Lack of the Bacterial Phytochrome Protein Decreases Deinococcus radiodurans Resistance to Mitomycin C

Deinococcus radiodurans known for its extraordinary resistance to ionizing radiation contains bacterial phytochrome (BphP), a member of the family of red/far-red light-sensing proteins. In this study, we constructed a bphP mutant strain (ΔbphP) to investigate the role of D. radiodurans BphP (DrBphP) in the DNA damage response. When cells were incubated under light and dark conditions following exposure to DNA damaging agents, such as γ- and UV-radiation and mitomycin C (MMC), no significant difference in cell survival was observed between the wild-type D. radiodurans strain (WT) and ΔbphP. However, when continuously exposed to MMC under light conditions, the WT strain notably exhibited increased survival compared to cells grown in the dark. The increased survival was not observed in the ΔbphP strain. These results are indicative of the protective role of light-activated DrBphP in the presence of MMC. Site-directed mutagenesis revealed that the conserved amino acids Cys-24 and His-532 involved in chromophore binding and signal transduction, respectively, were essential for the protective function of DrBphP. Inactivation of the cognate response regulator (RR; DrBphR) of DrBphP increased MMC resistance in the dark. In trans complementation of the bphP bphR double mutant strain (ΔbphPR) with DrBphR decreased MMC resistance. Considering that DrBphP acts as a light-activated phosphatase that dephosphorylates DrBphR, it appears that phosphorylated DrBphR exerts a negative effect on cell survival in the presence of MMC. DrBphP overexpression resulted in an increase in MMC resistance of ΔbphPR, implying that other RRs might be involved in the DrBphP-mediated signaling pathway. A mutant lacking the dr_0781 gene (Δdr_0781) demonstrated the same MMC phenotype as ΔbphR. Survival was further increased in the bphR dr_0781 double mutant strain compared to each single mutant ΔbphR or Δdr_0781, suggesting that DR_0781 is also involved in the DrBphP-dependent MMC sensitivity. This study uncovered a previously unknown phenomenon of red/far-red light-dependent DNA damage survival mediated by BphP by identifying the conditions under which DrBphP exhibits a fitness advantage.

Downstream effects of polypathology on neurodegeneration of medial temporal lobe subregions

The medial temporal lobe (MTL) is a nidus for neurodegenerative pathologies and therefore an important region in which to study polypathology. We investigated associations between neurodegenerative pathologies and the thickness of different MTL subregions measured using high-resolution post-mortem MRI. Tau, TAR DNA-binding protein 43 (TDP-43), amyloid-β and α-synuclein pathology were rated on a scale of 0 (absent)-3 (severe) in the hippocampus and entorhinal cortex (ERC) of 58 individuals with and without neurodegenerative diseases (median age 75.0 years, 60.3% male). Thickness measurements in ERC, Brodmann Area (BA) 35 and 36, parahippocampal cortex, subiculum, cornu ammonis (CA)1 and the stratum radiatum lacunosum moleculare (SRLM) were derived from 0.2 × 0.2 × 0.2 mm3 post-mortem MRI scans of excised MTL specimens from the contralateral hemisphere using a semi-automated approach. Spearman's rank correlations were performed between neurodegenerative pathologies and thickness, correcting for age, sex and hemisphere, including all four proteinopathies in the model. We found significant associations of (1) TDP-43 with thickness in all subregions (r =  - 0.27 to r =  - 0.46), and (2) tau with BA35 (r =  - 0.31) and SRLM thickness (r =  - 0.33). In amyloid-β and TDP-43 negative cases, we found strong significant associations of tau with ERC (r =  - 0.40), BA35 (r =  - 0.55), subiculum (r =  - 0.42) and CA1 thickness (r =  - 0.47). This unique dataset shows widespread MTL atrophy in relation to TDP-43 pathology and atrophy in regions affected early in Braak stageing and tau pathology. Moreover, the strong association of tau with thickness in early Braak regions in the absence of amyloid-β suggests a role of Primary Age-Related Tauopathy in neurodegeneration.

PROsetta: An R Package for Linking Patient-Reported Outcome Measures

A common problem when using a variety of patient-reported outcomes (PROs) for diverse populations and subgroups is establishing a harmonized scale for the incommensurate outcomes. The lack of comparability in metrics (e.g., raw summed scores vs. scaled scores) among different PROs poses practical challenges in studies comparing effects across studies and samples. Linking has long been used for practical benefit in educational testing. Applying various linking techniques to PRO data has a relatively short history; however, in recent years, there has been a surge of published studies on linking PROs and other health outcomes, owing in part to concerted efforts such as the Patient-Reported Outcomes Measurement Information System (PROMIS^®) project and the PRO Rosetta Stone (PROsetta Stone^®) project (www.prosettastone.org). Many R packages have been developed for linking in educational settings; however, they are not tailored for linking PROs where harmonization of data across clinical studies or settings serves as the main objective. We created the PROsetta package to fill this gap and disseminate a protocol that has been established as a standard practice for linking PROs.

Liver development is restored by blastocyst complementation of HHEX knockout in mice and pigs

Background

There are over 17,000 patients in the US waiting to receive liver transplants, and these numbers are increasing dramatically. Significant effort is being made to obtain functional hepatocytes and liver tissue that can for therapeutic use in patients. Blastocyst complementation is a challenging, innovative technology that could fundamentally change the future of organ transplantation. It requires the knockout (KO) of genes essential for cell or organ development in early stage host embryos followed by injection of donor pluripotent stem cells (PSCs) into host blastocysts to generate chimeric offspring in which progeny of the donor cells populate the open niche to develop functional tissues and organs.

Methods

The HHEX gene is necessary for proper liver development. We engineered loss of HHEX gene expression in early mouse and pig embryos and performed intraspecies blastocyst complementation of HHEX KO embryos with eGFP-labeled PSCs in order to rescue the loss of liver development.

Results

Loss of HHEX gene expression resulted in embryonic lethality at day 10.5 in mice and produced characteristics of lethality at day 18 in pigs, with absence of liver tissue in both species. Analyses of mouse and pig HHEX KO fetuses confirmed significant loss of liver-specific gene and protein expression. Intraspecies blastocyst complementation restored liver formation and liver-specific proteins in both mouse and pig. Livers in complemented chimeric fetuses in both species were comprised of eGFP-labeled donor-derived cells and survived beyond the previously observed time of HHEX KO embryonic lethality.

Conclusions

This work demonstrates that loss of liver development in the HHEX KO can be rescued via blastocyst complementation in both mice and pigs. This complementation strategy is the first step towards generating interspecies chimeras for the goal of producing human liver cells, tissues, and potentially complete organs for clinical transplantation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13287-021-02348-z.

Methylobacterium radiodurans sp. nov., a novel radiation-resistant Methylobacterium

A Gram-negative, aerobic, flagellated, rod-shaped, and pink-pigmented bacterium, strain 17Sr1-43 ^T, was isolated from a soil sample collected in Nowongu, Seoul, Korea. The isolate could grow at 18-37 °C (optimum, 28-30 °C), pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0-1.0% (w/v) NaCl (optimum, 0%) with aeration. The major cellular fatty acids were summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c) and summed feature 2 (iso-C_16:1 I and/or C_14:0 3-OH). The predominant respiratory quinone was Q-10 and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phospholipid, and diphosphatidylglycerol. The G + C content of genomic DNA was 69.1 mol%. Strain 17Sr1-43 ^T was closely related to Methylobacterium gregans KACC 14808 ^T (98.4% 16S rRNA gene sequence similarity), Methylobacterium hispanicum KACC 11432 ^T (97.9%), and Methylobacterium phyllosphaerae CBMB27^T (96.1%). The complete genome of strain 17Sr1-43 ^T contains essential genes related to DNA repair processes including bacterial RecBCD dependent pathway and UmuCD system. Based on the phenotypic, genotypic, and chemotaxonomic characteristics, strain 17Sr1-43 ^T represents a novel species in the genus Methylobacterium, for which the name Methylobacterium radiodurans sp. nov. is proposed. The type strain is strain 17Sr1-43 ^T (= KCTC 52906 ^T = NBRC 112875 ^T).

The Inhibitory Effects of Plant Derivate Polyphenols on the Main Protease of SARS Coronavirus 2 and Their Structure-Activity Relationship

The main protease (Mpro) is a major protease having an important role in viral replication of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus that caused the pandemic of 2020. Here, active Mpro was obtained as a 34.5 kDa protein by overexpression in E. coli BL21 (DE3). The optimal pH and temperature of Mpro were 7.5 and 37 °C, respectively. Mpro displayed a Km value of 16 μM with Dabcyl-KTSAVLQ↓SGFRKME-Edans. Black garlic extract and 49 polyphenols were studied for their inhibitory effects on purified Mpro. The IC50 values were 137 μg/mL for black garlic extract and 9-197 μM for 15 polyphenols. The mixtures of tannic acid with puerarin, daidzein, and/or myricetin enhanced the inhibitory effects on Mpro. The structure-activity relationship of these polyphenols revealed that the hydroxyl group in C3', C4', C5' in the B-ring, C3 in the C-ring, C7 in A-ring, the double bond between C2 and C3 in the C-ring, and glycosylation at C8 in the A-ring contributed to inhibitory effects of flavonoids on Mpro.

Longitudinal Flow Decorrelations in Xe+Xe Collisions at sqrt[s_{NN}]=5.44 TeV with the ATLAS Detector

The first measurement of longitudinal decorrelations of harmonic flow amplitudes v_{n} for n=2-4 in Xe+Xe collisions at sqrt[s_{NN}]=5.44  TeV is obtained using 3  μb^{-1} of data with the ATLAS detector at the LHC. The decorrelation signal for v_{3} and v_{4} is found to be nearly independent of collision centrality and transverse momentum (p_{T}) requirements on final-state particles, but for v_{2} a strong centrality and p_{T} dependence is seen. When compared with the results from Pb+Pb collisions at sqrt[s_{NN}]=5.02  TeV, the longitudinal decorrelation signal in midcentral Xe+Xe collisions is found to be larger for v_{2}, but smaller for v_{3}. Current hydrodynamic models reproduce the ratios of the v_{n} measured in Xe+Xe collisions to those in Pb+Pb collisions but fail to describe the magnitudes and trends of the ratios of longitudinal flow decorrelations between Xe+Xe and Pb+Pb. The results on the system-size dependence provide new insights and an important lever arm to separate effects of the longitudinal structure of the initial state from other early and late time effects in heavy-ion collisions.

Search for Dark Matter Produced in Association with a Dark Higgs Boson Decaying into W^{±}W^{∓} or ZZ in Fully Hadronic Final States from sqrt[s]=13 TeV pp Collisions Recorded with the ATLAS Detector

Several extensions of the Standard Model predict the production of dark matter particles at the LHC. An uncharted signature of dark matter particles produced in association with VV=W^{±}W^{∓} or ZZ pairs from a decay of a dark Higgs boson s is searched for using 139  fb^{-1} of pp collisions recorded by the ATLAS detector at a center-of-mass energy of 13 TeV. The s→V(qq[over ¯])V(qq[over ¯]) decays are reconstructed with a novel technique aimed at resolving the dense topology from boosted VV pairs using jets in the calorimeter and tracking information. Dark Higgs scenarios with m_{s}>160  GeV are excluded.

Medium-Induced Modification of Z-Tagged Charged Particle Yields in Pb+Pb Collisions at 5.02 TeV with the ATLAS Detector

The yield of charged particles opposite to a Z boson with large transverse momentum (p_{T}) is measured in 260  pb^{-1} of pp and 1.7  nb^{-1} of Pb+Pb collision data at 5.02 TeV per nucleon pair recorded with the ATLAS detector at the Large Hadron Collider. The Z boson tag is used to select hard-scattered partons with specific kinematics, and to observe how their showers are modified as they propagate through the quark-gluon plasma created in Pb+Pb collisions. Compared with pp collisions, charged-particle yields in Pb+Pb collisions show significant modifications as a function of charged-particle p_{T} in a way that depends on event centrality and Z boson p_{T}. The data are compared with a variety of theoretical calculations and provide new information about the medium-induced energy loss of partons in a p_{T} regime difficult to measure through other channels.

Suppressed Degradation and Enhanced Performance of CsPbI3 Perovskite Quantum Dot Solar Cells via Engineering of Electron Transport Layers

CsPbI₃ perovskite quantum dots (CsPbI₃-PQDs) have recently come into focus as a light-harvesting material that can act as a platform through which to combine the material advantages of both perovskites and QDs. However, the low cubic-phase stability of CsPbI₃-PQDs in ambient conditions has been recognized as a factor that inhibits device stability. TiO₂ nanoparticles are the most regularly used materials as an electron transport layer (ETL) in CsPbI₃-PQD photovoltaics; however, we found that TiO₂ can facilitate the cubic-phase degradation of CsPbI₃-PQDs due to its vigorous photocatalytic activity. To address these issues, we have developed chloride-passivated SnO₂ QDs (Cl@SnO₂ QDs), which have low photocatalytic activity and few surface traps, to suppress the cubic-phase degradation of CsPbI₃-PQDs. Given these advantages, the CsPbI₃-PQD solar cells based on Cl@SnO₂ ETLs show significantly improved device operational stability (under conditions of 50% relative humidity and 1-sun illumination), compared to those based on TiO₂ ETLs. In addition, the Cl@SnO₂-based devices showed improved open circuit voltage and photocurrent density, resulting in enhanced power conversion efficiency (PCE) up to 14.5% compared to that of TiO₂-based control devices (PCE of 13.8%).

Effects of Conserved Wedge Domain Residues on DNA Binding Activity of Deinococcus radiodurans RecG Helicase

Deinococcus radiodurans is extremely resistant to ionizing radiation and has an exceptional ability to repair DNA damage caused by various DNA-damaging agents. D. radiodurans uses the same DNA-repair strategies as other prokaryotes, but certain proteins involved in the classical DNA repair machinery have characteristics different from their counterparts. RecG helicase, which unwinds a variety of branched DNA molecules, such as Holliday junctions (HJ) and D-loops, plays important roles in DNA repair, recombination, and replication. Primary sequence analysis of RecG from a number of bacterial species revealed that three amino acids (QPW) in the DNA-binding wedge domain (WD) are well-conserved across the Deinococcus RecG proteins. Interactions involving these conserved residues and DNA substrates were predicted in modeled domain structures of D. radiodurans RecG (DrRecG). Compared to the WD of Escherichia coli RecG protein (EcRecG) containing FSA amino acids corresponding to QPW in DrRecG, the HJ binding activity of DrRecG-WD was higher than that of EcRecG-WD. Reciprocal substitution of FSA and QPW increased and decreased the HJ binding activity of the mutant WDs, EcRecG-WD_QPW, and DrRecG-WD_FSA, respectively. Following γ-irradiation treatment, the reduced survival rate of DrRecG mutants (ΔrecG) was fully restored by the expression of DrRecG, but not by that of EcRecG. EcRecG_QPW also enhanced γ-radioresistance of ΔrecG, whereas DrRecG_FSA did not. ΔrecG cells complemented in trans by DrRecG and EcRecG_QPW reconstituted an intact genome within 3 h post-irradiation, as did the wild-type strain, but ΔrecG with EcRecG and DrRecG_FSA exhibited a delay in assembly of chromosomal fragments induced by γ-irradiation. These results suggested that the QPW residues facilitate the association of DrRecG with DNA junctions, thereby enhancing the DNA repair efficiency of DrRecG.

Spirosoma taeanense sp. nov., a radiation resistant bacterium isolated from a coastal sand dune

An aerobic, Gram-negative, non-motile, non-spore-forming, rod-shaped, and pale yellow-colored bacterial strain, designated TS118^T, was isolated from a sand sample obtained from a coastal sand dune after exposure to 3 kGy of gamma radiation. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the genus Spirosoma and most closely related to Spirosoma metallicum PR1014k^T (95.1% similarity). The genome of strain TS118^T is constituted by one chromosome (5,691,492 bp) and one plasmid (28,440 bp) and has a G + C content of 52.7%. The genome contains 4641 protein coding sequences (CDSs), 38 tRNAs, and 11 rRNAs. The predominant fatty acids of strain TS118^T were C_16:1 ω5c, iso-C_15:0, C_16:0, summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c), and iso-C_17:0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified amino lipid and an unidentified aminophospholipid. The main respiratory quinone was menaquinone-7 (MK-7). The novel strain showed resistance to gamma radiation with a D₁₀ value (i.e., the dose required to reduce the bacterial population by tenfold) of 4.3 kGy. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain TS118^T represents a novel species, for which the name Spirosoma taeanense sp. nov. is proposed. The type strain is TS118^T (=KCTC 72898^T =JCM 34024^T).

Observation and Measurement of Forward Proton Scattering in Association with Lepton Pairs Produced via the Photon Fusion Mechanism at ATLAS

The observation of forward proton scattering in association with lepton pairs (e^{+}e^{-}+p or μ^{+}μ^{-}+p) produced via photon fusion is presented. The scattered proton is detected by the ATLAS Forward Proton spectrometer, while the leptons are reconstructed by the central ATLAS detector. Proton-proton collision data recorded in 2017 at a center-of-mass energy of sqrt[s]=13  TeV are analyzed, corresponding to an integrated luminosity of 14.6  fb^{-1}. A total of 57 (123) candidates in the ee+p (μμ+p) final state are selected, allowing the background-only hypothesis to be rejected with a significance exceeding 5 standard deviations in each channel. Proton-tagging techniques are introduced for cross-section measurements in the fiducial detector acceptance, corresponding to σ_{ee+p}=11.0±2.6(stat)±1.2(syst)±0.3(lumi) and σ_{μμ+p}=7.2±1.6(stat)±0.9(syst)±0.2(lumi)  fb in the dielectron and dimuon channel, respectively.