A vitamin-C-derived DNA modification catalysed by an algal TET homologue.

Methylation of cytosine to 5-methylcytosine (5mC) is a prevalent DNA modification found in many organisms. Sequential oxidation of 5mC by ten-eleven translocation (TET) dioxygenases results in a cascade of additional epigenetic marks and promotes demethylation of DNA in mammals1,2. However, the enzymatic activity and function of TET homologues in other eukaryotes remains largely unexplored. Here we show that the green alga Chlamydomonas reinhardtii contains a 5mC-modifying enzyme (CMD1) that is a TET homologue and catalyses the conjugation of a glyceryl moiety to the methyl group of 5mC through a carbon-carbon bond, resulting in two stereoisomeric nucleobase products. The catalytic activity of CMD1 requires Fe(II) and the integrity of its binding motif His-X-Asp, which is conserved in Fe-dependent dioxygenases3. However, unlike previously described TET enzymes, which use 2-oxoglutarate as a co-substrate4, CMD1 uses L-ascorbic acid (vitamin C) as an essential co-substrate. Vitamin C donates the glyceryl moiety to 5mC with concurrent formation of glyoxylic acid and CO2. The vitamin-C-derived DNA modification is present in the genome of wild-type C. reinhardtii but at a substantially lower level in a CMD1 mutant strain. The fitness of CMD1 mutant cells during exposure to high light levels is reduced. LHCSR3, a gene that is critical for the protection of C. reinhardtii from photo-oxidative damage under high light conditions, is hypermethylated and downregulated in CMD1 mutant cells compared to wild-type cells, causing a reduced capacity for photoprotective non-photochemical quenching. Our study thus identifies a eukaryotic DNA base modification that is catalysed by a divergent TET homologue and unexpectedly derived from vitamin C, and describes its role as a potential epigenetic mark that may counteract DNA methylation in the regulation of photosynthesis.

Efficient methods for multiple types of precise gene-editing in Chlamydomonas.

Precise gene-editing using CRISPR/Cas9 technology remains a long-standing challenge, especially for genes with low expression and no selectable phenotypes in Chlamydomonas reinhardtii, a classic model for photosynthesis and cilia research. Here, we developed a multi-type and precise genetic manipulation method in which a DNA break was generated by Cas9 nuclease and the repair was mediated using a homologous DNA template. The efficacy of this method was demonstrated for several types of gene editing, including inactivation of two low-expression genes (CrTET1 and CrKU80), the introduction of a FLAG-HA epitope tag into VIPP1, IFT46, CrTET1 and CrKU80 genes, and placing a YFP tag into VIPP1 and IFT46 for live-cell imaging. We also successfully performed a single amino acid substitution for the FLA3, FLA10 and FTSY genes, and documented the attainment of the anticipated phenotypes. Lastly, we demonstrated that precise fragment deletion from the 3'-UTR of MAA7 and VIPP1 resulted in a stable knock-down effect. Overall, our study has established efficient methods for multiple types of precise gene editing in Chlamydomonas, enabling substitution, insertion and deletion at the base resolution, thus improving the potential of this alga in both basic research and industrial applications.

Anisotropic Nonlocal Damping in Ferromagnet/α-GeTe Bilayers Enabled by Splitting Energy Bands.

The understanding and manipulation of anisotropic Gilbert damping is crucial for both fundamental research and versatile engineering and optimization. Although several works on anisotropic damping have been reported, no direct relationship between the band structure and anisotropic damping was established. Here, we observed an anisotropic damping in Fe/GeTe manipulated by the symmetric band structures of GeTe via angle-resolved photoemission spectroscopy. Moreover, the anisotropic damping can be modified by the symmetry of band structures. Our Letter provides insightful understandings of the anisotropic Gilbert damping in ferromagnets interfaced with Rashba semiconductors and suggests the possibility of manipulating the Gilbert damping by band engineering.

Dual Topology of Dirac Electron Transport and Photogalvanic Effect in Low-Dimensional Topological Insulator Superlattices.

Dual topological insulators, simultaneously protected by time-reversal symmetry and crystalline symmetry, open great opportunities to explore different symmetry-protected metallic surface states. However, the conventional dual topological states located on different facets hinder integration into planar opto-electronic/spintronic devices. Here, dual topological superlattices (TSLs) Bi2 Se3 -(Bi2 /Bi2 Se3 )N with limited stacking layer number N are constructed. Angle-resolved photoelectron emission spectra of the TSLs identify the coexistence and adjustment of dual topological surface states on Bi2 Se3 facet. The existence and tunability of spin-polarized dual-topological bands with N on Bi2 Se3 facet result in an unconventionally weak antilocalization effect (WAL) with variable WAL coefficient α (maximum close to 3/2) from quantum transport experiments. Most importantly, it is identified that the spin-polarized surface electrons from dual topological bands exhibit circularly and linearly polarized photogalvanic effect (CPGE and LPGE). It is anticipated that the stacked dual-topology and stacking layer number controlled bands evolution provide a platform for realizing intrinsic CPGE and LPGE. The results show that the surface electronic structure of the dual TSLs is highly tunable and well-regulated for quantum transport and photoexcitation, which shed light on engineering for opto-electronic/spintronic applications.

Surface topography index: a novel deformity severity assessment index for pectus excavatum.

BACKGROUND: The surface topography index (STI) has great potential in both routine computed tomography (CT) scan and emerging optical imaging systems. However, the diagnostic accuracy and stability of the STI as a deformity severity assessment index has not been fully confirmed. Therefore, the aim of the present study was to determine the diagnostic performance of the STI as a novel deformity severity assessment index for pectus excavatum. METHODS: The present study consisted of 722 chest CT images from a single center. The standard CT index (CTI) and STI were calculated for all patients. The between-group difference and the level of compliance between the CTI and STI was analyzed by t-test and Pearson correlation. The diagnostic value and optimum discriminatory values of the CTI and STI were calculated by a receiver-operating characteristic (ROC) curve and DeLong's test. RESULTS: The distributions of the CTI and STI were similar and showed a slight overlap between the pectus excavatum (PE) and non-PE groups. Both the CTI and STI significantly differed between the 2 groups (P<0.001). The STI demonstrated a strong Pearson correlation with the CTI (r=0.91, 95% confidence interval: 0.88-0.91, P<0.001). The ROC curves showed that STI =1.58 (sensitivity: 0.93, specificity: 0.95) could be considered equivalent to CTI =2.72 (sensitivity: 0.93, specificity: 0.97) as the optimum discriminatory values. DeLong's test showed no significant difference in the ROC curve results between the CTI and STI (Z=0.90, P=0.37). CONCLUSIONS: The STI has comparative discrimination ability in PE diagnosis and deformity severity assessment when used with the standard CTI. The STI as a novel index is not only an ideal evaluation metric of PE deformity but also an objective trait for PE patients just as weight and height for everyone.

Thymine DNA glycosylase recognizes the geometry alteration of minor grooves induced by 5-formylcytosine and 5-carboxylcytosine.

The dynamic DNA methylation-demethylation process plays critical roles in gene expression control and cell development. The oxidation derivatives of 5-methylcytosine (5mC) generated by Tet dioxygenases in the demethylation pathway, namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), could impact biological functions by altering DNA properties or recognition by potential reader proteins. Hence, in addition to the fifth base 5mC, 5hmC, 5fC, and 5caC have been considered as the sixth, seventh, and eighth bases of the genome. How these modifications would alter DNA and be specifically recognized remain unclear, however. Here we report that formyl- and carboxyl-modifications on cytosine induce the geometry alteration of the DNA minor groove by solving two high-resolution structures of a dsDNA decamer containing fully symmetric 5fC and 5caC. The alterations are recognized distinctively by thymine DNA glycosylase TDG via its finger residue R275, followed by subsequent preferential base excision and DNA repair. These observations suggest a mechanism by which reader proteins distinguish highly similar cytosine modifications for potential differential demethylation in order to achieve downstream biological functions.

Evaluation of coma patients after cardiopulmonary resuscitation.

BACKGROUND: Coma after cardiopulmonary resuscitation (CPR) is commonly seen in daily clinical practice. How to objectively evaluate brain function after CPR is essential to the following treatment. Coma patients after CPR had been studied prospectively at the Neuro-Intensive Care Unit of Xuanwu Hospital since 2002. In this study, we focused on the topic of how to evaluate the severity of coma after CPR. METHODS: From April 2002 to November 2004, patients in coma 24 hours after CPR were monitored, the evaluation methods included Glasgow coma score (GCS), brain stem reflection, and spinal reflection. Laboratory evaluation included electroencephalography (EEG), brainstem auditory evoked potential (BAEP), short latency somatosensory evoked potential (SLSEP), and transcranial Doppler (TCD). RESULTS: Twenty-four of 35 patients (68.57%) were in deep coma. The GCS was 3 except for 2 patients; EEG was evaluated not less than grade IV except for 4 patients, BAEP was evaluated as grade III except for 3 patients, and SLSEP was evaluated as grade III except for 1 patient. Twenty-four patients died within 1 month and 11 of them (45.83%) were determined as brain death. Glasgow outcome score (GOS) was evaluated as grade I. Eleven of the 35 patients survived and their consciousness changed from deep coma to coma vigil. EEG was evaluated as gradeIin 5 patients, BAEP and SLSEP were evaluated as grade I in 3 patients, and GOS was all evaluated as grade II among the 11 patients. Two patients (18.18%) regained consciousness in 35 and 90 days after cardiopulmonary resuscitation and GOS was evaluated as grade IV and III, respectively. CONCLUSION: Combined or continuous evaluation of clinical examinations and laboratory tests can accurately and objectively determine brain function after CPR.

[Evaluation of coma after cardiopulmonary resuscitation].

OBJECTIVE: To investigate the accurate and objective methods of evaluating coma after cardiopulmonary resuscitation. METHODS: Cases that were still in coma 24 hours after cardiopulmonary resuscitation were continuously observed and evaluated between April 2002 and November 2004. The methods of evaluation included various clinical examinations, for instance conscious state, Glasgow coma score (GCS), brain stem inflection, spinal reflexes and so on. Other methods of evaluation included laboratory examinations, such as electroencephalography (EEG), brain auditory evoked potential (BAEP), short latent somatosensory evoked potential (SLSEP) and transcranial doppler (TCD). RESULTS: 24 of a series of 35 cases (68.6%) were in deep coma. The GCS is score 3. EEG evaluated was not less than grade IV in all except 4; BAEP evaluated was grade III in all except 3; SLSEP evaluated was grade III in all except 1. 24 cases died within 1 month and 11 of them (45.8%) were evaluated as having brain death and Glasgow outcome score (GOS) was grade I. 11 of the 35 cases survived and their state of consciousness changed from deep coma to coma vigil, EEG evaluated was grade I in 5 cases. BAEP and SLSEP were grade I in the 3 cases evaluated and GOS is grade II. 2 cases (18.2%) regain consciousness at the time of 35 and 90 days after cardiopulmonary resuscitation and their GOS was grade IV and grade III respectively. CONCLUSION: Combined and continuous observation of clinical manifestations and laboratory parameters can accurately and objectively evaluate coma after cardiopulmonary resuscitation.

Early prediction of poor outcome in severe hemispheric stroke by EEG patterns and gradings.

OBJECTIVES: To find out the EEG abnormal patterns in massive cerebral hemispheric infarction (MCHI) and their correlation with poor outcome, and to construct an EEG grading for predicting the outcome of MCHI patients. METHODS: Between 2000 and 2010, 162 patients with MCHI who met the selection criterions were selected for this study. All the patients underwent EEG examinations within 3 days after stroke onset and repeated on day 2 and 3. We classified the EEG recordings into 9 patterns and anglicized the correlation between EEG patterns and outcome. Then according to the results of the correlation between EEG patterns and outcome we constructed an EEG grading for predicting the outcome of MCHI patients. RESULTS: We revealed that patterns of dominant alpha without reactivity, RAWOD, burst-suppression, α/θ-coma, epileptiform activity (without burst-suppression), and generalized suppression were correlated to poor outcome. We further modified the Young grading according to the correlation between EEG patterns and outcome. We found that the modified grading was superior to existing EEG gradings in predicting the outcome of MCHI patients, and it could predict the outcome of MCHI more accurately. CONCLUSIONS: MCHI is common in N-ICU (Neurology Intensive Care Unit). The EEG analysis would detect the degree of brain lesion during the ischemia within the acute stage after stroke onset. The EEG evaluation might assist the neurophysicians to predict outcome of patients and make decisions on the treatments.