Genomic analysis and characterization of phages infecting the marine Roseobacter CHAB-I-5 lineage reveal a globally distributed and abundant phage genus

Marine phages play an important role in marine biogeochemical cycles by regulating the death, physiological metabolism, and evolutionary trajectory of bacteria. The Roseobacter group is an abundant and important heterotrophic bacterial group in the ocean, and plays an important role in carbon, nitrogen, sulfur and phosphorus cycling. The CHAB-I-5 lineage is one of the most dominant Roseobacter lineages, but remains largely uncultured. Phages infecting CHAB-I-5 bacteria have not yet been investigated due to the lack of culturable CHAB-I-5 strains. In this study, we isolated and sequenced two new phages (CRP-901 and CRP-902) infecting the CHAB-I-5 strain FZCC0083. We applied metagenomic data mining, comparative genomics, phylogenetic analysis, and metagenomic read-mapping to investigate the diversity, evolution, taxonomy, and biogeography of the phage group represented by the two phages. The two phages are highly similar, with an average nucleotide identity of 89.17%, and sharing 77% of their open reading frames. We identified several genes involved in DNA replication and metabolism, virion structure, DNA packing, and host lysis from their genomes. Metagenomic mining identified 24 metagenomic viral genomes closely related to CRP-901 and CRP-902. Genomic comparison and phylogenetic analysis demonstrated that these phages are distinct from other known viruses, representing a novel genus-level phage group (CRP-901-type). The CRP-901-type phages do not contain DNA primase and DNA polymerase genes, but possess a novel bifunctional DNA primase-polymerase gene with both primase and polymerase activities. Read-mapping analysis showed that the CRP-901-type phages are widespread across the world’s oceans and are most abundant in estuarine and polar waters. Their abundance is generally higher than other known roseophages and even higher than most pelagiphages in the polar region. In summary, this study has greatly expanded our understanding of the genetic diversity, evolution, and distribution of roseophages. Our analysis suggests that the CRP-901-type phage is an important and novel marine phage group that plays important roles in the physiology and ecology of roseobacters

Misregulation of Alternative Splicing in a Mouse Model of Rett Syndrome

Mutations in the human MECP2 gene cause Rett syndrome (RTT), a severe neurodevelopmental disorder that predominantly affects girls. Despite decades of work, the molecular function of MeCP2 is not fully understood. Here we report a systematic identification of MeCP2-interacting proteins in the mouse brain. In addition to transcription regulators, we found that MeCP2 physically interacts with several modulators of RNA splicing, including LEDGF and DHX9. These interactions are disrupted by RTT causing mutations, suggesting that they may play a role in RTT pathogenesis. Consistent with the idea, deep RNA sequencing revealed misregulation of hundreds of splicing events in the cortex of Mecp2 knockout mice. To reveal the functional consequence of altered RNA splicing due to the loss of MeCP2, we focused on the regulation of the splicing of the flip/flop exon of Gria2 and other AMPAR genes. We found a significant splicing shift in the flip/flop exon toward the flop inclusion, leading to a faster decay in the AMPAR gated current and altered synaptic transmission. In summary, our study identified direct physical interaction between MeCP2 and splicing factors, a novel MeCP2 target gene, and established functional connection between a specific RNA splicing change and synaptic phenotypes in RTT mice. These results not only help our understanding of the molecular function of MeCP2, but also reveal potential drug targets for future therapies

Anticonvulsant activities of α-asaronol ((E)-3'-hydroxyasarone), an active constituent derived from α-asarone.

BACKGROUND: Epilepsy is one of chronic neurological disorders that affects 0.5-1.0% of the world's population during their lifetime. There is a still significant need to develop novel anticonvulsant drugs that possess superior efficacy, broad spectrum of activities and good safety profile. METHODS: α-Asaronol and two current antiseizure drugs (α-asarone and carbamazepine (CBZ)) were assessed by in vivo anticonvulsant screening with the three most employed standard animal seizure models, including maximal electroshock seizure (MES), subcutaneous injection-pentylenetetrazole (PTZ)-induced seizures and 3-mercaptopropionic acid (3-MP)-induced seizures in mice. Considering drug safety evaluation, acute neurotoxicity was assessed with minimal motor impairment screening determined in the rotarod test, and acute toxicity was also detected in mice. RESULTS: In our results, α-asaronol displayed a broad spectrum of anticonvulsant activity (ACA) and showed better protective indexes (PI = 11.11 in MES, PI = 8.68 in PTZ) and lower acute toxicity (LD50 = 2940 mg/kg) than its metabolic parent compound (α-asarone). Additionally, α-asaronol displayed a prominent anticonvulsant profile with ED50 values of 62.02 mg/kg in the MES and 79.45 mg/kg in the sc-PTZ screen as compared with stiripentol of ED50 of 240 mg/kg and 115 mg/kg in the relevant test, respectively. CONCLUSION: The results of the present study revealed α-asaronol can be developed as a novel molecular in the search for safer and efficient anticonvulsants having neuroprotective effects as well as low toxicity. Meanwhile, the results also suggested that α-asaronol has great potential to develop into another new aromatic allylic alcohols type anticonvulsant drug for add-on therapy of Dravet's syndrome

Phase diagrams on composition-spread Fey_yTe1−x_{1-x}Sex_x films

Fe$_y$Te$_{1-x}$Se$_x$, an archetypical iron-based high-temperature superconductor with a simple structure but rich physical properties, has attracted lots of attention because the two end compositions, Se content $x = 0$ and 1, exhibit antiferromagnetism and nematicity, respectively, making it an ideal candidate for studying their interactions with superconductivity. However, what is clearly lacking to date is a complete phase diagram of Fe$_y$Te$_{1-x}$Se$_x$ as functions of its chemical compositions since phase separation usually occurs from $x\sim 0.6$ to 0.9 in bulk crystals. Moreover, fine control of its composition is experimentally challenging because both Te and Se are volatile elements. Here we establish a complete phase diagram of Fe$_y$Te$_{1-x}$Se$_x$, achieved by high-throughput film synthesis and characterization techniques. An advanced combinatorial synthesis process enables us to fabricate an epitaxial composition-spread Fe$_y$Te$_{1-x}$Se$_x$ film encompassing the entire Se content $x$ from 0 to 1 on a single piece of CaF$_2$ substrate. The micro-region composition analysis and X-ray diffraction show a successful continuous tuning of chemical compositions and lattice parameters, respectively. The micro-scale pattern technique allows the mapping of electrical transport properties as a function of relative Se content with an unprecedented resolution of 0.0074. Combining with the spin patterns in literature, we build a detailed phase diagram that can unify the electronic and magnetic properties of Fe$_y$Te$_{1-x}$Se$_x$. Our composition-spread Fe$_y$Te$_{1-x}$Se$_x$ films, overcoming the challenges of phase separation and precise control of chemical compositions, provide an ideal platform for studying the relationship between superconductivity and magnetism.Comment: 13 pages,5 figures and Supplementary Material 3 pages,3 figure

Single underwater image enhancement based on adaptive correction of channel differential and fusion

Clear underwater images are necessary in many underwater applications, while absorption, scattering, and different water conditions will lead to blurring and different color deviations. In order to overcome the limitations of the available color correction and deblurring algorithms, this paper proposed a fusion-based image enhancement method for various water areas. We proposed two novel image processing methods, namely, an adaptive channel deblurring method and a color correction method, by limiting the histogram mapping interval. Subsequently, using these two methods, we took two images from a single underwater image as inputs of the fusion framework. Finally, we obtained a satisfactory underwater image. To validate the effectiveness of the experiment, we tested our method using public datasets. The results showed that the proposed method can adaptively correct color casts and significantly enhance the details and quality of attenuated underwater images

Preliminary Study:Learning the Impact of Simulation Time on Reentry Location and Morphology Induced by Personalized Cardiac Modeling

Personalized cardiac modeling is widely used for studying the mechanisms of cardiac arrythmias. Due to the high demanding of computational resource of modeling, the arrhythmias induced in the models are usually simulated for just a few seconds. In clinic, it is common that arrhythmias last for more than several minutes and the morphologies of reentries are not always stable, so it is not clear that whether the simulation of arrythmias for just a few seconds is long enough to match the arrhythmias detected in patients. This study aimed to observe how long simulation of the induced arrhythmias in the personalized cardiac models is sufficient to match the arrhythmias detected in patients. A total of 5 contrast enhanced MRI datasets of patient hearts with myocardial infarction were used in this study. Then, a classification method based on Gaussian mixture model was used to detect the infarct tissue. For each reentry, 3 s and 10 s were simulated. The characteristics of each reentry simulated for different duration were studied. Reentries were induced in all 5 ventricular models and sustained reentries were induced at 39 stimulation sites in the model. By analyzing the simulation results, we found that 41% of the sustained reentries in the 3 s simulation group terminated in the longer simulation groups (10 s). The second finding in our simulation was that only 23.1% of the sustained reentries in the 3 s simulation did not change location and morphology in the extended 10 s simulation. The third finding was that 35.9% reentries were stable in the 3 s simulation and should be extended for the simulation time. The fourth finding was that the simulation results in 10 s simulation matched better with the clinical measurements than the 3 s simulation. It was shown that 10 s simulation was sufficient to make simulation results stable. The findings of this study not only improve the simulation accuracy, but also reduce the unnecessary simulation time to achieve the optimal use of computer resources to improve the simulation efficiency and shorten the simulation time to meet the time node requirements of clinical operation on patients

A splicing isoform of TEAD4 attenuates the Hippo–YAP signalling to inhibit tumour proliferation

Aberrant splicing is frequently found in cancer, yet the biological consequences of such alterations are mostly undefined. Here we report that the Hippo–YAP signalling, a key pathway that regulates cell proliferation and organ size, is under control of a splicing switch. We show that TEAD4, the transcription factor that mediates Hippo–YAP signalling, undergoes alternative splicing facilitated by the tumour suppressor RBM4, producing a truncated isoform, TEAD4-S, which lacks an N-terminal DNA-binding domain, but maintains YAP interaction domain. TEAD4-S is located in both the nucleus and cytoplasm, acting as a dominant negative isoform to YAP activity. Consistently, TEAD4-S is reduced in cancer cells, and its re-expression suppresses cancer cell proliferation and migration, inhibiting tumour growth in xenograft mouse models. Furthermore, TEAD4-S is reduced in human cancers, and patients with elevated TEAD4-S levels have improved survival. Altogether, these data reveal a splicing switch that serves to fine tune the Hippo–YAP pathway

Knowledge mapping and research hotspots of immunotherapy in renal cell carcinoma: A text-mining study from 2002 to 2021

BackgroundRenal cell carcinoma (RCC) is one of the most lethal urological malignancies, and because early-stage RCC is asymptomatic, many patients present metastatic diseases at first diagnosis. With the development of immunotherapy, the treatment of RCC has entered a new stage and has made a series of progress. This study mainly outlines the knowledge map and detects the potential research hotspots by using bibliometric analysis.MethodsPublications concerning RCC immunotherapy from 2002 to 2021 in the Web of Science Core Collection were collected. Visualization and statistical analysis were mainly performed by freeware tools VOSviewer, CiteSpace, R software, and Microsoft Office Excel 2019.ResultsA total of 3,432 papers were collected in this study, and the annual number of papers and citations showed a steady growth trend. The United States is the leading country with the most high-quality publications and is also the country with the most international cooperation. The University of Texas MD Anderson Cancer Center is the most productive organization. The Journal of Clinical Oncology is the highest co-cited journal, and Brian I. Rini is both the most prolific author and the author with the largest centrality. The current research hotspots may be focused on “immune checkpoint inhibitors (ICIs),” “PD-1,” and “mammalian target of rapamycin.”ConclusionImmunotherapy has a bright future in the field of RCC treatment, among which ICIs are one of the most important research hotspots. The main future research directions of ICI-based immunotherapy may focus on combination therapy, ICI monotherapy, and the development of new predictive biomarkers