Species-wide genetic incompatibility analysis identifies immune genes as hot spots of deleterious epistasis.

Intraspecific genetic incompatibilities prevent the assembly of specific alleles into single genotypes and influence genome- and species-wide patterns of sequence variation. A common incompatibility in plants is hybrid necrosis, characterized by autoimmune responses due to epistatic interactions between natural genetic variants. By systematically testing thousands of F1 hybrids of Arabidopsis thaliana strains, we identified a small number of incompatibility hot spots in the genome, often in regions densely populated by nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes. In several cases, these immune receptor loci interact with each other, suggestive of conflict within the immune system. A particularly dangerous locus is a highly variable cluster of NLR genes, DM2, which causes multiple independent incompatibilities with genes that encode a range of biochemical functions, including NLRs. Our findings suggest that deleterious interactions of immune receptors limit the combinations of favorable disease resistance alleles accessible to plant genomes.

Oxidative stress response and programmed cell death guided by NAC013 modulate pithiness in radish taproots.

Radish, Raphanus sativus L., is an important root crop that is cultivated worldwide. Owing to its evolutionary proximity to Arabidopsis thaliana, radish can be used as a model root crop in research on the molecular basis of agronomic traits. Pithiness is a significant defect that reduces the production of radish with commercial value; however, traditional breeding to eliminate this trait has thus far been unsuccessful. Here, we performed transcriptomics and genotype-by-sequencing (GBS)-based quantitative trait locus (QTL) analyses of radish inbred lines to understand the molecular basis of pithiness in radish roots. The transcriptome data indicated that pithiness likely stems from the response to oxidative stress, leading to cell death of the xylem parenchyma during the root-thickening process. Subsequently, we narrowed down a list of candidates responsible for pithiness near a major QTL and found polymorphisms in a radish homologue of Arabidopsis ANAC013 (RsNAC013), an endoplasmic reticulum bound NAC transcription factor that is targeted to the nucleus to mediate the mitochondrial retrograde signal. We analysed the effects of polymorphisms in RsNAC013 using Arabidopsis transgenic lines overexpressing RsNAC013 alleles as well as in radish inbred lines bearing these alleles. This analysis indicated that non-synonymous variations within the coding sequence result in different levels of RsNAC013 activities, thereby providing a genetic condition for root pithiness. The elevated oxidative stress or hypoxia that activates RsNAC013 for mitochondrial signalling enhances this process. Collectively, this study serves as an exemplary case of translational research taking advantage of the extensive information available from a model organism.

An aptamer-based magnetic resonance imaging contrast agent for detecting oligomeric amyloid-ß in the brain of an Alzheimer's disease mouse model.

The oligomeric amyloid-ß (oAß) is a reliable feature for an early diagnosis of Alzheimer's disease (AD). Therefore, the objective of this study was to demonstrate imaging of oAß deposits using our developed DNA aptamer called ob5 conjugated with gadolinium (Gd)-dodecane tetraacetic acid (DOTA) as a contrast agent for early diagnosis of AD using MRI. An oAß-specific aptamer was developed by amide bond formation and conjugated to Gd-DOTA MRI contrast agent and/or cyanine5 (cy5). We verified the performance of our new contrast agent with an AD mouse model using in vivo and ex vivo fluorescent imaging and animal MRI experiments. The presence of soluble Aß in 3xTg AD mice was detected using GdDOTA-ob5-cy5 probe ex vivo. Fluorescence intensities of the GdDOTA-ob5-cy5 contrast agent were high in the brains of 3xTg-AD mice, but relatively low in the brains of control mice. The GdDOTA-ob5 contrast agent had higher relaxivity than a clinically available contrast agent. T1-weighted MRI signals in 5-month-old 3xTg AD mice increased at 5 min, were prolonged until 10 min, then decreased 15 min after injecting the GdDOTA-ob5 contrast agent. Our targeted DNA aptamer GdDOTA-ob5 contrast agent could be potentially useful for validating the efficacy of a novel diagnostic contrast agent for selectively targeting neurotoxic oAß. It could ultimately be used for early diagnosis of AD.

Correction of a pathogenic gene mutation in human embryos.

Genome editing has potential for the targeted correction of germline mutations. Here we describe the correction of the heterozygous MYBPC3 mutation in human preimplantation embryos with precise CRISPR-Cas9-based targeting accuracy and high homology-directed repair efficiency by activating an endogenous, germline-specific DNA repair response. Induced double-strand breaks (DSBs) at the mutant paternal allele were predominantly repaired using the homologous wild-type maternal gene instead of a synthetic DNA template. By modulating the cell cycle stage at which the DSB was induced, we were able to avoid mosaicism in cleaving embryos and achieve a high yield of homozygous embryos carrying the wild-type MYBPC3 gene without evidence of off-target mutations. The efficiency, accuracy and safety of the approach presented suggest that it has potential to be used for the correction of heritable mutations in human embryos by complementing preimplantation genetic diagnosis. However, much remains to be considered before clinical applications, including the reproducibility of the technique with other heterozygous mutations.

Margin of exposure to free formaldehyde in personal care products containing formaldehyde-donor preservatives: Evidence for consumer safety.

Formaldehyde has been classified as carcinogenic to humans by International Agency for Research on Cancer and found in personal care (PC) products containing formaldehyde-donor (FD) preservatives. However, the cancer risk associated with the use of FD-containing PC products has not been well established. Our study provides the quantitative cancer risk assessment of formaldehyde in FD-containing PC products. The carbon-13 nuclear magnetic resonance (13C-NMR) spectroscopy was used in this risk assessment to provide reliable exposure information to formaldehyde in PC products and aqueous solutions containing sodium hydroxymethylglycinate. The risk assessment was conducted using the margin of exposure (MOE) approach with benchmark doses (BMDs) for 10% effect. For hemolymphoreticular neoplasias in male rats, a BMD of 28.03 mg/kg/day and a BMD lower confidence limit (BMDL) of 2.52 mg/kg/day were calculated from available long-term animal experiments. The worst-case consumer exposure to formaldehyde from FD-containing PC products was 0.007 µg/kg/day. Comparing the consumer exposure with BMDL, the resulting MOE was 360,000 for the worst-case scenario. The consumer exposure to formaldehyde (0.007 µg/kg/day) from using FD-containing PC products represents less than 1.0 × 10-6 % of background level endogenous formaldehyde (878-1310 mg/kg/day). The cancer risk from formaldehyde to consumers using FD-containing PC products is negligible.

RPW8/HR repeats control NLR activation in Arabidopsis thaliana.

In many plant species, conflicts between divergent elements of the immune system, especially nucleotide-binding oligomerization domain-like receptors (NLR), can lead to hybrid necrosis. Here, we report deleterious allele-specific interactions between an NLR and a non-NLR gene cluster, resulting in not one, but multiple hybrid necrosis cases in Arabidopsis thaliana. The NLR cluster is RESISTANCE TO PERONOSPORA PARASITICA 7 (RPP7), which can confer strain-specific resistance to oomycetes. The non-NLR cluster is RESISTANCE TO POWDERY MILDEW 8 (RPW8) / HOMOLOG OF RPW8 (HR), which can confer broad-spectrum resistance to both fungi and oomycetes. RPW8/HR proteins contain at the N-terminus a potential transmembrane domain, followed by a specific coiled-coil (CC) domain that is similar to a domain found in pore-forming toxins MLKL and HET-S from mammals and fungi. C-terminal to the CC domain is a variable number of 21- or 14-amino acid repeats, reminiscent of regulatory 21-amino acid repeats in fungal HET-S. The number of repeats in different RPW8/HR proteins along with the sequence of a short C-terminal tail predicts their ability to activate immunity in combination with specific RPP7 partners. Whether a larger or smaller number of repeats is more dangerous depends on the specific RPW8/HR autoimmune risk variant.

Comprehensive Genome-Wide Analysis and Expression Pattern Profiling of the SlHVA22 Gene Family Unravels Their Likely Involvement in the Abiotic Stress Adaptation of Tomato.

HVA22 family proteins with a conserved TB2/DP1/HVA22 domain are ubiquitous in eukaryotes. HVA22 family genes have been identified in a variety of plant species. However, there has been no comprehensive genome-wide analysis of HVA22 family genes in tomato (Solanum lycopersicum L.). Here, we identified 15 non-redundant SlHVA22 genes with three segmentally duplicated gene pairs on 8 of the 12 tomato chromosomes. The predicted three-dimensional (3D) models and gene ontology (GO) annotations of SlHVA22 proteins pointed to their putative transporter activity and ability to bind to diverse ligands. The co-expression of SlHVA22 genes with various genes implicated in multiple metabolic pathways and the localization of SlHVA22-GFP fused proteins to the endoplasmic reticulum suggested that they might have a variety of biological functions, including vesicular transport in stressed cells. Comprehensive expression analysis revealed that SlHVA22 genes were differentially expressed in various organs and in response to abiotic stress conditions. The predominant expression of SlHVA22i at the ripening stage and that of SlHVA22g, SlHVA22k, and SlHVA22l in fruits at most developmental stages suggested their probable involvement in tomato fruit development and ripening. Moreover, the transcript expression of most tomato HVA22 genes, particularly SlHVA22b, SlHVA22i, SlHVA22k, SlHVA22l, SlHVA22m, and SlHVA22n, was affected by abscisic acid (ABA) and diverse abiotic stress treatments, indicating the likely involvement of these genes in tomato abiotic stress responses in an ABA-dependent manner. Overall, our findings provide a foundation to better understand the structures and functional roles of SlHVA22 genes, many of which might be useful to improve the abiotic stress tolerance and fruit quality of tomato through marker-assisted backcrossing or transgenic approaches.

Genetics of autoimmunity in plants: an evolutionary genetics perspective.

Autoimmunity in plants has been found in numerous hybrids as a form of hybrid necrosis and mutant panels. Uncontrolled cell death is a main cellular outcome of autoimmunity, which negatively impacts growth. Its occurrence highlights the vulnerable nature of the plant immune system. Genetic investigation of autoimmunity in hybrid plants revealed that extreme variation in the immune receptor repertoire is a major contributor, reflecting an evolutionary conundrum that plants face in nature. In this review, we discuss natural variation in the plant immune system and its contribution to fitness. The value of autoimmunity genetics lies in its ability to identify combinations of a natural immune receptor and its partner that are predisposed to triggering autoimmunity. The network of immune components for autoimmunity becomes instrumental in revealing mechanistic details of how immune receptors recognize cellular invasion and activate signaling. The list of autoimmunity-risk variants also allows us to infer evolutionary processes contributing to their maintenance in the natural population. Our approach to autoimmunity, which integrates mechanistic understanding and evolutionary genetics, has the potential to serve as a prognosis tool to optimize immunity in crops.

Treatment of chemotherapy-induced cachexia with BST204: a multimodal validation study.

INTRODUCTION: Chemotherapy is a major etiology of cachexia. Ginseng products are known to have various anti-cachectic and health-promoting effects, such as inhibiting inflammation and promoting energy production. In particular, BST204, purified ginseng dry extract, contains multiple ginsenosides that can reduce chemotherapy-related fatigue and toxicity. OBJECTIVES: To investigate the effects of BST204 on the alleviation of chemotherapy-induced cachexia using a multimodal approach. METHODS: In a CT26 mouse syngeneic colon cancer model, cachexia was predominantly induced by chemotherapy with 5-fluorouracil (5-FU) than by tumor growth. BST204 at a dose of 100 or 200 mg/kg was administered to 5-FU-treated mice. RESULTS: BST204 significantly mitigated the decrease in tumor-excluded body weight (change in 5-FU group and BST204 groups: - 13% vs. - 6% on day 7; - 30% vs. - 20% on day 11), muscle volume (- 19% vs. - 11%), and fat volume (- 91% vs. - 56%). The anti-cachectic effect of BST204 was histologically demonstrated by an improved balance between muscle regeneration and degeneration and a decrease in muscle cross-sectional area reduction. CONCLUSION: Chemotherapy-induced cachexia was biochemically and metabolically characterized by activated inflammation, enhanced oxidative stress, increased protein degradation, decreased protein stabilization, reduced glucose-mediated energy production, and deactivated glucose-mediated biosynthesis. These adverse effects were significantly improved by BST204 treatment. Overall, our multimodal study demonstrated that BST204 could effectively alleviate chemotherapy-induced cachexia.

Techniques for measuring carbon and oxygen isotope compositions of atmospheric CO2 via isotope ratio mass spectrometry.

Measuring the stable isotope compositions of atmospheric CO2 is common in earth and atmospheric sciences, and various analytical methods have been developed utilizing continuous-flow (CF) or dual-inlet (DI) isotope ratio mass spectrometry (IRMS). Air is typically collected via passive, manual, or automated collection methods and the volume of the air sample ranges from 10 to 300 mL for CF-IRMS to >1 L for DI-IRMS to yield a measurable amount of atmospheric CO2 gas. It has been determined that the integrity of vials and flasks for air sample storage can be compromised after 3 days of air collection for δ13 C values and within 10 hours for δ18 O values. Air samples must be purified after collection to remove constituents of air, such as Ar, O2 , N2 , N2 O, and water vapor, to avoid isobaric interferences during mass spectrometric measurement. Purification is generally undertaken by utilizing commercial or custom-made preconcentration devices, the blanking method for CF-IRMS, or an offline/online cryogenic separation using a vacuum line for DI-IRMS. Ambient N2 O is a component of air that may affect analytical results and thus must either be corrected for or be removed using a gas chromatographic column. In some cases, water is removed during air collection by using a common chemical desiccant, magnesium perchlorate (Mg(ClO4 )2 ), or by a dry ice/alcohol mixture (-78°C). Lastly, a linearity issue for IRMS due to the low amount of purified CO2 from a typical ambient air sample must be considered. In general, analytical precisions of 0.02-0.21‰ and 0.04-0.34‰ for CF-IRMS and 0.01-0.02‰ and 0.01-0.02‰ for DI-IRMS are expected for δ13 C and δ18 O measurements, respectively.

Modulation of ACD6 dependent hyperimmunity by natural alleles of an Arabidopsis thaliana NLR resistance gene.

Plants defend themselves against pathogens by activating an array of immune responses. Unfortunately, immunity programs may also cause unintended collateral damage to the plant itself. The quantitative disease resistance gene ACCELERATED CELL DEATH 6 (ACD6) serves to balance growth and pathogen resistance in natural populations of Arabidopsis thaliana. An autoimmune allele, ACD6-Est, which strongly reduces growth under specific laboratory conditions, is found in over 10% of wild strains. There is, however, extensive variation in the strength of the autoimmune phenotype expressed by strains with an ACD6-Est allele, indicative of genetic modifiers. Quantitative genetic analysis suggests that ACD6 activity can be modulated in diverse ways, with different strains often carrying different large-effect modifiers. One modifier is SUPPRESSOR OF NPR1-1, CONSTITUTIVE 1 (SNC1), located in a highly polymorphic cluster of nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes, which are prototypes for qualitative disease resistance genes. Allelic variation at SNC1 correlates with ACD6-Est activity in multiple accessions, and a common structural variant affecting the NL linker sequence can explain differences in SNC1 activity. Taken together, we find that an NLR gene can mask the activity of an ACD6 autoimmune allele in natural A. thaliana populations, thereby linking different arms of the plant immune system.

The Functional Association of ACQOS/VICTR with Salt Stress Resistance in Arabidopsis thaliana Was Confirmed by CRISPR-Mediated Mutagenesis.

Clustered regularly interspaced palindromic repeat (CRISPR)-mediated mutagenesis has become an important tool in plant research, enabling the characterization of genes via gene knock-out. CRISPR genome editing tools can be applied to generate multi-gene knockout lines. Typically, multiple single-stranded, single guide RNAs (gRNAs) must be expressed in an organism to target multiple genes simultaneously; however, a single gRNA can target multiple genes if the target genes share similar sequences. A gene cluster comprising ACQUIRED OSMOTOLERANCE (ACQOS; AT5G46520) and neighboring nucleotide-binding leucine-rich repeats (NLRs; AT5G46510) is associated with osmotic tolerance. To investigate the role of ACQOS and the tandemly arranged NLR in osmotic tolerance, we introduced small insertion/deletion mutations into two target genes using a single gRNA and obtained transformant plant lines with three different combinations of mutant alleles. We then tested our mutant lines for osmotic tolerance after a salt-stress acclimation period by determining the chlorophyll contents of the mutant seedlings. Our results strongly suggest that ACQOS is directly associated with salt resistance, while the neighboring NLR is not. Here, we confirmed previous findings suggesting the involvement of ACQOS in salt tolerance and demonstrated the usefulness of CRISPR-mediated mutagenesis in validating the functions of genes in a single genetic background.

Isotopic links between atmospheric chemistry and the deep sulphur cycle on Mars.

The geochemistry of Martian meteorites provides a wealth of information about the solid planet and the surface and atmospheric processes that occurred on Mars. The degree to which Martian magmas may have assimilated crustal material, thus altering the geochemical signatures acquired from their mantle sources, is unclear. This issue features prominently in efforts to understand whether the source of light rare-earth elements in enriched shergottites lies in crustal material incorporated into melts or in mixing between enriched and depleted mantle reservoirs. Sulphur isotope systematics offer insight into some aspects of crustal assimilation. The presence of igneous sulphides in Martian meteorites with sulphur isotope signatures indicative of mass-independent fractionation suggests the assimilation of sulphur both during passage of magmas through the crust of Mars and at sites of emplacement. Here we report isotopic analyses of 40 Martian meteorites that represent more than half of the distinct known Martian meteorites, including 30 shergottites (28 plus 2 pairs, where pairs are separate fragments of a single meteorite), 8 nakhlites (5 plus 3 pairs), Allan Hills 84001 and Chassigny. Our data provide strong evidence that assimilation of sulphur into Martian magmas was a common occurrence throughout much of the planet's history. The signature of mass-independent fractionation observed also indicates that the atmospheric imprint of photochemical processing preserved in Martian meteoritic sulphide and sulphate is distinct from that observed in terrestrial analogues, suggesting fundamental differences between the dominant sulphur chemistry in the atmosphere of Mars and that in the atmosphere of Earth.

Cerebral mapping of glutamate using chemical exchange saturation transfer imaging in a rat model of stress-induced sleep disturbance at 7.0T.

BACKGROUND: Glutamate chemical exchange saturation transfer (GluCEST) imaging has been widely used in brain psychiatric disorders. Glutamate signal changes may help to evaluate the sleep-related disorders, and could be useful in diagnosis. PURPOSE: To evaluate signal changes in the hippocampus and cortex of a rat model of stress-induced sleep disturbance using GluCEST. STUDY TYPE: Prospective animal study. ANIMAL MODEL: Fourteen male Sprague-Dawley rats. FIELD STRENGTH/SEQUENCE: 7.0T small bore MRI / fat-suppressed, turbo-rapid acquisition with relaxation enhancement (RARE) for CEST, and spin-echo, point-resolved proton MR spectroscopy (1 H MRS). ASSESSMENT: Rats were divided into two groups: the stress-induced sleep-disturbance group (SSD, n = 7) and the control group (CTRL, n = 7), to evaluate and compare the cerebral glutamate signal changes. GluCEST data were quantified using a conventional magnetization transfer ratio asymmetry in the left- and right-side hippocampus and cortex. The correlation between GluCEST signal and glutamate concentrations, derived from 1 H MRS, was evaluated. STATISTICAL ANALYSIS: Wilcoxon rank-sum test between CEST signals and multiparametric MR signals, Wilcoxon signed-rank test between CEST signals on the left and right hemispheres, and a correlation test between CEST signals and glutamate concentrations derived from 1 H MRS. RESULTS: Measured GluCEST signals showed significant differences between the two groups (left hippocampus; 4.23 ± 0.27% / 5.27 ± 0.42% [SSD / CTRL, P = 0.002], right hippocampus; 4.50 ± 0.44% / 5.04 ± 0.34% [P = 0.035], left cortex; 2.81 ± 0.38% / 3.56 ± 0.41% [P = 0.004], and right cortex; 2.95 ± 0.47% / 3.82 ± 0.26% [P = 0.003]). GluCEST signals showed positive correlation with glutamate concentrations (R2 = 0.312; P = 0.038). DATA CONCLUSION: GluCEST allowed the visualization of cerebral glutamate changes in rats subjected to sleep disturbance, and may yield valuable insights for interpreting alterations in cerebral biochemical information. LEVEL OF EVIDENCE: 2 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2019;50:1866-1872.

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation.

Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe-microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe-microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial "hubs," are strongly interconnected and have a severe effect on communities. By documenting these microbe-microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on "hub" microbes, which, via microbe-microbe interactions, transmit the effects to the microbial community. We analyzed two "hub" microbes (the obligate biotrophic oomycete pathogen Albugo and the basidiomycete yeast fungus Dioszegia) more closely. Albugo had strong effects on epiphytic and endophytic bacterial colonization. Specifically, alpha diversity decreased and beta diversity stabilized in the presence of Albugo infection, whereas they otherwise varied between plants. Dioszegia, on the other hand, provided evidence for direct hub interaction with phyllosphere bacteria. The identification of microbial "hubs" and their importance in phyllosphere microbiome structuring has crucial implications for plant-pathogen and microbe-microbe research and opens new entry points for ecosystem management and future targeted biocontrol. The revelation that effects can cascade through communities via "hub" microbes is important to understand community structure perturbations in parallel fields including human microbiomes and bioprocesses. In particular, parallels to human microbiome "keystone" pathogens and microbes open new avenues of interdisciplinary research that promise to better our understanding of functions of host-associated microbiomes.

Enzymatically catalyzed CO2 -H2 O equilibration for oxygen isotope analyses of aqueous samples.

RATIONALE: The classic CO2 -H2 O equilibration method is a very popular technique for the measurement of the oxygen isotope composition of aqueous samples in stable isotope geochemistry. This study examined whether enzymatically controlled CO2 -H2 O equilibration by carbonic anhydrase (CA) could reduce the time for oxygen isotope equilibrium between CO2 and H2 O at 25°C. METHODS: Four types of aqueous samples containing CA were equilibrated with CO2 gases using a continuous flow isotope ratio mass spectrometer equipped with an automated gas sample collection device. We examined the effect of CA concentration in an aqueous sample, the influence of drying technique for the preparation of sample vials containing dried CA, the age of CA stock solution, and the ionic strength and the oxygen isotope composition of aqueous samples. RESULTS: CA rapidly catalyzed the oxygen isotope exchange between CO2 and H2 O and was unaffected by drying technique or stock solution age. Compared with aqueous samples with no CA or 0.2 µmolal CA, samples containing 4 µmolal CA significantly reduced the CO2 -H2 O equilibration time for deionized water and artificial seawater (ionic strength = ~0.6) from ~19 h and ~23 h to ~0.30 h and ~0.77 h, respectively at 25°C. CONCLUSIONS: This enzymatically catalyzed CO2 -H2 O equilibration method is time-efficient, cost-effective, requires no additional data correction procedure, and can be used for most commercially available CO2 -H2 O equilibration devices without any modification.

Web-based design and analysis tools for CRISPR base editing.

BACKGROUND: As a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool. Recently, CRISPR base editors, which consist of deactivated Cas9 (dCas9) or Cas9 nickase (nCas9) linked with a cytidine or a guanine deaminase, have been developed. Base editing tools will be very useful for gene correction because they can produce highly specific DNA substitutions without the introduction of any donor DNA, but dedicated web-based tools to facilitate the use of such tools have not yet been developed. RESULTS: We present two web tools for base editors, named BE-Designer and BE-Analyzer. BE-Designer provides all possible base editor target sequences in a given input DNA sequence with useful information including potential off-target sites. BE-Analyzer, a tool for assessing base editing outcomes from next generation sequencing (NGS) data, provides information about mutations in a table and interactive graphs. Furthermore, because the tool runs client-side, large amounts of targeted deep sequencing data (< 1 GB) do not need to be uploaded to a server, substantially reducing running time and increasing data security. BE-Designer and BE-Analyzer can be freely accessed at http://www.rgenome.net/be-designer/ and http://www.rgenome.net/be-analyzer /, respectively. CONCLUSION: We develop two useful web tools to design target sequence (BE-Designer) and to analyze NGS data from experimental results (BE-Analyzer) for CRISPR base editors.

Intravenously Administered Lidocaine and Magnesium During Thyroid Surgery in Female Patients for Better Quality of Recovery After Anesthesia.

BACKGROUND: Although systemic lidocaine and magnesium have been widely studied as perioperative analgesic adjuvants, they have been rarely evaluated with respect to recovery quality under the same conditions. We compared the quality of recovery 40 (QoR-40) scores of female patients who received intravenous lidocaine, magnesium, and saline during thyroidectomy to investigate their effects on comprehensive recovery from anesthesia. METHODS: In this prospective, double-blind trial, 135 female patients scheduled for open thyroidectomy were randomly assigned to the lidocaine group (group L), magnesium group (group M), or control group (group C). Immediately after induction, lidocaine (2 mg/kg for 15 minutes followed by 2 mg/kg/h) was administered in group L and magnesium sulfate (20 mg/kg over 15 minutes followed by 20 mg/kg/h) was administered in group M. Group C received an equivalent volume of saline. The QoR-40 survey was conducted on postoperative days 1 and 2. RESULTS: The mean global QoR-40 scores on postoperative day 1 were 186.3 (standard deviation, 5.5) in group L, 184.3 (4.7) in group M, and 179.4 (17.8) in group C, and there was a significant difference only between group L and group C (mean difference, 6.9; adjusted P = .018). Among the 5 dimensions of QoR-40, emotional state, physical comfort, and pain were superior in group L compared to group C. CONCLUSIONS: Lidocaine administered intravenously during anesthesia led to better quality of postoperative recovery measured by QoR-40 compared with the group C. Magnesium was found to be insufficient to induce any significant improvement with the dose used in the present study.

Preparation of Conductive Carbon Films from Novolac Resins by Ion Beam Irradiation and Carbonization.

In this study, thin carbon films with good electrical properties were prepared using commercial novolac resins by ion beam irradiation and carbonization. Novolac films were irradiated with ion beams and then carbonized under inert atmosphere. Based on the FTIR and UV results, the novolac resins were found to be crosslinked by ion beam irradiation without any additives. The Raman and XRD results indicate that carbon films with pseudo-graphitic structures were formed by carbonization of the ion beam irradiated novolac films. The sheet resistance of the prepared carbon films decreased to 1.35 × 102 Ω/ with an increasing fluence. The prepared carbon films showed a good electrical conductivity of ∼2.34 × 102 S/cm.