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Summary: Single-stranded DNA-binding proteins (SSBs) have been regarded as indispensable replication factors. Herein, we report that the genes encoding the canonical SSB (SisSSB) and the non-canonical SSB (SisDBP) in Saccharolobus islandicus REY15A are not essential for cell viability. Interestingly, at a lower temperature (55°C), the protein level of SisSSB increases and the growth of ΔSisssb and ΔSisssbΔSisdbp is retarded. SisSSB exhibits melting activity on dsRNA and DNA/RNA hybrid in vitro and is able to melt RNA hairpin in Escherichia coli. Furthermore, the core SisSSB domain is able to complement the absence of cold-shock proteins in E. coli. Importantly, these activities are conserved in the canonical SSBs from Crenarchaeota species that lack bacterial Csp homologs. Overall, our study has clarified the function of the archaeal canonical SSBs which do not function as a DNA-processing factor, but play a role in the processes requiring melting of dsRNA or DNA/RNA hybrid.

Abstract The eye, which is under constant exposure to environmental pathogens, has evolved various anatomic and immunological barriers critical to the protection of tissues lacking regenerative capacity, and the maintenance of a clear optic pathway essential to vision. By bypassing the ocular barriers, intravitreal (IVT) injection has become the mainstay for the delivery of drugs to treat conditions that affect the back of the eye. Both small molecules and biotherapeutics have been successfully administered intravitreally, and several drugs have been approved for the treatment of (wet) age‐related macular degeneration and diabetic macular edema. However, IVT injection is an invasive procedure, which requires sufficient technical expertise from the healthcare professional administering the drug. Potential side effects include bleeding, retinal tear, cataracts, infection, uveitis, loss of vision, and increased ocular pressure. Pharmaceutical companies often differ in their drug development plan, including drug administration techniques, collection of ocular tissues and fluids, ophthalmology monitoring, and overall conduct of nonclinical and clinical studies. The present effort, under the aegis of the Innovation & Quality Ophthalmic Working Group, aims at understanding these differences, identifying pros and cons of the various approaches, determining the gaps in knowledge, and suggesting feasible good practices for nonclinical and early clinical IVT drug development.

Abstract Kinase, putative Endopeptidase, and Other Proteins of Small size (KEOPS) is a multisubunit protein complex conserved in eukaryotes and archaea. It is composed of Pcc1, Kae1, Bud32, Cgi121, and Gon7 in eukaryotes and is primarily involved in N6‐threonylcarbamoyl adenosine (t6A) modification of transfer RNAs (tRNAs). Recently, it was reported that KEOPS participates in homologous recombination (HR) repair in yeast. To characterize the KEOPS in archaea (aKEOPS), we conducted genetic and biochemical analyses of its encoding genes in the hyperthermophilic archaeon Saccharolobus islandicus. We show that aKEOPS also possesses five subunits, Pcc1, Kae1, Bud32, Cgi121, and Pcc1‐like (or Gon7‐like), just like eukaryotic KEOPS. Pcc1‐like has physical interactions with Kae1 and Pcc1 and can mediate the monomerization of the dimeric subcomplex (Kae1‐Pcc1‐Pcc1‐Kae1), suggesting that Pcc1‐like is a functional homolog of the eukaryotic Gon7 subunit. Strikingly, none of the genes encoding aKEOPS subunits, including Pcc1 and Pcc1‐like, can be deleted in the wild type and in a t6A modification complementary strain named TsaKI, implying that the aKEOPS complex is essential for an additional cellular process in this archaeon. Knock‐down of the Cgi121 subunit leads to severe growth retardance in the wild type that is partially rescued in TsaKI. These results suggest that aKEOPS plays an essential role independent of the cellular t6A modification level. In addition, archaeal Cgi121 possesses dsDNA‐binding activity that relies on its tRNA 3ʹ CCA tail binding module. Our study clarifies the subunit organization of archaeal KEOPS and suggests an origin of eukaryotic Gon7. The study also reveals a possible link between the function in t6A modification and the additional function, presumably HR.

ABSTRACT Forkhead-associated (FHA) domain proteins specifically recognize phosphorylated threonine via the FHA domain and are involved in signal transduction in various processes especially DNA damage response (DDR) and cell cycle regulation in eukaryotes. Although FHA domain proteins are found in prokaryotes, archaea, and bacteria, their functions are far less clear as compared to the eukaryotic counterparts, and it has not been studied whether archaeal FHA proteins play a role in DDR. Here, we have characterized an FHA protein from the hyperthermophilic Crenarchaeon Saccharolobus islandicus (SisArnA) by genetic, biochemical, and transcriptomic approaches. We find that ΔSisarnA exhibits higher resistance to DNA damage agent 4-nitroquinoline 1-oxide (NQO). The transcription of ups genes, encoding the proteins for pili-mediated cell aggregation and cell survival after DDR, is elevated in ΔSisarnA. The interactions of SisArnA with two predicted partners, SisvWA1 (SisArnB) and SisvWA2 (designated as SisArnE), were enhanced by phosphorylation in vitro. ΔSisarnB displays higher resistance to NQO than the wild type. In addition, the interaction between SisArnA and SisArnB, which is reduced in the NQO-treated cells, is indispensable for DNA binding in vitro. These indicate that SisArnA and SisArnB work together to inhibit the expression of ups genes in vivo. Interestingly, ΔSisarnE is more sensitive to NQO than the wild type, and the interaction between SisArnA and SisArnE is strengthened after NQO treatment, suggesting a positive role of SisArnE in DDR. Finally, transcriptomic analysis reveals that SisArnA represses a number of genes, implying that archaea apply the FHA/phospho-peptide recognition module for extensive transcriptional regulation. IMPORTANCE Cellular adaption to diverse environmental stresses requires a signal sensor and transducer for cell survival. Protein phosphorylation and its recognition by forkhead-associated (FHA) domain proteins are widely used for signal transduction in eukaryotes. Although FHA proteins exist in archaea and bacteria, investigation of their functions, especially those in DNA damage response (DDR), is limited. Therefore, the evolution and functional conservation of FHA proteins in the three domains of life is still a mystery. Here, we find that an FHA protein from the hyperthermophilic Crenarchaeon Saccharolobus islandicus (SisArnA) represses the transcription of pili genes together with its phosphorylated partner SisArnB. SisArnA derepression facilitates DNA exchange and repair in the presence of DNA damage. The fact that more genes including a dozen of those involved in DDR are found to be regulated by SisArnA implies that the FHA/phosphorylation module may serve as an important signal transduction pathway for transcriptional regulation in archaeal DDR.

Abstract Distant metastasis is the main cause of mortality in breast cancer patients. Using the breast cancer genomic data from The Cancer Genome Atlas (TCGA), we identified brain specific Cav2.2 as a critical regulator of metastasis. Cav2.2 expression is significantly upregulated in breast cancer and its higher expression is inversely correlated with survival suggesting a previously unappreciated role of Cav2.2 in breast cancer. Cav2.2 is required for breast cancer migration, invasion, and metastasis. Interestingly, Cav2.2 promotes invadopodia formation and extracellular matrix (ECM) degradation through the stabilization of invadopodia component cortactin in a proteosome-dependent manner. Moreover, deubiquitinating enzyme USP43 mediated the functions of Cav2.2 in cortactin stabilization, invadopodia formation, ECM degradation, and metastasis. Interestingly, Cav2.2 upregulates USP43 expression through NFAT2 dephosphorylation and nuclear localization. Our study uncovered a novel pathway that regulates cortactin expression and invadopodia formation in breast cancer metastasis.

Abstract BRAF V600E-mutant colorectal cancer (CRC) is a rare subtype of colorectal cancer with poor prognosis. Compelling evidence indicates that the heparanase (HPSE) gene has multiple functions in cancer, however, its role in BRAF V600E-mutant CRC remains elusive. Differentially expressed genes between BRAF V600E-mutant and wild-type patients were explored by analyzing public data from The Cancer Genome Atlas and the Gene Expression Omnibus. Clinical samples of 172 patients with BRAF V600E-mutant CRC diagnosed at Zhongshan Hospital Fudan University were collected. Overall survival was analyzed using Kaplan–Meier curves and Cox regression models. Cell models and xenografts were utilized to investigate the effect of HPSE on tumor proliferation. HPSE was significantly highly expressed in the BRAF V600E-mutant group. High HPSE expression level was independently associated with inferior survival in the BRAF V600E-mutant cohort. HPSE knockdown impeded tumor proliferation of BRAF V600E-mutant CRC cells in vitro and in vivo. Mechanistically, HPSE silencing arrested cell cycle in G0/G1 phase by downregulating Cyclin E2 expression via the AKT/p27Kip1 pathway. These findings support a role for HPSE in promoting BRAF V600E-mutant CRC progression, which suggests it holds great promise as a prognostic biomarker and a potential therapeutic target for the aggressive CRC subtype.

Abstract Based on the holographic principle and the Barrow entropy, Barrow holographic dark energy had been proposed. In order to analyze the stability and the evolution of Barrow holographic dark energy, we, in this paper, apply the dynamical analysis and statefinder methods to Barrow holographic dark energy with different IR cutoff and interacting terms. In the case of using Hubble horizon as IR cutoff with the interacting term $$Q=\frac{\lambda }{H}\rho _{m}\rho _{D}$$ Q = λ H ρ m ρ D , we find this model is stable and can be used to describe the whole evolution of the universe when the energy transfers from the pressureless matter to the Barrow holographic dark energy. When the dynamical analysis method is applied to this stable model, an attractor corresponding to an accelerated expansion epoch exists and this attractor can behave as the cosmological constant. Furthermore, the coincidence problem can be solved in this case. Then, after using the statefinder analysis method to this model, we find this model can be discriminated from the standard $$\Lambda $$ Λ CDM model. Finally, we have discussed the turning point of Hubble diagram in Barrow holographic dark energy and find the turning point does not exist in this model.

Abstract Background To investigate the clinical features of patients with Stanford type A acute aortic dissection (AAD) and analyze the risk factors affecting postoperative in-hospital mortality rate. Methods The demographic and clinical data were retrospectively collected and analyzed from 118 AAD patients admitted to the Affiliated Hospital of Hangzhou Normal University from June 2016 to April 2019. All patients underwent surgical treatment and were grouped into death and survival groups. The risk factors affecting postoperative in-hospital death were analyzed using multivariate logistic regression analysis. Results The male to female ratio in the patients was 3.8:1 and the mean age was 50.11 ± 9.91 years. The patient’s main comorbidities were hypertension (70.33%) and coronary heart disease (10.17%). The main symptoms included chest pain and back pain (72.89%). The highest incidence of complications was pericardial effusion (48.31%), followed by pleural effusion (22.88%). The mean systolic blood pressure, white blood cell count and D-dimer in the patients were over the ranges of normal people. The incidences of cardiac and renal insufficiency were 18.64% and 16.95% respectively, and the postoperative in-hospital mortality rate was 12.71%. Univariable analysis showed that age, renal insufficiency, cardiac insufficiency, D-dimer level, cardiopulmonary bypass time, operation time, blood transfusion volume and postoperative hemostasis were significant factors leading to the death (P 65, renal insufficiency, cardiopulmonary bypass time ≥ 250 min and postoperative hemostasis were independent risk factors for the death (P 65 years, renal insufficiency, cardiopulmonary bypass time ≥ 250 min and postoperative hemostasis are significantly risk factors for postoperative mortality.

The emergent universe provides a possible method to avoid the Big Bang singularity by considering that the universe stems from a stable Einstein static universe rather than the singularity. Since the Einstein static universe exists before inflation, it may leave some relics in the CMB power spectrum. In this paper, we analyze the stability condition for the Einstein static universe in general relativity with k-essence against both the scalar and tensor perturbations. Furthermore, we find the emergent universe can be successfully realized by constructing a scalar potential and an equation of state parameter. Solving the curved Mukhanov–Sasaki equation, we obtain the analytical approximation for the primordial power spectrum, and then depict the TT-spectrum of the emergent universe. The results show that both the primordial power spectrum and CMB TT-spectrum are suppressed on large scales.

Gallbladder cancer (GBC) is the most common malignancy of the biliary tract, with extremely dismal prognosis. Limited therapeutic options are available for GBC patients. We used whole-exome sequencing of human GBC to identify the ErbB and epigenetic pathways as two vulnerabilities in GBC. We screened two focused small-molecule libraries that target these two pathways using GBC cell lines and identified the mTOR inhibitor INK-128 and the histone deacetylase (HDAC) inhibitor JNJ-26481585 as compounds that inhibited proliferation at low concentrations. Both significantly suppressed tumor growth and metastases in mouse models. Both synergized with the standard of care chemotherapeutic agent gemcitabine in cell lines and in mouse models. Furthermore, the activation of the mTOR pathway, measured by immunostaining for phosphorylated mTOR and downstream effector S6K1, is correlated with poor prognosis in GBC. Phosphorylated mTOR or p-S6K1 in clinical samples is an independent indicator for overall survival in GBC patients. Taken together, our findings suggest that mTOR inhibitors and HDAC inhibitors can serve as potential therapeutics for GBC, and the phosphorylation of mTOR and S6K1 may serve as biomarkers for GBC.

Abstract Macrotermes barneyi, widely distributed in southern China, is the major fungus-growing termite in the subfamily Macrotermitinae. It has no flagellated protists in the guts. Here, we report occurrence of gregarine, a protozoan parasite in the digestive tract of M. barneyi. The general morphology and ultrastructure of the gregarine gamonts and syzygies by light micrograph and scanning electron micrograph are presented. SSU rDNA sequence analysis showed that the termite gregarine has the highest identity (90.10%) to that of Gregarina blattarum from cockroaches. Phylogenetic analysis based on the SSU rDNA sequences from diverse insect eugregarines indicated that the gregarine from M. barneyi is phylogenetically close to G. blattarus, L. erratica and G. tropica from Gregarinidae and Leidyanidae families, and may represent a novel species. This study expands our knowledge about the diversity of terrestrial eugregarines parasitizing in termites.

In this paper, using the latest Pantheon+ sample of Type Ia supernovae, baryon acoustic oscillation measurements, and observational Hubble data, we carry out a joint constraint on the Hubble constant H _0 , the spatial curvature Ω _K , and the sound horizon at the end of the drag epoch r _d . To be model-independent, four cosmography models—i.e., the Taylor series in terms of redshift y _1 = z /(1 + z ), ${y}_{2}=\arctan (z)$ , ${y}_{3}=\mathrm{ln}(1+z)$ , and the Padé approximants—are used without the assumption of a flat Universe. The results show that H _0 is anticorrelated with Ω _K and r _d , indicating that smaller Ω _K or r _d would be helpful in alleviating the Hubble tension. The values of H _0 and r _d are consistent with the estimate derived from the Planck cosmic microwave background data based on the flat ΛCDM model, but H _0 is in 2.3 ∼ 3.0 σ tension with that obtained by Riess et al. in all these cosmographic approaches. Meanwhile, a flat Universe is preferred by the present observations under all approximations except the third order of y _1 and y _2 of the Taylor series. Furthermore, according to the values of the Bayesian evidence, we found that the flat ΛCDM remains to be the most favored model by the joint data sets, and the Padé approximant of order (2,2), the third order of y _3 and y _1 are the top three cosmographic expansions that fit the data sets best, while the Taylor series in terms of y _2 are essentially ruled out.

Imaging through the wavy water–air interface is challenging since the random fluctuations of water will cause complex geometric distortion and motion blur in the images, seriously affecting the effective identification of the monitored object. Considering the problems of image recovery accuracy and computational efficiency, an efficient reconstruction scheme that combines lucky-patch search and image registration technologies was proposed in this paper. Firstly, a high-quality reference frame is rebuilt using a lucky-patch search strategy. Then an iterative registration algorithm is employed to remove severe geometric distortions by registering warped frames to the reference frame. During the registration process, we integrate JADE and LBFGS algorithms as an optimization strategy to expedite the control parameter optimization process. Finally, the registered frames are refined using PCA and the lucky-patch search algorithm to remove residual distortions and random noise. Experimental results demonstrate that the proposed method significantly outperforms the state-of-the-art methods in terms of sharpness and contrast.

Abstract In this paper, we probe the cosmic opacity with the newest Pantheon type Ia supernovae (SNIa) and the observational Hubble parameter $$\left( H(z)\right) $$ H ( z ) data based on the $$\Lambda $$ Λ CDM and wCDM models with or without spatial curvature. In the analysis, we marginalize the likelihood function of SNIa data over the pertinent nuisance parameter $${\mathcal {M}}$$ M , a combination of the absolute magnitude of SNIa $$M_{\mathrm{B}}$$ M B and the Hubble constant $$H_0$$ H 0 , with a flat prior. Two parameterizations of the optical depth $$\tau (z)$$ τ ( z ) associated to the cosmic absorption, namely $$\tau (z)=2\varepsilon z$$ τ ( z ) = 2 ε z and $$\tau (z)= (1+z)^{2\varepsilon }-1$$ τ ( z ) = ( 1 + z ) 2 ε - 1 , are adopted. We find that the results are not sensitive to the fiducial cosmological models, the spatial curvature and parameterizations of $$\tau (z)$$ τ ( z ) . Moreover, the results from the Pantheon data alone are consistent with a transparent universe ( $$\varepsilon =0$$ ε = 0 ). And once the H(z) data is combined, $$\varepsilon =0$$ ε = 0 falls within the 68% confidence level (CL) of the best fit when a flat $$H_0$$ H 0 prior or the distance priors are used, while it falls within the 95% CL when a Gaussian distribution prior of $$H_0=74.03\pm 1.42$$ H 0 = 74.03 ± 1.42 km $$\mathrm {s}^{-1}\, \mathrm {Mpc}^{-1}$$ s - 1 Mpc - 1 is used.

BackgroundIntravenous lidocaine has been shown to reduce opioid consumption and is associated with favourable outcomes after surgery. In this study, we explored whether intraoperative lidocaine reduces intraoperative opioid use and length of stay (LOS) and improves long-term survival after primary debulking surgery for ovarian cancer and explored the correlation between SCN9A expression and ovarian cancer prognosis.MethodsThis retrospective study included patients who underwent primary debulking surgery(PDS) for ovarian cancer from January 2015 to December 2018. The patients were divided into non-lidocaine and lidocaine [bolus injection of 1.5 mg/kg lidocaine at the induction of anaesthesia followed by a continuous infusion of 2 mg/(kg∙h) intraoperatively] groups. Intraoperative opioid consumption, the verbal numeric rating scale (VNRS) at rest and LOS were recorded. Propensity score matching was used to minimize bias, and disease-free survival (DFS) and overall survival (OS) were compared between the two groups.ResultsAfter propensity score matching(PSM), the demographics were not significantly different between the groups. The intraoperative sufentanil consumption in the lidocaine group was significantly lower than that in the non-lidocaine group (Mean: 35.6 μg vs. 43.2 μg, P=0.035). LOS was similar between the groups (12.0 days vs. 12.4 days, P=0.386). There was a significant difference in DFS between the groups (32.3% vs. 21.6%, P=0.015), and OS rates were significantly higher in the lidocaine group than in the non-lidocaine group (35.2% vs. 25.6%, P=0.042). Multivariate analysis indicated that intraoperative lidocaine infusion was associated with prolonged OS and DFS.ConclusionIntraoperative intravenous lidocaine infusion appears to be associated with improved OS and DFS in patients undergoing primary debulking surgery for ovarian cancer. Our study has the limitations of a retrospective review. Hence, our results should be confirmed by a prospective randomized controlled trial.

Abstract During the 2020 Spring Festival in China, the outbreak of a novel coronavirus, named COVID‐19 by WHO, brought on a worldwide panic. According to the clinical data of infected patients, radiologic evidence of lung edema is common and deserves clinical attention. Lung edema is a manifestation of acute lung injury (ALI) and may progress to hypoxemia and potentially acute respiratory distress syndrome (ARDS). Patients diagnosed with ARDS have poorer prognosis and potentially higher mortality. Although no effective treatment is formally approved for COVID‐19 infection, support of ventilation with oxygen therapy and sometimes mechanical ventilation is often required. Treatment with systemic and/or local glucocorticoids might be helpful to alleviate the pulmonary inflammation and edema, which may decrease the development and/or consequences of ARDS. In this article, we focus on the lung edema and ALI of patients with this widely transmitted COVID‐19 infection in order to provide clinical indications and potential therapeutic targets for clinicians and researchers.

Abstract A new coronavirus SARS‐CoV‐2 has caused outbreaks in multiple countries and the number of cases is rapidly increasing through human‐to‐human transmission. Clinical phenomes of patients with SARS‐CoV‐2 infection are critical in distinguishing it from other respiratory infections. The extent and characteristics of those phenomes varied depending on the severities of the infection, for example, beginning with fever or a mild cough, progressed with signs of pneumonia, and worsened with severe or even fatal respiratory difficulty in acute respiratory distress syndrome. We summarized clinical phenomes of 3795 patients with COVID‐19 based on 80 published reports from the onset of outbreak to March 2020 to emphasize the importance and specificity of those phenomes in diagnosis and treatment of infection, and evaluate the impact on medical services. The data show that the incidence of male patients was higher than that of females and the level of C‐reaction protein was increased as well as most patients' imaging included ground‐glass opacity. Clinical phenomes of SARS‐CoV‐2 infection were compared with those of SARS‐CoV and MERS‐CoV infections. There is an urgent need to develop an artificial intelligence‐based machine learning capacity to analyze and integrate radiomics‐ or imaging‐based, patient‐based, clinician‐based, and molecular measurements‐based data to fight the outbreak of COVID‐19 and enable more efficient responses to unknown infections in future.

Orc1-2 is a non-initiator ortholog of archaeal/eukaryotic Orc1 proteins, which functions as a global regulator in DNA damage-responsive (DDR) expression. As for Orc1 initiators, the DDR regulator harbors an AAA+ ATPase domain, an Initiator-Specific Motif (ISM) and a winged-helix (wH) DNA-binding domain, which are also organized in a similar fashion. To investigate how Orc1-2 mediates the DDR regulation, the orc1-2 mutants inactivating each of these functional domains were constructed with Saccharolobus islandicus and genetically characterized. We found that disruption of each functional domain completely abolished the DDR regulation in these orc1-2 mutants. Strikingly, inactivation of ATP hydrolysis of Orc1-2 rendered an inviable mutant. However, the cell lethality can be suppressed by the deficiency of the DNA binding in the same protein, and it occurs independent of any DNA damage signal. Mutant Orc1-2 proteins were then obtained and investigated for DNA-binding in vitro. This revealed that both the AAA+ ATPase and the wH domains are involved in DNA-binding, where ISM and R381R383 in wH are responsible for specific DNA binding. We further show that Orc1-2 regulation occurs in two distinct steps: (a) eliciting cell division inhibition at a low Orc1-2 content, and this regulation is switched on by ATP binding and turned off by ATP hydrolysis; any failure in turning off the regulation leads to growth inhibition and cell death; (b) activation of the expression of DDR gene encoding DNA repair proteins at an elevated level of Orc1-2.

Using the Barrow entropy and considering the timescale as IR cutoff, a new holographic dark energy model named Barrow agegraphic dark energy (BADE) was proposed. We use phase space analysis method to discuss the evolution of the universe in three different mode of BADE (Q=0; Q=3αH(ρm+ρD); Q=H(αρm+βρD)). We find the attractor which represents the dark energy-dominated era exists in all cases. In the case Q=0 and Q=H(αρm+βρD) with β=0, the attractor can behave as the cosmological constant, and these models can used to mimic the cosmological constant.

Fungus-growing termites are engaged in a tripartite mutualism with intestinal microbes and a monocultivar (Termitomyces sp.) in the fungus garden. The termites are often plagued by entomopathogen (Metarhizium anisopliae) and fungus garden is always threatened by competitors (Xylaria spp.). Here, we aim to understand the defensive role of intestinal microbes, the actinomycetes which were isolated from the gut of Macrotermes barneyi. We obtained 44 antifungal isolates, which showed moderate to strong inhibition to Xylaria sp. HPLC analysis indicated that different types of polyenes (tetraene, pentene, and heptaene) existed in the metabolites of 10 strong antifungal Streptomyces strains. Two pentene macrolides (pentamycin and 1′14-dihydroxyisochainin) were firstly purified from Streptomyces strain HF10, both exhibiting higher activity against Xylaria sp. and M. anisopliae than cultivar Termitomyces. Subsequently, tetraene and heptaene related gene disruption assay showed that the mutant strains lost the ability to produce corresponding polyenes, and they also had significantly decreased activities against Xylaria sp. and M. anisopliae compared to that of wild type strains. These results indicate that polyene-producing Streptomyces from the guts of M. barneyi have strong inhibition to competitor fungus and polyenes contribute to inhibitory effects on Xylaria sp.

DNA damage response (DDR) in eukaryotes is largely regulated by protein phosphorylation. In archaea, many proteins are phosphorylated, however, it is unclear how the cells respond to DNA damage through global protein phosphorylation. We previously found that Δrio1, a Rio1 kinase homolog deletion strain of Sulfolobus islandicus REY15A, was sensitive to UV irradiation. In this study, we showed that Δrio1 grew faster than the wild type. Quantitative phosphoproteomic analysis of the wild type and Δrio1, untreated and irradiated with UV irradiation, revealed 562 phosphorylated sites (with a Ser/Thr/Tyr ratio of 65.3%/23.8%/10.9%) of 333 proteins in total. The phosphorylation levels of 35 sites of 30 proteins changed with >1.3-fold in the wild type strain upon UV irradiation. Interestingly, more than half of the UV-induced changes in the wild type did not occur in the Δrio1 strain, which were mainly associated with proteins synthesis and turnover. In addition, a protein kinase and several transcriptional regulators were differentially phosphorylated after UV treatment, and some of the changes were dependent on Rio1. Finally, many proteins involved in various cellular metabolisms exhibited Riol-related and UV-independent phosphorylation changes. Our results suggest that Rio1 is involved in the regulation of protein recycling and signal transduction in response to UV irradiation, and plays regulatory roles in multiple cellular processes in S. islandicus.

EndoMS is a recently identified mismatch specific endonuclease in Thermococcales of Archaea and Mycobacteria of Bacteria. The homologs of EndoMS are conserved in Archaea and Actinobacteria, where classic MutS-MutL-mediated DNA mismatch repair pathway is absent or non-functional. Here, we report a study on the in vitro mismatch cleavage activity and in vivo function of an EndoMS homolog (SisEndoMS) from Sulfolobus islandicus REY15A, the model archaeon belonging to Crenarchaeota. SisEndoMS is highly active on duplex DNA containing G/T, G/G, and T/T mismatches. Interestingly, the cleavage activity of SisEndoMS is stimulated by the heterotrimeric PCNAs, and when Mn2+ was used as the co-factor instead of Mg2+, SisEndoMS was also active on DNA substrates containing C/T or A/G mismatches, suggesting that the endonuclease activity can be regulated by ion co-factors and accessory proteins. We compared the spontaneous mutation rate of the wild type strain REY15A and ∆endoMS by counter selection against 5-fluoroorotic acid (5-FOA). The endoMS knockout mutant had much higher spontaneous mutation rate (5.06 × 10−3) than that of the wild type (4.6 × 10−6). A mutation accumulation analysis also showed that the deletion mutant had a higher mutation occurrence than the wild type, with transition mutation being the dominant, suggesting that SisEndoMS is responsible for mutation avoidance in this hyperthermophilic archaeon. Overexpression of the wild type SisEndoMS in S. islandicus resulted in retarded growth and abnormal cell morphology, similar to strains overexpressing Hje and Hjc, the Holliday junction endonucleases. Transcriptomic analysis revealed that SisEndoMS overexpression led to upregulation of distinct gene including the CRISPR-Cas IIIB system, methyltransferases, and glycosyltransferases, which are mainly localized to specific regions in the chromosome. Collectively, our results support that EndoMS proteins represent a noncanonical DNA repair pathway in Archaea. The mechanism of the mismatch repair pathway in Sulfolobus which have a single chromosome is discussed.

Abstract The emergent mechanism provides a possible way to resolve the big-bang singularity problem by assuming that our universe originates from the Einstein static (ES) state. Thus, the existence of a stable ES solution becomes a very crucial prerequisite for the emergent scenario. In this paper, we study the stability of an ES universe in gravity theory with a non-minimal coupling between the kinetic term of a scalar field and the Einstein tensor. We find that the ES solution is stable under both scalar and tensor perturbations when the model parameters satisfy certain conditions, which indicates that the big-bang singularity can be avoided successfully by the emergent mechanism in the non-minimally kinetic coupled gravity.

Protein phosphorylation is one of the main protein post-translational modifications and regulates DNA repair in eukaryotes. Archaeal genomes encode eukaryotic-like DNA repair proteins and protein kinases (ePKs), and several proteins involved in homologous recombination repair (HRR) including Hjc, a conserved Holliday junction (HJ) resolvase in Archaea, undergo phosphorylation, indicating that phosphorylation plays important roles in HRR. Herein, we performed phosphorylation analysis of Hjc by various ePKs from Sulfolobus islandicus. It was shown that SiRe_0171, SiRe_2030, and SiRe_2056, were able to phosphorylate Hjc in vitro. These ePKs phosphorylated Hjc at different Ser/Thr residues: SiRe_0171 on S34, SiRe_2030 on both S9 and T138, and SiRe_2056 on T138. The HJ cleavage activity of the phosphorylation-mimic mutants was analyzed and the results showed that the cleavage activity of S34E was completely lost and that of S9E had greatly reduced. S. islandicus strain expressing S34E in replacement of the wild type Hjc was resistant to higher doses of DNA damaging agents. Furthermore, SiRe_0171 deletion mutant exhibited higher sensitivity to DNA damaging agents, suggesting that Hjc phosphorylation by SiRe_0171 enhanced the DNA repair capability. Our results revealed that HJ resolvase is regulated by protein phosphorylation, reminiscent of the regulation of eukaryotic HJ resolvases GEN1 and Yen1.

GABRA3, a subunit of the GABA receptor, is often highly expressed in brain metastasis and breast cancers. Here, the authors demonstrated that GABRA3 activates AKT to promote breast cancer cell invasion and that the A-to-I edited form of GABRA3, specifically expressed in noninvasive breast cancers, can suppress the function of wild type GABRA3.

Protein phosphorylation, one of the most important post-translational modifications, regulates almost every cellular process. Although signal transduction by protein phosphorylation is extensively studied in Eukaryotes and Bacteria, the knowledge of this process in archaea is greatly lagging behind, especially for Ser/Thr/Tyr phosphorylation by eukaryotic-like protein kinases (ePKs). So far, only a few studies on archaeal ePKs have been reported, most of which focused on the phosphorylation activities in vitro, but their physiological functions and interacting network are still largely unknown. In this study, we systematically investigated the autophosphorylation and cross-phosphorylation activities of ePKs from Sulfolobus islandicus REY15A using proteins expressed in Escherichia coli or S. islandicus. In vitro kinase assay showed that 7 out of the 11 putative ePKs have autophosphorylation activity. A protein Ser/Thr phosphatase, SiRe_1009, was able to dephosphorylate various autophosphorylated ePKs, confirming that these proteins are Ser/Thr kinases. Two ePKs, SiRe_2030 and SiRe_2056, homologs of typical eukaryotic PKs involved in peptide synthesis in response to various cellular stresses, exhibit highly efficient phosphorylation activities on both themselves and other ePKs. Overexpression of the protein kinases in vivo revealed that elevated level of either SiRe_1531 or SiRe_2056 inhibited the cell growth of S. islandicus cells. Finally, a phosphorylation network of the protein kinases was proposed and their putative physiological roles were discussed.

In this paper, a multi-focus image fusion method based on Dual-Tree Compactly Supported Shearlet Transform (DT CSST) and Direction Decision Map (DDM) is proposed. DT CSST is a shift invariant modification of conventional Compactly Supported Shearlet Transform (CSST). Based on the mitigation of shift variance of CSST in DT CSST, a clearer fused image could be acquired through the General Image Fusion (GIF) method, and this image is called the initial fused image in this paper. The decision map is determined by the similarity of the initial fused image and the source images. The generation algorithm of the decision map in this paper takes advantage of the directional nature of DT CSST: every direction of the transform generates an initial directional decision map and then yields the final map through vote and smooth steps. This scheme is called DDM in this paper. The proposed method is evaluated by four groups of standard images. The results show that the proposed method is able to improve the quality indices compared with two algorithms which have excellent quality indices.

Metastasis represents one of the most clinically important transitions in neoplastic progression. The evolution of metastasis is a puzzle because a metastatic clone is at a disadvantage in competition for space and resources with non-metastatic clones in the primary tumor. Metastatic clones waste some of their reproductive potential on emigrating cells with little chance of establishing metastases. We suggest that resource heterogeneity within primary tumors selects for cell migration, and that cell emigration is a by-product of that selection.We developed an agent-based model to simulate the evolution of neoplastic cell migration. We simulated the essential dynamics of neoangiogenesis and blood vessel occlusion that lead to resource heterogeneity in neoplasms. We observed the probability and speed of cell migration that evolves with changes in parameters that control the degree of spatial and temporal resource heterogeneity. Across a broad range of realistic parameter values, increasing degrees of spatial and temporal heterogeneity select for the evolution of increased cell migration and emigration.We showed that variability in resources within a neoplasm (e.g. oxygen and nutrients provided by angiogenesis) is sufficient to select for cells with high motility. These cells are also more likely to emigrate from the tumor, which is the first step in metastasis and the key to the puzzle of metastasis. Thus, we have identified a novel potential solution to the puzzle of metastasis.