Advancing PAM-less genome editing in soybean using CRISPR-SpRY.

Although CRISPR-Cas9 technology has been rapidly applied in soybean genetic improvement, it is difficult to achieve the targeted editing of the specific loci in the soybean complex genome due to the limitations of the classical protospacer adjacent motif (PAM). Here, we developed a PAM-less genome editing system mediated by SpRY in soybean. By performing targeted editing of representative agronomic trait targets in soybean and evaluating the results, we demonstrate that the SpRY protein can achieve efficient targeted mutagenesis at relaxed PAM sites in soybean. Furthermore, the SpRY-based cytosine base editor SpRY-hA3A and the adenine base editor SpRY-ABE8e both can accurately induce C-to-T and A-to-G conversion in soybean, respectively. Thus, our data illustrate that the SpRY toolbox can edit the soybean genomic sequence in a PAM-free manner, breaking restrictive PAM barriers in the soybean genome editing technology system. More importantly, our research enriches soybean genome editing tools, which has important practical application value for precise editing and molecular design in soybean breeding.

Anopheles gambiae lacking AgTRIO probe inefficiently on a mammalian host.

Malaria is initiated as Plasmodium sporozoites are injected into the dermis when an infected mosquito probes on a vertebrate host for a blood meal. Factors in the mosquito saliva, such as AgTRIO, can alter the ability of Anopheles gambiae to transmit Plasmodium. We therefore used CRISPR-Cas9-mediated genome editing to generate AgTRIO knockout (KO) A. gambiae and examined the ability of these mosquitoes to probe on a vertebrate host. AgTRIO KO mosquitoes showed a diminished host probing capacity and required repetitive probing to locate a blood resource to complete a blood meal. This increased probing resulted in enhanced Plasmodium transmission to the vertebrate host. Our data demonstrate the importance of the A. gambiae saliva protein AgTRIO in probing and its influence on the ability of mosquitoes to transmit malaria.

Correlations between growth differentiation factor 15 (GDF-15) serum levels and gene polymorphism with type 2 diabetes mellitus.

Purpose: To date, the relationship between Growth Differentiation Factor 15 (GDF-15) gene polymorphism and the risk of type 2 diabetes mellitus (T2DM) has not been clarified. Our study aims to explore the association between serum GDF-15 levels and related gene polymorphism with the risk of T2DM in a Chinese rural Yao population. Methods: This was a 1:1 case-control study with 179 T2DM patients and 179 age- and sex-matched control participants. Serum GDF-15 levels were measured by enzyme-linked immunosorbent assay, and polymorphisms (rs1059519, rs1059369, rs1804826 and rs1054564) were genotyped by MassArray mass spectrometry. Results: Serum GDF-15 (sGDF-15) levels were higher in patients with T2DM and glycosylated hemoglobin (HbA1c) ≥ 6.5 % compared to that in controls (p < 0.001). The area under the curve (AUC) corresponding to sGDF-15 levels was 0.626. Serum GDF-15 was positively correlated with fasting plasma glucose (FPG) (rs = 0.150, p < 0.001) and HbA1c (rs = 0.160, p < 0.001). The frequency of GDF-15 gene rs1054564 GC + CC genotype was significantly associated with increased risk of T2DM compared to GG genotype (OR = 1.724, 95CI: 1.046-2.841, p = 0.033). Frequencies of rs1804826 T allele (ß additive = 113.318, p = 0.026) and rs1054564 C allele (ß additive = 247.282, p = 0.001, ß dominant = 286.109, p = 0.001) was significantly correlated with higher sGDF-15. The rs1059519 C allele was negatively correlated with FPG (ß recessive = -0.607, p = 0.047) and HbA1c (ß recessive = -0.456, p = 0.020). Conclusion: Serum GDF-15 levels were positively correlated with FPG and HbA1c. The GDF-15 rs1054564 GC + CC genotype was associated with a significantly higher T2DM risk. The rs1059519 C allele was negatively correlated with FPG and HbA1c.

Optimizing Rice Genomics: Employing the Hypercompact Cas12j2 System for Targeted Transcriptional Regulation and Epigenome Modification.

In the burgeoning field of genome engineering, the CRISPR-Cas systems have emerged as pivotal tools for precise genetic modifications in various organisms, including humans, animals, and plants. One significant obstacle in this arena is the substantial size of Cas proteins, such as SpCas9, which is approximately 190 kDa, complicating their delivery, particularly via viral vectors. To overcome this challenge, our research introduces the hypercompact Cas12j2 system, a groundbreaking development with a size of merely ~80 kDa, originally identified in Biggiephage. We demonstrate its application in plant genome editing, with a particular focus on rice. In this context, we have successfully adapted Cas12j2 for gene activation, achieving significant increases in gene expression, specifically up to a tenfold activation for OsER1 and a fourfold activation for OsNRT1.1A in stable transgenic rice plants. Moreover, we have ventured beyond mere gene editing to develop a Cas12j2-based approach for targeted epigenome editing, particularly in the context of DNA methylation. This was demonstrated through the targeted methylation of the OsGBSS1 promoter, as verified by Next-Generation Sequencing of bisulfite sequencing PCR products. This chapter presents a detailed protocol about utilizing the hypercompact Cas12j2 system in conjunction with specific effectors, such as transcriptional activation or repression domains, or methylation domains, to achieve targeted gene transcriptional regulation and epigenome modification in rice.

Association between Copper Exposure and Cognitive Function: A Cross-Sectional Study in a County, Guangxi, China.

There has been growing attention to the impact of copper exposure on cognitive function; however, current research on the specific information regarding urinary copper and cognitive function is limited, particularly detailed analyses in the Chinese adult population. This study aimed to explore the association between copper exposure and cognitive function in a cross-sectional design. A total of 2617 participants in a county, Guangxi Zhuang Autonomous Region (Guangxi), China, were included. The mini-mental state examination (MMSE) was used to assess cognitive function, and inductively coupled plasma mass spectrometry was used to measure urinary metal levels. Spearman's rank correlation was used to analyze the correlation between urinary copper levels and various cognitive function assessment indices. After adjusting for potential confounders, binary logistic regression was used to explore the association between urinary copper levels and the risk of cognitive impairment (CI) as revealed by MMSE, and restricted cubic spline regression was further used to explore the dose-response relationship. The results showed a negative correlation between urinary copper levels and orientation, attention and calculation, memory, language ability, and MMSE total scores (P < 0.05). Compared with the low copper exposure group, the high exposure group showed a 58.5% increased risk of CI (OR = 1.585, 95%CI: 1.125 to 2.235, P = 0.008). A significant linear dose-response relationship was observed between urinary copper levels and the risk of CI (P overall = 0.045, P nonlinearity = 0.081). Our findings suggest that higher copper exposure may be associated with CI in the population of a county, Guangxi, China.

Parental Warmth, Friendship Quality, Empathy and Bystander Defending Behavior in Cyberbullying Among Adolescents in China.

Adolescents' bystander defending behavior in cyberbullying contributes to reducing the harm done to cyberbullying victims. This study examined the relationships and underlying mechanisms of parental warmth, friendship quality, empathy and bystander defending behavior in cyberbullying among 848 Chinese adolescents (43.986% girls, mean age = 14.960 years old [SD = 1.398]). The results showed that parental warmth, friendship quality and empathy were all positively correlated with bystander defending behavior in cyberbullying among adolescents. Both friendship quality and empathy played a mediating role between parental warmth and bystander defending behavior in cyberbullying, indicating that parental warmth was associated with increased bystander defending behavior through higher levels of friendship quality and empathy, respectively. Friendship quality and empathy also played a chain mediating role between these two, indicating that parental warmth was linked to increased bystander defending behavior by first associating with higher level of friendship quality and subsequently with greater empathy. These results suggest that high degrees of parental warmth, friendship quality and empathy may all increase the likelihood of bystander defending behavior in cyberbullying among adolescents. This study provides practical implications for improving adolescent bystander defending behavior in cyberbullying.

A cyanine based fluorescent probe for detecting hypochlorite in vitro and in vivo.

Hypochlorite (ClO-) is recognized as a bioactive substance that plays a crucial role in various physiological and pathological processes. The increase of ClO- content in cells is a key factor in the early atherosclerosis lesions, which are closely linked to cardiovascular and cerebrovascular diseases. Therefore, the development of an efficient and sensitive method for detecting hypochlorite in tap water, serum, and living cells, including animal model in vivo is of paramount importance. In this study, a novel fluorescent probe (Cy-F) based on the cyanine group was designed for the specific detection of ClO-, demonstrating exceptional selectivity, high sensitivity, and rapid response. The probe successfully detected ClO- in tap water and serum with a limit of detection (LOD) of 2.93 × 10-7 M, showcasing excellent anti-interference capabilities. Notably, the probe exhibited good biocompatibility, low biological toxicity, and proved effective for detecting and analyzing ClO- in live cells and zebrafish. This newly developed probe offers a promising approach and valuable tool for detecting ClO- with biosafety considerations, paving the way for the design of functional probes tailored for future biomedical applications.

Relations between near-field enhancements and Purcell factors in hybrid nanostructures of plasmonic antennas and dielectric cavities.

Strong near-field enhancements (NFEs) of nanophotonic structures are believed to be closely related to high Purcell factors (FP). Here, we theoretically show that the correlation is partially correct; the extinction cross section (σ) response is also critical in determining FP. The divergence between NFE and FP is especially pronounced in plasmonic-dielectric hybrid systems, where the plasmonic antenna supports dipolar plasmon modes and the dielectric cavity hosts Mie-like resonances. The cavity's enhanced-field environment can boost the antenna's NFEs, but the FP is not increased concurrently due to the larger effective σ that is intrinsic to the FP calculations. Interestingly, the peak FP for the coupled system can be predicted by using the NFE and σ responses. Furthermore, the limits for FP of coupled systems are considered; they are determined by the sum of the FP of a redshifted (or modified, if applicable) antenna and an individual cavity. This contrasts starkly with the behavior of NFE which is closely associated with the multiplicative effects of the NFEs provided by the antenna and the dielectric cavity. The differing behaviors of NFE and FP in hybrid cavities have varied impacts on relevant nanophotonic applications such as fluorescence, Raman scattering and enhanced light-matter interactions.

Robust CRISPR/Mb2Cas12a genome editing tools in cotton plants.

The efficiency and accuracy of the CRISPR/Mb2Cas12a system were demonstrated in cotton, achieving an efficiency of over 90% at target sites. Notably, Mb2Cas12a exhibited significant tolerance under different temperatures ranging from 22°C to 32°C. Additionally, the Mb2Cas12a system revealed effective editing at more relaxed VTTV PAM sites in the cotton genome, which expanded the genome editing range by approximately 2.6-fold than the wide-type LbCas12a. Finally, a multiplex genome editing system was also developed based on Mb2Cas12a, enabling simultaneous editing of eight target sites using a single crRNA cassette.

High performance TadA-8e derived cytosine and dual base editors with undetectable off-target effects in plants.

Cytosine base editors (CBEs) and adenine base editors (ABEs) enable precise C-to-T and A-to-G edits. Recently, ABE8e, derived from TadA-8e, enhances A-to-G edits in mammalian cells and plants. Interestingly, TadA-8e can also be evolved to confer C-to-T editing. This study compares engineered CBEs derived from TadA-8e in rice and tomato cells, identifying TadCBEa, TadCBEd, and TadCBEd_V106W as efficient CBEs with high purity and a narrow editing window. A dual base editor, TadDE, promotes simultaneous C-to-T and A-to-G editing. Multiplexed base editing with TadCBEa and TadDE is demonstrated in transgenic rice, with no off-target effects detected by whole genome and transcriptome sequencing, indicating high specificity. Finally, two crop engineering applications using TadDE are shown: introducing herbicide resistance alleles in OsALS and creating synonymous mutations in OsSPL14 to resist OsMIR156-mediated degradation. Together, this study presents TadA-8e derived CBEs and a dual base editor as valuable additions to the plant editing toolbox.

Performance analysis of a liquid lens for laser ablation using OCT imaging.

Laser ablation has been used in different surgical procedures to perform precise treatments. Compared with previous free-beam laser delivery systems, flexible-optical-fiber-based systems can deliver laser energy to a curved space, avoiding the requirement of a straight working path to the target. However, the fiber tip maintains direct contact with the tissue to prevent laser divergence, resulting in fiber damage, uneven ablation, and tissue carbonization. Here, a liquid lens is used to address the problem of laser defocusing when radiating targets at different depths for flexible-optical-fiber-based systems. The liquid lens focuses a laser with a maximum power of 3 W onto a medium-density fiberboard at a focal length of 40-180 mm. The relationships between the ablation crater diameter and depth with the radiation time and laser power have been quantitatively evaluated through OCT (optical coherence tomography) imaging. Experiments demonstrate that the liquid lens can continuously focus the high-power laser to different depths, with the advantages of compact size, fast response, light weight, and easy operation. This study explores liquid-lens-based focused laser ablation, which can potentially improve the performance of future medical image-guided laser ablation.

Interfacial Heterojunction Enables High Efficient PbS Quantum Dot Solar Cells.

Colloidal quantum dots (CQDs) are promising optoelectronic materials for solution-processed thin film optoelectronic devices. However, the large surface area with abundant surface defects of CQDs and trap-assisted non-radiative recombination losses at the interface between CQDs and charge-transport layer limit their optoelectronic performance. To address this issue, an interface heterojunction strategy is proposed to protect the CQDs interface by incorporating a thin layer of polyethyleneimine (PEIE) to suppress trap-assisted non-radiative recombination losses. This thin layer not only acts as a protective barrier but also modulates carrier recombination and extraction dynamics by forming heterojunctions at the buried interface between CQDs and charge-transport layer, thereby enhancing the interface charge extraction efficiency. This enhancement is demonstrated by the shortened lifetime of carrier extraction from 0.72 to 0.46 ps. As a result, the resultant PbS CQD solar cells achieve a power-conversion-efficiency (PCE) of 13.4% compared to 12.2% without the heterojunction.

Genome editing in rice and tomato with a small Un1Cas12f1 nuclease.

The clustered regularly interspaced short palindromic repeats (CRISPR) systems have been demonstrated to be the foremost compelling genetic tools for manipulating prokaryotic and eukaryotic genomes. Despite the robustness and versatility of Cas9 and Cas12a/b nucleases in mammalian cells and plants, their large protein sizes may hinder downstream applications. Therefore, investigating compact CRISPR nucleases will unlock numerous genome editing and delivery challenges that constrain genetic engineering and crop development. In this study, we assessed the archaeal miniature Un1Cas12f1 type-V CRISPR nuclease for genome editing in rice and tomato protoplasts. By adopting the reengineered guide RNA modifications ge4.1 and comparing polymerase II (Pol II) and polymerase III (Pol III) promoters, we demonstrated uncultured archaeon Cas12f1 (Un1Cas12f1) genome editing efficacy in rice and tomato protoplasts. We characterized the protospacer adjacent motif (PAM) requirements and mutation profiles of Un1Cas12f1 in both plant species. Interestingly, we found that Pol III promoters, not Pol II promoters, led to higher genome editing efficiency when they were used to drive guide RNA expression. Unlike in mammalian cells, the engineered Un1Cas12f1-RRA variant did not perform better than the wild-type Un1Cas12f1 nuclease, suggesting continued protein engineering and other innovative approaches are needed to further improve Un1Cas12f1 genome editing in plants.

[A new cucurbitane glycoside from Picrorhiza scrophulariiflora].

Chemical constituents from the ethanol extract of Picrorhiza scrophulariiflora were isolated and purified by column chromatography. Their structures were identified by HR-MS, 1D and 2D-NMR, and their cytotoxicity was assessed by CCK-8 assay. Four compounds were isolated and identified as follows: 2ß-D-glucosyloxy-3ß,16α,20ß-trihydroxy-9-methyl-19-norlanosterol-5,25-diene-22-one(1), 2ß-D-glucosyloxy-3ß,16α,20ß-trihydroxy-9-methyl-19-norlanosta-5,24-diene-22-one(2), 25-acetoxy-2ß-glucosyloxy-3ß,16α,20ß-trihydroxy-9-methyl-19-norlanosta-5-ene-22-one(3) and 25-acetoxy-2ß-glucosyloxy-3ß,16α,20ß-trihydroxy-9-methyl-19-norlanosta-5,23-(E)-diene-22-one(4). Compound 1 represents a new cucurbitane glycoside. The half inhibitory concentrations of the 4 compounds exceeded 100 µmol·L~(-1) against four tumor cell lines, indicating no significant cytotoxicity.

Negative Deterministic Information-Based Multiple Instance Learning for Weakly Supervised Object Detection and Segmentation.

Weakly supervised object detection (WSOD) and semantic segmentation with image-level annotations have attracted extensive attention due to their high label efficiency. Multiple instance learning (MIL) offers a feasible solution for the two tasks by treating each image as a bag with a series of instances (object regions or pixels) and identifying foreground instances that contribute to bag classification. However, conventional MIL paradigms often suffer from issues, e.g., discriminative instance domination and missing instances. In this article, we observe that negative instances usually contain valuable deterministic information, which is the key to solving the two issues. Motivated by this, we propose a novel MIL paradigm based on negative deterministic information (NDI), termed NDI-MIL, which is based on two core designs with a progressive relation: NDI collection and negative contrastive learning (NCL). In NDI collection, we identify and distill NDI from negative instances online by a dynamic feature bank. The collected NDI is then utilized in a NCL mechanism to locate and punish those discriminative regions, by which the discriminative instance domination and missing instances issues are effectively addressed, leading to improved object-and pixel-level localization accuracy and completeness. In addition, we design an NDI-guided instance selection (NGIS) strategy to further enhance the systematic performance. Experimental results on several public benchmarks, including PASCAL VOC 2007, PASCAL VOC 2012, and MS COCO, show that our method achieves satisfactory performance. The code is available at: https://github.com/GC-WSL/NDI.

Expanding plant genome editing scope and profiles with CRISPR-FrCas9 systems targeting palindromic TA sites.

CRISPR-Cas9 is widely used for genome editing, but its PAM sequence requirements limit its efficiency. In this study, we explore Faecalibaculum rodentium Cas9 (FrCas9) for plant genome editing, especially in rice. FrCas9 recognizes a concise 5'-NNTA-3' PAM, targeting more abundant palindromic TA sites in plant genomes than the 5'-NGG-3' PAM sites of the most popular SpCas9. FrCas9 shows cleavage activities at all tested 5'-NNTA-3' PAM sites with editing outcomes sharing the same characteristics of a typical CRISPR-Cas9 system. FrCas9 induces high-efficiency targeted mutagenesis in stable rice lines, readily generating biallelic mutants with expected phenotypes. We augment FrCas9's ability to generate larger deletions through fusion with the exonuclease, TREX2. TREX2-FrCas9 generates much larger deletions than FrCas9 without compromise in editing efficiency. We demonstrate TREX2-FrCas9 as an efficient tool for genetic knockout of a microRNA gene. Furthermore, FrCas9-derived cytosine base editors (CBEs) and adenine base editors (ABE) are developed to produce targeted C-to-T and A-to-G base edits in rice plants. Whole-genome sequencing-based off-target analysis suggests that FrCas9 is a highly specific nuclease. Expression of TREX2-FrCas9 in plants, however, causes detectable guide RNA-independent off-target mutations, mostly as single nucleotide variants (SNVs). Together, we have established an efficient CRISPR-FrCas9 system for targeted mutagenesis, large deletions, C-to-T base editing, and A-to-G base editing in plants. The simple palindromic TA motif in the PAM makes the CRISPR-FrCas9 system a promising tool for genome editing in plants with an expanded targeting scope.

Brain-Inspired Learning, Perception, and Cognition: A Comprehensive Review.

The progress of brain cognition and learning mechanisms has provided new inspiration for the next generation of artificial intelligence (AI) and provided the biological basis for the establishment of new models and methods. Brain science can effectively improve the intelligence of existing models and systems. Compared with other reviews, this article provides a comprehensive review of brain-inspired deep learning algorithms for learning, perception, and cognition from microscopic, mesoscopic, macroscopic, and super-macroscopic perspectives. First, this article introduces the brain cognition mechanism. Then, it summarizes the existing studies on brain-inspired learning and modeling from the perspectives of neural structure, cognitive module, learning mechanism, and behavioral characteristics. Next, this article introduces the potential learning directions of brain-inspired learning from four aspects: perception, cognition, understanding, and decision-making. Finally, the top-ten open problems that brain-inspired learning, perception, and cognition currently face are summarized, and the next generation of AI technology has been prospected. This work intends to provide a quick overview of the research on brain-inspired AI algorithms and to motivate future research by illuminating the latest developments in brain science.

Associations between whole grains intake and new-onset hypertension: a prospective cohort study.

IMPORTANCE: Epidemiological evidences regarding the association between whole grain intake and the risk of new-onset hypertension are still controversial. OBJECTIVE: We aimed to investigate the relationship between whole grain intake and new-onset hypertension and examine possible effect modifiers in the general population. METHODS: A total of 10,973 participants without hypertension from the China Health and Nutrition Survey were enrolled, with follow-up beginning in 1997 and ending in 2015. Whole grain intake was assessed by 3 consecutive 24-h dietary recalls combined with a household food inventory. Multivariable hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards regression model after adjusting for potential risk factors. RESULTS: During a median follow-up of 7.0 years, 3,733 participants developed new-onset hypertension. The adjusted HRs (95% CIs) were as follows: for quartile 2 (HR: 0.52; 95% CI: 0.47-0.57), quartile 3 (HR: 0.46; 95% CI: 0.42-0.51), and quartile 4 (HR: 0.35; 95% CI: 0.31-0.38), compared with quartile 1. Different types of whole grain types, including wheat (adjusted HR, 0.35; 95% CI, 0.32-0.39), maize (adjusted HR, 0.50; 95% CI, 0.42-0.59), and millet (adjusted HR, 0.38; 95% CI, 0.30-0.48), showed significant associations with a reduced risk of hypertension. The association between whole grain intake and new-onset hypertension was stronger in individuals with older age (P for interaction < 0.001) and higher BMI (P for interaction < 0.001). CONCLUSION: Higher consumption of whole grains was significantly associated with a lower risk of new-onset hypertension. This study provides further evidence supporting the importance of increasing whole grain intake for hypertension prevention among Chinese adults.