designed and synthesized a novel CDK4/6-positive PET imaging agent, which was radiolabeled by 68Ga for radioactive tagging. The radiotracer demonstrates high radiochemical purity, excellent stability in vitro and in vivo, and favorable pharmacokinetic characteristics. Cell uptake experiments using MCF-7 cells indicate that an excess of ribociclib (RBB) can inhibit cellular uptake of 68Ga-DOTA-RBB. Imaging and biodistribution experiments in MCF-7 tumor-bearing nude mice show significant radioactive accumulation in the tumor. However, preadministration of excess ribociclib results in a substantial reduction in radioactive accumulation within the tumor. On the basis of our explorations, 68Ga-DOTA-RBB, as a targeted imaging agent for CDK4/6-positive tumors, holds significant potential application values.

C-to-G editing generates double-strand breaks causing deletion, transversion and translocation.

Base editors (BEs) introduce base substitutions without double-strand DNA cleavage. Besides precise substitutions, BEs generate low-frequency 'stochastic' byproducts through unclear mechanisms. Here, we performed in-depth outcome profiling and genetic dissection, revealing that C-to-G BEs (CGBEs) generate substantial amounts of intermediate double-strand breaks (DSBs), which are at the centre of several byproducts. Imperfect DSB end-joining leads to small deletions via end-resection, templated insertions or aberrant transversions during end fill-in. Chromosomal translocations were detected between the editing target and off-targets of Cas9/deaminase origin. Genetic screenings of DNA repair factors disclosed a central role of abasic site processing in DSB formation. Shielding of abasic sites by the suicide enzyme HMCES reduced CGBE-initiated DSBs, providing an effective way to minimize DSB-triggered events without affecting substitutions. This work demonstrates that CGBEs can initiate deleterious intermediate DSBs and therefore require careful consideration for therapeutic applications, and that HMCES-aided CGBEs hold promise as safer tools.

Enhanced sensing of nucleic acids with silicon nanowire field effect transistor biosensors.

Silicon nanowire (SiNW) field effect transistors (FETs) have emerged as powerful sensors for ultrasensitive, direct electrical readout, and label-free biological/chemical detection. The sensing mechanism of SiNW-FET can be understood in terms of the change in charge density at the SiNW surface after hybridization. So far, there have been limited systematic studies on fundamental factors related to device sensitivity to further make clear the overall effect on sensing sensitivity. Here, we present an analytical result for our triangle cross-section wire for predicting the sensitivity of nanowire surface-charge sensors. It was confirmed through sensing experiments that the back-gated SiNW-FET sensor had the highest percentage current response in the subthreshold regime and the sensor performance could be optimized in low buffer ionic strength and at moderate probe concentration. The optimized SiNW-FET nanosensor revealed ultrahigh sensitivity for rapid and reliable detection of target DNA with a detection limit of 0.1 fM and high specificity for single-nucleotide polymorphism discrimination. In our work, enhanced sensing of biological species by optimization of operating parameters and fundamental understanding for SiNW FET detection limit was obtained.