Structure and DNA damage-dependent derepression mechanism for the XRE family member DG-DdrO.

DdrO is an XRE family transcription repressor that, in coordination with the metalloprotease PprI, is critical in the DNA damage response of Deinococcus species. Here, we report the crystal structure of Deinococcus geothermalis DdrO. Biochemical and structural studies revealed the conserved recognizing α-helix and extended dimeric interaction of the DdrO protein, which are essential for promoter DNA binding. Two conserved oppositely charged residues in the HTH motif of XRE family proteins form salt bridge interactions that are essential for promoter DNA binding. Notably, the C-terminal domain is stabilized by hydrophobic interactions of leucine/isoleucine-rich helices, which is critical for DdrO dimerization. Our findings suggest that DdrO is a novel XRE family transcriptional regulator that forms a distinctive dimer. The structure also provides insight into the mechanism of DdrO-PprI-mediated DNA damage response in Deinococcus.

Importance of Volume Ratio in Photonic Effects of Lanthanide-Doped LaPO4 Nanocrystals.

Experimental variation of the volume ratio (filling factor: i.e., volume of nanoparticles (NPs) compared with that of medium) of nanocomposite materials with doped lanthanide ions demonstrates that it has a significant affect upon local field effects. Lanthanum orthophosphate NPs are doped with Eu3+ and/or Tb3+ and immersed in organic solvents and lead borate glasses for Tb3+ 5 D4 lifetime measurements. For media with a refractive index (nmed ) less than that of LaPO4 (nnp = 1.79), the 5 D4 emission decay rate increases with increasing volume ratio of the NPs, whereas for nmed > 1.79, the decay rate decreases with increasing volume ratio. Fitting with the model of Pukhov provides an estimation of the radiative lifetime of 5 D4 and the quantum yield. Energy transfer (ET) from Tb3+ to Eu3+ occurs in co-doped LaPO4 NPs with excitation into a Tb3+ absorption band. The ET rate is independent on nmed and the energy transfer efficiency decreases with an increase in nmed . The behavior of ET rate with regard to the local field is consistent with the Dexter, but not Förster, equation for ET rate involving the electric dipole-electric dipole mechanism. This has consequences when using the spectroscopic ruler approach to measure distances between donor-acceptor chromophores.

Electronic Spectra of Cs2NaYb(NO2)6: Is There Quantum Cutting?

The crystal structure and electronic spectra of the T h symmetry hexanitritoytterbate(III) anion have been studied in Cs2NaY0.96Yb0.04(NO2)6, which crystallizes in the cubic space group Fm3̅. The emission from Yb3+ can be excited via the NO2- antenna. The latter electronic transition is situated at more than twice the energy of the former, but at room temperature, one photon absorbed at 470 nm in the triplet state produces no more than one photon emitted. Some degree of quantum cutting is observed at 298 K under 420 nm excitation into the singlet state and at 25 K using excitation into either state. The quantum efficiency is ∼10% at 25 K. The energy level scheme of Yb3+ has been deduced from excitation and emission spectra and calculated by crystal field theory. New improved energy level calculations are also reported for the Cs2NaLn(NO2)6 (Ln = Pr, Eu, Tb) series using the f- Spectra package. The neat crystal Cs2NaYb(NO2)6 has also been studied, but results were unsatisfactory due to sample decomposition, and this chemical instability makes it unsuitable for applications.

Effect of Implementing an Informatization Case Management Model on the Management of Chronic Respiratory Diseases in a General Hospital: Retrospective Controlled Study.

Background: The use of chronic disease information systems in hospitals and communities plays a significant role in disease prevention, control, and monitoring. However, there are several limitations to these systems, including that the platforms are generally isolated, the patient health information and medical resources are not effectively integrated, and the "Internet Plus Healthcare" technology model is not implemented throughout the patient consultation process. Objective: The aim of this study was to evaluate the efficiency of the application of a hospital case management information system in a general hospital in the context of chronic respiratory diseases as a model case. Methods: A chronic disease management information system was developed for use in general hospitals based on internet technology, a chronic disease case management model, and an overall quality management model. Using this system, the case managers provided sophisticated inpatient, outpatient, and home medical services for patients with chronic respiratory diseases. Chronic respiratory disease case management quality indicators (number of managed cases, number of patients accepting routine follow-up services, follow-up visit rate, pulmonary function test rate, admission rate for acute exacerbations, chronic respiratory diseases knowledge awareness rate, and patient satisfaction) were evaluated before (2019-2020) and after (2021-2022) implementation of the chronic disease management information system. Results: Before implementation of the chronic disease management information system, 1808 cases were managed in the general hospital, and an average of 603 (SD 137) people were provided with routine follow-up services. After use of the information system, 5868 cases were managed and 2056 (SD 211) patients were routinely followed-up, representing a significant increase of 3.2 and 3.4 times the respective values before use (U=342.779; P<.001). With respect to the quality of case management, compared to the indicators measured before use, the achievement rate of follow-up examination increased by 50.2%, the achievement rate of the pulmonary function test increased by 26.2%, the awareness rate of chronic respiratory disease knowledge increased by 20.1%, the retention rate increased by 16.3%, and the patient satisfaction rate increased by 9.6% (all P<.001), while the admission rate of acute exacerbation decreased by 42.4% (P<.001) after use of the chronic disease management information system. Conclusions: Use of a chronic disease management information system improves the quality of chronic respiratory disease case management and reduces the admission rate of patients owing to acute exacerbations of their diseases.

Peroxymonosulfate activation by CuFe-prussian blue analogues for the degradation of bisphenol S: Effect, mechanism, and pathway.

The fenton-like process based on peroxymonosulfate (PMS) activation is considered as a promising strategy for the removal of organic pollutants. However, the development of efficient photocatalysts for PMS activation remains challenging. Herein, copper-iron prussian blue analogue (CunFe1-PBA, n = 1, 2, 3, 4) nanomaterials were first fabricated through a simple combination of co-precipitation and calcination processes. The as-synthesized CunFe1-PBA composite catalyst was used to activate PMS for the degradation of endocrine disruptor bisphenol S (BPS). As the result, Cu3Fe1-PBA calcined at 300 °C (Cu3Fe1-PBA*300 °C) mainly composed of CuFe2O4 and CuO showed a higher catalytic activity for activating PMS for BPS degradation than those of CunFe1-PBA composite. Additionally, Cu3Fe1-PBA*300 °C/PMS system was suitable for degradation of BPS at 400 mg/L catalyst or PMS and wide pH ranges from 3 to 11 while coexisting inorganic anions (SO42-, NO3-, and HCO3-) and humic acid all inhibited the reaction. Radical trapping experiment, electron paramagnetic resonance (EPR), and X-ray photoelectron spectroscopy (XPS) proved that Cu and Fe could regulate the charge balance through changes of valence state, and active PMS to produce free radicals effectively, especially the production of 1O2. Furthermore, the analysis of the BPS intermediates of degradation was carried out by ultra-performance liquid chromatography-mass spectrometry, and two degradation pathways of BPS were proposed. In summary, this work provides a facile avenue to design efficient catalysts to activate PMS for the degradation of emerging organic pollutants in water remediation.

Degradation mechanism of ammonia nitrogen synergistic with bromate under UV or UV/TiO2.

Bromate (BrO3-) and ammonia nitrogen (NH4+) are both typical environmental pollutants: BrO3- has been categorized as one of the Group 2B carcinogen by IARC; an excess of NH4+ might result in the eutrophication of water. The existence of NH4+ could inhibit the transformation of bromide (Br-) to bromate (BrO3-). However, the interaction of NH4+ and BrO3- during the removal process is not clear. This study intends to disclose the mutual relationships of ammonia nitrogen and bromate ions under UV irradiation or UV/TiO2 conditions. Without UV irradiation, BrO3- and NH4+ were both stable even under the presentation of each other. Under UV irradiation or UV/TiO2 conditions, BrO3- and NH4+ promoted the degradation of each other, showing the synergistic degradation mechanism. In the neutral environment, both of BrO3- and NH4+ could be transformed effectively. Furthermore, NH4+ accelerated the transformation of BrO3- to Br- at the reaction beginning and the existence of BrO3- is beneficial for the transformation of NH4+ to N2.

Responsive Regulation of Energy Transfer in Lanthanide-Doped Nanomaterials Dispersed in Chiral Nematic Structure.

The responsive control of energy transfer (ET) plays a key role in the broad applications of lanthanide-doped nanomaterials. Photonic crystals (PCs) are excellent materials for ET regulation. Among the numerous materials that can be used to fabricate PCs, chiral nematic liquid crystals are highly attractive due to their good photoelectric responsiveness and biocompatibility. Here, the mechanisms of ET and the photonic effect of chiral nematic structures on ET are introduced; the regulation methods of chiral nematic structures and the resulting changes in ET of lanthanide-doped nanomaterials are highlighted; and the challenges and promising opportunities for ET in chiral nematic structures are discussed.

Luminescence regulation of lanthanide-doped nanorods in chiral photonic cellulose nanocrystal films.

A new design for chiral photonic cellulose nanocrystal films was developed by co-assembling lanthanide-doped nanorods (NRs) into chiral cellulose nanocrystals, in which the photonic band gap (PBG) could be tuned in the visible range by changing the mass fraction of flexible agents, such as polyvinyl alcohol (PVA) and ethylene glycol (EG). Due to the PBG effect, the luminescence modulation in such nanocrystal films had been realized. The down-conversion luminescence from NaGd30Y60F4:5%Tb3+, 5%Eu3+ NRs and up-conversion luminescence from NaGd40Y40F4:18%Yb3+, 2%Er3+ NRs could be enhanced by 28 % and 18 % respectively, on account of the band edge effect. The luminescence would be inhibited when the luminescence overlapped with the stop band of the PBG. These results implied that the biocompatible photonic cellulose nanocrystal films are ideally suited for applications in optical coding, optical resonators and biocompatible lasers.

Genome-Wide Study of Hsp90 Gene Family in Cabbage (Brassica oleracea var. capitata L.) and Their Imperative Roles in Response to Cold Stress.

Heat shock protein 90 (Hsp90) plays an important role in plant developmental regulation and defensive reactions. Several plant species have been examined for the Hsp90 family gene. However, the Hsp90 gene family in cabbage has not been well investigated to date. In this study, we have been discovered 12 BoHsp90 genes in cabbage (Brassica oleracea var. capitata L.). These B. oleracea Hsp90 genes were classified into five groups based on phylogenetic analysis. Among the five groups, group one contains five Hsp90 genes, including BoHsp90-1, BoHsp90-2, BoHsp90-6, BoHsp90-10, and BoHsp90-12. Group two contains three Hsp90 genes, including BoHsp90-3, BoHsp90-4, and BoHsp90. Group three only includes one Hsp90 gene, including BoHsp90-9. Group four were consisting of three Hsp90 genes including BoHsp90-5, BoHsp90-7, and BoHsp90-8, and there is no Hsp90 gene from B. oleracea in the fifth group. Synteny analysis showed that a total of 12 BoHsp90 genes have a collinearity relationship with 5 Arabidopsis genes and 10 Brassica rapa genes. The promoter evaluation revealed that the promoters of B. oleracea Hsp90 genes included environmental stress-related and hormone-responsive cis-elements. RNA-seq data analysis indicates that tissue-specific expression of BoHsp90-9 and BoHsp90-5 were highly expressed in stems, leaves, silique, and flowers. Furthermore, the expression pattern of B. oleracea BoHsp90 exhibited that BoHsp90-2, BoHsp90-3, BoHsp90-7, BoHsp90-9, BoHsp90-10, and BoHsp90-11 were induced under cold stress, which indicates these Hsp90 genes perform a vital role in cold acclimation and supports in the continual of normal growth and development process. The cabbage Hsp90 gene family was found to be differentially expressed in response to cold stress, suggesting that these genes play an important role in cabbage growth and development under cold conditions.

CREB1 contributes colorectal cancer cell plasticity by regulating lncRNA CCAT1 and NF-κB pathways.

The CREB1 gene encodes an exceptionally pleiotropic transcription factor that frequently dysregulated in human cancers. CREB1 can regulate tumor cell status of proliferation and/or migration; however, the molecular basis for this switch involvement in cell plasticity has not fully been understood yet. Here, we first show that knocking out CREB1 triggers a remarkable effect of epithelial-mesenchymal transition (EMT) and leads to the occurrence of inhibited proliferation and enhanced motility in HCT116 colorectal cancer cells. By monitoring 45 cellular signaling pathway activities, we find that multiple growth-related pathways decline significantly while inflammatory pathways including NF-κB are largely upregulated in comparing between the CREB1 wild-type and knocked out cells. Mechanistically, cells with CREB1 knocked out show downregulation of MYC as a result of impaired CREB1-dependent transcription of the oncogenic lncRNA CCAT1. Interestingly, the unbalanced competition between the coactivator CBP/p300 for CREB1 and p65 leads to the activation of the NF-κB pathway in cells with CREB1 disrupted, which induces an obvious EMT phenotype of the cancer cells. Taken together, these studies identify previously unknown mechanisms of CREB1 in CRC cell plasticity via regulating lncRNA CCAT1 and NF-κB pathways, providing a critical insight into a combined strategy for CREB1-targeted tumor therapies.

Effects of europium spectral probe interchange in Ln-dyads with cyclen and phen moieties.

Herein, we have investigated spectral structure and intensity changes in a bimetallic lanthanide complex comprising La3+ and Eu3+, with the ions coordinated to silent and antenna ligands, when their positions are interchanged. Comparison of the fluorescence decay of a ligand in the presence and absence of La3+ has enabled internal nonradiative decay rates to be determined. The effects upon Eu3+ emission spectra resulting from changes in its environment at a distance of ∼10 Å, and upon changing from the solid state to solution, were also investigated. Conclusive results to these investigations were achieved from the electronic excitation spectra, emission spectra and emission decay measurements of cyc-phen, cycLn1-phLn2, cycLn-phen and phLn (Ln = La, Eu; cyc = substituted 1,4,7,10-tetrazacyclododecane; phen = 1,10-phenanthroline; ph = phen(pdtc)3, pdtc = pyrrolidine-1-carbodithioate) recorded in the solid state, at 298 K and ∼10 K, and in solution. Ligand fluorescence was observed in all cases at room temperature, and phosphorescence was observed at 77 K, except for cyc-phen. The phosphorescence lifetimes of the La3+ complexes extend up to 180 ms. Our results support the concept that the lowest excited states of the complexes are localized on individual ligands, in the present case phen, rather than delocalized over the entire molecule.

Energy Transfer between Tb3+ and Eu3+ in LaPO4: Pulsed versus Switched-off Continuous Wave Excitation.

The energy transfer (ET) between Tb3+ and Eu3+ is investigated experimentally and with available theoretical models in the regime of high Tb3+ concentrations in ≈30 nm LaPO4 nanoparticles at room temperature. The ET efficiency approaches 100% even for lightly Eu3+-doped materials. The major conclusion from the use of pulsed laser excitation and switched-off continuous wave laser diode excitation is that the energy migration between Tb3+ ions, situated on La3+ sites with ≈4 Å separation, is not fast. The quenching of Tb3+ emission in singly doped LaPO4 only reduces the luminescence lifetime by ≈50% in heavily doped samples. Various theoretical models are applied to simulate the luminescence decays of Tb3+ and Tb3+, Eu3+-doped LaPO4 samples of various concentrations and the transfer mechanism is identified as forced electric dipole at each ion.

Massive Stokes shift in 12-coordinate Ce(NO2)63-: crystal structure, vibrational and electronic spectra.

The Ce3+ ion in Cs2NaCe(NO2)6 (I), which comprises the unusual Th site symmetry of the Ce(NO2)63- ion, demonstrates the largest Ce-O Stokes shift of 8715 cm-1 and the low emission quenching temperature of 53 K. The activation energy for quenching changes with temperature, attributed to relative shifts of the two potential energy curves involved. The splitting of the Ce3+ 5d1 state into two levels separated by 4925 cm-1 is accounted for by a first principles calculation using the crystal structure data of I. The NO2- energy levels and spectra were investigated also in Cs2NaLa(NO2)6 and modelled by hybrid DFT. The vibrational and electronic spectral properties have been thoroughly investigated and rationalized at temperatures down to 10 K. A comparison of Stokes shifts with other Ce-O systems emphasizes the dependence upon the coordination number of Ce3+.

Comprehensive Genomic Characterization of RNA-Binding Proteins across Human Cancers.

RNA-binding proteins (RBPs) regulate the expression of thousands of transcripts, and some are reported to be involved in human tumorigenesis. However, little is known about the dysregulation of RBPs at the genomic level in human cancers. Here, we conducted comprehensive analyses for expression, somatic copy number alteration (SCNA), and mutation profiles of 1,542 RBPs in ∼7,000 clinical specimens across 15 cancer types. We identified markedly dysregulated RBPs and found that downregulation was a predominant pattern in cancer. Combined with recurrent SCNA data, we identified 76 RBPs as potential drivers. We also discovered a set of 139 RBPs that were significantly mutated in cancers. We confirmed the oncogenic property of six RBPs in colorectal and liver cancer cell lines by using in vitro functional experiments. Our study highlights the potential roles of RBPs in carcinogenesis and lays the groundwork to better understand the functions and mechanisms of RBPs in cancer.

AAVS1-Targeted Plasmid Integration in AAV Producer Cell Lines.

Adeno-associated virus (AAV) producer cell lines are created via transfection of HeLaS3 cells with a single plasmid containing three components (the vector sequence, the AAV rep and cap genes, and a selectable marker gene). As this plasmid contains both the cis (Rep binding sites) and trans (Rep protein encoded by the rep gene) elements required for site-specific integration, it was predicted that plasmid integration might occur within the AAVS1 locus on human chromosome 19 (chr19). The objective of this study was to investigate whether integration in AAVS1 might be correlated with vector yield. Plasmid integration sites within several independent cell lines were assessed via Southern, fluorescence in situ hybridization (FISH) and PCR analyses. In the Southern analyses, the presence of fragments detected by both rep- and AAVS1-specific probes suggested that for several mid- and high-producing lines, plasmid DNA had integrated into the AAVS1 locus. Analysis with puroR and AAVS1-specific probes suggested that integration in AAVS1 was a more widespread phenomenon. High-producing AAV2-secreted alkaline phosphatase (SEAP) lines (masterwell 82 [MW82] and MW278) were evaluated via FISH using probes specific for the plasmid, AAVS1, and a chr19 marker. FISH analysis detected two plasmid integration sites in MW278 (neither in AAVS1), while a total of three sites were identified in MW82 (two in AAVS1). An inverse PCR assay confirmed integration within AAVS1 for several mid- and high-producing lines. In summary, the FISH, Southern, and PCR data provide evidence of site-specific integration of the plasmid within AAVS1 in several AAV producer cell lines. The data also suggest that integration in AAVS1 is a general phenomenon that is not necessarily restricted to high producers. The results also suggest that plasmid integration within the AAVS1 locus is not an absolute requirement for a high vector yield.

A Smart Europium-Ruthenium Complex as Anticancer Prodrug: Controllable Drug Release and Real-Time Monitoring under Different Light Excitations.

A unique, dual-function, photoactivatable anticancer prodrug, RuEuL, has been tailored that features a ruthenium(II) complex linked to a cyclen-europium chelate via a π-conjugated bridge. Under irradiation at 488 nm, the dark-inactive prodrug undergoes photodissociation, releasing the DNA-damaging ruthenium species. Under evaluation-window irradiation (λirr = one-photon 350 nm or two-photon 700 nm), the drug delivery process can be quantitatively monitored in real-time because of the long-lived red europium emission. Linear relationships between released drug concentration and ESI-MS or luminescence responses are established. Finally, the efficiency of the new prodrug is demonstrated both in vitro RuEuL anticancer prodrug over some existing ones and open the way for decisive improvements in multipurpose prodrugs.

Generation and characterization of adeno-associated virus producer cell lines for research and preclinical vector production.

Adeno-associated virus (AAV) producer cell lines represent an effective method for large-scale production of AAV vectors. We set out to evaluate and characterize the use of an abbreviated protocol to generate "masterwells" (MWs; a nonclonal cell population) as a platform for research and preclinical vector production. In this system, a single plasmid containing three components, the vector sequence, the AAV rep, and cap genes, and a selectable marker gene is stably transfected into HeLaS3 cells. Producer cell lines generating an AAV2 vector expressing a secreted form of human placental alkaline phosphatase (SEAP) have been created. Several MWs showed vector yields in the 5×10(4) to 2×10(5) DNase-resistant particles/cell range, and the productivity was stable over >60 population doublings. Integrated plasmid copy number in three high-producing MWs ranged from approximately 12 to 50; copies were arranged in a head-to-tail configuration. Upon infection with adenovirus, rep/cap copy number was amplified approximately 100-fold and high yield appeared to be dependent on the extent of amplification. Rep/cap gene expression and vector packaging both reached a peak at 48 hr postinfection. AAV2-SEAP vector was produced in 1-liter shaker culture and purified for assessment of vector quality and potency. The data showed that the majority of the capsids from the MWs contained vector DNA (≥70%) and that purified vector was free of replication-competent AAV. In vitro and in vivo analyses demonstrated that potency of the producer cell-derived vector was comparable to vector generated via the standard transfection method.

A constitutively active hypoxia-inducible factor-1alpha/VP16 hybrid factor activates expression of the human B-type natriuretic peptide gene.

Hypoxia-inducible factor-1 (HIF-1) is a primary regulator of the physiological response to hypoxia. A recombinant adenovirus expressing a constitutively active hybrid form of the HIF-1alpha subunit (Ad2/HIF-1alpha/VP16) is being evaluated as a gene therapy for the treatment of peripheral vascular disease. Ad2/HIF-1alpha/VP16 up-regulates known HIF-1-responsive genes, including those involved in angiogenesis. Expression profile analysis revealed that the brain natriuretic peptide (BNP) gene was significantly up-regulated in response to HIF-1alpha/VP16 in human fetal cardiac cells. Real-time reverse transcription-polymerase chain reaction analyses confirmed transcriptional activation of the BNP gene by HIF-1alpha/VP16 in human but not rat cardiac cells. Because hypoxia itself did not increase human BNP gene expression in these analyses, the mechanism of the HIF-1alpha/VP16 effect was determined. Analyses of promoter deletion mutants suggested that the cis-acting sequence in the human BNP promoter mediating activation by HIF-1alpha/VP16 was a putative HIF-1 responsive element (HRE) located at -466. An SV40 basal promoter-luciferase plasmid containing a minimal BNP HRE was up-regulated by HIF-1alpha/VP16, whereas a similar construct carrying a mutation within the HIF-1 binding site was not. Mutation of an E-box motif within the BNP HRE reduced HIF-1alpha/VP16-mediated transcriptional activation by 50%. Gel-shift analyses showed that both the native HIF-1alpha and HIF-1alpha/VP16 are able to bind to a probe containing the HIF-1 binding site. These experiments demonstrate the existence of a functional HRE in the BNP promoter and further define the scope and mechanism of action of Ad2/HIF-1alpha/VP16.

Stabilization of vascular endothelial growth factor mRNA by hypoxia-inducible factor 1.

Hypoxia regulates expression of vascular endothelial growth factor (VEGF) by increasing its transcription and by stabilizing its mRNA. Despite the pivotal role of hypoxia-inducible factor 1 (HIF-1) in transcriptional activation of hypoxia-responsive genes, it is not known whether HIF-1 mediates hypoxia-induced stabilization of VEGF mRNA. We constructed adenoviral vectors expressing either the wild-type HIF-1 alpha (Ad2/HIF-1 alpha/FL), a constitutively stable hybrid form of HIF-1 alpha (Ad2/HIF-1 alpha/VP16), or no transgene (Ad2/CMVEV). In rat glioma (C6) cells and human cardiac, vascular smooth muscle, and endothelial cells, infection with Ad2/HIF-1 alpha/VP16 or Ad2/HIF-1 alpha/FL increased VEGF expression at both the mRNA and protein levels. Under normoxic conditions, the half-life of VEGF mRNA was 42 min in C6 cells. Hypoxia and Ad2/HIF-1 alpha/VP16 increased the half-life of VEGF mRNA to 3.3 and 2.7 h, respectively, while Ad2/CMVEV had no effect. These studies are the first to demonstrate that overexpression of HIF-1 alpha increases VEGF mRNA stability. Our results also suggest that stabilization of VEGF mRNA by hypoxia is mediated, at least in part, by HIF-1.