High-Throughput CRISPR/Cas9 Mutagenesis Streamlines Trait Gene Identification in Maize

Maize (Zea mays) is one of the most important crops in the world. However, few agronomically important maize genes have been cloned and used for trait improvement, due to its complex genome and genetic architecture. Here, we integrated multiplexed CRISPR/Cas9-based high-throughput targeted mutagenesis with genetic mapping and genomic approaches to successfully target 743 candidate genes corresponding to traits relevant for agronomy and nutrition. After low-cost barcode-based deep sequencing, 412 edited sequences covering 118 genes were precisely identified from individuals showing clear phenotypic changes. The profiles of the associated gene-editing events were similar to those identified in human cell lines and consequently are predictable using an existing algorithm originally designed for human studies. We observed unexpected but frequent homology-directed repair through endogenous templates that was likely caused by spatial contact between distinct chromosomes. Based on the characterization and interpretation of gene function from several examples, we demonstrate that the integration of forward and reverse genetics via a targeted mutagenesis library promises rapid validation of important agronomic genes for crops with complex genomes. Beyond specific findings, this study also guides further optimization of high-throughput CRISPR experiments in plants.

The quorum-sensing molecule 2-phenylethanol impaired conidial germination, hyphal membrane integrity and growth of Penicillium expansum and Penicillium nordicum

AIMS

The aim of the study was to investigate the antifungal effects of a quorum sensing-molecule, 2-phenylethanol, against the food spoilage moulds Penicillium expansum and Penicillium nordicum.

METHODS AND RESULTS

Conidial germination of the tested Penicillium spp. (three strains in total) were inhibited by treatments with 2-phenylethanol in a concentration-dependent manner. Germinated conidia was significantly reduced from 4·4-16·7% at 7·5 mmol l^-1 and completely inhibited at 15 mmol l^-1 2-phenylethanol. Integrity of conidial cell membranes was unaffected by 2-phenylethanol resulting in reversible inhibition pattern of germination. In contrast, membrane permeability of actively growing hyphae was severely compromised, showing 63·5 - 75·7% membrane damage upon treatment with 15 mmol l^-1 2-phenylethanol. The overall inhibitory effect of 2-phenylethanol on colony development and growth of P. expansum and P. nordicum was additionally confirmed.

CONCLUSIONS

2-phenylethanol inhibits conidial germination and growth of P. expansum and P. nordicum in a nonlethal, reversible and concentration-dependent manner.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study indicates that 2-phenylethanol can find potential application as an antifungal agent for biological control of moulds in the food industry.

Rice plastidial NAD-dependent malate dehydrogenase 1 negatively regulates salt stress response by reducing the vitamin B6 content

Salinity is an important environmental factor that adversely impacts crop growth and productivity. Malate dehydrogenases (MDHs) catalyse the reversible interconversion of malate and oxaloacetate using NAD(H)/NADP(H) as a cofactor and regulate plant development and abiotic stress tolerance. Vitamin B6 functions as an essential cofactor in enzymatic reactions involved in numerous cellular processes. However, the role of plastidial MDH in rice (Oryza sativa) in salt stress response by altering vitamin B6 content remains unknown. In this study, we identified a new loss-of-function osmdh1 mutant displaying salt stress-tolerant phenotype. The OsMDH1 was expressed in different tissues of rice plants including leaf, leaf sheath, panicle, glume, bud, root and stem and was induced in the presence of NaCl. Transient expression of OsMDH1-GFP in rice protoplasts showed that OsMDH1 localizes to chloroplast. Transgenic rice plants overexpressing OsMDH1 (OsMDH1OX) displayed a salt stress-sensitive phenotype. Liquid chromatography-mass spectrometry (LC-MS) metabolic profiling revealed that the amount of pyridoxine was significantly reduced in OsMDH1OX lines compared with the NIP plants. Moreover, the pyridoxine content was higher in the osmdh1 mutant and lower in OsMDH1OX plants than in the NIP plants under the salt stress, indicating that OsMDH1 negatively regulates salt stress-induced pyridoxine accumulation. Furthermore, genome-wide RNA-sequencing (RNA-seq) analysis indicated that ectopic expression of OsMDH1 altered the expression level of genes encoding key enzymes of the vitamin B6 biosynthesis pathway, possibly reducing the level of pyridoxine. Together, our results establish a novel, negative regulatory role of OsMDH1 in salt stress tolerance by affecting vitamin B6 content of rice tissues.

The Nab experiment: A precision measurement of unpolarized neutron beta decay

Neutron beta decay is one of the most fundamental processes in nuclear physics and provides sensitive means to uncover the details of the weak interaction. Neutron beta decay can evaluate the ratio of axial-vector to vector coupling constants in the standard model, λ = gA/gV, through multiple decay correlations. The Nab experiment will carry out measurements of the electron-neutrino correlation parameter a with a precision of δa/a = 10−3 and the Fierz interference term b to δb = 3 × 10−3 in unpolarized free neutron beta decay. These results, along with a more precise measurement of the neutron lifetime, aim to deliver an independent determination of the ratio λ with a precision of δλ/λ = 0.03% that will allow an evaluation of Vud and sensitively test CKM unitarity, independent of nuclear models. Nab utilizes a novel, long asymmetric spectrometer that guides the decay electron and proton to two large area silicon detectors in order to precisely determine the electron energy and an estimation of the proton momentum from the proton time of flight. The Nab spectrometer is being commissioned at the Fundamental Neutron Physics Beamline at the Spallation Neutron Source at Oak Ridge National Lab. We present an overview of the Nab experiment and recent updates on the spectrometer, analysis, and systematic effects.

Liquid Chromatographic Determination of Maleic Hydrazide in Technical and Formulated Products: Collaborative Study

Fourteen collaborating laboratories assayed maleic hydrazide (MH), 6-hydroxypyridazin-3(2H)-one, in technical and formulated products by reversed-phase liquid chromatography (LC) with sulfanilic acid as an internal standard. The active MH in the samples (6 lots) ranged from 16% (expressed as the potassium salt) to 98% (MH in the technical). A small amount of 1 M KOH was added to the technical MH and analytical standards to create the potassium salt of the analyte which is soluble in water. Test samples and standards were extracted with water containing the internal standard before analysis by LC on a C8 column with an ion-pairing eluting solution and UV detection at 254 nm. The concentration of MH was calculated by comparing the peak area response ratios of the analyte and the internal standard with those in the analytical standard solution. Eleven laboratories weighed each test sample twice with single analysis. Three laboratories weighed each sample once and made duplicate injections on the LC system. The data were analyzed using the 11 laboratories' results. A second data analysis was done including all laboratory results using a Youden pair approach, selecting one of 2 duplicate assay values randomly for each laboratory and sample. In the first data analysis, the repeatability standard deviation ranged from 0.07 to 1.39%; reproducibility standard deviation ranged from 0.22 to 1.39%. In the second data analysis (using all laboratory data), repeatability standard deviation ranged from 0.09 to 0.86%; reproducibility standard deviation ranged from 0.22 to 1.31%.

Mutation of a Nucleotide-Binding Leucine-Rich Repeat Immune Receptor-Type Protein Disrupts Immunity to Bacterial Blight

Most characterized plant resistance proteins belong to the nucleotide-binding domain and Leu-rich repeat-containing (NLR) family. NLRs are present in an auto-inhibited state in the absence of specific pathogens, while gain-of-function mutations in NLRs usually cause autoimmunity. Here, we show that a gain-of-function mutation, weaker defense (wed), which caused a Phe-to-Leu substitution in the nucleotide-binding domain of a typical NLR in rice (Oryza sativa), led to enhanced susceptibility to Xanthomonas oryzae pv. Oryzae The unexpected accumulation of salicylic acid (SA), along with downregulation of NONEXPRESSOR OF PR1 (NPR1), in wed indicates the potential presence of a feedback regulation loop of SA biosynthesis in rice. Epistasis analyses illustrated that SA accumulation and the NLR-associated components RAR1, OsRac1, and PhyB are dispensable for the wed phenotypes. Intriguingly, besides pattern-triggered immunity, effector-triggered immunity conferred by different resistance proteins, including Xa3/Xa26, Xa4, and Xa21, was also disturbed by wed to a certain extent, indicating the existence of shared regulatory mechanisms for various defense systems. The identification of wed therefore provides a unique system for genetic dissection of shared immune signaling pathways activated by different types of immune receptors.

Transcriptome analysis reveals corresponding genes and key pathways involved in heat stress in Hu sheep

Heat stress (HS) seriously affects animal performance. In view of global warming, it is essential to understand the regulatory mechanisms by which animals adapt to heat stress. In this study, our aim was to explore the genes and pathways involved in heat stress in sheep. To this end, we used transcriptome analysis to understand the molecular responses to heat stress and thereby identify means to protect sheep from heat shock. To obtain an overview of the effects of heat stress on sheep, we used the hypothalamus for transcriptome sequencing and identified differentially expressed genes (DEGs; false discovery rate (FDR) < 0.01; fold change > 2) during heat stress. A total of 1423 DEGs (1122 upregulated and 301 downregulated) were identified and classified into Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Heat stress triggered dramatic and complex alterations in gene expression in the hypothalamus. We hypothesized that heat stress induced apoptosis and dysfunction in cells and vital organs and affected growth, development, reproduction, and circadian entrainment via the calcium signaling pathway, which influences ribosome assembly and function. Real-time PCR was used to evaluate the expression of the genes regulating important biological functions or whose expression profiles were significantly changed after acute heat stress (FDR < 0.01; fold change > 4), and the results showed that the expression patterns of these genes were consistent with the results of transcriptome sequencing, indicating that the credibility of the sequencing results. Our data indicated that heat stress induced calcium dyshomeostasis, blocked biogenesis, caused ROS accumulation, impaired the antioxidant system and innate defense, and induced apoptosis through the P53 signaling pathway activated by PEG3, decreased growth and development, and enhanced organ damage. These data is very important and helpful to elucidate the molecular mechanism of heat stress and finally to find ways to deal with heat stress damage in sheep.

Klinefelter's syndrome with systemic lupus erythematosus and atrial fibrillation

We describe a 65-year-old man who presented with arthralgia, reduced body hair and gynecomastia. He showed severe pancytopaenia. Laboratory examination revealed high follicle-stimulating hormone, low testosterone and oestradiol, elevated antinuclear antibodies, anti-dsDNA and ESR levels, as well as low complement levels. An electrocardiogram showed atrial fibrillation. Computed tomography and dual-energy x-ray absorptiometry showed pleural effusion and osteoporosis. Chromosome analysis revealed 47, XXY karyotype. The unifying diagnosis was therefore Klinefelter's syndrome (KS) with systemic lupus erythematosus (SLE), with manifestations of pancytopaenia, atrial fibrillation, serositis and osteoporosis. After immunosuppressive therapy, his physical condition and pancytopaenia improved. Sex hormones and gene escape from X chromosome inactivation may contribute to the pathogenesis of SLE. Clinicians should consider autoimmune processes when patients with KS present with pancytopaenia or additional features of a systemic autoimmune disorder.

[Comparisons of clinical characteristics and prognosis between patients with primary and secondary thyroid lymphoma]

Objective: To compare clinical characteristics and prognosis between patients with primary (PTL) and secondary thyroid lymphoma (STL) . Methods: A retrospective analysis was performed on 46 patients with thyroid lymphoma (PTL 19, STL 27) from January 2002 to October 2018. Results: ①PTL group included 4 males and 15 females, with a median age of 57 years. The STL group included 10 males and 17 females, with a median age of 61 years. Diffuse large B-cell lymphoma (DLBCL) was the main pathological subtype in both PTL and STL groups, with 14 cases (73.7%) and 20 cases (74.1%) respectively. In terms of clinical manifestations, goiter was the most common symptom in PTL patients 100.0% (19/19) , while 29.6% (8/27) STL had goiter (P<0.001) . The incidences of increased thyroglobulin antibody (TRAb) /thyroid peroxidase antibody (TPO) were 81.3% (13/16) in PTL group and 43.8% (7/16) in STL group (P=0.028) respectively. Concerning the clinical features of patients, only two PTL patients (10.5%) with advanced Ann Arbor stage (Ⅲ/Ⅳ) , while 21 (77.8%) STL experienced advanced Ann Arbor stage (P<0.001) . Elevated serum β(2)-MG were appeared in 1 (7.1%) PTL and 9 (47.4%) STL patients (P=0.013) , and advanced IPI score (3-5) was more common in STL than PTL (59.3% vs 5.3%, P<0.001) . ②Among the 17 PTL patients who received treatments, 15 (88.2%) achieved remission; as for STL patients received treatments, 23/25 (92.0%) were in remission. The 5-year overall survival (OS) rates of PTL (n=17) and STL groups (n=25) were (87.4±8.4) % and (70.0±13.1) % (P=0.433) respectively. ③The 5-year OS rate in 41 patients with B-cell thyroid lymphoma was (81.1±7.5) %. Univariate analysis showed that IPI score of 3-5 (P=0.040) and high level of serum IL-8 (P=0.022) were significantly associated with poor outcome. Conclusion: DLBCL was the most common subtype in both PTL and STL, and goiter was the major symptom in PTL. IPI score of 3-5 and high level of serum IL-8 were unfavorable prognostic factors for patients with B-cell thyroid lymphoma.

Author Correction: Nitrate-NRT1.1B-SPX4 cascade integrates nitrogen and phosphorus signalling networks in plants

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

[Surgical treatment in 184 patients with supraglottic carcinoma at a single institute]

Objective: To summarize clinical experience in surgical treatment of supraglottic carcinoma and reconstructive techniques. Methods: Medical files of 184 patients (173 men, 11 women) were collected and retrospectively analyzed, who underwent surgeries between January 2008 and December 2012 at Qilu Hospital of Shandong University. Among them, T1, T2, T3 and T4 staging tumors accounted respectively for 14.1% (26/184), 41.9%(77/184), 31.5%(58/184) and 12.5%(23/184). Cervical metastasis was histologically identified in 86 cases (98 for N0, 31 for N1 and 55 for N2). Advanced cases (56 cases at stage Ⅲ and 67 at stage Ⅳ), early cases (22 at stage Ⅰ and 39 at stage Ⅱ) accounted respectively for 66.8% and 33.2%. Supraglottic horizontal laryngectomy or total laryngectomy was performed to allow for tumor excision without compromising margins and the tongue flap or sternohyoidmyofascial flap was subsequently used for repairing the defect after removal of tumor. Survival rates were analyzed by the Kaplan-Meier method. Results: Patients receiving conservation laryngeal surgery accounted for 75.5% (139/184). The 3-year and 5-year survival rates for all cases were 84.2% and 70.7%, respectively. Log-rank test demonstrated that cervical lymph node metastasis, primary tumor staging and clinical TNM staging were significantly associated with prognoses of patients (P=0.003, 0.010, 0.035). Dysphagia was not observed in any case and speech function was maintained in petients with partial laryngectomy. Conclusion: Adequate pre-operative evaluation, individualized treatment, and comprehensive application of flaps for repair are critical to precise tumor excision and reconstruction of laryngeal functions.

Nitrate-NRT1.1B-SPX4 cascade integrates nitrogen and phosphorus signalling networks in plants

To ensure high crop yields in a sustainable manner, a comprehensive understanding of the control of nutrient acquisition is required. In particular, the signalling networks controlling the coordinated utilization of the two most highly demanded mineral nutrients, nitrogen and phosphorus, are of utmost importance. Here, we reveal a mechanism by which nitrate activates both phosphate and nitrate utilization in rice (Oryza sativa L.). We show that the nitrate sensor NRT1.1B interacts with a phosphate signalling repressor SPX4. Nitrate perception strengthens the NRT1.1B-SPX4 interaction and promotes the ubiquitination and degradation of SPX4 by recruiting NRT1.1B interacting protein 1 (NBIP1), an E3 ubiquitin ligase. This in turn allows the key transcription factor of phosphate signalling, PHR2, to translocate to the nucleus and initiate the transcription of phosphorus utilization genes. Interestingly, the central transcription factor of nitrate signalling, NLP3, is also under the control of SPX4. Thus, nitrate-triggered degradation of SPX4 activates both phosphate- and nitrate-responsive genes, implementing the coordinated utilization of nitrogen and phosphorus.

Wnt Production in Dental Epithelium Is Crucial for Tooth Differentiation

The Wnt ligands display varied spatiotemporal expression in the epithelium and mesenchyme in the developing tooth. Thus far, the actions of these differentially expressed Wnt ligands on tooth development are not clear. Shh expression specifies the odontogenic epithelium during initiation and is consistently restricted to the dental epithelium during tooth development. In this study, we inactivate Wntless ( Wls), the key regulator for Wnt trafficking, by Shh-Cre to investigate how the Wnt ligands produced in the dental epithelium lineage act on tooth development. We find that conditional knockout of Wls by Shh-Cre leads to defective ameloblast and odontoblast differentiation. Wls^Shh-Cre teeth display reduced canonical Wnt signaling activity in the inner enamel epithelium and the underlying mesenchyme at the early bell stage, as exhibited by target gene expression and BAT-gal staining. The expression of Wnt5a and Wnt10b is not changed in Wls^Shh-Cre teeth. By contrast, Wnt10a expression is significantly increased in response to epithelial Wls deficiency. In addition, the expression of Hedgehog signaling pathway components Shh, Gli1, and Patched1 was greatly decreased in Wls^Shh-Cre teeth. Epithelial Wls loss of function in Shh lineage also leads to aberrant cell proliferation in dental epithelium and mesenchyme at embryonic day 16.5; however, the cell apoptosis is unaffected. Moreover, we find that Decorin and Col1a1, the key markers for odontoblast differentiation that are downregulated in Wls^Shh-Cre teeth, act as direct downstream targets of the canonical Wnt signaling pathway by chromatin immunoprecipitation analysis. Additionally, Decorin and Col1a1 expression can be increased by lithium chloride (LiCl) treatment in the in vitro tooth explants. Taken together, our results suggest that the spatial expression of Wnt ligands within the dental epithelial lineage regulates the differentiation of tooth structures in later stages.

[Efficacy and prognostic analysis of relapsed/refractory diffuse large B-cell lymphoma patients with hepatitis B virus infection]

Objective: To evaluate the clinical and prognostic significance of hepatitis B virus infection on patients with relapsed/refractory diffuse large B-cell lymphoma (DLBCL). Methods: A retrospective analysis was performed in 81 relapsed/refractory DLBCL cases who were treated with salvage regimens from January 2004 to November 2016. The patients were divided into two group, HBsAg positive and HBsAg negative group, and assessed the clinical features and survival time of two groups. Results: Twenty-four (29.6%) patients were HBsAg positive and 57(70.4%) were negative. HBsAg-positive DLBCL patients showed unique clinical features, including more younger patients (P=0.005), more advanced Ann Arbor stage (P<0.001), high-risk IPI (P=0.010), more hypohemoglobin (P=0.015), especially extra-nodal involvement (P=0.038) and recurrence (P=0.002). Overall response rate (29.2% vs 68.4%, χ(2)=10.720, P=0.001) and median overall survival time [(11.3±2.9) months vs (30.0±7.6) months, χ(2)=28.175, P<0.001] were inferior in HBsAg-positive patients, respectively. Conclusion: To strictly control HBV infection plays an important role on the survival and prognosis of relapsed/refractory lymphoma patients.

MRI Evidence of Altered Callosal Sodium in Mild Traumatic Brain Injury

BACKGROUND AND PURPOSE

Mild traumatic brain injury is a leading cause of death and disability worldwide with 42 million cases reported annually, increasing the need to understand the underlying pathophysiology because this could help guide the development of targeted therapy. White matter, particularly the corpus callosum, is susceptible to injury. Animal models suggest stretch-induced mechanoporation of the axonal membrane resulting in ionic shifts and altered sodium ion distribution. The purpose of this study was to compare the distribution of total sodium concentration in the corpus callosum between patients with mild traumatic brain injury and controls using sodium (²³Na) MR imaging.

MATERIALS AND METHODS

Eleven patients with a history of mild traumatic brain injury and 10 age- and sex-matched controls underwent sodium (²³Na) MR imaging using a 3T scanner. Total sodium concentration was measured in the genu, body, and splenium of the corpus callosum with 5-mm ROIs; total sodium concentration of the genu-to-splenium ratio was calculated and compared between patients and controls.

RESULTS

Higher total sodium concentration in the genu (49.28 versus 43.29 mmol/L, P = .01) and lower total sodium concentration in the splenium (which was not statistically significant; 38.35 versus 44.06 mmol/L, P = .08) was seen in patients with mild traumatic brain injury compared with controls. The ratio of genu total sodium concentration to splenium total sodium concentration was also higher in patients with mild traumatic brain injury (1.3 versus 1.01, P = .001).

CONCLUSIONS

Complex differences are seen in callosal total sodium concentration in symptomatic patients with mild traumatic brain injury, supporting the notion of ionic dysfunction in the pathogenesis of mild traumatic brain injury. The total sodium concentration appears to be altered beyond the immediate postinjury phase, and further work is needed to understand the relationship to persistent symptoms and outcome.

[Intervention study of compassion fatigue of oncology nurses in Balint group activities]

Objective: To explore the effectiveness of Balint group on compassion fatigue among oncology nurses. Methods: From January to December 2016, 35 oncology nurses from one general hospital were enrolled. 18 cases were allocated in the observation group and 17 cases in the control group by computer randomization. Nurses in the observation group were received a total of 8 times Balint Group activities, with 2 times a month and 1.5 hours each time, which is aiming to discuss difficult cases encountered in the clinic to help nurses have a deeper experience and a better understanding of the emotions and behaviors, fantasies and needs between nurse-patient interaction. Nurses in the control group without intervention. All the Participants were requested to complete the survey of the Professional Quality of Life (ProQOL) , the Jefferson Scale of Empathy-Health Professionals (JSE-HP) , and the General Health Questionnaire (GHQ) at pre and post intervention. Results: Before intervention, two group of nurses in age, working years, marriage, and education were not statistically significant (P>0.05). There was no difference in the scores of empathy, compassion satisfaction, secondary traumatic stress, and General health (P>0.05). After intervention, the scores of JSE-HP and its three dimensions of perspective taking, emotional care, and trans-positional consideration in the observation group had significantly higher than the control group (P<0.05). The level of compassion satisfaction in the observation group was higher, and the general health status was lower (P<0.05). There was no statistically difference in the level of burnout and secondary traumatic stress between two groups (P>0.05) . Conclusion: Balint group has a positive role in promoting nurses'empathetic skills, compassion satisfaction and mental health.