HPV integration generates a cellular super-enhancer which functions as ecDNA to regulate genome-wide transcription.

Human papillomavirus (HPV) integration is a critical step in cervical cancer development; however, the oncogenic mechanism at the genome-wide transcriptional level is still poorly understood. In this study, we employed integrative analysis on multi-omics data of six HPV-positive and three HPV-negative cell lines. Through HPV integration detection, super-enhancer (SE) identification, SE-associated gene expression and extrachromosomal DNA (ecDNA) investigation, we aimed to explore the genome-wide transcriptional influence of HPV integration. We identified seven high-ranking cellular SEs generated by HPV integration in total (the HPV breakpoint-induced cellular SEs, BP-cSEs), leading to intra-chromosomal and inter-chromosomal regulation of chromosomal genes. The pathway analysis revealed that the dysregulated chromosomal genes were correlated to cancer-related pathways. Importantly, we demonstrated that BP-cSEs existed in the HPV-human hybrid ecDNAs, explaining the above transcriptional alterations. Our results suggest that HPV integration generates cellular SEs that function as ecDNA to regulate unconstrained transcription, expanding the tumorigenic mechanism of HPV integration and providing insights for developing new diagnostic and therapeutic strategies.

Comparison of the differentiation of dental pulp stem cells and periodontal ligament stem cells into neuron-like cells and their effects on focal cerebral ischemia.

Recent studies have reported an increasing incidence of ischemic stroke, particularly in younger age groups. Dental pulp stem cells (DPSCs) and periodontal ligament stem cells (PDLSCs) are the most common stem cells acquired from the teeth of adults, even elderly people. However, there are no detailed reports on whether DPSCs or PDLSCs are suitable for the treatment of ischemic stroke. In this study, the in vitro differentiation of DPSCs and PDLSCs into neuron-like cells was evaluated. Then, we established a rat model of cerebral ischemia. DPSCs or PDLSCs were administered to animals, and the therapeutic effects of these two types of cells were investigated. The results showed that PDLSCs had a higher differentiation rate than DPSCs. Immunofluorescence studies showed that the expression of the neuronal differentiation marker Thy-1 was higher in PDLSCs than in DPSCs, and other gene markers of neuronal differentiation showed corresponding trends, which were confirmed by western blot analysis. In this process, the Notch and Wnt signaling pathways were inhibited and activated, respectively. Finally, rats with transient occlusion of the right middle cerebral artery were used as a model to assess the therapeutic effect of PDLSCs and DPSCs on ischemia. The results showed that rats in the PDLSC-treated group emitted significantly greater red fluorescence signal than the DPSC-treated group. PDLSC transplantation promoted the recovery of neurological function more effectively than DPSC transplantation. Hence, PDLSCs represent an autogenous source of adult mesenchymal stem cells with desirable biological properties and may be an ideal candidate for clinical applications.

Non-uniformity correction of polarization response for liquid crystal modulated polarimeters.

Liquid crystal modulated polarimeters (LCMPs) are often used to detect the full polarization information of target scenes. In this study, a non-uniformity correction method based on reference source calibration for LCMP is proposed. We analyze the error sources of the polarimeter and establish a grayscale response model with non-uniformity noises. The gain and bias correction coefficient of each pixel is calculated based on the linear response property of the detector. The polarization parameters of each detection unit of the uniform light source with the same polarization state calculated by the corrected Stokes vector are uniform. Results show that the error of the degree of linear polarization is reduced by 5.08%, and the degree of circular polarization is reduced by 19%. Therefore, the proposed method effectively improves the non-uniformity and detection accuracy of polarimeters.

miR-30 family members negatively regulate osteoblast differentiation.

miRNAs are endogenously expressed 18- to 25-nucleotide RNAs that regulate gene expression through translational repression by binding to a target mRNA. Recently, it has been indicated that miRNAs are closely related to osteogenesis. Our previous data suggested that miR-30 family members might be important regulators during the biomineralization process. However, whether and how they modulate osteogenic differentiation have not been explored. In this study, we demonstrated that miR-30 family members negatively regulate BMP-2-induced osteoblast differentiation by targeting Smad1 and Runx2. Evidentially, overexpression of miR-30 family members led to a decrease of alkaline phosphatase activity, whereas knockdown of them increased the activity. Then bioinformatic analysis identified potential target sites of the miR-30 family located in the 3' untranslated regions of Smad1 and Runx2. Western blot analysis and quantitative RT-PCR assays demonstrated that miR-30 family members inhibit Smad1 gene expression on the basis of repressing its translation. Furthermore, dual-luciferase reporter assays confirmed that Smad1 is a direct target of miR-30 family members. Rescue experiments that overexpress Smad1 and Runx2 significantly eliminated the inhibitory effect of miR-30 on osteogenic differentiation and provided strong evidence that miR-30 mediates the inhibition of osteogenesis by targeting Smad1 and Runx2. Also, the inhibitory effects of the miR-30 family were validated in mouse bone marrow mesenchymal stem cells. Therefore, our study uncovered that miR-30 family members are key negative regulators of BMP-2-mediated osteogenic differentiation.

Cerebral Hemodynamic Changes during Unaffected Handgrip Exercises in Stroke Patients: An fNIRS Study.

This study aimed to assess the effect of the altered strength of the sound limb on the hemodynamics in the affected brain of stroke patients. We recruited 20 stroke patients to detect changes in the HbO concentrations in the bilateral prefrontal cortex (PFC), sensorimotor cortex (SMC), and occipital lobe (OL). We performed functional near-infrared spectroscopy (fNIRS) to detect changes in oxyhemoglobin (HbO) concentrations in regions of interest (ROIs) in the bilateral cerebral hemispheres of stroke patients while they performed 20%, 50%, and 80% maximal voluntary contraction (MVC) levels of handgrip tasks with the unaffected hands. The results suggest that when patients performed handgrip tasks with 50% of the MVC force, SMC in the affected cerebral hemisphere was strongly activated and the change in the HbO concentration was similar to that of the handgrip with 80% of MVC. When the force was 50% of MVC, the SMC in the affected hemisphere showed a more proportional activation than that at 80% MVC. Overall, this research suggests that stroke patients with a poor upper limb function should perform motor training with their sound hands at 50% of the MVC grip task to activate the ipsilesional hemisphere.

Mechanical digit sensory stimulation: a randomized control trial on neurological and motor recovery in acute stroke.

Background: Mechanical digit sensory stimulation (MDSS) is a novel therapy designed to accelerate the recovery of upper limb (including hand) function in patients with hemiplegia following a stroke. The primary goal of this study was to investigate the effect of MDSS on patients with acute ischemic stroke (AIS). Methods: Sixty-one inpatients with AIS were randomly divided into conventional rehabilitation group (RG) and stimulation group (SG), and the latter group received MDSS therapy. A healthy group consisting of 30 healthy adults was also included. The interleukin-17A (IL-17A), vascular endothelial growth factor A (VEGF-A), and tumor necrosis factor-alpha (TNF-α) plasma levels were measured in all subjects. The neurological and motor functions of patients were evaluated using the National Institutes of Health Stroke Scale (NIHSS), Mini-Mental State Examination (MMSE), Fugel-Meyer Assessment (FMA), and Modified Barthel Index (MBI). Results: After 12 days of intervention, the IL-17A, TNF-α, and NIHSS levels were significantly decreased, while the VEGF-A, MMSE, FMA, and MBI levels were significantly increased in both disease groups. No significant difference was observed between both disease groups after intervention. The levels of IL-17A and TNF-α were positively correlated with NIHSS but negatively correlated with MMSE, FMA, and MBI. The VEGF-A levels were negatively correlated with NIHSS but positively correlated with MMSE, FMA, and MBI. Conclusion: Both MDSS and conventional rehabilitation significantly reduce the production of IL-17A and TNF-α, increase the VEGF-A levels, and effectively improve cognition and motor function of hemiplegic patients with AIS, and the effects of MDSS and conventional rehabilitation are comparable.

Massively parallel CRISPR off-target detection enables rapid off-target prediction model building.

BACKGROUND: CRISPR (clustered regularly interspaced short palindromic repeats) genome editing holds tremendous potential in clinical translation. However, the off-target effect has always been a major concern. METHODS: Here, we have developed a novel sensitive and specific off-target detection method, AID-seq (adaptor-mediated off-target identification by sequencing), that can comprehensively and faithfully detect the low-frequency off targets generated by different CRISPR nucleases (including Cas9 and Cas12a). FINDINGS: Based on AID-seq, we developed a pooled strategy to simultaneously identify the on/off targets of multiple gRNAs, as well as using mixed human and human papillomavirus (HPV) genomes to screen the most efficient and safe targets from 416 HPV gRNA candidates for antiviral therapy. Moreover, we used the pooled strategy with 2,069 single-guide RNAs (sgRNAs) at a pool size of about 500 to profile the properties of our newly discovered CRISPR, FrCas9. Importantly, we successfully built an off-target detection model using these off-target data via the CRISPR-Net deep learning method (area under the receiver operating characteristic curve [AUROC] = 0.97, area under the precision recall curve [AUPRC] = 0.29). CONCLUSIONS: To our knowledge, AID-seq is the most sensitive and specific in vitro off-target detection method to date. And the pooled AID-seq strategy can be used as a rapid and high-throughput platform to select the best sgRNAs and characterize the properties of new CRISPRs. FUNDING: This work was supported by The National Natural Science Foundation of China (grant nos. 32171465 and 82102392), the General Program of Natural Science Foundation of Guangdong Province of China (grant no. 2021A1515012438), Guangdong Basic and Applied Basic Research Foundation (grant no. 2020A1515110170), and the National Ten Thousand Plan-Young Top Talents of China (grant no. 80000-41180002).

The complete chloroplast genome of Vandenboschia striata, a common and widespread filmy fern (Hymenophyllaceae).

Vandenboschia striata is a common and widespread filmy fern of Hymenophyllaceae. Its complete chloroplast genome is 147,014 bp in length, including a large single copy (LSC) region of 89,886 bp, a small single copy (SSC) region of 20,850 bp, and a pair of inverted repeats (IRs) of 18,139 bp. Totally, 132 genes are predicted in the cp genome embodies, including 88 protein coding genes, 36 tRNA genes, and eight rRNA genes. A maximum-likelihood tree was constructed to explore phylogenetic relationship. The result showed that V. striata was sister to V.speciosa with 100% bootstrap support. The complete chloroplast genome sequences of V. striata would be beneficial to further phylogenetic survey on classification of the related species or genera in Hymenophyllaceae.

Application of a Brain-Computer Interface System with Visual and Motor Feedback in Limb and Brain Functional Rehabilitation after Stroke: Case Report.

(1) Objective: To investigate the feasibility, safety, and effectiveness of a brain-computer interface (BCI) system with visual and motor feedback in limb and brain function rehabilitation after stroke. (2) Methods: First, we recruited three hemiplegic stroke patients to perform rehabilitation training using a BCI system with visual and motor feedback for two consecutive days (four sessions) to verify the feasibility and safety of the system. Then, we recruited five other hemiplegic stroke patients for rehabilitation training (6 days a week, lasting for 12-14 days) using the same BCI system to verify the effectiveness. The mean and Cohen's w were used to compare the changes in limb motor and brain functions before and after training. (3) Results: In the feasibility verification, the continuous motor state switching time (CMSST) of the three patients was 17.8 ± 21.0s, and the motor state percentages (MSPs) in the upper and lower limb training were 52.6 ± 25.7% and 72.4 ± 24.0%, respectively. The effective training revolutions (ETRs) per minute were 25.8 ± 13.0 for upper limb and 24.8 ± 6.4 for lower limb. There were no adverse events during the training process. Compared with the baseline, the motor function indices of the five patients were improved, including sitting balance ability, upper limb Fugel-Meyer assessment (FMA), lower limb FMA, 6 min walking distance, modified Barthel index, and root mean square (RMS) value of triceps surae, which increased by 0.4, 8.0, 5.4, 11.4, 7.0, and 0.9, respectively, and all had large effect sizes (Cohen's w ≥ 0.5). The brain function indices of the five patients, including the amplitudes of the motor evoked potentials (MEP) on the non-lesion side and lesion side, increased by 3.6 and 3.7, respectively; the latency of MEP on the non-lesion side was shortened by 2.6 ms, and all had large effect sizes (Cohen's w ≥ 0.5). (4) Conclusions: The BCI system with visual and motor feedback is applicable in active rehabilitation training of stroke patients with hemiplegia, and the pilot results show potential multidimensional benefits after a short course of treatment.

Changes and roles of IL-17A, VEGF-A and TNF-α in patients with cerebral infarction during the acute phase and early stage of recovery.

BACKGROUND AND PURPOSE: Interleukin 17A (IL-17A), vascular endothelial growth factor A (VEGF-A) and tumour necrosis factor alpha (TNF-α) are important cytokines detected mostly within two weeks after stroke in previous clinical studies. Longer clinical studies investigating these cytokines are lacking. We aimed to explore the roles of these cytokines in patients within 35 days after cerebral infarction. METHODS: Thirty patients with cerebral infarction and 30 healthy individuals were enrolled. Venous blood was collected from each patient at specific times and from each healthy individual only once. Coma and neurological functional deficits of the patients were evaluated by the Glasgow Coma Scale (GCS) and the National Institutes of Health Stroke Scale (NIHSS), respectively. Three cytokines were measured. The correlations among the three cytokines and between each cytokine and the GCS/NIHSS scores were analysed. RESULTS: IL-17A and TNF-α began to increase on day 1 after cerebral infarction, peaked on day 4, then decreased, and increased again on day 18. IL-17A returned to normal on day 35, but TNF-α remained higher than normal on day 35. VEGF-A began to increase on day 1, peaked on day 7, and returned to normal on day 35. From days 18 to 35, IL-17A was positively correlated with the GCS scores, and both IL-17A and VEGF-A were negatively correlated with the NIHSS scores. CONCLUSION: After cerebral infarction, VEGF-A from the acute phase and IL-17A from the early stage of recovery may be important for nerve protection and repair; TNF-α plays a complex role within 35 days.

Wide field-of-view imaging spectrometer using imaging fiber bundles.

A field-of-view-folding approach is proposed to extend the field of view (FOV) of a dispersive imaging spectrometer after introducing several linear arrays of imaging fiber bundles to which to replace the slit. The fiber bundles can flexibly connect fore-optics with a spectrometer to yield an imaging fiber-optic spectrometer (IFOS). The technology of FOV segmenting and folding, which can decrease simultaneously the dimension and spectral distortion of the imaging spectrometer, is described in detail. Because of the sampling function of the fiber bundles, the IFOS is a double-sampling imaging system. We analyze the effect of fiber coupling on the modulation transfer function (MTF) and then develop a cascade MTF model to estimate the imaging performance of the IFOS. A spaceborne IFOS example is presented to describe how the method can be used.

[Effect of spectrum distortion on modulation transfer function in imaging fiber-optic spectrometer].

Imaging fiber bundles were introduced to dispersion imaging spectrometer and substituted for slit, connecting the telescope and spectrometer to yield the imaging fiber-optic spectrometer. It is a double sampling system, the misalignment between image of optical fiber and detector pixel has arisen because of the spectrum distortion of spectrometer, which affected the second sampling process, and the modulation transfer function (MTF) therefore degraded. Optical transfer function of sampling process was derived from line spread function. The effect of spectrum distortion on system MTF was analyzed, and a model evaluating the MTF of imaging fiber-optic spectrometer was developed. Compared to the computation model of MTF of slit imaging spectrometer, a MTF item of sampling by optical fiber and a MTF item of misalignment arising from spectrum distortion were added in this model. Employing this, the MTF of an airborne imaging fiber-optic spectrometer for visible near infrared band was evaluated. The approach ro deriving and developing the MTF model has a reference signification for the computation of MTF of double sampling system, which can direct the design of imaging fiber-optic spectrometer also.

First Multi-Organ Full-Length Transcriptome of Tree Fern Alsophila spinulosa Highlights the Stress-Resistant and Light-Adapted Genes.

Alsophila spinulosa, a relict tree fern, is a valuable plant for investigating environmental adaptations. Its genetic resources, however, are scarce. We used the PacBio and Illumina platforms to sequence the polyadenylated RNA of A. spinulosa root, rachis, and pinna, yielding 125,758, 89,107, and 89,332 unigenes, respectively. Combining the unigenes from three organs yielded a non-redundant reference transcriptome with 278,357 unigenes and N50 of 4141 bp, which were further reconstructed into 38,470 UniTransModels. According to functional annotation, pentatricopeptide repeat genes and retrotransposon-encoded polyprotein genes are the most abundant unigenes. Clean reads mapping to the full-length transcriptome is used to assess the expression of unigenes. The stress-induced ASR genes are highly expressed in all three organs, which is validated by qRT-PCR. The organ-specific upregulated genes are enriched for pathways involved in stress response, secondary metabolites, and photosynthesis. Genes for five types of photoreceptors, CRY signaling pathway, ABA biosynthesis and transduction pathway, and stomatal movement-related ion channel/transporter are profiled using the high-quality unigenes. The gene expression pattern coincides with the previously identified stomatal characteristics of fern. This study is the first multi-organ full-length transcriptome report of a tree fern species, the abundant genetic resources and comprehensive analysis of A. spinulosa, which provides the groundwork for future tree fern research.

Interleukin-17A promotes the differentiation of bone marrow mesenchymal stem cells into neuronal cells.

Ischemia or hemorrhagic stroke is one of the leading causes of death and permanent disability in the worldwide population. As a consequence of the potential increasing in stroke, stem cell therapy is currently an area of intense focus. However, there are less data available regarding the promotion of healing efficacy after stroke. The present study aimed to investigate whether the cytokine interleukin-17A (IL-17A) could have a role in promoting the neuronal differentiation of mesenchymal stem cells (MSCs) and to investigate the associated molecular mechanism. Firstly, different concentration of IL-17A at range from 5-40 ng/mL was applied to stimulate bone marrow MSCs (BMSCs) during the course of neurogenic differentiation. Then reverse transcription-PCR, histological analyses and immunofluorescence assays were used to determine the optimum concentration of IL-17A in promoting the neuronal differentiation of BMSCs, which was 20 ng/mL. Mechanistically, Wnt signaling pathway was activated and Notch signaling pathway was suppressed. In addition, there were antergic effect of these two signaling pathways modulating the neurogenic differentiation of BMSCs induced by IL-17A. The present study demonstrated the potential role of IL-17A-based BMSCs strategy for promoting neuronal differentiation in vitro. However, the treatment efficacy could be considerably confirmed in animals with ischemia stroke. Therefore, a more sophisticated strategy that addresses the complicated treatment associated with stroke is needed.

The complete chloroplast genome of Alsophila latebrosa, a common and widespread tree fern (Cyatheaceae).

Alsophila latebrosa is a common and widespread tree fern of Cyatheaceae. Its complete chloroplast genome is first assembled and reported with 155,724 bp in length, including a large single copy (LSC) region of 85,800 bp, a small single copy (SSC) region of 21,620 bp, and a pair of inverted repeats (IRs) of 24,152 bp. The genome has 133 genes, including 89 protein-coding genes, 33 tRNA genes, eight rRNA genes and three pseudogenes. Maximum likelihood approach was employed to construct the phylogenetic relationship among ten ferns including A. latebrosa. The result showed that A. latebrosa was most related to A. costularis as a sister group with 100% bootstrap support. The complete chloroplast genome sequences of A. latebrosa will provide valuable genomic information to further illuminate phylogenetic classification of Cyatheacea.

The complete chloroplast genome of Lemmaphyllum intermedium, a valuable medicinal fern.

Lemmaphyllum intermedium is a valuable medicinal fern in China. We have determined its complete chloroplast genome using Illumina paired-end sequencing. The genome is 157,795 bp in length with 132 genes, including 88 protein-coding genes, eight ribosomal RNA genes, 35 tRNA genes, and one pseudogene. It has a quadripartite structure consisting of a small single-copy (SSC) of 21,764 bp, a large single-copy (LSC) of 81,189 bp, and two inverted repeats (IRs) of 27,421 bp each. A maximum-likelihood phylogenetic tree reconstructed by using complete chloroplast genome sequences reveals that L. intermedium is closely related to Lemmaphyllum carnosum var. microphyllum with strong support.

Dendrobium officinale polysaccharide-induced neuron-like cells from bone marrow mesenchymal stem cells improve neuronal function a rat stroke model.

Various methods have been used to induce the neuronal differentiation of marrow mesenchymal stem cells (MSCs). However, the limited induction efficiency of cells in vitro has restricted their use. Therefore, identifying a simple and efficient treatment method is necessary. Dendrobium officinale is an important traditional Chinese medicine, and its main component, polysaccharides, has many pharmacological activities. However, the effects of D. officinale polysaccharide (DOP) on the neuronal differentiation of bone marrow mesenchymal stem cells (BMSCs) and treatment of ischaemic stroke remain unknown. We found that DOP promoted the neuronal differentiation of BMSCs by increasing the expression levels of neural markers, and the optimal concentration of DOP was 25 µg/mL. Additionally, the Notch signalling pathway was inhibited during the neuronal differentiation of BMSCs induced by DOP, and this effect was strengthened using an inhibitor of this pathway. The Wnt signalling pathway was activated during the differentiation of BMSCs, and inhibition of the Wnt signalling pathway downregulated the expression of neuronal genes. Furthermore, the transplantation of neuron-like cells induced by DOP improved neuronal recovery, as the brain infarct volume, neurologic severity scores and levels of inflammatory factors were all significantly reduced in vivo. In conclusion, DOP is an effective inducer of the neuronal differentiation of BMSCs and treatment option for ischaemic stroke.

Genome Survey Sequencing of In Vivo Mother Plant and In Vitro Plantlets of Mikania cordata.

Mikania cordata, the only native congener of the invasive weed Mikania micrantha in China, is an ideal species for comparative study to reveal the invasion mechanism. However, its genome resources are lagging far behind its congener, which limits the comparative genomic analysis. Our goal is to characterize the genome of M. cordata by next-generation sequencing and propose a scheme for long-read genome sequencing. Previous studies have shown that the genomic resources of the host plant would be affected by the endophytic microbial DNA. An aseptic sample of M. cordata will ensure the proper genome in downstream analysis. Because endophytes are ubiquitous in the greenhouse-grown M. cordata, the in vitro culture with cefotaxime or timentin treatment was undertaken to obtain the aseptic plantlets. The in vivo mother plant and in vitro plantlets were used to survey the genome. The microbial contamination in M. cordata was recognized by blast search and eliminated from the raw reads. The decontaminated sequencing reads were used to predict the genome size, heterozygosity, and repetitive rate. The in vivo plant was so contaminated that microbes occupied substantial sequencing resources and misled the scaffold assembly. Compared with cefotaxime, treatment with timentin performed better in cultivating robust in vitro plantlets. The survey result from the in vitro plantlets was more accurate due to low levels of contamination. The genome size was estimated to be 1.80 Gb with 0.50% heterozygosity and 78.35% repetitive rate. Additionally, 289,831 SSRs were identified in the genome. The genome is heavily contaminated and repetitive; therefore, the in vitro culture technique and long-read sequencing technology are recommended to generate a high-quality and highly contiguous genome.

The complete chloroplast genome sequence of Plagiogyria euphlebia, a fascinating fern with important taxonomic significance.

It is the first report on the complete chloroplast genome of Plagiogyria euphlebia, a fascinating fern with important taxonomic significance. Its genome size is 161,046 bp with 43.5% GC content, including a large single copy (LSC) region (90,975 bp), a small single copy (SSC) region (21,441 bp), and a pair of inverted repeats (IRa and IRb) regions (24,315 bp). The cp genome has 133 genes involving 89 protein-coding genes, 33 tRNA genes, and three pseudogenes. ML tree reveals that P. euphlebia is sister to Cyatheales, especially closely related to Cibotium barometz.

Characterization of the complete chloroplast genome of Leptochilus decurrens (Polypodiaceae), a least concern folk medicinal fern.

Leptochilus decurrens is a small tropical fern of Polypodiaceae, but also a least concern folk medicinal fern. Its genome size is 153,753 bp with a pair of 21,664 bp inverted repeat regions (IR), a large single-copy (LSC) region of 84,395 bp and a small single-copy (SSC) region of 26,030 bp. A total of 133 genes were predicted, including 88 protein-coding genes, 37 tRNA genes and eight rRNA genes. The ML analysis reveals that L. decurrens is sister to Leptochilus hemionitideus forming monophyletic group closely related with polypodiaceous ferns. The work provides vigorous molecular data to further promote phylogenetics of Polypodiaceae.