A fructan: the fructan 1-fructosyl-transferase gene from Helianthus tuberosus increased the PEG-simulated drought stress tolerance of tobacco

BACKGROUND

Jerusalem artichoke (Helianthus tuberosus) is a fructan-accumulating plant, and an industrial source of raw material for fructan production, but the crucial enzymes involved in fructan biosynthesis remain poorly understood in this plant.

RESULTS

In this study, a fructan: fructan 1-fructosyl-transferase (1-FFT) gene, Ht1-FFT, was isolated from Jerusalem artichoke. The coding sequence of Ht1-FFT was 2025 bp in length, encoding 641 amino acids. Ht1-FFT had the type domain of the 1-FFT protein family, to which it belonged, according to phylogenetic tree analysis, which implied that Ht1-FFT had the function of catalyzing the formation and extension of beta-(2,1)-linked fructans. Overexpression of Ht1-FFT in the leaves of transgenic tobacco increased fructan concentration. Moreover, the soluble sugar and proline concentrations increased, and the malondialdehyde (MDA) concentration was reduced in the transgenic lines. The changes in these parameters were associated with increased stress tolerance exhibited by the transgenic tobacco plants. A PEG-simulated drought stress experiment confirmed that the transgenic lines exhibited increased PEG-simulated drought stress tolerance.

CONCLUSIONS

The 1-FFT gene from Helianthus tuberosus was a functional fructan: fructan 1-fructosyl-transferase and played a positive role in PEG-simulated drought stress tolerance. This transgene could be used to increase fructan concentration and PEG-simulated drought stress tolerance in plants by genetic transformation.

Prime genome editing in rice and wheat

Prime editors, which are CRISPR-Cas9 nickase (H840A)-reverse transcriptase fusions programmed with prime editing guide RNAs (pegRNAs), can edit bases in mammalian cells without donor DNA or double-strand breaks. We adapted prime editors for use in plants through codon, promoter, and editing-condition optimization. The resulting suite of plant prime editors enable point mutations, insertions and deletions in rice and wheat protoplasts. Regenerated prime-edited rice plants were obtained at frequencies of up to 21.8%.

Efficacy and safety of nab-paclitaxel plus S-1(nab-P/S-1) versus nab-paclitaxel plus gemcitabine (nab-P/Gem) for first-line chemotherapy in advanced pancreatic ductal adenocarcinoma (aPDAC): A randomized study

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Background: Nab-P/Gem significantly improved survival compared with gem in patients (pts) with metastatic PDAC, but the ORR was limited to 23% with increased myelosuppression. Two phase II trials demonstrated high ORR of 50.0-53.1% with nab-P/S-1 and showed less hematologic toxicity. Methods: A randomized (1:1) phase II trial was conducted. Eligibility required treatment-naïve pts with unresectable PDAC. Pts received nab-P 125mg/m2on day 1 + S-1 80-120mg orally per day on day 1-7 every 2 weeks or nab-P 125mg/m2+ Gem 1000mg/m2 on days 1,8 every 3 weeks. With an increase of ORR from 25% to 50%, 100 pts were required for 90% power at a two-sided significance level of 0.05. We enrolled 40 pts for a pilot study. Primary endpoints were ORR and 6-month PFS rate. Secondary endpoints were ORR of primary lesion, DCR, PFS, OS and safety. Results: 40 pts were enrolled between 06/2018 and 06/2019, including locally advanced (27.5%) and metastatic (72.5%) PDACs. 42.5% were male and the median age was 61 (range, 36-75) years old. The median duration of treatment was 2.3 months in nab-P/S-1 (n = 20) and 2.7 months in nab-P/Gem (n = 20). In the intention-to-treat (ITT) population, the ORR and DCR were 35.0% vs 25.0% ( P= 0.49) and 70.0% vs 70.0%, respectively.The ORR of primary lesion was 30.0% vs 25.0% ( P= 0.72). In the evaluable pts (nab-P/S-1 n = 18, nab-P/Gem n = 18), the ORR, DCR and the ORR of primary lesion were 38.9% vs 27.8%, 77.8% vs 77.8% and 35.3% vs 29.4%, respectively.With the median follow-up of 5.0 (range 0.3-11.4) months, the median PFS and 6-month PFS rate was 6.3 vs 5.7 months and 56.1% vs 36.2%( P= 0.61) for nab-P/S-1 and nab-P/Gem, respectively. The median OS have not reached. Grade 3/4 toxicities occurred in 30.0% nab-P/S-1 and 30.0% nab-P/Gem: leukopenia/neutropenia(15.0% vs 25.0%), febrile neutropenia (0 vs 5.0%), rash (0 vs 5.0%) and diarrhea (10.0% vs 0). Conclusions: Compared with nab-P/Gem, nab-P/S-1 had higher ORR, ORR of primary lesion and longer PFS without significant difference. Nab-P/S-1 developed a trend towards less hematologic toxicity. Follow up for survival is ongoing. Clinical trial information: 03636308.

Measurement of the depths at different regions of the anterior chamber in healthy Chinese adults

AIM

To measure the depths of different regions of the anterior chamber (AC) in healthy Chinese adults, and to explore possible correlations with age or gender.

METHODS

The AC was imaged by swept-source optical coherence tomography in healthy Chinese adults. The horizontal scan of the right eye was used to measure the anterior chamber depth (ACD) at 199 points.

RESULTS

A total of 309 images from 309 subjects were analyzed. The ACD values at nearly all locations were negatively correlated with age (all P<0.05), except for ACD1, 2, 198, and 199 (correspond to the iris roots). The mean annual decrease 0.013±0.005 mm/y for all ACDs combined, 0.008±0.004 mm/y for the peripheral region, 0.017±0.003 mm/y for the middle peripheral region, and 0.014±0.001 mm/y for the central region. The mean annual decrease was significantly different among these three regions (P<0.001). The ACD was greater in males than in females (P<0.05). The mean difference in ACD between males and females was 0.081±0.025 mm.

CONCLUSION

This study showed that optical coherence tomography can be used to measure the ACD of different regions of the AC. We found reductions in ACD with age, although the reduction varied among different points, in healthy Chinese adults.

Overexpression of ThMYC4E Enhances Anthocyanin Biosynthesis in Common Wheat

The basic helix-loop helix (bHLH) transcription factor has been inferred to play an important role in blue and purple grain traits in common wheat, but to date, its overexpression has not been reported. In this study, the bHLH transcription factor ThMYC4E, the candidate gene controlling the blue grain trait from Th. Ponticum, was transferred to the common wheat JW1. The positive transgenic lines displayed higher levels of purple anthocyanin pigments in their grains, leaves and glumes. Stripping the glumes (light treatment) caused white grains to become purple in transgenic lines. RNA-Seq and qRT-PCR analysis demonstrated that the transcript levels of structural genes associated with anthocyanin biosynthesis were higher in transgenic wheat than the wild-type (WT), which indicated that ThMYC4E activated anthocyanin biosynthesis in the transgenic lines. Correspondingly, the anthocyanin contents in grains, roots, stems, leaves and glumes of transgenic lines were higher than those in the WT. Metabolome analysis demonstrated that the anthocyanins were composed of cyanidin and delphinidin in the grains of the transgenic lines. Moreover, the transgenic lines showed higher antioxidant activity, in terms of scavenging DPPH radicals, in the ethanol extracts of their grains. The overexpression of ThMYC4E sheds light on the traits related to anthocyanin biosynthesis in common wheat and provide a new way to improve anthocyanin content.

Comprehensive Influences of Overexpression of a MYB Transcriptor Regulating Anthocyanin Biosynthesis on Transcriptome and Metabolome of Tobacco Leaves

Overexpression of R2R3-MYB transcriptor can induce up-expression of anthocyanin biosynthesis structural genes, and improve the anthocyanin content in plant tissues, but it is not clear whether the MYB transcription factor overexpression does effect on other genes transcript and chemical compounds accumulation. In this manuscript, RNA-sequencing and the stepwise multiple ion monitoring-enhanced product ions (stepwise MIM-EPI) strategy were employed to evaluate the comprehensive effect of the MYB transcription factor LrAN2 in tobacco. Overexpression of LrAN2 could promote anthocyanin accumulation in a lot of tissues of tobacco cultivar Samsun. Only 185 unigenes express differently in a total of 160,965 unigenes in leaves, and 224 chemical compounds were differently accumulated. Three anthocyanins, apigeninidin chloride, pelargonidin 3-O-beta-D-glucoside and cyanidin 3,5-O-diglucoside, were detected only in transgenic lines, which could explain the phenotype of purple leaves. Except for anthocyanins, the phenylpropanoid, polyphenol (catechin), flavonoid, flavone and flavonol, belong to the same subgroups of flavonoids biosynthesis pathway with anthocyanin and were also up-accumulated. Overexpression of LrAN2 activated the bHLH (basic helix-loop-helix protein) transcription factor AN1b, relative to anthocyanin biosynthesis and the MYB transcription factor MYB3, relative to proanthocyanin biosynthesis. Then, the structural genes, relative to the phenylpropanoid pathway, were activated, which led to the up-accumulation of phenylpropanoid, polyphenol (catechin), flavonoid, flavone, flavonol and anthocyanin. The MYB transcription factor CPC, negative to anthocyanin biosynthesis, also induced up-expression in transgenic lines, which implied that a negative regulation mechanism existed in the anthocyanin biosynthesis pathway. The relative contents of all 19 differently accumulated amino and derivers were decreased in transgenic lines, which meant the phenylalanine biosynthesis pathway completed the same substrates with other amino acids. Interestingly, the acetylalkylglycerol acetylhydrolase was down-expressed in transgenic lines, which caused 19 lyso-phosphatidylcholine and derivatives of lipids to be up-accumulated, and 8 octodecane and derivatives were down-accumulated. This research will give more information about the function of MYB transcription factors on the anthocyanin biosynthesis and other chemical compounds and be of benefit to obtaining new plant cultivars with high anthocyanin content by biotechnology.

A bHLH transcription factor TsMYC2 is associated with the blue grain character in triticale (Triticum × Secale)

RNA-Seq was employed to compare the transcriptome differences between the triticale lines and to identify the key gene responsible for the blue aleurone trait. The accumulation of anthocyanins in the aleurone of triticale results in the formation of the blue-grained trait, but the identity of the genes associated with anthocyanin biosynthesis in the aleurone has not yet been reported. In this manuscript, RNA-Seq was employed to compare the transcriptome differences between the triticale lines HM13 (blue aleurone) and HM5 (white aleurone), and to identify the key genes responsible for the blue aleurone trait. There were 32,406 differentially expressed genes between HM13 and HM5. Seventy-three unigenes were homologous to the structural genes related to anthocyanin biosynthesis, and the average transcript level of the structural genes was higher in HM13 than in HM5, so that quantitative differences between the two lines in transcription rates could be the cause of the blue aleurone. The MYB and bHLH transcription factors had two homologous unigenes, but contained only one differentially expressed unigene each. The relative transcript level of bHLH Unigene5672_All (TsMYC2) in HM13 was 42.71 times that in HM5, while the relative transcript level of the MYB transcription factor Unigene12228_All in HM13 was 2.20 times that in HM5. qPCR experiments determined the relative transcript level of TsMYC2 in developing grain, with the expression of TsMYC2 in grain being the highest compared with that in root, stem or leaf tissue. TsMYC2 was homologous to the bHLH transcription factor regulating anthocyanin biosynthesis and contained three entire functional domains: bHLH-MYC_N, HLH and ACT-like, which were important for exercising regulation of anthocyanin biosynthesis as a bHLH transcription factor. Transient expression of ZmC1 and TsMYC2 could induce anthocyanin biosynthesis in white wheat coleoptile cells, demonstrating that TsMYC2 was a functional bHLH transcription factor. These results indicated that TsMYC2 was associated with the blue aleurone trait and could prove to be a valuable gene with which to breed new triticale cultivars with the blue aleurone trait.

[Progress on base editing systems]

Base editing is a newly developed precise genome editing technique based on the CRISPR/Cas system. According to different base modification enzymes, the current base editing systems can be divided into cytosine base editors (CBE) and adenine base editors (ABE). They use cytosine deaminases or artificially evolved adenine deaminases to perform single-base editing, and achieve C to T (G to A) or A to G (T to C) substitutions, respectively. Due to high efficiency, independence of DNA double-strand breaks, and no need for donor DNA, base editing systems have been successfully applied in diverse species including animals, plants and other organisms since the first report in 2016. Therefore, base editing systems will have a high prospect of providing important support for gene therapy and crop genetic improvement in the future. In this review, we describe the development and current applications of base editing systems for basic research and biotechnology, highlight the challenges, and discuss the directions for future research in this important field. The information presented may facilitate interested researchers to grasp the principles of base editing, to use relevant base editing tools in their own studies, or to innovate new versions of base editing in the future.

Automatic Classification of Anterior Chamber Angle Using Ultrasound Biomicroscopy and Deep Learning

Purpose

To develop a software package for automated classification of anterior chamber angle of the eye by using ultrasound biomicroscopy.

Methods

Ultrasound biomicroscopy images were collected, and the trabecular-iris angle was manually measured and classified into three categories: open angle, narrow angle, and angle closure. Inception v3 was used as the classifying convolutional neural network and the algorithm was trained.

Results

With a recall rate of 97% in the test set, the neural network's classification accuracy can reach 97.2% and the overall area under the curve was 0.988. The sensitivity and specificity were 98.04% and 99.09% for the open angle, 96.30% and 98.13% for the narrow angle, and 98.21% and 99.05% for the angle closure categories, respectively.

Conclusions

Preliminary results show that an automated classification of the anterior chamber angle achieved satisfying sensitivity and specificity and could be helpful in clinical practice.

Translational Relevance

The present work suggests that the algorithm described here could be useful in the categorizing of anterior chamber angle and screening for subjects who are at high risk of angle closure.

Nab-paclitaxel/S-1(AS) versus nab-paclitaxel/gemcitabine(AG) for first-line chemotherapy in advanced pancreatic ductal adenocarcinoma (aPDAC): A retrospective analysis of efficacy and safety

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Background: AG significantly improved PFS and OS compared with gemcitabine monotherapy in patients (pts) with metastatic PDAC, but the confirmed ORR was limited to 23% with increased grade 3 or 4 myelosuppression. In GEST and JASPAC01 studies, S-1 showed non-inferior or superior activity to gemcitabine in advanced and postoperative PDAC. S-1 also developed less hematologic adverse events especially in neutropenia and was a convenient oral alternative. Two single-arm phase II trials in China demonstrated high ORR of 50.0-53.1% with AS. We investigated the efficacy and safety of first-line chemotherapy with AS versus AG in pts with aPDAC. Methods: A retrospective review was conducted of aPDAC pts treated with first-line AS and AG in GI dpt. Of PUCH between 11/2013 and 12/2018. Pts received 125mg/m2 nab-paclitaxel intravenously (IV) on day1, and 80-100mg S-1 orally per day on day1-7 every two weeks in AS cohort, while pts received 125mg/m2 nab-paclitaxel IV on day1,8, and 1000mg/m2 gemcitabine IV on day1,8 every three weeks in AG cohort. ORR, ORR of primary lesion, DCR, PFS, OS and safety were analysed between two cohorts. Survival outcomes were evaluated by Kaplan-Meier method and compared with the log-rank test. A Cox proportional hazard model was made to determine independent predictors of survival. Results: A total of 70 pts (45 in AS cohort, 25 in AG cohort) with locally advanced (4%) and metastatic (96%) PDACs were identified. 75% were male and the median age was 65(range 36-72). Among intention-to-treat population, the ORR and DCR were 40.0% vs 32.0% (p = 0.70) and 75.6% vs 64.0% (p = 0.57) in AS and AG cohort, respectively. The ORR of primary lesion was 31.1% with AS vs 20.0% with AG (p = 0.73). With the median follow-up of 9.8 months(range 2.3-22.2), the median PFS and OS were 4.7m vs 6.7m (HR, 1.2; 95% CI, 0.6 to 2.4; p = 0.62) and 10.3m vs 11.3m (HR, 0.9; 95% CI, 0.5 to 1.8; p = 0.78) in AS and AG cohort, respectively. Grade 3/4 toxicities occurred in 31.1% AS vs 36.0% AG (p = 0.59). Most G3/4 toxicities were: leukopenia/neutropenia (26.7% vs 20.0%), febrile neutropenia (2.2% vs 8.0%), thrombocytopenia (0 vs 12%), fatigue (4.4% vs 12%), peripheral neuropathy (0 vs 8.0%). In multivariate analysis, liver metastasis was the only independent predictor of poor OS (HR 0.3, 95%CI 0.1-0.8, p = 0.014). Conclusions: AS was a comparable and convenient alternative with manageable toxicities in aPDAC. There was a trend towards improved ORR of primary lesion compared with AG.

Intereye and intraeye asymmetry analysis of retinal microvascular and neural structure parameters for diagnosis of primary open-angle glaucoma

PURPOSE

To investigate the diagnostic values of intereye or intraeye asymmetry of retinal perfused vessel density and neural structure parameters for detection of glaucoma.

METHODS

In total, 152 healthy subjects and 72 bilateral primary open-angle glaucoma (POAG) patients were enrolled. Total POAG group contains all glaucoma patients. Early to moderate POAG group contains patients whose binocular mean defect values were larger than -12 dB. The retinal perfused vessel densities were acquired using optic coherence tomography angiography. The neural structure parameters include RNFL, GCC thickness and its derivative indices like focal loss volume percentage (FLV%) and global loss volume percentage (GLV%). Intereye asymmetry equaled to the absolute difference of parameters between paired eyes. Intraeye asymmetry was defined as absolute difference between the inferior and superior hemisphere values from one random selected eye. The areas under the receiver operating characteristic curves (AUROCs) were calculated to evaluate diagnostic ability.

RESULTS

From pairwise comparison analysis of ROC curves, the intereye asymmetric parameters with the largest diagnostic accuracy were FLV and GLV% (AUROC = 0.944), which were significantly superior to the intereye asymmetry of perfused vessel density in peripapillary area and parafoveal area (P < 0.05). Particularly, the intereye asymmetry of FLV% (AUROC = 0.926) and GLV% (AUROC = 0.950) showed excellent diagnostic precision for detecting early to moderate glaucoma patients. However, the intraeye asymmetry of microvascular parameters and neural structure parameters showed fair diagnostic ability for identifying POAG patients.

CONCLUSIONS

The intereye asymmetry of neural structure parameters, particularly the FLV% and GLV%, outperformed the microvascular parameters for identifying POAG patients.

Generation of herbicide tolerance traits and a new selectable marker in wheat using base editing

Developing herbicide-tolerant varieties by genome editing holds great promise for addressing the worsening weed problems in wheat cultivation¹. Here, we generated transgene-free wheat germplasms harbouring herbicide tolerance mutations that confer tolerance to sulfonylurea-, imidazolinone- and aryloxyphenoxy propionate-type herbicides by base editing the acetolactate synthase (ALS) and acetyl-coenzyme A carboxylase genes. These stackable herbicide tolerance traits provide a potentially powerful tool for weed management. In addition, we found that base editing at the wheat ALS Pro-174 codon (TaALS-P174) endowed wheat with sufficient resistance to nicosulfuron herbicide in MS growth medium to allow selection. When the TaALS-P174 editor was coupled with editors for other targets of interest, co-editing occurred in the nicosulfuron-resistant plants, and selection for resistance in growth medium enriched the frequency of coupled targets by several-fold. This selectable co-editing system has the potential to greatly bolster adoption of base editing for crop improvement applications.

Functional MYB transcription factor encoding gene AN2 is associated with anthocyanin biosynthesis in Lycium ruthenicum Murray

BACKGROUND

Lycium ruthenicum Murray is an important economic plant in China and contains higher levels of anthocyanins in its fruits than other Lyciums. However, the genetic mechanism of anthocyanin production in this plant is unknown.

RESULTS

Based on previous transcriptome analysis, LrAN2 and LbAN2, encoding MYB transcription factors, were isolated from L. ruthenicum and L. barbarum, respectively. Both genes contained two introns, encoded 257 amino acids with two-Aa difference, and carried the unabridged HTH-MYB, MYB-like DNA-binding, and SANT domains. In the phylogenetic trees, LrAN2 and LbAN2 were found to be closely related to NtAN2, which regulates anthocyanin biosynthesis in tobacco. Overexpression of LrAN2 and LbAN2 induced anthocyanin biosynthesis in all tissues of tobacco. The anthocyanin content in the leaves of transgenic lines with LbAN2 was lower than LrAN2. It indicated that the function of LbAN2 was weaker than LrAN2. The AN2 transcript could be detected only in the fruits of L. ruthenicum and increased during fruit development, accompanied by anthocyanin accumulation. In natural population, the alleles LrAN2 and LrAN2 were associated strictly with L. ruthenicum and L. barbarum, respectively. Moreover, an AN2 genetic diversity study suggested that Lyciums with yellow, white, purple, and jujube red fruits were derived from L. ruthenicum.

CONCLUSIONS

Two AN2 alleles, from L. ruthenicum and L. barbarum, were functional MYB transcriptor regulating anthocyanin biosynthesis. The functional diversity and high expression level of LrAN2 could be the reason for high anthocyanin content in the fruit of L. ruthenicum. Lyciums with yellow, white, purple, and jujube red fruits were derived from L. ruthenicum based on AN2 sequence diversity. The results may be advantageous in identifying new varieties and breeding new cultivars.

Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice

Cytosine and adenine base editors (CBEs and ABEs) are promising new tools for achieving the precise genetic changes required for disease treatment and trait improvement. However, genome-wide and unbiased analyses of their off-target effects in vivo are still lacking. Our whole-genome sequencing analysis of rice plants treated with the third-generation base editor (BE3), high-fidelity BE3 (HF1-BE3), or ABE revealed that BE3 and HF1-BE3, but not ABE, induce substantial genome-wide off-target mutations, which are mostly the C→T type of single-nucleotide variants (SNVs) and appear to be enriched in genic regions. Notably, treatment of rice with BE3 or HF1-BE3 in the absence of single-guide RNA also results in the rise of genome-wide SNVs. Thus, the base-editing unit of BE3 or HF1-BE3 needs to be optimized in order to attain high fidelity.

Transcriptome Analysis Identifies Key Genes Responsible for Red Coleoptiles in Triticum Monococcum

Red coleoptiles can help crops to cope with adversity and the key genes that are responsible for this trait have previously been isolated from Triticum aestivum, Triticum urartu, and Aegilops tauschii. This report describes the use of transcriptome analysis to determine the candidate gene that controls the trait for white coleoptiles in T. monococcum by screening three cultivars with white coleoptiles and two with red coleoptiles. Fifteen structural genes and two transcription factors that are involved in anthocyanin biosynthesis were identified from the assembled UniGene database through BLAST analysis and their transcript levels were then compared in white and red coleoptiles. The majority of the structural genes reflected lower transcript levels in the white than in the red coleoptiles, which implied that transcription factors related to anthocyanin biosynthesis could be candidate genes. The transcript levels of MYC transcription factor TmMYC-A1 were not significantly different between the white and red coleoptiles and all of the TmMYC-A1s contained complete functional domains. The deduced amino acid sequence of the MYB transcription factor TmMYB-A1 in red coleoptiles was homologous to TuMYB-A1, TaMYB-A1, TaMYB-B1, and TaMYB-D1, which control coleoptile color in corresponding species and contained the complete R2R3 MYB domain and the transactivation domain. TmMYB-a1 lost its two functional domains in white coleoptiles due to a single nucleotide deletion that caused premature termination at 13 bp after the initiation codon. Therefore, TmMYB-A1 is likely to be the candidate gene for the control of the red coleoptile trait, and its loss-of-function mutation leads to the white phenotype in T. monococcum.

Spatial-Temporal Recurrent Neural Network for Emotion Recognition

In this paper, we propose a novel deep learning framework, called spatial-temporal recurrent neural network (STRNN), to integrate the feature learning from both spatial and temporal information of signal sources into a unified spatial-temporal dependency model. In STRNN, to capture those spatially co-occurrent variations of human emotions, a multidirectional recurrent neural network (RNN) layer is employed to capture long-range contextual cues by traversing the spatial regions of each temporal slice along different directions. Then a bi-directional temporal RNN layer is further used to learn the discriminative features characterizing the temporal dependencies of the sequences, where sequences are produced from the spatial RNN layer. To further select those salient regions with more discriminative ability for emotion recognition, we impose sparse projection onto those hidden states of spatial and temporal domains to improve the model discriminant ability. Consequently, the proposed two-layer RNN model provides an effective way to make use of both spatial and temporal dependencies of the input signals for emotion recognition. Experimental results on the public emotion datasets of electroencephalogram and facial expression demonstrate the proposed STRNN method is more competitive over those state-of-the-art methods.

Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice

Cytosine and adenine base editors (CBEs and ABEs) are promising new tools for achieving the precise genetic changes required for disease treatment and trait improvement. However, genome-wide and unbiased analyses of their off-target effects in vivo are still lacking. Our whole-genome sequencing analysis of rice plants treated with the third-generation base editor (BE3), high-fidelity BE3 (HF1-BE3), or ABE revealed that BE3 and HF1-BE3, but not ABE, induce substantial genome-wide off-target mutations, which are mostly the C→T type of single-nucleotide variants (SNVs) and appear to be enriched in genic regions. Notably, treatment of rice with BE3 or HF1-BE3 in the absence of single-guide RNA also results in the rise of genome-wide SNVs. Thus, the base-editing unit of BE3 or HF1-BE3 needs to be optimized in order to attain high fidelity.

Transcriptome Analysis Clarified Genes Involved in Betalain Biosynthesis in the Fruit of Red Pitayas (Hylocereus costaricensis)

The red flesh trait gives red pitayas more healthful components and a higher price, while the genetic mechanism behind this trait is unknown. In this manuscript, transcriptome analysis was employed to discover the genetic differences between white and red flesh in pitayas. A total of 27.99 Gb clean data were obtained for four samples. Unigenes, 79,049 in number, were generated with an average length of 1333 bp, and 52,618 Unigenes were annotated. Compared with white flesh, the expression of 10,215 Unigenes was up-regulated, and 4853 Unigenes were down-regulated in red flesh. The metabolic pathways accounted for 64.6% of all differentially expressed Unigenes in KEGG pathways. The group with high betalain content in red flesh and all structural genes, related to betalain biosynthesis, had a higher expression in red flesh than white flesh. The expression of the key gene, tyrosine hydroxylase CYP76AD1, was up-regulated 245.08 times, while 4,5-DOPA dioxygenase DODA was up-regulated 6.46 times. Moreover, the special isomers CYP76AD1α and DODAα were only expressed in red flesh. The competitive anthocyanin biosynthesis pathway had a lower expression in red flesh. Two MYB transcription factors were of the same branch as BvMYB1, regulating betalain biosynthesis in beet, and those transcription factors had expression differences in two kinds of pitayas, which indicated that they should be candidate genes controlling betalain accumulation in red pitayas. This research would benefit from identifying the major gene controlling red flesh trait and breed new cultivars with the red flesh trait. Future research should aim to prove the role of each candidate gene in betalain biosynthesis in red pitayas.

Clinical Features and Efficacy of Lens Surgery in Patients with Lens Subluxation Misdiagnosed as Primary Angle-Closure Glaucoma

PURPOSE

To investigate the clinical features and efficacy of lens surgery in patients with lens subluxation misdiagnosed as primary angle-closure glaucoma.

METHODS

In total, 2054 inpatients with primary angle-closure glaucoma were consecutively recruited. Eighty-five of the patients were rediagnosed as lens subluxation following ultrasound biomicroscopy after hospitalization. Lens surgeries were performed in all patients, and 35 had a follow-up of at least 12 months. Risk factors of postoperative intraocular pressure control were identified with multivariate logistic regression analysis.

RESULTS

Eighty-five inpatients (4.1%, 85/2054) with lens subluxation were misdiagnosed as primary angle-closure glaucoma, of which 71.8% (2.97% of all cases, 61 out of 2054 subjects) had ocular blunt trauma and 18.8% (0.78% of all cases, 16 out of 2054 subjects) had spontaneous dislocation. Lens surgery significantly decreased the intraocular pressure and improved best-corrected visual acuity, meanwhile increased the anterior chamber depth (all P < 0.001). Postoperatively, the intraocular pressure was controlled with antiglaucomatous eye drops administration in 17 eyes, in which greater range of preoperative angle closure and zonular dialysis, and longer operation time delay were detected. Risk factors for poor postoperative IOP control were more quadrants of angle closure (P = 0.038) and operation time delay (P = 0.045).

CONCLUSION

Lens subluxation was the major cause of the misdiagnosed cases as primary angle-closure glaucoma. Misdiagnosed patients could benefit from the lens surgery, while more angle-closure quadrants and operation time delay indicated worse postoperative intraocular pressure control.