Abortive HIV infection mediates CD4 T cell depletion and inflammation in human lymphoid tissue.

The mechanism by which CD4 T cells are depleted in HIV-infected hosts remains poorly understood. In ex vivo cultures of human tonsil tissue, CD4 T cells undergo a pronounced cytopathic response following HIV infection. Strikingly, >95% of these dying cells are not productively infected but instead correspond to bystander cells. We now show that the death of these "bystander" cells involves abortive HIV infection. Inhibitors blocking HIV entry or early steps of reverse transcription prevent CD4 T cell death while inhibition of later events in the viral life cycle does not. We demonstrate that the nonpermissive state exhibited by the majority of resting CD4 tonsil T cells leads to accumulation of incomplete reverse transcripts. These cytoplasmic nucleic acids activate a host defense program that elicits a coordinated proapoptotic and proinflammatory response involving caspase-3 and caspase-1 activation. While this response likely evolved to protect the host, it centrally contributes to the immunopathogenic effects of HIV.

Distinguishable neural circuit mechanisms associated with the clinical efficacy of rTMS in aMCI patients.

Repetitive transcranial magnetic stimulation is used in early-stage Alzheimer's disease to slow progression, but heterogeneity in response results in different treatment outcomes. The mechanisms underlying this heterogeneity are unclear. This study used resting-state neuroimaging to investigate the variability in episodic memory improvement from angular gyrus repetitive transcranial magnetic stimulation and tracked the neural circuits involved. Thirty-four amnestic mild cognitive impairment patients underwent angular gyrus repetitive transcranial magnetic stimulation (4 weeks, 20 Hz, 100% resting motor threshold) and were divided into high-response and low-response groups based on minimal clinically important differences in auditory verbal learning test scores. Baseline and pre/post-treatment neural circuit activities were compared. Results indicated that the orbital middle frontal gyrus in the orbitofrontal cortex network and the precuneus in the default mode network had higher local activity in the low-response group. After treatment, changes in local and remote connectivity within brain regions of the orbitofrontal cortex, default mode network, visual network, and sensorimotor network showed opposite trends and were related to treatment effects. This suggests that the activity states of brain regions within the orbitofrontal cortex and default mode network could serve as imaging markers for early cognitive compensation in amnestic mild cognitive impairment patients and predict the aftereffects of repetitive transcranial magnetic stimulation response.

Nimodipine Protects Vascular and Cognitive Function in an Animal Model of Cerebral Small Vessel Disease.

BACKGROUND: Cerebral small vessel disease is a common cause of vascular cognitive impairment and dementia. There is an urgent need for preventative treatments for vascular cognitive impairment and dementia, and reducing vascular dysfunction may provide a therapeutic route. Here, we investigate whether the chronic administration of nimodipine, a central nervous system-selective dihydropyridine calcium channel blocking agent, protects vascular, metabolic, and cognitive function in an animal model of cerebral small vessel disease, the spontaneously hypertensive stroke-prone rat. METHODS: Male spontaneously hypertensive stroke-prone rats were randomly allocated to receive either a placebo (n=24) or nimodipine (n=24) diet between 3 and 6 months of age. Animals were examined daily for any neurological deficits, and vascular function was assessed in terms of neurovascular and neurometabolic coupling at 3 and 6 months of age, and cerebrovascular reactivity at 6 months of age. Cognitive function was evaluated using the novel object recognition test at 6 months of age. RESULTS: Six untreated control animals were terminated prematurely due to strokes, including one due to seizure, but no treated animals experienced strokes and so had a higher survival (P=0.0088). Vascular function was significantly impaired with disease progression, but nimodipine treatment partially preserved neurovascular coupling and neurometabolic coupling, indicated by larger (P<0.001) and more prompt responses (P<0.01), and less habituation upon repeated stimulation (P<0.01). Also, animals treated with nimodipine showed greater cerebrovascular reactivity, indicated by larger dilation of arterioles (P=0.015) and an increase in blood flow velocity (P=0.001). This protection of vascular and metabolic function achieved by nimodipine treatment was associated with better cognitive function (P<0.001) in the treated animals. CONCLUSIONS: Chronic treatment with nimodipine protects from strokes, and vascular and cognitive deficits in spontaneously hypertensive stroke-prone rat. Nimodipine may provide an effective preventive treatment for stroke and cognitive decline in cerebral small vessel disease.

Identification of novel single nucleotide variants in the drug resistance mechanism of Mycobacterium tuberculosis isolates by whole-genome analysis.

BACKGROUND: Tuberculosis (TB) represents a major global health challenge. Drug resistance in Mycobacterium tuberculosis (MTB) poses a substantial obstacle to effective TB treatment. Identifying genomic mutations in MTB isolates holds promise for unraveling the underlying mechanisms of drug resistance in this bacterium. METHODS: In this study, we investigated the roles of single nucleotide variants (SNVs) in MTB isolates resistant to four antibiotics (moxifloxacin, ofloxacin, amikacin, and capreomycin) through whole-genome analysis. We identified the drug-resistance-associated SNVs by comparing the genomes of MTB isolates with reference genomes using the MuMmer4 tool. RESULTS: We observed a strikingly high proportion (94.2%) of MTB isolates resistant to ofloxacin, underscoring the current prevalence of drug resistance in MTB. An average of 3529 SNVs were detected in a single ofloxacin-resistant isolate, indicating a mutation rate of approximately 0.08% under the selective pressure of ofloxacin exposure. We identified a set of 60 SNVs associated with extensively drug-resistant tuberculosis (XDR-TB), among which 42 SNVs were non-synonymous mutations located in the coding regions of nine key genes (ctpI, desA3, mce1R, moeB1, ndhA, PE_PGRS4, PPE18, rpsA, secF). Protein structure modeling revealed that SNVs of three genes (PE_PGRS4, desA3, secF) are close to the critical catalytic active sites in the three-dimensional structure of the coding proteins. CONCLUSION: This comprehensive study elucidates novel resistance mechanisms in MTB against antibiotics, paving the way for future design and development of anti-tuberculosis drugs.

A TCR mimic CAR T cell specific for NDC80 is broadly reactive with solid tumors and hematologic malignancies.

Target identification for chimeric antigen receptor (CAR) T-cell therapies remains challenging due to the limited repertoire of tumor-specific surface proteins. Intracellular proteins presented in the context of cell surface HLA provide a wide pool of potential antigens targetable through T-cell receptor mimic antibodies. Mass spectrometry (MS) of HLA ligands from 8 hematologic and nonhematologic cancer cell lines identified a shared, non-immunogenic, HLA-A*02-restricted ligand (ALNEQIARL) derived from the kinetochore-associated NDC80 gene. CAR T cells directed against the ALNEQIARL:HLA-A*02 complex exhibited high sensitivity and specificity for recognition and killing of multiple cancer types, especially those of hematologic origin, and were efficacious in mouse models against a human leukemia and a solid tumor. In contrast, no toxicities toward resting or activated healthy leukocytes as well as hematopoietic stem cells were observed. This shows how MS can inform the design of broadly reactive therapeutic T-cell receptor mimic CAR T-cell therapies that can target multiple cancer types currently not druggable by small molecules, conventional CAR T cells, T cells, or antibodies.

Protein function annotation and virulence factor identification of Klebsiella pneumoniae genome by multiple machine learning models.

Klebsiella pneumoniae is a type of Gram-negative bacterium which can cause a range of infections in human. In recent years, an increasing number of strains of K. pneumoniae resistant to multiple antibiotics have emerged, posing a significant threat to public health. The protein function of this bacterium is not well known, thus a systematic investigation of K. pneumoniae proteome is in urgent need. In this study, the protein functions of this bacteria were re-annotated, and their function groups were analyzed. Moreover, three machine learning models were built to identify novel virulence factors. Results showed that the functions of 16 uncharacterized proteins were first annotated by sequence alignment. In addition, K. pneumoniae proteins share a high proportion of homology with Haemophilus influenzae and a low homology proportion with Chlamydia pneumoniae. By sequence analysis, 10 proteins were identified as potential drug targets for this bacterium. Our model achieved a high accuracy of 0.901 in the benchmark dataset. By applying our models to K. pneumoniae, we identified 39 virulence factors in this pathogen. Our findings could provide novel clues for the treatment of K. pneumoniae infection.

Transcriptomic analysis reveals molecular characterization and immune landscape of PANoptosis-related genes in atherosclerosis.

BACKGROUND: Atherosclerosis is a chronic inflammatory disease characterized by abnormal lipid deposition in the arteries. Programmed cell death is involved in the inflammatory response of atherosclerosis, but PANoptosis, as a new form of programmed cell death, is still unclear in atherosclerosis. This study explored the key PANoptosis-related genes involved in atherosclerosis and their potential mechanisms through bioinformatics analysis. METHODS: We evaluated differentially expressed genes (DEGs) and immune infiltration landscape in atherosclerosis using microarray datasets and bioinformatics analysis. By intersecting PANoptosis-related genes from the GeneCards database with DEGs, we obtained a set of PANoptosis-related genes in atherosclerosis (PANoDEGs). Functional enrichment analysis of PANoDEGs was performed and protein-protein interaction (PPI) network of PANoDEGs was established. The machine learning algorithms were used to identify the key PANoDEGs closely linked to atherosclerosis. Receiver operating characteristic (ROC) analysis was used to assess the diagnostic potency of key PANoDEGs. CIBERSORT was used to analyze the immune infiltration patterns in atherosclerosis, and the Spearman method was used to study the relationship between key PANoDEGs and immune infiltration abundance. The single gene enrichment analysis of key PANoDEGs was investigated by GSEA. The transcription factors and target miRNAs of key PANoDEGs were predicted by Cytoscape and online database, respectively. The expression of key PANoDEGs was validated through animal and cell experiments. RESULTS: PANoDEGs in atherosclerosis were significantly enriched in apoptotic process, pyroptosis, necroptosis, cytosolic DNA-sensing pathway, NOD-like receptor signaling pathway, lipid and atherosclerosis. Four key PANoDEGs (ZBP1, SNHG6, DNM1L, and AIM2) were found to be closely related to atherosclerosis. The ROC curve analysis demonstrated that the key PANoDEGs had a strong diagnostic potential in distinguishing atherosclerotic samples from control samples. Immune cell infiltration analysis revealed that the proportion of initial B cells, plasma cells, CD4 memory resting T cells, and M1 macrophages was significantly higher in atherosclerotic tissues compared to normal tissues. Spearman analysis showed that key PANoDEGs showed strong correlations with immune cells such as T cells, macrophages, plasma cells, and mast cells. The regulatory networks of the four key PANoDEGs were established. The expression of key PANoDEGs was verified in further cell and animal experiments. CONCLUSIONS: This study evaluated the expression changes of PANoptosis-related genes in atherosclerosis, providing a reference direction for the study of PANoptosis in atherosclerosis and offering potential new avenues for further understanding the pathogenesis and treatment strategies of atherosclerosis.

High efficiency of biosurfactants in stabilizing oil micro-droplets within the aging time scale of milliseconds: a microfluidic study.

Rapid adsorption of surfactants onto a freshly formed interface is vital for emulsification because emulsification is a competitive process occurring between the very short time span of interface formation and surfactant mass transport. The biosurfactant surfactin has been previously reported to reach adsorption equilibrium at the hydrophobic/hydrophilic interface within hundreds of milliseconds and rapidly reduce the interfacial tension compared to chemically synthesized surfactants. According to a prior study, surfactin is expected to exhibit good performance in stabilizing micro-droplets of oil within the aging time scale of milliseconds. Herein, the stabilities of micro-droplets of n-hexadecane in the presence of a biosurfactant, surfactin (C15-SFT), and a chemically synthesized surfactant, sodium cetyl benzene sulfonate (8-SCBS), were investigated using a microfluidic method. The coalescence frequency of micro-droplets, the evolution of micro-droplet size, and the coalescence time of micro-droplets were evaluated. The results indicated that C15-SFT exhibited superiority over 8-SCBS in stabilizing the micro-droplets of n-hexadecane. Biosurfactant C15-SFT effectively reduced the fusion probability between oil droplets and elongated the coalescence time compared to 8-SCBS, and these phenomena were obvious at a shorter aging time (150 ms) and lower surfactant concentration (0.1 × critical micelle concentration). The stabilities of micro-droplets increased with aging time and the bulk concentration of surfactants. Stable micro-droplets of n-hexadecane were formed in 1 × 10-4 mol L-1 C15-SFT solution at 600 ms aging time, and the bulk concentration was 1 × 10-3 mol L-1 in the case of 8-SCBS. The micro-droplets rarely coalesced in the presence of 1 × 10-4 mol L-1 C15-SFT after 600 ms aging time, but the micro-droplets in 1 × 10-4 mol L-1 8-SCBS coalesced frequently in the midstream and downstream of the coalescence chamber, and big droplets were dominant in the emulsion. The coalescence time of micro-droplets stabilized by C15-SFT was obviously longer than that of those stabilized by 8-SCBS under the same condition, indicating that the interfacial film formed by C15-SFT has much strength to resist coalescence during collisions. This work is helpful for understanding the activity of lipopeptides in the very short early stage of the emulsification process, laying the foundation for biosurfactant research in the fields of enhanced oil recovery, bioremediation of contaminated water or soil, etc.

Associations between the multitrajectory neuroplasticity of neuronavigated rTMS-mediated angular gyrus networks and brain gene expression in AD spectrum patients with sleep disorders.

INTRODUCTION: The multifactorial influence of repetitive transcranial magnetic stimulation (rTMS) on neuroplasticity in neural networks is associated with improvements in cognitive dysfunction and sleep disorders. The mechanisms of rTMS and the transcriptional-neuronal correlation in Alzheimer's disease (AD) patients with sleep disorders have not been fully elucidated. METHODS: Forty-six elderly participants with cognitive impairment (23 patients with low sleep quality and 23 patients with high sleep quality) underwent 4-week periods of neuronavigated rTMS of the angular gyrus and neuroimaging tests, and gene expression data for six post mortem brains were collected from another database. Transcription-neuroimaging association analysis was used to evaluate the effects on cognitive dysfunction and the underlying biological mechanisms involved. RESULTS: Distinct variable neuroplasticity in the anterior and posterior angular gyrus networks was detected in the low sleep quality group. These interactions were associated with multiple gene pathways, and the comprehensive effects were associated with improvements in episodic memory. DISCUSSION: Multitrajectory neuroplasticity is associated with complex biological mechanisms in AD-spectrum patients with sleep disorders. HIGHLIGHTS: This was the first transcription-neuroimaging study to demonstrate that multitrajectory neuroplasticity in neural circuits was induced via neuronavigated rTMS, which was associated with complex gene expression in AD-spectrum patients with sleep disorders. The interactions between sleep quality and neuronavigated rTMS were coupled with multiple gene pathways and improvements in episodic memory. The present strategy for integrating neuroimaging, rTMS intervention, and genetic data provide a new approach to comprehending the biological mechanisms involved in AD.

Tissue Hypoxia and Associated Innate Immune Factors in Experimental Autoimmune Optic Neuritis.

Visual loss in acute optic neuritis is typically attributed to axonal conduction block due to inflammatory demyelination, but the mechanisms remain unclear. Recent research has highlighted tissue hypoxia as an important cause of neurological deficits and tissue damage in both multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE) and, here, we examine whether the optic nerves are hypoxic in experimental optic neuritis induced in Dark Agouti rats. At both the first and second peaks of disease expression, inflamed optic nerves labelled significantly for tissue hypoxia (namely, positive for hypoxia inducible factor-1α (HIF1α) and intravenously administered pimonidazole). Acutely inflamed nerves were also labelled significantly for innate markers of oxidative and nitrative stress and damage, including superoxide, nitric oxide and 3-nitrotyrosine. The density and diameter of capillaries were also increased. We conclude that in acute optic neuritis, the optic nerves are hypoxic and come under oxidative and nitrative stress and damage. Tissue hypoxia can cause mitochondrial failure and thus explains visual loss due to axonal conduction block. Tissue hypoxia can also induce a damaging oxidative and nitrative environment. The findings indicate that treatment to prevent tissue hypoxia in acute optic neuritis may help to restore vision and protect from damaging reactive oxygen and nitrogen species.

Efficient utilization of coral waste for internal curing material to prepare eco-friendly marine geopolymer concrete.

To address shortages in construction materials for island engineering, tackle the accumulation of solid waste, and inhibit the shrinkage of geopolymers, coral waste was utilized as the internal curing material to prepare high-performance marine geopolymer concrete (MGC) with seawater, sea-sand, and normal limestone aggregate (LsA). The coral coarse aggregate (CorA) used in this investigation has a total porosity ranging from 50% to 58.3% with internal pore diameters spanning 50-400 µm. The water desorption of CorA followed a two-stage pattern within a relative humidity (RH) range of 75%-85%, becoming nonlinear above 90% RH, which released about 85% of its moisture within 200 h at 97% RH, demonstrating potential for internal curing. Adding a small amount of CorA to MGC increased slump and setting time by providing internal curing water. However, as CorA content exceeded 30%, the slump significantly decreased due to reduced mixing water and elevated activator concentration, while the initial setting time slightly decreased. Furthermore, the inclusion of saturated CorA in MGC significantly reduced autogenous shrinkage, with higher CorA contents (exceeding 30%) leading to slight expansion in the early stages and nearly eliminating shrinkage at contents above 40%. The greater drying shrinkage in geopolymer systems compared to ordinary Portland cement is due to capillary pressure compressing the product framework, converting larger gel pores into smaller ones. Additionally, the layered calcium aluminosilicate hydrate (C-A-S-H) gel exhibits more pronounced creep characteristics under low internal humidity conditions. The higher CorA content in MGC promoted the formation of hybrid C, N-A-S-H gel and hydrotalcite-like phases, and reduced carbonation issues. The interfacial transition zone (ITZ) between CorA and the geopolymer matrix formed a robust mechanical interlock, enhancing tensile strength and minimizing shrinkage-induced cracks. Based on overall performance and marine material utilization, an optimal substitution rate of CorA between 40% and 50% is recommended.

Dynamic monitoring of aboveground biomass in inner Mongolia grasslands over the past 23 Years using GEE and analysis of its driving forces.

Aboveground biomass (AGB) in grasslands directly reflects the net primary productivity, making it a sensitive indicator of grassland resource quality and ecological degradation. Accurately estimating AGB over large regions to reveal long-term AGB evolution trends remains a formidable challenge. In this study, we divided Inner Mongolia Autonomous Region (IMAR) grasslands into three study regions based on their spatial distribution of grassland types. We combined remote sensing data with ground-based sample data collected over the past 19 years from 6114 field plots using the Google Earth Engine platform. We constructed random forest (RF) and traditional regression AGB inversion models for each region and selected the best-performing model through accuracy assessment to estimate IMAR grassland AGB for the period 2000-2022. We also examined the trends in AGB changes and identified the driving forces affecting IMAR grasslands through the application of Theil-Sen estimation, Mann-Kendall trend analysis, and the Geodetector model. The main findings are as follows: (1) Compared with the univariate parametric traditional regression model, the AGB monitoring accuracy of the multivariate non-parametric RF model in the three study regions increased by 5.94%, 5.08% and 19.14%, respectively. (2) The average AGB per unit area of IMAR grasslands from 2000 to 2022 was 731.41 kg/hm2, with alpine meadow having the highest average AGB (1271.70 kg/hm2) and temperate grassland desertification having the lowest (469.06 kg/hm2). IMAR grasslands exhibited an overall increasing trend in AGB over the past 23 years (6.01 kg/hm2•yr), with the increasing trend covering 83.52% of the grassland area and the decreasing trend covering 16.48%. (3) Spatially, IMAR grassland AGB showed a gradual decline from northeast to southwest and exhibited an increasing trend with increasing longitude (45.423 kg/hm2 per degree) and latitude (71.9 kg/hm2 per degree). (4) Meteorological factors were the most significant factors affecting IMAR grassland AGB, with precipitation (five-year average q value of 0.61) being the most prominent. In the western part of IMAR, where precipitation is consistently limited throughout the year, the primary drivers of influence were human activities, with particular emphasis on the number of livestock (with a five-year average q value of 0.44). It is evident that reducing human activity disturbance and pressure in fragile grassland areas or implementing near-natural restoration measures will be beneficial for the sustainable development of grassland ecosystems. The results of this research hold substantial reference importance for the protection and restoration of grasslands, the supervision and administration of grassland resources, as well as the development of policies related to grassland management.

The Physical Mechanism of Linear and Nonlinear Optical Properties of Nanographene-Induced Chiral Inversion.

Based on density functional theory (DFT) and wave function analysis, the ultraviolet and visible spectrophotometry (UV-Vis) spectra and Raman spectra of 1-meso and 1-rac obtained by the chiral separation of chiral nanographenes are theoretically investigated. The electron excitation properties of 1-meso and 1-rac are studied by means of transition density matrix (TDM) and charge density difference (CDD) diagrams. The intermolecular interaction is discussed based on an independent gradient model based on Hirshfeld partition (IGMH). The interaction of 1-meso and 1-rac with the external environment is studied using the electrostatic potential (ESP), and the electron delocalization degree of 1-meso and 1-rac is studied based on the magnetically induced current under the external magnetic field. Through the chiral separation of 1-rac, two enantiomers, 1-(P, P) and 1-(M, M), were obtained. The electrical-magnetic interaction of the molecule is revealed by analyzing the electron circular dichroism (ECD) spectra of 1-meso, 1-(P, P) and 1-(M, M), the transition electric dipole moment (TEDM) and the transition magnetic dipole moment (TMDM). It is found that 1-(P, P) and 1-(M, M) have opposite chiral properties due to the inversion of the structure.

Preparation and Application of Co-Doped Zinc Oxide: A Review.

Due to a wide band gap and large exciton binding energy, zinc oxide (ZnO) is currently receiving much attention in various areas, and can be prepared in various forms including nanorods, nanowires, nanoflowers, and so on. The reliability of ZnO produced by a single dopant is unstable, which in turn promotes the development of co-doping techniques. Co-doping is a very promising technique to effectively modulate the optical, electrical, magnetic, and photocatalytic properties of ZnO, as well as the ability to form various structures. In this paper, the important advances in co-doped ZnO nanomaterials are summarized, as well as the preparation of co-doped ZnO nanomaterials by using different methods, including hydrothermal, solvothermal, sol-gel, and acoustic chemistry. In addition, the wide range of applications of co-doped ZnO nanomaterials in photocatalysis, solar cells, gas sensors, and biomedicine are discussed. Finally, the challenges and future prospects in the field of co-doped ZnO nanomaterials are also elucidated.

View-Driven Multi-View Clustering via Contrastive Double-Learning.

Multi-view clustering requires simultaneous attention to both consistency and the diversity of information between views. Deep learning techniques have shown impressive abilities to learn complex features when working with extensive datasets; however, existing deep multi-view clustering methods often focus only on either consistency information or diversity information, making it difficult to balance both aspects. Therefore, this paper proposes a view-driven multi-view clustering using the contrastive double-learning method (VMC-CD), aiming to generate better clustering results. This method first adopts a view-driven approach to consider information from other views to encourage diversity, thus guiding feature learning. Additionally, it presents the idea of dual contrastive learning to enhance the alignment of views at both the clustering and feature levels. The VMC-CD method's superiority over various cutting-edge methods is substantiated by experimental findings across three datasets, affirming its effectiveness.

Identifying Network Biomarkers in Early Diagnosis of Hepatocellular Carcinoma via miRNA-Gene Interaction Network Analysis.

BACKGROUND: Hepatocellular carcinoma (HCC) is a highly heterogeneous cancer at the histological level. Despite the emergence of new biological technology, advanced-stage HCC remains largely incurable. The prediction of a cancer biomarker is a key problem for targeted therapy in the disease. METHODS: We performed a miRNA-gene integrated analysis to identify differentially expressed miRNAs (DEMs) and genes (DEGs) of HCC. The DEM-DEG interaction network was constructed and analyzed. Gene ontology enrichment and survival analyses were also performed in this study. RESULTS: By the analysis of healthy and tumor samples, we found that 94 DEGs and 25 DEMs were significantly differentially expressed in different datasets. Gene ontology enrichment analysis showed that these 94 DEGs were significantly enriched in the term "Liver" with a statistical p-value of 1.71 × 10-26. Function enrichment analysis indicated that these genes were significantly overrepresented in the term "monocarboxylic acid metabolic process" with a p-value = 2.94 × 10-18. Two sets (fourteen genes and five miRNAs) were screened by a miRNA-gene integrated analysis of their interaction network. The statistical analysis of these molecules showed that five genes (CLEC4G, GLS2, H2AFZ, STMN1, TUBA1B) and two miRNAs (hsa-miR-326 and has-miR-331-5p) have significant effects on the survival prognosis of patients. CONCLUSION: We believe that our study could provide critical clinical biomarkers for the targeted therapy of HCC.

CRISPR/Cas9 and Agrobacterium tumefaciens virulence proteins synergistically increase efficiency of precise genome editing via homology directed repair in plants.

CRISPR/Cas9 genome editing and Agrobacterium tumefaciens-mediated genetic transformation are widely-used plant biotechnology tools derived from bacterial immunity-related systems, each involving DNA modification. The Cas9 endonuclease introduces DNA double-strand breaks (DSBs), and the A. tumefaciens T-DNA is released by the VirD2 endonuclease assisted by VirDl and attached by VirE2, transferred to the plant nucleus and integrated into the genome. Here, we explored the potential for synergy between the two systems and found that Cas9 and three virulence (Vir) proteins achieve precise genome editing via the homology directed repair (HDR) pathway in tobacco and rice plants. Compared with Cas9T (Cas9, VirD1, VirE2) and CvD (Cas9-VirD2) systems, the HDR frequencies of a foreign GFPm gene in the CvDT system (Cas9-VirD2, VirD1, VirE2) increased 52-fold and 22-fold, respectively. Further optimization of the CvDT process with a donor linker (CvDTL) achieved a remarkable increase in the efficiency of HDR-mediated genome editing. Additionally, the HDR efficiency of the three rice endogenous genes ACETOLACTATE SYNTHASE (ALS), PHYTOENE DESATURASE (PDS), and NITROGEN TRANSPORTER 1.1 B (NRT1.1B) increased 24-, 32- and 16-fold, respectively, in the CvDTL system, compared with corresponding Cas9TL (Cas9T process with a donor linker). Our results suggest that collaboration between CRISPR/Cas9 and Agrobacterium-mediated genetic transformation can make great progress towards highly efficient and precise genome editing via the HDR pathway.

Relationship Between Stress Modulated Metallicity and Plasmon in Graphene Nanoribbons.

Nanoscale quantum plasmon is an important technology that restricts the application of optics, electricity, and graphene photoelectric devices. Establishing a structure-effect relationship between the structure of graphene nanoribbons (GNRs) under stress regulation and the properties of plasmons is a key scientific issue for promoting the application of plasmons in micro-nano photoelectric devices. In this study, zigzag graphene nanoribbon (Z-GNR) and armchair graphene nanoribbon (A-GNR) models of specific widths were constructed, and density functional theory (DFT) was used to study their lattice structure, energy band, absorption spectrum, and plasmon effects under different stresses. The results showed that the Z-GNR band gap decreased with increasing stress, and the A-GNR band gap changed periodically with increasing stress. The plasmon effects of the A-GNRs and Z-GNRs appeared in the visible region, whereas the absorption spectrum showed a redshift trend, indicating the range of the plasmon spectrum also underwent significant changes. This study provides a theoretical basis for the application of graphene nanoribbons in the field of optoelectronics under strain-engineering conditions.

ZIP Genes Are Involved in the Retransfer of Zinc Ions during the Senescence of Zinc-Deficient Rice Leaves.

Rice lacks sufficient amounts of zinc despite its vitality for human health. Leaf senescence enables redistribution of nutrients to other organs, yet Zn retransfer during deficiency is often overlooked. In this hydroponic experiment, we studied the effect of Zn deficiency on rice seedlings, focusing on the fourth leaf under control and deficient conditions. Growth phenotype analysis showed that the growth of rice nodal roots was inhibited in Zn deficiency, and the fourth leaf exhibited accelerated senescence and increased Zn ion transfer. Analyzing differentially expressed genes showed that Zn deficiency regulates more ZIP family genes involved in Zn ion retransfer. OsZIP3 upregulation under Zn-deficient conditions may not be induced by Zn deficiency, whereas OsZIP4 is only induced during Zn deficiency. Gene ontology enrichment analysis showed that Zn-deficient leaves mobilized more biological pathways (BPs) during aging, and the enrichment function differed from that of normal aging leaves. The most apparent "zinc ion transport" BP was stronger than that of normal senescence, possibly due to Zn-deficient leaves mobilizing large amounts of BP related to lipid metabolism during senescence. These results provide a basis for further functional analyses of genes and the study of trace element transfer during rice leaf senescence.

Effects of elevated nitrogen fertilizer on the multi-level structure and thermal properties of rice starch granules and their relationship with chalkiness traits.

BACKGROUND: Chalkiness in rice reduces its market value and affects consumer acceptance. Research on the mechanism of chalkiness formation has focused primarily on the activity of key enzymes of carbon metabolism and starch accumulation. The relationship between the formation of chalkiness induced by N fertilizer and rice starch's multi-level structure and thermal properties still needs to be fully elucidated. RESULTS: In this study, the rates of chalky grains and degree of chalkiness decreased with the increase in N fertilizer dosage. This was attributed to an increased proportion of short chains, ordered structure carbon chains, small starch granules, and branched starches, and a higher degree of crystallinity and ΔHg in protein, and a decreased proportion of amylose, large starch granules, and weighted average diameter of starch granule surface area and volume. Application of N fertilizer promoted an increased proportion of short-branched chain amylopectin to develop a more ordered carbohydrate structure and crystalline lamella. These effects enhanced the normal development and compactness of starch granules in grains, and improved their arrangement morphology, thereby reducing the chalkiness in rice. CONCLUSION: These changes in starch multi-level structure and protein improve the physicochemical characteristics of starch and enhance the fullness, crystallinity and compactness of starch granules, while synergistically increasing the regularity and homogeneity of starch granules and thus optimizing the stacking pattern of starch granules, leading to a reduction in rice chalkiness under nitrogen fertilization and thus improving the appearance of rice. © 2023 Society of Chemical Industry.