mazF, a novel counter-selectable marker for unmarked chromosomal manipulation in Bacillus subtilis

Here, we present a novel method for the directed genetic manipulation of the Bacillus subtilis chromosome free of any selection marker. Our new approach employed the Escherichia coli toxin gene mazF as a counter-selectable marker. The mazF gene was placed under the control of an isopropyl-β-d-thiogalactopyranoside (IPTG)-inducible expression system and associated with a spectomycin-resistance gene to form the MazF cassette, which was flanked by two directly-repeated (DR) sequences. A double-crossover event between the linearized delivery vector and the chromosome integrated the MazF cassette into a target locus and yielded an IPTG-sensitive strain with spectomycin-resistance, in which the wild-type chromosome copy had been replaced by the modified copy at the targeted locus. Another single-crossover event between the two DR sequences led to the excision of the MazF cassette and generated a strain with IPTG resistance, thereby realizing the desired alteration to the chromosome without introducing any unwanted selection markers. We used this method repeatedly and successfully to inactivate a specific gene, to introduce a gene of interest and to realize the in-frame deletion of a target gene in the same strain. As there is no prerequisite strain for this method, it will be a powerful and universal tool

Co-delivery of Cisplatin(IV) and Capecitabine as an Effective and Non-toxic Cancer Treatment

A strategy for preparing composite micelles (CM) containing both cisplatin(IV) [CisPt(IV)] prodrug and capecitabine using a co-assembly method is described in this study. The CM are capable of an effective release of the anticancer drug cisplatin(II) [CisPt(II)] and capecitabine via acid hydrolysis once they are internalized by cancer cells. Moreover, the CM display a synergistic effect in vitro and the combination therapy in the micellar dosage form leads to reduced systemic toxicity and enhanced antitumor efficacy in vivo

Is Fermi 1544-0649 a misaligned blazar? discovering the jet structure with VLBI

Fermi J1544-0649 is a transient GeV source first detected during its GeV flares in 2017. Multi-wavelength observations during the flaring time demonstrate variability and spectral energy distribution(SED) that are typical of a blazar. Other than the flare time, Fermi J1544-0649 is quiet in the GeV band and looks rather like a quiet galaxy (2MASX J15441967-0649156) for a decade. Together with the broad absorption lines feature we further explore the "misaligned blazar scenario". We analyzed the Very Long Baseline Array (VLBA) and East Asian VLBI Network (EAVN) data from 2018 to 2020 and discovered the four jet components from Fermi J1544-0649. We found a viewing angle around 3.7{\deg} to 7.4{\deg}. The lower limit of the viewing angle indicates a blazar with an extremely low duty cycle of the gamma-ray emission, the upper limit of it supports the "misaligned blazar scenario". Follow-up multi-wavelength observations after 2018 show Fermi J1544-0649 remains quiet in GeV, X-ray, and optical bands. Multi-messenger search of neutrinos is also performed, and an excess of 3.1 {\sigma} significance is found for this source.Comment: Accepted for publication in ApJ. 13 pages, 7 figure

Genetic prediction of the causal relationship between schizophrenia and tumors: a Mendelian randomized study

BackgroundPatients with schizophrenia are at a higher risk of developing cancer. However, the causal relationship between schizophrenia and different tumor types remains unclear.MethodsUsing a two-sample, two-way Mendelian randomization method, we used publicly available genome-wide association analysis (GWAS) aggregate data to study the causal relationship between schizophrenia and different cancer risk factors. These tumors included lung adenocarcinoma, lung squamous cell carcinoma, small-cell lung cancer, gastric cancer, alcohol-related hepatocellular cancer, tumors involving the lungs, breast, thyroid gland, pancreas, prostate, ovaries and cervix, endometrium, colon and colorectum, and bladder. We used the inverse variance weighting (IVW) method to determine the causal relationship between schizophrenia and different tumor risk factors. In addition, we conducted a sensitivity test to evaluate the effectiveness of the causality.ResultsAfter adjusting for heterogeneity, evidence of a causal relationship between schizophrenia and lung cancer risk was observed (odds ratio [OR]=1.001, 95% confidence interval [CI], 1.000–1.001; P=0.0155). In the sensitivity analysis, the causal effect of schizophrenia on the risk of lung cancer was consistent in both direction and degree. However, no evidence of causality or reverse causality between schizophrenia and other tumors was found.ConclusionThis study elucidated a causal relationship between the genetic predictors of schizophrenia and the risk of lung cancer, thereby providing a basis for the prevention, pathogenesis, and treatment of schizophrenia in patients with lung cancer

Succession of Composition and Function of Soil Bacterial Communities During Key Rice Growth Stages

Elucidating the succession of soil microbial communities and microbial functions at key plant growth stages is a major goal of microbial ecology research. In this study, we investigated the succession of soil bacteria during four fertilizer treatments (control, NPK, NPK + pig manure, and NPK + straw) and at three crucial rice growth stages (tillering, heading, and ripening) in paddy soil from a rice-wheat cropping system over a 10-year period. The results showed that the bacterial community and function composition of the control treatment was significantly different from that of the other treatments with NPK fertilizers, and S1 from others stages (ANOSIM, p < 0.05). The application of pig manure could reduce the effects of applying NPK fertilizers on bacterial communities in heading and ripening stages, but the effects of straw returning is not obvious. Variance partitioning analyses (VPA) suggested that pH, OM, and AK appeared to be key factors responsible for the microbial community changes observed in all the treatments or stages. The correlation results showed the bacterial families different between S1 and other stages such as Micromonosporaceae, Nocardioidaceae, Gaiellaceae, and Anaerolineaceae etc., were correlated with bacterial KEGG metabolic pathways. In addition, the topological of the soil bacterial community network with more nodes, links and higher Maximal degree at the heading stage and maintained relatively similar topological structures at the heading and ripening stages. However, the topological of the functional networks at the ripening stage were a small yet complicated co-occurring network with 209 nodes, 789 links, higher Average connectivity (avgK), and Maximal degree. These results suggest an obvious succession of soil bacteria and bacterial function at the key rice growth stages, but the topological of functional network structure of bacteria changes a little in the early and middle stages of rice, while its changes significantly in the ripening stage of rice growth

How to Identify and Separate Bright Galaxy Clusters from the Low-frequency Radio Sky?

In this work we simulate the $50-200$ MHz radio sky that is constrained in the field of view ($5^{\circ}$ radius) of the 21 Centimeter Array (21CMA), by carrying out Monte-Carlo simulations to model redshifted cosmological reionization signals and strong contaminating foregrounds, including emissions from our Galaxy, galaxy clusters, and extragalactic point sources. As an improvement of previous works, we consider in detail not only random variations of morphological and spectroscopic parameters within the ranges allowed by multi-band observations, but also evolution of radio halos in galaxy clusters, assuming that relativistic electrons are re-accelerated in the ICM in merger events and lose energy via both synchrotron emission and inverse Compton scattering with CMB photons. By introducing a new approach designed on the basis of independent component analysis (ICA) and wavelet detection algorithm, we prove that, with a cumulative observation of one month with the 21CMA array, about $80\%$ of galaxy clusters with central brightness temperatures of $> 10~{\rm K}$ at 65 MHz can be safely identified and separated from the overwhelmingly bright foreground. We find that the morphological and spectroscopic distortions are extremely small as compared to the input simulated clusters, and the reduced $\chi^2$ of brightness temperature profiles and spectra are controlled to be $\lesssim 0.5$ and $\lesssim 1.3$, respectively. These results robustly indicate that in the near future a sample of dozens of bright galaxy clusters will be disentangled from the foreground in 21CMA observations, the study of which will greatly improve our knowledge about cluster merger rates, electron acceleration mechanisms in cluster radio halos, and magnetic field in the ICM.Comment: 35 pages, 10 figures, Accepted for publication in The Astrophysical Journa

A Chandra Study of Temperature Substructures in Intermediate-Redshift Galaxy Clusters

By analyzing the gas temperature maps created from the Chandra archive data, we reveal the prevailing existence of temperature substructures on ~100 kpc scales in the central regions of nine intermediate-redshift (z~0.1) galaxy clusters, which resemble those found in the Virgo and Coma Clusters. Each substructure contains a clump of hot plasma whose temperature is about 2-3 keV higher than the environment, corresponding to an excess thermal energy of ~1E58-1E60 erg per clump. Since if there were no significant non-gravitational heating sources, these substructures would have perished in 1E8-1E9 yrs due to thermal conduction and turbulent flows, whose velocity is found to range from about 200 to 400 km/s, we conclude that the substructures cannot be created and sustained by inhomogeneous radiative cooling. We also eliminate the possibilities that the temperature substructures are caused by supernova explosions, or by the non-thermal X-ray emission due to the inverse-Comptonization of the CMB photons. By calculating the rising time of AGN-induced buoyant bubbles, we speculate that the intermittent AGN outbursts (~ 1E60 erg per burst) may have played a crucial role in the forming of the high temperature substructures. Our results are supported by recent study of McNamara & Nulsen (2007), posing a tight observational constraint on future theoretical and numerical studies.Comment: 31 pages, 7 figures, ApJ accepte

Genome analysis of a plasmid-bearing myxobacterim Myxococcus sp. strain MxC21 with salt-tolerant property

Myxobacteria are widely distributed in various habitats of soil and oceanic sediment. However, it is unclear whether soil-dwelling myxobacteria tolerate a saline environment. In this study, a salt-tolerant myxobacterium Myxococcus sp. strain MxC21 was isolated from forest soil with NaCl tolerance >2% concentration. Under 1% salt-contained condition, strain MxC21 could kill and consume bacteria prey and exhibited complex social behaviors such as S-motility, biofilm, and fruiting body formation but adopted an asocial living pattern with the presence of 1.5% NaCl. To investigate the genomic basis of stress tolerance, the complete genome of MxC21 was sequenced and analyzed. Strain MxC21 consists of a circular chromosome with a total length of 9.13 Mbp and a circular plasmid of 64.3 kb. Comparative genomic analysis revealed that the genomes of strain MxC21 and M. xanthus DK1622 share high genome synteny, while no endogenous plasmid was found in DK1622. Further analysis showed that approximately 21% of its coding genes from the genome of strain MxC21 are predominantly associated with signal transduction, transcriptional regulation, and protein folding involved in diverse niche adaptation such as salt tolerance, which enables social behavior such as gliding motility, sporulation, and predation. Meantime, a high number of genes are also found to be involved in defense against oxidative stress and production of antimicrobial compounds. All of these functional genes may be responsible for the potential salt-toleration. Otherwise, strain MxC21 is the second reported myxobacteria containing indigenous plasmid, while only a small proportion of genes was specific to the circular plasmid of strain MxC21, and most of them were annotated as hypothetical proteins, which may have a direct relationship with the habitat adaptation of strain MxC21 under saline environment. This study provides an inspiration of the adaptive evolution of salt-tolerant myxobacterium and facilitates a potential application in the improvement of saline soil in future

Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations

Approximately half of the world's 500,000 new oesophageal squamous-cell carcinoma (ESCC) cases each year occur in China. Here, we show whole-genome sequencing of DNA and RNA in 94 Chinese individuals with ESCC. We identify six mutational signatures (E1–E6), and Signature E4 is unique in ESCC linked to alcohol intake and genetic variants in alcohol-metabolizing enzymes. We discover significantly recurrent mutations in 20 protein-coding genes, 4 long non-coding RNAs and 10 untranslational regions. Functional analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (oesophageal, head and neck and lung) significantly promote cancer cell proliferation, migration and invasion. The most frequently affected genes by structural variation are LRP1B and TTC28. The aberrant cell cycle and PI3K-AKT pathways seem critical in ESCC. These results establish a comprehensive genomic landscape of ESCC and provide potential targets for precision treatment and prevention of the cancer

Co-Deletion of Chromosome 1p/19q and IDH1/2 Mutation in Glioma Subsets of Brain Tumors in Chinese Patients

OBJECTIVE: To characterize co-deletion of chromosome 1p/19q and IDH1/2 mutation in Chinese brain tumor patients and to assess their associations with clinical features. METHODS: In a series of 528 patients with gliomas, pathological and radiological materials were reviewed. Pathological constituents of tumor subsets, incidences of 1p/19q co-deletion and IDH1/2 mutation in gliomas by regions and sides in the brain were analyzed. RESULTS: Overall, 1p and 19q was detected in 339 patients by FISH method while the sequence of IDH1/2 was determined in 280 patients. Gliomas of frontal, temporal and insular origin had significantly different pathological constituents of tumor subsets (P<0.001). Gliomas of frontal origin had significantly higher incidence of 1p/19q co-deletion (50.4%) and IDH1/2 mutation (73.5%) than those of non-frontal origin (27.0% and 48.5%, respectively) (P<0.001), while gliomas of temporal origin had significantly lower incidence of 1p/19q co-deletion (23.9%) and IDH1/2 mutation (41.7%) than those of non-temporal origin (39.9% and 63.2%, respectively) (P = 0.013 and P = 0.003, respectively). Subgroup analysis confirmed these findings in oligoastrocytic and oligodendroglial tumors, respectively. Although the difference of 1p/19q co-deletion was not statistically significant in temporal oligodendroglial tumors, the trend was marginally significant (P = 0.082). However, gliomas from different sides of the brain did not show significant different pathological constituents, incidences of 1p/19q co-deletion or IDH1/2 mutation. CONCLUSION: Preferential distribution of pathological subsets, 1p/19q co-deletion and IDH1/2 mutation were confirmed in some brain regions in Chinese glioma patients, implying their distinctive tumor genesis and predictive value for prognosis