Mapping glymphatic solute transportation through the perivascular space of hippocampal arterioles with 14 Tesla MRI.

The perivascular space (PVS) plays a crucial role in facilitating the clearance of waste products and the exchange of cerebrospinal fluid and interstitial fluid in the central nervous system. While optical imaging methods identify the glymphatic transport of fluorescent tracers through PVS of surface-diving arteries, their limited depth penetration impedes the study of glymphatic dynamics in deep brain regions. In this study, we introduced a novel high-resolution dynamic contrast-enhanced MRI mapping approach based on single-vessel multi-gradient-echo methods. This technique allowed the differentiation of penetrating arterioles and venules from adjacent parenchymal tissue voxels and enabled the detection of Gd-enhanced signals coupled to PVS of penetrating arterioles in the deep cortex and hippocampus. By directly infusing Gd into the lateral ventricle, we eliminated delays in cerebrospinal fluid flow and focused on PVS Gd transport through PVS of hippocampal arterioles. The study revealed significant PVS-specific Gd signal enhancements, shedding light on glymphatic function in deep brain regions. These findings advance our understanding of brain-wide glymphatic dynamics and hold potential implications for neurological conditions characterized by impaired waste clearance, warranting further exploration of their clinical relevance and therapeutic applications.

Stochastic circular persistent currents of exciton polaritons.

We monitor the orbital degree of freedom of exciton-polariton condensates confined within an optical trap and unveil the stochastic switching of persistent annular polariton currents under pulse-periodic excitation. Within an elliptical trap, the low-lying in energy polariton current states manifest as a two-petaled density distribution with a swirling phase. In the stochastic regime, the density distribution, averaged over multiple excitation pulses, becomes homogenized in the azimuthal direction. Meanwhile, the weighted phase, extracted from interference experiments, exhibits two compensatory jumps when varied around the center of the trap. Introducing a supplemental control optical pulse to break the reciprocity of the system enables the transition from a stochastic to a deterministic regime, allowing for controlled polariton circulation direction.

Study on Improving the Modulatory Effect of Rhythmic Oscillations by Transcranial Magneto-Acoustic Stimulation.

In hippocampus, synaptic plasticity and rhythmic oscillations reflect the cytological basis and the intermediate level of cognition, respectively. Transcranial ultrasound stimulation (TUS) has demonstrated the ability to elicit changes in neural response. However, the modulatory effect of TUS on synaptic plasticity and rhythmic oscillations was insufficient in the present studies, which may be attributed to the fact that TUS acts mainly through mechanical forces. To enhance the modulatory effect on synaptic plasticity and rhythmic oscillations, transcranial magneto-acoustic stimulation (TMAS) which induced a coupled electric field together with TUS's ultrasound field was applied. The modulatory effect of TMAS and TUS with a pulse repetition frequency of 100 Hz were compared. TMAS/TUS were performed on C57 mice for 7 days at two different ultrasound intensities (3 W/cm2 and 5 W/cm [Formula: see text]. Behavioral tests, long-term potential (LTP) and local field potentials in vivo were performed to evaluate TUS/TMAS modulatory effect on cognition, synaptic plasticity and rhythmic oscillations. Protein expression based on western blotting were used to investigate the under- lying mechanisms of these beneficial effects. At 5 W/cm2, TMAS-induced LTP were 113.4% compared to the sham group and 110.5% compared to TUS. Moreover, the relative power of high gamma oscillations (50-100Hz) in the TMAS group ( 1.060±0.155 %) was markedly higher than that in the TUS group ( 0.560±0.114 %) and sham group ( 0.570±0.088 %). TMAS significantly enhanced the synchronization of theta and gamma oscillations as well as theta-gamma cross-frequency coupling. Whereas, TUS did not show relative enhancements. TMAS provides enhanced effect for modulating the synaptic plasticity and rhythmic oscillations in hippocampus.

Transcranial Magneto-Acoustic Stimulation Protects Synaptic Rehabilitation from Amyloid-Beta Plaques via Regulation of Microglial Functions.

Transcranial magneto-acoustic stimulation (TMAS), which is characterized by high spatiotemporal resolution and high penetrability, is a non-invasive neuromodulation technology based on the magnetic-acoustic coupling effect. To reveal the effects of TMAS treatment on amyloid-beta (Aß) plaque and synaptic plasticity in Alzheimer's disease, we conducted a comparative analysis of TMAS and transcranial ultrasound stimulation (TUS) based on acoustic effects in 5xFAD mice and BV2 microglia cells. We found that the TMAS-TUS treatment effectively reduced amyloid plaque loads and plaque-associated neurotoxicity. Additionally, TMAS-TUS treatment ameliorated impairments in long-term memory formation and long-term potentiation. Moreover, TMAS-TUS treatment stimulated microglial proliferation and migration while enhancing the phagocytosis and clearance of Aß. In 5xFAD mice with induced microglial exhaustion, TMAS-TUS treatment-mediated Aß plaque reduction, synaptic rehabilitation improvement, and the increase in phospho-AKT levels were diminished. Overall, our study highlights that stimulation of hippocampal microglia by TMAS treatment can induce anti-cognitive impairment effects via PI3K-AKT signaling, providing hope for the development of new strategies for an adjuvant therapy for Alzheimer's disease.

Pathological and immunohistochemical analysis of gastric mucosa after one anastomosis gastric bypass surgery.

BACKGROUND: One anastomosis gastric bypass (OAGB) is now the third most common bariatric surgery worldwide. This procedure is garnering increasing attention, but its complication of bile reflux and the associated risk of gastric carcinogenesis remains controversial. OBJECTIVE: The study aims to assess the impact of bile reflux on the gastric mucosa by comparing pathological and immunohistochemical results of gastric mucosa before and 2 years after OAGB surgery. METHODS: This retrospective study analyzed gastric lesions observed in gastroscopy before and after OAGB surgery. Pathological examinations were conducted on mucosal samples from proximal, middle and distal part of stomach, with a particular focus on the expression of Ki-67, P53, and CDX2 in immunohistochemistry. Ki-67 indicates cellular proliferation, P53 is a tumor suppressor protein, and CDX2 is a marker for intestinal differentiation. RESULTS: A total of 16 patients completed the follow-up. Regarding gastritis, presurgery nonerosive gastritis was found in two cases (12.5%), and postsurgery in six cases (37.5%). Erosive gastritis increased from one case (6.2%) presurgery to three cases (18.7%) postsurgery, totaling an increase from three to nine cases (p = .028). Bile reflux in the stomach increased from one case (6.2%) presurgery to three cases (18.7%) postsurgery. Most lesions in the proximal, middle, and distal part of stomach were relatively mild, with normal tissue states being predominant. Mild inflammation was found in all three areas, whereas moderate inflammation, intestinal metaplasia, and glandular atrophy were less common. No cases of severe inflammation were noted. The expression of gastric biomarkers CDX-2, Ki67, and P53 showed no significant statistical variation in different areas. CONCLUSION: Bile reflux does occur after OAGB, but its incidence is not high. Based on the immunohistochemical and pathological results of the gastric mucosa 2 years post-OAGB, there seems to be no significant causal relationship between OAGB and oncogenic inflammation around the gastric tube.

Treg-Related Genes Representing a Potential Shared Biological Mechanism Between Clear Cell Renal Carcinoma and Obesity.

OBJECTIVE: To determine the potential shared biological mechanism between obesity and clear cell renal carcinoma (ccRCC). STUDY DESIGN: Observational study. Place and Duration of the Study: Department of Urology, Lishui People's Hospital, Lishui City, China, from December 2022 to March 2023. METHODOLOGY: The test and validation cohorts were selected from the GEO database. WGCNA and PPI networks were applied to identify shared hub genes. GO/KEGG, GSEA, and ROC curve analyses were applied to explore the potential underlying mechanisms and diagnostic power. Logistic regression was used to select genes to construct the signature. The risk score and various immune-related analyses were performed to assess the clinical and immune performance of the signature. The CellMiner platform was used to screen potential FDA-approved drugs. RESULTS: PTPRC, TYROBP, ITGB2, CD86, and ITGAM were defined as shared hub genes with good diagnostic power for obesity and ccRCC. Eight immune cells exhibited a positive correlation with the hub genes, while two immune cells showed negative associations. MDSCs and Tregs had the strongest positive associations with the hub genes. The Treg-related pathway exhibited predominant enrichment. The TYROBP, ITGB2, and CD86 genes were selected to construct an immune signature that has good clinical and immune performance. Six FDA-approved drugs were screened. CONCLUSION: Five Treg-related genes were identified as shared hub genes in obese patients and ccRCC patients. A signature was constructed to describe the immune features of ccRCC. KEY WORDS: Treg-related genes, Shared biological mechanism, Immune signature, Obesity, Clear cell renal carcinoma (ccRCC).

Clinical significance of miR-200a in systemic lupus erythematosus and renal damage in children.

The purpose was to analyze the clinical significance of miR-200a in children with initially diagnosed SLE and renal damage. Children with initially diagnosed SLE (n=100) and healthy children (n=50) undergoing physical examinations during the same period were recruited. Disease activity of SLE children was determined based on SLEDAI (systemic lupus erythematosus disease activity index), and they were divided to SLEDAI≤9 group and SLEDAI>9 group, respectively. Moreover, SLE children were divided to LN group and non-LN group based on the occurrence of lupus nephritis. Differential level of miR-200a between groups was detected by qRT-PCR. Spearman correlation test was conducted to analyze the influence of miR-200a on SLEDAI and other laboratory indexes of SLE children. Its diagnostic potential in SLE and LN was assessed through depicting ROC curves. MiR-200a level was remarkably lower in SLE children than that of healthy children. Lower level of miR-200a was detected in SLE children with high SLEDAI or accompanied LN. MiR-200a level was negatively correlated to SLEDAI (r=-0.425), ESR (r=-0.284), CRP (r=-0.338), BUN (r=-0.263) and Scr (r=-0.345), while it was positively correlated to C3 (r=0.631), C4 (r=0.524) and ALB (r=0.394) in SLE children. The AUC of miR-200a in diagnosing SLE was 0.8379 (cut-off value=2.225, sensitivity=70%, specificity=70%). Besides, the AUC of miR-200a in diagnosing LN was 0.7619 (cut-off value=2.005, sensitivity=80%, specificity=76%). MiR-200a level has a certain correlation to the disease activity of children with initially diagnosed SLE, which can be utilized as an adjuvant indicator in evaluating SLE severity. Meanwhile, miR-200a has predictive value for SLE-induced renal damage.

Sleeve gastrectomy with one anastomosis bipartition versus one anastomosis gastric bypass: A pilot study.

BACKGROUND: One anastomosis gastric bypass (OAGB) is a new recognized metabolic surgery, but the problem that we cannot screen the excluded stomach is a troubling issue in China. The emergence of sleeve gastrectomy plus one anastomosis bipartition (SG + OAB) makes us see a hope to solve this problem. OBJECTIVES: By comparing the efficacy of the two surgical methods, to evaluate whether SG + OAB surgery can solve the dilemma faced by OAGB that the excluded stomach cannot be screened. METHODS: A retrospective study to compare the patients who underwent OAGB and SG + OAB was conducted. The main outcome measures were (1) operation risk, (2) weight loss, and (3) diabetes remission at 6 months. RESULTS: This study was conducted in the bariatric/metabolic surgical center. From November 2021 to February 2022, a total of 30 patients with obesity who received SG + OAB surgery were recruited. Another matched 60 patients undergoing OAGB were recruited as control group. There was no difference in preoperative age (32.15 ± 9.02 vs. 34.47 ± 7.22; p = .224), female ratio (83% vs. 85%; p = .837), and BMI (36.18 ± 5.30 vs. 34.68 ± 5.58; p = .217) between the two groups. OAGB had a shorter mean operation time (121.67 ± 20.41 vs. 143.50 ± 25.07 min; p < .001) and a lower intraoperative blood loss (21.92 ± 12.35 vs. 32.43 ± 22.01 mL; p = .005), but a longer postoperative flatus passage (2.13 ± 0.43 vs. 1.87 ± 0.43 days; p = .007) compared with the SG + OAB group. Two patients (6.7%) developed major surgical complication in SG + OAB group but no major complication developed in OAGB group. At 6 months after surgery, SG + OAB had a higher %total weight loss than OAGB (31.05 ± 3.12 vs. 28.14 ± 5.43%; p = .015), but diabetes remission rate was similarly high in both groups. CONCLUSIONS: SG + OAB operation had a non-inferior or even better weight loss than OAGB, with a similar glycemic control efficacy. However, the high complication rate of SG + OAB is the major drawback that needs attention.

Structural Engineering of Co-Metal-Organic Frameworks via Ce Incorporation for Improved Oxygen Evolution.

The rational design of metal-organic framework (MOF)-based electrocatalysts plays a key role in achieving high-efficiency oxygen evolution reaction (OER). Herein, a synergetic morphology and electronic structure engineering strategy are proposed to design a Co-MOF nanoflower grown on carbon paper via rare-earth cerium doping (CoCe-MOF/CP). Compared with Co-MOF/CP, the developed CoCe-MOF/CP exhibited superior OER performance with a low overpotential of 267 mV at 10 mA cm-2 and outstanding long-term stability over 100 h. Theoretical calculations show that the unique 4f valence electron structure of Ce induced charge redistribution of the Co-MOF surface through the strong Co 3d-O 2p-Ce 4f orbital electronic coupling below the Fermi level. Ce-doped plays a key role in the engineering of the electronic states of the Co sites to endow them with the optimal free energy landscape for enhanced OER catalytic activity. This work provides new insights into comprehending the RE-enhanced mechanism of electrocatalysis and provides an effective strategy for the design of MOF-based electrocatalysts.

Study on the Role of Physical Fields in TMAS to Modulate Synaptic Plasticity in Mice.

OBJECTIVE: Transcranial magneto-acoustic stimulation (TMAS) is a composite technique combining static magnetic and coupled electric fields with transcranial ultrasound stimulation (TUS) and has shown advantages in neuromodulation. However, the role of these physical fields in neuromodulation is unclear. Synaptic plasticity is the cellular basis for learning and memory. In this paper, we varied the intensity of static magnetic, electric and ultrasonic fields respectively to investigate the modulation of synaptic plasticity by these physical fields. METHODS: There are control, static magnetic field (0.1 T/0.2 T), TUS (0.15/0.3 MPa), and TMAS (0.15 MPa + 0.2 V/m, 0.3 MPa + 0.2 V/m, 0.3 MPa + 0.4 V/m) groups. Hippocampal areas were stimulated at 5 min daily for 7 days and in vivo electrophysiological experiments were performed. RESULTS: TMAS induced greater LTP, LTD, and paired-pulse ratio (PPR) than TUS, reflecting that TMAS has a more significant modulation in both long- and short- term synaptic plasticity. In TMAS, a doubling of the electric field amplitude increases LTP, LTD and PPR to a greater extent than a doubling of the acoustic pressure. Increasing the static magnetic field intensity has no significant effect on the modulation of synaptic plasticity. CONCLUSION: This paper argues that electric fields should be the main reason for the difference in modulation between TMAS and TUS and that changing the amplitude of the electric field affected the modulation of TMAS more than changing the acoustic pressure. SIGNIFICANCE: This study elucidates the roles of the physical fields in TMAS and provides a parameterisation way to guide TMAS applications based on the dominant roles of the physical fields.

High-resolution awake mouse fMRI at 14 Tesla.

High-resolution awake mouse fMRI remains challenging despite extensive efforts to address motion-induced artifacts and stress. This study introduces an implantable radiofrequency (RF) surface coil design that minimizes image distortion caused by the air/tissue interface of mouse brains while simultaneously serving as a headpost for fixation during scanning. Using a 14T scanner, high-resolution fMRI enabled brain-wide functional mapping of visual and vibrissa stimulation at 100×100×200µm resolution with a 2s per frame sampling rate. Besides activated ascending visual and vibrissa pathways, robust BOLD responses were detected in the anterior cingulate cortex upon visual stimulation and spread through the ventral retrosplenial area (VRA) with vibrissa air-puff stimulation, demonstrating higher-order sensory processing in association cortices of awake mice. In particular, the rapid hemodynamic responses in VRA upon vibrissa stimulation showed a strong correlation with the hippocampus, thalamus, and prefrontal cortical areas. Cross-correlation analysis with designated VRA responses revealed early positive BOLD signals at the contralateral barrel cortex (BC) occurring 2 seconds prior to the air-puff in awake mice with repetitive stimulation, which was not detectable with the randomized stimulation paradigm. This early BC activation indicated learned anticipation through the vibrissa system and association cortices in awake mice under continuous training of repetitive air-puff stimulation. This work establishes a high-resolution awake mouse fMRI platform, enabling brain-wide functional mapping of sensory signal processing in higher association cortical areas.

Stability of African swine fever virus genome under different environmental conditions.

Background and Aim: African swine fever (ASF), a globally transmitted viral disease caused by ASF virus (ASFV), can severely damage the global trade economy. Laboratory diagnostic methods, including pathogen and serological detection techniques, are currently used to monitor and control ASF. Because the large double-stranded DNA genome of the mature virus particle is wrapped in a membrane, the stability of ASFV and its genome is maintained in most natural environments. This study aimed to investigate the stability of ASFV under different environmental conditions from both genomic and antibody perspectives, and to provide a theoretical basis for the prevention and elimination of ASFV. Materials and Methods: In this study, we used quantitative real-time polymerase chain reaction for pathogen assays and enzyme-linked immunosorbent assay for serological assays to examine the stability of the ASFV genome and antibody, respectively, under different environmental conditions. Results: The stability of the ASFV genome and antibody under high-temperature conditions depended on the treatment time. In the pH test, the ASFV genome and antibody remained stable in both acidic and alkaline environments. Disinfection tests revealed that the ASFV genome and antibody were susceptible to standard disinfection methods. Conclusion: Collectively, the results demonstrated that the ASFV genome is highly stable in favorable environments but are also susceptible to standard disinfection methods. This study focuses on the stability of the ASFV genome under different conditions and provides various standard disinfection methods for the prevention and control of ASF.

The mitochondrial regulation in ferroptosis signaling pathway and its potential strategies for cancer.

Ferroptosis is an iron-dependent regulated cell death, mainly manifested by the production of reactive oxygen species and accumulation of lipid peroxides. It is distinct from other forms of cell death with regard to morphology and biochemistry, particularly in disrupting mitochondrial function. Mitochondria are essential compartments where the organism generates energy and are closely associated with the fate of ferroptosis. Currently, researchers focus on the potential value of ferroptosis and mitochondria for overcoming drug sensitivity and assisting in cancer therapy. In this review, we summarize the main mechanisms of ferroptosis (the GPX4-realated pathway, FSP1-related pathway, and iron metabolism pathway) and the functions and regulating pathways of mitochondria (the TCA cycle, oxidative phosphorylation, mitochondrial regulation of iron ions, and mtDNA) in ferroptosis. We believe that exploring the role of mitochondria in ferroptosis will help us understand the potential regulatory mechanisms of ferroptosis in cancer and help us find new therapeutic targets.

A photoactivatable and phenylboronic acid-functionalized nanoassembly for combating multidrug-resistant gram-negative bacteria and their biofilms.

Background: Multidrug-resistant (MDR) gram-negative bacteria-related infectious diseases have caused an increase in the public health burden and mortality. Moreover, the formation of biofilms makes these bacteria difficult to control. Therefore, developing novel interventions to combat MDR gram-negative bacteria and their biofilms-related infections are urgently needed. The purpose of this study was to develop a multifunctional nanoassembly (IRNB) based on IR-780 and N, N'-di-sec-butyl-N, N'- dinitroso-1,4-phenylenediamine (BNN6) for synergistic effect on the infected wounds and subcutaneous abscesses caused by gram-negative bacteria. Methods: The characterization and bacteria-targeting ability of IRNB were investigated. The bactericidal efficacy of IRNB against gram-negative bacteria and their biofilms was demonstrated by crystal violet staining assay, plate counting method and live/dead staining in vitro. The antibacterial efficiency of IRNB was examined on a subcutaneous abscess and cutaneous infected wound model in vivo. A cell counting kit-8 assay, Calcein/PI cytotoxicity assay, hemolysis assay and intravenous injection assay were performed to detect the biocompatibility of IRNB in vitro and in vivo. Results: Herein, we successfully developed a multifunctional nanoassembly IRNB based on IR-780 and BNN6 for synergistic photothermal therapy (PTT), photodynamic therapy (PDT) and nitric oxide (NO) effect triggered by an 808 nm laser. This nanoassembly could accumulate specifically at the infected sites of MDR gram-negative bacteria and their biofilms via the covalent coupling effect. Upon irradiation with an 808 nm laser, IRNB was activated and produced both reactive oxygen species (ROS) and hyperthermia. The local hyperthermia could induce NO generation, which further reacted with ROS to generate ONOO-, leading to the enhancement of bactericidal efficacy. Furthermore, NO and ONOO- could disrupt the cell membrane, which converts bacteria to an extremely susceptible state and further enhances the photothermal effect. In this study, IRNB showed a superior photothermal-photodynamic-chemo (NO) synergistic therapeutic effect on the infected wounds and subcutaneous abscesses caused by gram-negative bacteria. This resulted in effective control of associated infections, relief of inflammation, promotion of re-epithelization and collagen deposition, and regulation of angiogenesis during wound healing. Moreover, IRNB exhibited excellent biocompatibility, both in vitro and in vivo. Conclusions: The present research suggests that IRNB can be considered a promising alternative for treating infections caused by MDR gram-negative bacteria and their biofilms.

Comprehensive Transcriptomic Profiling of m6A Modification in Age-Related Hearing Loss.

Age-related hearing loss (ARHL), also known as presbycusis, is one of the most common neurodegenerative disorders in elderly individuals and has a prevalence of approximately 70-80% among individuals aged 65 and older. As ARHL is an intricate and multifactorial disease, the exact pathogenesis of ARHL is not fully understood. There is evidence that transcriptional dysregulation mediated by epigenetic modifications is widespread in ARHL. However, the potential role of N6-methyladenosine (m6A) modification, as a crucial component of epigenetics, in ARHL progression remains unclear. In this study, we confirmed that the downregulation of m6A modification in cochlear tissues is related to ARHL and found that the expression of the m6A methylation regulators Wilms tumour suppressor-1-associated protein (WTAP), methyltransferase-like 3 (METTL3), ALKB homologous protein 5 (ALKBH5) and fat mass and obesity-associated protein (FTO) is decreased significantly at the mRNA and protein levels in ARHL mice. Then, we used methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and RNA sequencing (RNA-Seq) to identify the differentially m6A-methylated genes in the cochlear tissues of ARHL mice. A total of 3438 genes with differential m6A methylation were identified, of which 1332 genes were m6A-hypermethylated and 2106 genes were m6A-hypomethylated in the ARHL group compared to the control group according to MeRIP-seq. Further joint analysis of RNA-Seq and MeRIP-Seq data showed that 262 genes had significant differences in both mRNA expression and m6A methylation. GO and KEGG analyses indicated that 262 unique genes were enriched mainly in the PI3K-AKT signalling pathway. In conclusion, the results of this study reveal differential m6A methylation patterns in the cochlear tissues of ARHL mice, providing a theoretical basis for further study of the pathogenesis of ARHL and potential therapeutic strategies.

Prospects and challenges of CRISPR/Cas9 gene-editing technology in cancer research.

Cancer, one of the leading causes of death, usually commences and progresses as a result of a series of gene mutations and dysregulation of expression. With the development of clustered regularly interspaced palindromic repeat (CRISPR)/Cas9 gene-editing technology, it is possible to edit and then decode the functions of cancer-related gene mutations, markedly advance the research of biological mechanisms and treatment of cancer. This review summarizes the mechanism and development of CRISPR/Cas9 gene-editing technology in recent years and describes its potential application in cancer-related research, such as the establishment of human tumor disease models, gene therapy and immunotherapy. The challenges and future development directions are highlighted to provide a reference for exploring pathological mechanisms and potential treatment protocols of cancer.

VCFshiny: an R/Shiny application for interactively analyzing and visualizing genetic variants.

Summary: Next-generation sequencing generates variants that are typically documented in variant call format (VCF) files. However, comprehensively examining variant information from VCF files can pose a significant challenge for researchers lacking bioinformatics and programming expertise. To address this issue, we introduce VCFshiny, an R package that features a user-friendly web interface enabling interactive annotation, interpretation, and visualization of variant information stored in VCF files. VCFshiny offers two annotation methods, Annovar and VariantAnnotation, to add annotations such as genes or functional impact. Annotated VCF files are deemed acceptable inputs for the purpose of summarizing and visualizing variant information. This includes the total number of variants, overlaps across sample replicates, base alterations of single nucleotides, length distributions of insertions and deletions (indels), high-frequency mutated genes, variant distribution in the genome and of genome features, variants in cancer driver genes, and cancer mutational signatures. VCFshiny serves to enhance the intelligibility of VCF files by offering an interactive web interface for analysis and visualization. Availability and implementation: The source code is available under an MIT open source license at https://github.com/123xiaochen/VCFshiny with documentation at https://123xiaochen.github.io/VCFshiny.

Mini-PE, a prime editor with compact Cas9 and truncated reverse transcriptase.

Prime editor (PE) is a versatile genome editing tool that does not need extra DNA donors or inducing double-strand breaks. However, in vivo implementation of PE remains a challenge because of its oversized composition. In this study, we screened out the smallest truncated Moloney murine leukemia virus (MMLV) reverse transcriptase (RT) with the F155Y mutation to keep gene editing efficiency. We discovered the most efficient gene editing variants of MMLV RT with the smallest size. After optimization of the pegRNAs and incorporation with nick sgRNAs, the mini-PE delivered up to 10% precise editing at target sites in human and mouse cells. It also edited the mouse Hsf1 gene in the mouse retina precisely after delivery with adeno-associated viruses (AAVs), although the editing efficiency was lower than 1%. We will focus on improving the editing efficiency of mini-PE and exploiting its therapeutic potential against human genetic diseases.

Potential roles for lncRNA Mirg/Foxp1 in an ARHL model created using C57BL/6J mice.

Age-related hearing loss (ARHL) is associated with hair cell apoptosis, but the underlying mechanism of hair cell apoptosis remains unclear. Here, we investigated the expression profiles of long noncoding RNAs (lncRNAs) and mRNAs in an ARHL model created with C57BL/6 J mice using RNA sequencing and found that the expression of several lncRNAs was significantly correlated with apoptosis-associated mRNAs in the cochlear tissues of old mice compared to young mice. We found that lncRNA Mirg was upregulated in the cochlear tissues of old mice compared to young mice and its overexpression promoted apoptosis in House Ear Institute-Organ of Corti 1 (HEI-OC1). H2O2-induced oxidative stress increased HEI-OC1 cell apoptosis by upregulating lncRNA Mirg. Furthermore, the expression of lncRNA Mirg and Foxp1 showed the highest correlation coefficient in the cochlear tissues of old mice, and lncRNA Mirg promoted HEI-OC1 cell apoptosis by increasing Foxp1 expression. In conclusion, our findings suggest that lncRNA Mirg expression correlates with cell apoptosis-associated mRNAs in the ARHL model created using C57BL/6 J mice and that oxidative stress-induced lncRNA Mirg promotes HEI-OC1 cell apoptosis by increasing Foxp1 expression. These data suggest the potential therapeutic significance of targeting lncRNA Mirg/Foxp1 signaling in ARHL.

Improved USER cloning for TALE assembly and its application to base editing.

Transcription activator-like effectors (TALEs) have been widely used for genome editing, transcriptional regulation, and locus-specific DNA imaging. However, TALEs are difficult to handle in routine laboratories because of their complexity and the considerable time consumed in TALE construction. Here, we described a simple and rapid TALE assembly method based on uracil-specific excision reagent (USER) cloning. Polymerase chain reaction was amplified with TALE trimer templates and deoxyuridine-containing primers. The products were treated with USER at 37°C for 30 min, followed by the treatment of T4 DNA Ligase at 16°C for 30 min. The TALE trimer unit could be rejoined hierarchically to form complete TALE expression vectors with high efficiency. This method was adopted to construct TALE-deaminases, which were used in combination with Cas9 nickases to generate efficient C-to-T or A-to-G base editing while eliminating predictable DNA off-target effects. This improved USER assembly is a simple, rapid, and laboratory-friendly TALE construction technique that will be valuable for DNA targeting.