FANCA Promotes DNA Double-Strand Break Repair by Catalyzing Single-Strand Annealing and Strand Exchange.

FANCA is a component of the Fanconi anemia (FA) core complex that activates DNA interstrand crosslink repair by monoubiquitination of FANCD2. Here, we report that purified FANCA protein catalyzes bidirectional single-strand annealing (SA) and strand exchange (SE) at a level comparable to RAD52, while a disease-causing FANCA mutant, F1263Δ, is defective in both activities. FANCG, which directly interacts with FANCA, dramatically stimulates its SA and SE activities. Alternatively, FANCB, which does not directly interact with FANCA, does not stimulate this activity. Importantly, five other patient-derived FANCA mutants also exhibit deficient SA and SE, suggesting that the biochemical activities of FANCA are relevant to the etiology of FA. A cell-based DNA double-strand break (DSB) repair assay demonstrates that FANCA plays a direct role in the single-strand annealing sub-pathway (SSA) of DSB repair by catalyzing SA, and this role is independent of the canonical FA pathway and RAD52.

The complex hexaploid oil-Camellia genome traces back its phylogenomic history and multi-omics analysis of Camellia oil biosynthesis.

Oil-Camellia (Camellia oleifera), belonging to the Theaceae family Camellia, is an important woody edible oil tree species. The Camellia oil in its mature seed kernels, mainly consists of more than 90% unsaturated fatty acids, tea polyphenols, flavonoids, squalene and other active substances, which is one of the best quality edible vegetable oils in the world. However, genetic research and molecular breeding on oil-Camellia are challenging due to its complex genetic background. Here, we successfully report a chromosome-scale genome assembly for a hexaploid oil-Camellia cultivar Changlin40. This assembly contains 8.80 Gb genomic sequences with scaffold N50 of 180.0 Mb and 45 pseudochromosomes comprising 15 homologous groups with three members each, which contain 135 868 genes with an average length of 3936 bp. Referring to the diploid genome, intragenomic and intergenomic comparisons of synteny indicate homologous chromosomal similarity and changes. Moreover, comparative and evolutionary analyses reveal three rounds of whole-genome duplication (WGD) events, as well as the possible diversification of hexaploid Changlin40 with diploid occurred approximately 9.06 million years ago (MYA). Furthermore, through the combination of genomics, transcriptomics and metabolomics approaches, a complex regulatory network was constructed and allows to identify potential key structural genes (SAD, FAD2 and FAD3) and transcription factors (AP2 and C2H2) that regulate the metabolism of Camellia oil, especially for unsaturated fatty acids biosynthesis. Overall, the genomic resource generated from this study has great potential to accelerate the research for the molecular biology and genetic improvement of hexaploid oil-Camellia, as well as to understand polyploid genome evolution.

Comprehensive analysis of MAPK gene family in upland cotton (Gossypium hirsutum) and functional characterization of GhMPK31 in regulating defense response to insect infestation.

KEY MESSAGE: The transcriptomic, phenotypic and metabolomic analysis of transgenic plants overexpressing GhMPK31 in upland cotton revealed the regulation of H2O2 burst and the synthesis of defensive metabolites by GhMPK31. Mitogen-activated protein kinases (MAPKs) are a crucial class of protein kinases, which play an essential role in various biological processes in plants. Upland cotton (G. hirsutum) is the most widely cultivated cotton species with high economic value. To gain a better understanding of the role of the MAPK gene family, we conducted a comprehensive analysis of the MAPK gene family in cotton. In this study, a total of 55 GhMPK genes were identified from the whole genome of G. hirsutum. Through an investigation of the expression patterns under diverse stress conditions, we discovered that the majority of GhMPK family members demonstrated robust responses to abiotic stress, pathogen stress and pest stress. Furthermore, the overexpression of GhMPK31 in cotton leaves led to a hypersensitive response (HR)-like cell death phenotype and impaired the defense capability of cotton against herbivorous insects. Transcriptome and metabolomics data analysis showed that overexpression of GhMPK31 enhanced the expression of H2O2-related genes and reduced the accumulation of defensive related metabolites. The direct evidence of GhMPK31 interacting with GhRBOHB (H2O2-generating protein) were found by Y2H, BiFC, and LCI. Therefore, we propose that the increase of H2O2 content caused by overexpression of GhMPK31 resulted in HR-like cell death in cotton leaves while reducing the accumulation of defensive metabolites, ultimately leading to a decrease in the defense ability of cotton against herbivorous insects. This study provides valuable insights into the function of MAPK genes in plant resistance to herbivorous insects.

The chromosome-scale reference genome of mirid bugs (Adelphocoris suturalis) genome provides insights into omnivory, insecticide resistance, and survival adaptation.

BACKGROUND: Adelphocoris suturalis (Hemiptera: Miridae) is a notorious agricultural pest, which causes serious economic losses to a diverse range of agricultural crops around the world. The poor understanding of its genomic characteristics has seriously hindered the establishment of sustainable and environment-friendly agricultural pest management through biotechnology and biological insecticides. RESULTS: Here, we report a chromosome-level assembled genome of A. suturalis by integrating Illumina short reads, PacBio, 10x Chromium, and Hi-C mapping technologies. The resulting 1.29 Gb assembly contains twelve chromosomal pseudomolecules with an N50 of 1.4 and 120.6 Mb for the contigs and scaffolds, respectively, and carries 20,010 protein-coding genes. The considerable size of the A. suturalis genome is predominantly attributed to a high amount of retrotransposons, especially long interspersed nuclear elements (LINEs). Transcriptomic and phylogenetic analyses suggest that A. suturalis-specific candidate effectors, and expansion and expression of gene families associated with omnivory, insecticide resistance and reproductive characteristics, such as digestion, detoxification, chemosensory receptors and long-distance migration likely contribute to its strong environmental adaptability and ability to damage crops. Additionally, 19 highly credible effector candidates were identified and transiently overexpressed in Nicotiana benthamiana for functional assays and potential targeting for insect resistance genetic engineering. CONCLUSIONS: The high-quality genome of A. suturalis provides an important genomic landscape for further investigations into the mechanisms of omnivory, insecticide resistance and survival adaptation, and for the development of integrated management strategies.

Compound Qiying Granules alleviates diabetic peripheral neuropathy by inhibiting endoplasmic reticulum stress and apoptosis.

BACKGROUND: Diabetic peripheral neuropathy (DPN) is a major complication of diabetes. This study aimed to investigate the therapeutic effects and molecular mechanisms of Compound Qiying Granules (CQYG) for DPN. METHODS: Rats and RSC96 cells of DPN models were established to evaluate the therapeutic effects of CQYG. Then the morphology and apoptotic changes of sciatic nerves were detected. Further, tandem mass tag based quantitative proteomics technology was used to identify differentially expressed proteins (DEPs) and the underlying molecular mechanisms. Protein expression of key signaling pathways was also detected. RESULTS: CQYG treatment significantly improved blood glucose and oxidative stress levels, and further reduced nerve fiber myelination lesions, denervation, and apoptosis in DPN rats. Further, 2176 DEPs were found in CQYG treated DPN rats. Enrichment analysis showed that protein processing in the endoplasmic reticulum (ER), and apoptosis were all inhibited after CQYG treatment. Next, CQYG treatment reduced inflammatory factor expression, mitochondrial damage, and apoptosis in RSC96 cells which induced by high glucose. Transmission electron microscopy results found that CQYG treatment improved the morphology of nerve myelin, mitochondria, and ER. CQYG treatment decreased ER stress and apoptosis pathway proteins that were highly expressed in DPN models. In addition, we also predicted the potential targets of CQYG in DEPs. CONCLUSIONS: CQYG exerts neuroprotective effects in experimental diabetic neuropathy through anti-ER stress and anti-apoptosis.

Contrast-enhanced US with Perfluorobutane to Diagnose Small Lateral Cervical Lymph Node Metastases of Papillary Thyroid Carcinoma.

Background Although metastasis of lateral cervical lymph nodes (LNs) is common in papillary thyroid carcinoma (PTC), correctly diagnosing small metastatic LNs with US remains challenging. The use of contrast-enhanced US (CEUS), especially the postvascular phase of CEUS with perfluorobutane contrast material, might contribute to improved diagnosis of metastatic LNs in PTC. Purpose To assess the diagnostic value of the postvascular phase of CEUS with perfluorobutane in suspicious small lateral cervical LNs (short-axis diameter ≤8 mm) in patients with PTC. Materials and Methods This single-center study prospectively enrolled consecutive participants with confirmed PTC and suspicious LNs at US from October 2020 to October 2021. All participants underwent CEUS, 1 week before biopsy or surgery, with intravenous perfluorobutane contrast material to visualize the LNs in the vascular phase (5-60 seconds after injection) and postvascular phase (10-30 minutes after injection). The reference standard was cytologic and surgical histologic assessment of the LNs. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of sonographic features were calculated, and the diagnostic performance of US, CEUS, and the combination of postvascular phase and US features was assessed using multivariable logistic regression models. Results A total of 135 participants (median age, 36 years [IQR, 30-46 years]; 100 women) with 161 suspicious LNs at US were evaluated, including 67 metastatic and 94 benign LNs. The specificity of perfusion defect as a sonographic feature in the vascular phase reached 96% (90 of 94 LNs), and the negative predictive value of non-isoenhancement (ie, hypoenhancement, partial enhancement, and no enhancement) in the postvascular phase reached 100% (83 of 83 LNs). The area under the receiver operating characteristic curve (AUC) of the combination of postvascular phase and US features was 0.94 (95% CI: 0.89, 0.97), significantly higher than that of US features alone (AUC, 0.73; 95% CI: 0.65, 0.79; P < .001). Conclusion The postvascular phase of CEUS with perfluorobutane demonstrated excellent performance for diagnosing suspicious small lateral cervical LNs in participants with PTC. Published under a CC BY 4.0 license Supplemental material is available for this article. See also the editorial by Gunabushanam in this issue.

The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum).

Zanthoxylum armatum and Zanthoxylum bungeanum, known as 'Chinese pepper', are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species-special metabolites. Here, we report reference-grade genomes of Z. armatum and Z. bungeanum. Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum. The genomic rearrangements and two whole-genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (>82%) and high chromosome number (2n = 4x = 132). Further analysis of the high-quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes.

Activated carbon enhanced traditional activated sludge process for chemical explosion accident wastewater treatment.

With the development of industries, explosion accidents occur frequently during production, transportation, usage and storage of hazard chemicals. It remained challenging to efficiently treat the resultant wastewater. As an enhancement of traditional process, the activated carbon-activated sludge (AC-AS) process has a promising potential in treating wastewater with high concentrations of toxic compounds, chemical oxygen demand (COD) and ammonia nitrogen (NH4+-N), etc. In this paper, activated carbon (AC), activated sludge (AS) and AC-AS were used to treat the wastewater produced from an explosion accident in the Xiangshui Chemical Industrial Park. The removal efficiency was assessed by the removal performances of COD, dissolved organic carbon (DOC), NH4+-N, aniline and nitrobenzene. Increased removal efficiency and shortened treatment time were achieved in the AC-AS system. To achieve the same COD, DOC and aniline removal (90%), the AC-AS system saved 30, 38 and 58 h compared with the AS system, respectively. The enhancement mechanism of AC on the AS was explored by metagenomic analysis and three-dimensional excitation-emission-matrix spectra (3DEEMs). More organics, especially aromatic substances were removed in the AC-AS system. These results showed that the addition of AC promoted the microbial activity in pollutant degradation. Bacteria, such as Pyrinomonas, Acidobacteria and Nitrospira and genes, such as hao, pmoA-amoA, pmoB-amoB and pmoC-amoC, were found in the AC-AS reactor, which might have played important roles in the degradation of pollutants. To sum up, AC might have enhanced the growth of aerobic bacteria which further improved the removal efficiency via the combined effects of adsorption and biodegradation. The successful treatment of Xiangshui accident wastewater using the AC-AS demonstrated the potential universal characteristics of the process for the treatment of wastewater with high concentration of organic matter and toxicity. This study is expected to provide reference and guidance for the treatment of similar accident wastewaters.

Development of an efficient and precise adenine base editor (ABE) with expanded target range in allotetraploid cotton (Gossypium hirsutum).

BACKGROUND: Base editors (BEs) display diverse applications in a variety of plant species such as Arabidopsis, rice, wheat, maize, soybean, and cotton, where they have been used to mediate precise base pair conversions without the collateral generation of undesirable double-stranded breaks (DSB). Studies of single-nucleotide polymorphisms (SNPs) underpinning plant traits are still challenging, particularly in polyploidy species where such SNPs are present in multiple copies, and simultaneous modification of all alleles would be required for functional analysis. Allotetraploid cotton has a number of homoeologous gene pairs located in the A and D sub-genomes with considerable SNPs, and it is desirable to develop adenine base editors (ABEs) for efficient and precise A-to-G single-base editing without DSB in such complex genome. RESULTS: We established various ABE vectors based on different engineered adenosine deaminase (TadA) proteins fused to Cas9 variants (dCas9, nCas9), enabling efficient A to G editing up to 64% efficiency on-target sites of the allotetraploid cotton genome. Comprehensive analysis showed that GhABE7.10n exhibited the highest editing efficiency, with the main editing sites specifically located at the position A5 (counting the PAM as positions 21-23). Furthermore, DNA and RNA off-target analysis of cotton plants edited with GhABE7.10n and GhABE7.10d by whole genome and whole-transcriptome sequencing revealed no DNA off-target mutations, while very low-level RNA off-target mutations were detected. A new base editor, namely GhABE7.10dCpf1 (7.10TadA + dCpf1), that recognizes a T-rich PAM, was developed for the first time. Targeted A-to-G substitutions generated a single amino acid change in the cotton phosphatidyl ethanolamine-binding protein (GhPEBP), leading to a compact cotton plant architecture, an ideotype for mechanized harvesting of modern cotton production. CONCLUSIONS: Our data illustrate the robustness of adenine base editing in plant species with complex genomes, which provides efficient and precise toolkit for cotton functional genomics and precise molecular breeding.

LncRNA-p21 suppresses cell proliferation and induces apoptosis in gastric cancer by sponging miR-514b-3p and up-regulating ARHGEF9 expression.

The long non-coding RNA p21 (lncRNA-p21) was a tumor suppressor gene in most cancer types including gastric cancer (GC). We aimed to identify a specific lncRNA-p21-involved pathway in regulating the proliferation and apoptosis of GC cells. A lower lncRNA-p21 expression in tumors was associated with advanced disease stage and predicted worse survival of GC patients. LncRNA-p21 overexpression in GC cell line somatic gastric cancer (SGC)-7901 and human gastric cancer (HGC)-27 suppressed cell proliferation and enhanced apoptosis, while lncRNA-p21 knockdown caused the opposite effects. Through bioinformatics analysis and luciferase-based reporter assays, we identified miR-514b-3p as a sponge target of lncRNA-p21. Cdc42 guanine nucleotide exchange factor 9 (ARHGEF9), functioned as a tumor suppress factor in GC, was found as the downstream target of miR-514-3p, and their expressions were negatively correlated in GC tumor tissues. In addition, like lncRNA-p21 overexpression alone, miR-514-3p inactivation alone also led to decreased proliferation and increased apoptosis in SGC-7901 and HGC-27 cells, which were markedly attenuated by additional ARHGEF9 knockdown. Xenograft SGC-7901 cells with more lncRNA-p21 or ARHGEF9 expressions or with less miR-514-3p expression exhibited obviously slower in vivo growth than the control SGC-7901 cells in nude mice. Our study reveals a novel lncRNA-p21/miR-514b-3p/ARHGEF9 pathway that can be targeted for GC therapy.

Spatial Distribution and Ecological Risk Assessment of Heavy Metals in Sediments of a Heavily Polluted Maozhou River, Southern China.

In this study, eighteen 3.30-m-long sediment profiles were sampled in Maozhou River. In order to investigate the sediment pollution status and potential sources of heavy metals, we performed heavy metal contents, grain size, organic matter concentration, moisture concentration and total phosphorus analysis, and assessed the ecological risk of heavy metal pollution in the study area using enrichment coefficient, geo-accumulation index and potential ecological risk index. The results indicated that the heavy metal concentrations in the Maozhou River sediments were 3.73-417 times higher than the soil background in Guangdong Province and the average concentrations were 0.447-15.1 times higher than Chinese lacustrine sediments. The Cr, Ni, Cu, Zn, Cd and Pb contents were significantly correlated with each other (p < 0.01), indicating similar deposition process. In addition, spatial and vertical distribution of heavy metals showed similar variation patterns and extreme high contents are distributed in the interchange area. The ecological risk of Maozhou River was much higher than other river sediments in Guangdong Province, especially for Cu, Cd and Ni. The variation pattern of potential ecological risk index is similar with that of heavy metals and the assessment results indicated high ecological risk in the Maozhou River sediments, which is in good agreement with the EF and Igeo results. This study would provide some references for the treatment of heavy metals' pollution in Maozhou River.

Crash Diagnosis and Price Rebound Prediction in NYSE Composite Index Based on Visibility Graph and Time-Evolving Stock Correlation Network.

This study proposes a framework to diagnose stock market crashes and predict the subsequent price rebounds. Based on the observation of anomalous changes in stock correlation networks during market crashes, we extend the log-periodic power-law model with a metric that is proposed to measure network anomalies. To calculate this metric, we design a prediction-guided anomaly detection algorithm based on the extreme value theory. Finally, we proposed a hybrid indicator to predict price rebounds of the stock index by combining the network anomaly metric and the visibility graph-based log-periodic power-law model. Experiments are conducted based on the New York Stock Exchange Composite Index from 4 January 1991 to 7 May 2021. It is shown that our proposed method outperforms the benchmark log-periodic power-law model on detecting the 12 major crashes and predicting the subsequent price rebounds by reducing the false alarm rate. This study sheds light on combining stock network analysis and financial time series modeling and highlights that anomalous changes of a stock network can be important criteria for detecting crashes and predicting recoveries of the stock market.

Therapeutic Effect of Berberine on Insomnia Rats by ErbB Signaling Pathway.

BACKGROUND Insomnia seriously affects people's health and quality of life. Short-term use of Western drugs may also be harmful. Traditional Chinese medicine has been widely used to treat diseases in world. Therefore, this paper aims to study the therapeutic effect of berberine based on the insomnious rat model. MATERIAL AND METHODS The insomnia rat model was established by intragastric administration of caffeine and parachlorophenylalanine (PCPA). Berberine and diazepam were used to treat the established insomnia rats. Then, the pathological changes of insomnia rats were detected. In addition, transcriptome sequencing and data analysis were carried out using rat hippocampus. The expression of key genes was verified by quantitative polymerase chain reaction and western blot. RESULTS After 7 days of intragastric administration of berberine, the body weight, memory, and sleep quality of insomnia rats were significantly improved. The key roles of Erbb4, Erbb2, Ar, and Grin2a in berberine treatment were identified. Through the analysis of biological functions and signaling pathways, berberine was shown to play a salutary role through nervous system development and ErbB signaling pathway. Gene-set enrichment analysis (GSEA) results showed that berberine treatment affected more metabolic pathways. Compared with diazepam, berberine can play a faster role, and also improve the overall health level of insomnia rats. CONCLUSIONS These results suggest that berberine can alleviate insomnia in rats through a neuroprotective effect and improved metabolic level. Berberine has great potential in treatment of insomnia and might have better clinical significance.

Reversal of right ventricular failure by chronic α1A-subtype adrenergic agonist therapy.

Right ventricular (RV) failure (RVF) is a serious disease with no effective treatment available. We recently reported a disease prevention study showing that chronic stimulation of α1A-adrenergic receptors (α1A-ARs), started at the time of RV injury, prevented the development of RVF. The present study used a clinically relevant disease reversal design to test if chronic α1A-AR stimulation, started after RVF was established, could reverse RVF. RVF was induced surgically by pulmonary artery constriction in mice. Two weeks after pulmonary artery constriction, in vivo RV fractional shortening as assessed by MRI was reduced by half relative to sham-operated controls (25 ± 2%, n = 27, vs. 52 ± 2%, n = 13, P < 10-11). Subsequent chronic treatment with the α1A-AR agonist A61603 for a further 2 wk resulted in a substantial recovery of RV fractional shortening (to 41 ± 2%, n = 17, P < 10-7 by a paired t-test) along with recovery of voluntary exercise capacity. Mechanistically, chronic A61603 treatment resulted in increased activation of the prosurvival kinase ERK, increased abundance of the antiapoptosis factor Bcl-2, and decreased myocyte necrosis evidenced by a decreased serum level of cardiac troponin. Moreover, A61603 treatment caused increased abundance of the antioxidant glutathione peroxidase-1, decreased level of reactive oxygen species, and decreased oxidative modification (carbonylation) of myofilament proteins. Consistent with these effects, A61603 treatment resulted in increased force development by cardiac myofilaments, which might have contributed to increased RV function. These findings suggest that the α1A-AR is a therapeutic target to reverse established RVF. NEW & NOTEWORTHY Currently, there are no effective therapies for right ventricular (RV) failure (RVF). This project evaluated a novel therapy for RVF. In a mouse model of RVF, chronic stimulation of α1A-adrenergic receptors with the agonist A61603 resulted in recovery of in vivo RV function, improved exercise capacity, reduced oxidative stress-related carbonylation of contractile proteins, and increased myofilament force generation. These results suggest that the α1A-adrenergic receptor is a therapeutic target to treat RVF.

Rs1884444 variant in IL23R gene is associated with a decreased risk in esophageal cancer in Chinese population.

Single nucleotide polymorphisms (SNPs) in interleukin-23 receptor (IL23R) are involved in the pathogenesis of many cancers and autoimmune diseases. IL23R gene is still controversial in the study of esophageal cancer. The aim of this research is to investigate the influence of IL23R SNPs on the risk of esophageal cancer. Five hundred six esophageal cancer and 507 controls frequency matched by age and gender were conducted, and the genotypes were determined by the Agena MassARRAY. Logistic regression analysis was used to evaluate the odd ratios (ORs) and 95% confidence intervals (CIs) of rs1884444 and rs6682925 with susceptibility of esophageal cancer. A total of 30 articles are eligible. Pooled ORs and the 95% CI were calculated using the random-effect model. Database predicts the expression of IL23R gene in esophageal cancer. IL23R rs1884444 allele G decreased the risk of esophageal cancer under allele, genotype, and additive models (allele model: OR = 0.82, 95% CI: 0.68-0.98, P = .032; genotype model: OR = 0.65, 95% CI: 0.44-0.97, P = .035; additive model: OR = 0.82, 95% CI: 0.68-0.98, P = .031). Meta-analysis shown that IL23R rs1884444 increased the risk of overall disease in allele model (OR = 1.16, 95% CI: 1.08-1.25, P < .001), and also increased the risk of gastrointestinal tumor (OR = 1.18, 95% CI: 1.05-1.31, P = .005). The database analysis showed that the expression of IL23R gene was upregulated in esophageal cancer tissues. IL23R rs1884444 may play an important role in the susceptibility of esophageal cancer.

Whole genome sequencing reveals rare off-target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9-edited cotton plants.

The CRISPR/Cas9 system has been extensively applied for crop improvement. However, our understanding of Cas9 specificity is very limited in Cas9-edited plants. To identify on- and off-target mutation in an edited crop, we described whole genome sequencing (WGS) of 14 Cas9-edited cotton plants targeted to three genes, and three negative (Ne) control and three wild-type (WT) plants. In total, 4188-6404 unique single-nucleotide polymorphisms (SNPs) and 312-745 insertions/deletions (indels) were detected in 14 Cas9-edited plants compared to WT, negative and cotton reference genome sequences. Since the majority of these variations lack a protospacer-adjacent motif (PAM), we demonstrated that the most variations following Cas9-edited are due either to somaclonal variation or/and pre-existing/inherent variation from maternal plants, but not off-target effects. Of a total of 4413 potential off-target sites (allowing ≤5 mismatches within the 20-bp sgRNA and 3-bp PAM sequences), the WGS data revealed that only four are bona fide off-target indel mutations, validated by Sanger sequencing. Moreover, inherent genetic variation of WT can generate novel off-target sites and destroy PAMs, which suggested great care should be taken to design sgRNA for the minimizing of off-target effect. These findings suggested that CRISPR/Cas9 system is highly specific for cotton plants.

Association between TIMP-2 gene polymorphism and breast cancer in Han Chinese women.

BACKGROUND: TIMP-2 gene plays an important role in the development of breast cancer. The present study was conducted to evaluate whether TIMP-2 gene polymorphisms are associated with breast cancer risk in a Han Chinese cohort. METHODS: Six single nucleotide polymorphisms (SNPs) within the TIMP-2 gene in 571 breast cancer and 578 healthy control subjects were genotyped through the Agena MassARRAY. Logistic regression analysis was used to assess the influence of TIMP-2 polymorphisms on breast cancer. Functional annotation of TIMP-2 variants and TIMP-2 expression were analyzed by bioinformatics. RESULTS: Bioinformatics analysis found that rs4789936 was likely to affect transcription factor binding, motifs, DNase footprint, and DNase peaks; and TIMP-2 was under-expressed in breast cancer, the risk allele of rs4789936 was associated with increased expression of TIMP-2 in peripheral blood samples. Importantly, individuals carrying TIMP-2 rs2277698 T allele have a 19% lower risk of breast cancer than individuals with allele C, providing protection (OR = 0.81, 95%CI = 0.67-0.99, p = 0.041). In the breast cancer patients with c-erb positive and PR positive, when the CC genotype was used as a reference, individuals carrying the TT genotype increased the risk of breast cancer. Haplotype analysis showed "TCC" was associated with a reduced risk of breast cancer (OR = 0.79, 95%CI = 0.63-0.97, p = 0.028). CONCLUSION: Our study indicated that TIMP-2 rs2277698 was associated with breast cancer susceptibility.

The clinical significance of ubiquitin carboxyl hydrolase L1 and its autoantibody in neuropsychiatric systemic lupus erythematosus.

OBJECTIVES: To identify specific cerebrospinal fluid (CSF) biomarkers for the diagnosis and disease severity evaluation of neuropsychiatric systemic lupus erythematosus (NPSLE). METHODS: Patients presented with neuropsychiatric symptoms were recruited and categorised as 36 NPSLE, 19 SLE controls, 4 other connective tissue disease (CTD) controls and 10 nervous system disorder (NSD) controls. The NPSLE group consisted of severe NPSLE (sNPSLE) and mild NPSLE (mNPSLE). Potential biomarkers were determined by Luminex multiplex assay and enzyme-linked immunosorbent assay. RESULTS: 1) Among a variety of neurological disease-related proteins, only ubiquitin carboxyl hydrolase L1 (UCH-L1) levels were significantly elevated in the CSF samples of sNPSLE patients compared with those of mNPSLE patients (p=0.020) and SLE controls (p=0.037). CSF UCH-L1 levels were significantly positively correlated with SLE disease activity index and overlap number of NPSLE manifestations. 2) CSF anti-UCH-L1 autoantibodies were significantly elevated in patients with NPSLE in comparison to all of the control groups, with a sensitivity of 53% and a specificity of 91% for NPSLE. CSF anti-UCH-L1 levels were associated with organ involvement and were positively correlated with serum anti-UCH-L1 levels in the NPSLE patients (r=0.4551, p=0.0382). CONCLUSIONS: Anti-UCH-L1 is a promising CSF biomarker for NPSLE diagnosis with high specificity, and the elevated levels of CSF UCH-L1 reflect the clinical severity of NPSLE. The elevation of UCH-L1 and its autoantibody in NPSLE patients showed us novel aetiological insights on NPSLE.

Thymoquinone inhibits the metastasis of renal cell cancer cells by inducing autophagy via AMPK/mTOR signaling pathway.

Thymoquinone (TQ, 2-methyl-5-isopropyl-1,4-benzoquinone), a bioactive constituent extracted from the seeds of Nigella sativa, has been proved to exert anti-tumor efficiency in various cancers. Autophagy is a self-digestion phenomenon, and its role in tumor formation and progression remains controversial. In the present study, we investigated the effects of TQ on renal cell cancer (RCC) cell lines (786-O and ACHN) using wound healing assay, transwell assay and western blot analysis. We found that TQ effectively inhibited the metastatic capacity of RCC cells in vitro, which was also verified in a xenograft model. Meanwhile, we observed LC3 puncta and detected the expression of LC3 in TQ-treated RCC cells, and then found that autophagy was induced by TQ in 786-O and ACHN cell lines. In addition, TQ inhibited the migration and invasion as well as the EMT in RCC cells in an autophagy-dependent manner. To further explore the underlying mechanism, we detected the AMPK/mTOR signaling pathway. The results indicated that TQ inhibited the metastasis of RCC cells by inducing autophagy via AMPK/mTOR signaling pathway. In conclusion, our findings provide a novel therapeutic strategy that aims at TQ-induced autophagy in RCC treatment.

Responses of atrazine degradation and native bacterial community in soil to Arthrobacter sp. strain HB-5.

The bioremediation of soil contaminated with organic pesticides is a safe and effective approach to remove pollutants from the soil. However, whether the invasion of foreign aid organisms affects the local organisms has received increasing attention in recent years. Therefore, the purpose of this study was to examine the degradation ability of atrazine by the strain HB-5 and evaluate its effects on natural bacterial communities in a miniature pot experiment. Results showed that HB-5 accelerated the degradation of atrazine and the degradation half-life of atrazine was 3.3 times less than the natural soil. Additionally, HB-5 increased the quantities of indigenous bacteria, the microbial biomass carbon and the Shannon, Simpson and McIntosh diversity indices of soil microbes in its early stage of use, But these parameters in soil treated with HB-5 decreased to values as low as those found in the control at the later stage of incubation. These suggested that the bacteria vanished as atrazine was completely removed. These results demonstrated that Arthrobacter sp. strain HB-5 had great potential and would be an effective and environmental friendly technique to remove atrazine from the contaminated soil.