Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis.

Transcription factors (TFs) and chromatin-modifying factors (CMFs) access chromatin by recognizing specific DNA motifs in their target genes. Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) has been widely used to discover the potential DNA-binding motifs for both TFs and CMFs. Yet, an in vivo method for verifying DNA motifs captured by ChIP-seq is lacking in plants. Here, we describe the use of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) to verify DNA motifs in their native genomic context in Arabidopsis. Using a single-guide RNA (sgRNA) targeting the DNA motif bound by REF6, a DNA sequence-specific H3K27 demethylase in plants, we generated stable transgenic plants where the motif was disrupted in a REF6 target gene. We also deleted a cluster of multiple motifs from another REF6 target gene using a pair of sgRNAs, targeting upstream and downstream regions of the cluster, respectively. We demonstrated that endogenous genes with motifs disrupted and/or deleted become inaccessible to REF6. This strategy should be widely applicable for in vivo verification of DNA motifs identified by ChIP-seq in plants

The Differential Role of Human Cationic Trypsinogen (PRSS1) p.R122H Mutation in Hereditary and Nonhereditary Chronic Pancreatitis: A Systematic Review and Meta-Analysis.

Background:Environmental factors and genetic mutations have been increasingly recognized as risk factors for chronic pancreatitis (CP). The PRSS1 p.R122H mutation was the first discovered to affect hereditary CP, with 80% penetrance. We performed here a systematic review and meta-analysis to evaluate the associations of PRSS1 p.R122H mutation with CP of diverse etiology. Methods:The PubMed, EMBASE, and MEDLINE database were reviewed. The pooled odds ratio (OR) with 95% confidence intervals was used to evaluate the association of p.R122H mutation with CP. Initial analysis was conducted with all etiologies of CP, followed by a subgroup analysis for hereditary and nonhereditary CP, including alcoholic or idiopathic CP. Results:A total of eight case-control studies (1733 cases and 2415 controls) were identified and included. Overall, PRSS1 p.R122H mutation was significantly associated with an increased risk of CP (OR = 4.78[1.13-20.20]). Further analysis showed p.R122H mutation strongly associated with the increased risk of hereditary CP (OR = 65.52[9.09-472.48]) but not with nonhereditary CP, both alcoholic and idiopathic CP. Conclusions:Our study showing the differential role of p.R122H mutation in various etiologies of CP indicates that this complex disorder is likely influenced by multiple genetic factors as well as environmental factors

The LDL1/2-HDA6 Histone Modification Complex Interacts With TOC1 and Regulates the Core Circadian Clock Components in Arabidopsis

In Arabidopsis, the circadian rhythm is associated with multiple important biological processes and maintained by multiple interconnected loops that generate robust rhythms. The circadian clock central loop is a negative feedback loop composed of the core circadian clock components. TOC1 (TIMING OF CAB EXPRESSION 1) is highly expressed in the evening and negatively regulates the expression of CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)/LHY (LATE ELONGATED HYPOCOTYL). CCA1/LHY also binds to the promoter of TOC1 and represses the TOC1 expression. Our recent research revealed that the histone modification complex comprising of LYSINE-SPECIFIC DEMETHYLASE 1 (LSD1)-LIKE 1/2 (LDL1/2) and HISTONE DEACETYLASE 6 (HDA6) can be recruited by CCA1/LHY to repress TOC1 expression. In this study, we found that HDA6, LDL1, and LDL2 can interact with TOC1, and the LDL1/2-HDA6 complex is associate with TOC1 to repress the CCA1/LHY expression. Furthermore, LDL1/2-HDA6 and TOC1 co-target a subset of genes involved in the circadian rhythm. Collectively, our results indicate that the LDL1/2-HDA6 histone modification complex is important for the regulation of the core circadian clock components

Association of concomitant continuous pain in trigeminal neuralgia with a narrow foramen ovale

BackgroundThe pathogenesis of concomitant continuous pain remains unclear and is worthy of further study. In this clinical study, we aimed to explore the potential role of a narrow foramen ovale in the development of concomitant continuous pain.MethodsA total of 108 patients with classical trigeminal neuralgia affecting the third branch of the trigeminal nerve and 46 healthy individuals were enrolled in this study. Three-dimensional reconstructed computerized tomography images of all participants were collected, and the morphometric features of the foramen ovale were examined by two investigators who were blinded to the clinical data of the patients.ResultsIn this cohort, patients with concomitant continuous pain suffered from more sensory abnormalities (18.4% vs. 2.9%, p = 0.015) and responded more poorly to medication (74.3% vs. 91.9%, p = 0.018) than patients without concomitant continuous pain. While no significant differences regarding the mean length (5.02 mm vs. 5.36 mm, p > 0.05) and area (22.14 mm2 vs. 23.80 mm2, p > 0.05) were observed between patients with and without concomitant continuous pain, the mean width of the foramen ovale on the affected side in patients with concomitant continuous pain was significantly narrower than that in patients without concomitant continuous pain (2.01 mm vs. 2.48 mm, p = 0.003).ConclusionThis neuroimaging and clinical study demonstrated that the development of concomitant continuous pain was caused by the compression of the trigeminal nerve owing to a narrow foramen ovale rather than responsible vessels in classical trigeminal neuralgia

De novo assembly and comparative analysis of cherry (Prunus subgenus Cerasus) mitogenomes

Prunus subgenus Cerasus (Mill) A. Gray, commonly known as cherries and cherry blossoms, possesses significant edible and ornamental value. However, the mitochondrial genomes (mitogenomes) of cherry species remain largely unexplored. Here, we successfully assembled the mitogenomes of five cherry species (P. campanulata, P. fruticosa, P. mahaleb, P. pseudocerasus, and P. speciosa), revealing common circular structures. The assembled mitogenomes exhibited sizes ranging from 383,398 bp to 447,498 bp, with GC content varying between 45.54% and 45.76%. A total of 62 to 69 genes were annotated, revealing variability in the copy number of protein-coding genes (PCGs) and tRNA genes. Mitogenome collinearity analysis indicated genomic rearrangements across Prunus species, driven by repetitive sequences, particularly dispersed repeats. Additionally, the five cherry species displayed highly conserved codon usage and RNA editing patterns, highlighting the evolutionary conservation of the mitochondrial PCGs. Phylogenetic analyses confirmed the monophyly of subg. Cerasus, although notable phylogenetic incongruences were observed between the mitochondrial and plastid datasets. These results provide significant genomic resources for forthcoming studies on the evolution and molecular breeding of cherry mitogenomes, enhancing the overall comprehension of mitogenome structure and evolution within Prunus

Triple-nerve decompression surgery for the treatment of painful diabetic peripheral neuropathy in lower extremities: A study protocol for a randomized controlled trial

ObjectivesPainful diabetic peripheral neuropathy (DPN) is often refractory to conventional medications. Triple-nerve decompression was proposed for painful DPN due to the frequent involvement of multiple nerve entrapments in diabetes. However, the role of decompressive surgery remains controversial. This trial aims to assess the efficacy of triple-nerve decompression for patients with painful DPN suggestive of nerve entrapment using a randomized controlled trial (RCT) design.Methods and analysisThis trial is a single-center RCT and will be conducted in Shanghai Ninth People's Hospital. Enrolled subjects (n = 74) with painful DPN due to nerve compression, which can be detected by nerve conduction studies, will be randomly allocated at a 1:1 ratio into surgical and non-surgical groups. The primary outcome will be measured by 50% responder rates, which is defined as the proportion of subjects with at least 50% reduction of the mean weekly visual analog score (VAS) of pain from baseline after 6 months of treatment. Mean weekly VAS will be additionally evaluated 1 week (W1), 1 month (M1), and 3 months (M3) after treatment to monitor the changes in pain intensity. The secondary outcomes include two-point discrimination (TPD), Toronto clinical scoring system (TCSS), electrophysiological indexes, hospital anxiety and depression scale (HADS), and the medical outcome study short-form 36-item questionnaire (SF-36). A quantitative analgesic questionnaire (QAQ) will be used as a secondary outcome to quantify the analgesic medication weekly. TPD and TCSS will be conducted at W1, M1, M3, and M6 after treatment. Electrophysiological tests, HADS, and SF-36 will be performed at M3 and M6.Ethics and disseminationEthics approval has been obtained from the Ethics Committee of Shanghai Ninth People's Hospital (SH9H-2-21-T323-2). It was registered on the Chinese Clinical Trial Registry website (http://www.chictr.org.cn) on 16 August 2021 with the number ChiCTR2100050049. Written informed consent will be obtained from all participants. The results of this trial will be disseminated via peer-reviewed journals, mass media, and presentations at national and international academic conferences

Dynamical Evolution of Anisotropic Response in Black Phosphorus under Ultrafast Photoexcitation

Black phosphorus has recently emerged as a promising material for high performance electronic and optoelectronic device for its high mobility, tunable mid-infrared bandgap and anisotropic electronic properties. Dynamical evolution of photo excited carriers and its induced change of transient electronic properties are critical for materials' high field performance, but remains to be explored for black phosphorus. In this work, we perform angle resolved transient reflection spectroscopy to study the dynamical evolution of anisotropic properties of black phosphorus under photo excitation. We find that the anisotropy of reflectivity is enhanced in the pump induced quasi-equilibrium state, suggesting an extraordinary enhancement of the anisotropy in dynamical conductivity in hot carrier dominated regime. These results raise enormous possibilities of creating high field, angle sensitive electronic, optoelectronic and remote sensing devices exploiting the dynamical electronic anisotropic with black phosphorus.Comment: 22 pages,10 figure