Graph-Based Pangenome of Actinidia chinensis Reveals Structural Variations Mediating Fruit Degreening.

Fruit ripening is associated with the degreening process (loss of chlorophyll) that occurs in most fruit species. Kiwifruit is one of the special species whose fruits may maintain green flesh by accumulating a large amount of chlorophyll even after ripening. However, little is known about the genetic variations related to the fruit degreening process. Here, a graph-based kiwifruit pangenome by analyzing 14 chromosome-scale haplotype-resolved genome assemblies from seven representative cultivars or lines in Actinidia chinensis is built. A total of 49,770 non-redundant gene families are identified, with core genes constituting 46.6%, and dispensable genes constituting 53.4%. A total of 84,591 non-redundant structural variations (SVs) are identified. The pangenome graph integrating both reference genome sequences and variant information facilitates the identification of SVs related to fruit color. The SV in the promoter of the AcBCM gene determines its high expression in the late developmental stage of fruits, which causes chlorophyll accumulation in the green-flesh fruits by post-translationally regulating AcSGR2, a key enzyme of chlorophyll catabolism. Taken together, a high-quality pangenome is constructed, unraveled numerous genetic variations, and identified a novel SV mediating fruit coloration and fruit quality, providing valuable information for further investigating genome evolution and domestication, QTL genes function, and genomics-assisted breeding.

Dipole Moments Regulation of Biphosphonic Acid Molecules for Self-assembled Monolayers Boosts the Efficiency of Organic Solar Cells Exceeding 19.7.

PEDOT: PSS has been widely used as a hole extraction layer (HEL) in organic solar cells (OSCs). However, their acidic nature can potentially corrode the indium tin oxide (ITO) electrode over time, leading to adverse effects on the longevity of the OSCs. Herein, we have developed a class of biphosphonic acid molecules with tunable dipole moments for self-assembled monolayers (SAMs), namely, 3-BPIC(i), 3-BPIC, and 3-BPIC-F, which exhibit an increasing dipole moment in sequence. Compared to centrosymmetric 3-BPIC(i), the axisymmetric 3-BPIC and 3-BPIC-F exhibit higher adsorption energies (Eads) with ITO, shorter interface spacing, more uniform coverage on ITO surface, and better interfacial compatibility with the active layer. Thanks to the incorporation of fluorine atoms, 3-BPIC-F exhibits a deeper highest occupied molecular orbital (HOMO) energy level and a larger dipole moment compared to 3-BPIC, resulting in an enlarged work function (WF) for the ITO/3-BPIC-F substrate. These advantages of 3-BPIC-F could not only improve hole extraction within the device but also lower the interfacial impedance and reduce nonradiative recombination at the interface. As a result, the OSCs using SAM based on 3-BPIC-F obtained a record high efficiency of 19.71%, which is higher than that achieved from the cells based on 3-BPIC(i) (13.54%) and 3-BPIC (19.34%). Importantly, 3-BPIC-F-based OSCs exhibit significantly enhanced stability compared to that utilizing PEDOT:PSS as HEL. Our work offers guidance for the future design of functional molecules for SAMs to realize even higher performance in organic solar cells.

LncRNA Gm15834 Aggravates Cardiac Hypertrophy by Interacting with Sam68 and Activating NF-κB Mediated Inflammation.

BACKGROUND: Cardiac hypertrophy is the common pathological process of multiple cardiovascular diseases. However, the molecular mechanisms of cardiac hypertrophy are unclear. Long non-coding RNA (lncRNA), a newly discovered type of transcript that has been demonstrated to function as crucial regulators in the development of cardiovascular diseases. This study revealed a novel regulatory pathway of lncRNA in cardiac hypertrophy. METHODS: The cardiac hypertrophy models were established by transverse aortic constriction (TAC) in mice and angiotensin II (Ang II) in HL-1 cardiomyocytes. Adeno-associated virus 9 (AAV9) in vivo and lncRNA Gm15834 and shRNA plasmids in vitro were used to overexpress and knock down lncRNA Gm15834. The myocardial tissue structure, cardiomyocyte area, cardiac function, protein expressions, and binding of lncRNA Gm15834 and Src-associated substrate during mitosis of 68 KDa (Sam68) were detected by hematoxylin and eosin (HE) staining, immunofluorescence staining, echocardiography, western blot and RNA immunoprecipitation (RIP), respectively. RESULTS: In cardiac hypertrophy models, inhibiting lncRNA Gm15834 could decrease Sam68 expression and nuclear factor kappa-B (NF-κB) mediated inflammatory activities in vivo and in vitro, but overexpressing lncRNA Gm15834 showed the opposite results. RIP experiments validated the binding activities between lncRNA Gm15834 and Sam68. Overexpression of Sam68 could counteract the anti-hypertrophy effects of lncRNA Gm15834 knockdown. Meanwhile, in vivo inhibition of lncRNA Gm15834 could inhibit Sam68 expression, reduce NF-κB mediated inflammatory activity and attenuate cardiac hypertrophy. CONCLUSION: Our study revealed a novel regulatory axis of cardiac hypertrophy, which comprised lncRNA Gm15834/Sam68/NF-κB/inflammation, shedding a new light for identifying therapy target of cardiac hypertrophy in clinic.

Copper isotopes track the Neoproterozoic oxidation of cratonic mantle roots.

The oxygen fugacity (fO2) of the lower cratonic lithosphere influences diamond formation, melting mechanisms, and lithospheric evolution, but its redox evolution over time is unclear. We apply Cu isotopes (δ65Cu) of ~ 1.4 Ga lamproites and < 0.59 Ga silica-undersaturated alkaline rocks from the lithosphere-asthenosphere boundary (LAB) of the North Atlantic Craton to characterize fO2 and volatile speciation in their sources. The lamproites' low δ65Cu (-0.19 to -0.12‰) show that the LAB was metal-saturated with CH4 + H2O as the dominant volatiles during the Mesoproterozoic. The mantle-like δ65Cu of the < 0.59 Ga alkaline rocks (0.03 to 0.15‰) indicate that the LAB was more oxidized, stabilizing CO2 + H2O and destabilizing metals. The Neoproterozoic oxidation resulted in an increase of at least 2.5 log units in fO2 at the LAB. Combined with previously reported high fO2 in peridotites from the Slave, Kaapvaal, and Siberia cratonic roots, this oxidation might occur in cratonic roots globally.

Stability and integrity of self-assembled bovine parvovirus virus­like particles (BPV­VLPs) of VP2 and combination of VP1VP2 assisted by baculovirus-insect cell expression: a potential logistical platform for vaccine deployment.

BACKGROUND: Bovine parvovirus (BPV) is an autonomous DNA virus with a smaller molecular size and subtle differences in its structural proteins, unlike other animal parvoviruses. More importantly, this virus has the potential to produce visible to silent economic catastrophes in the livestock business, despite receiving very little attention. Parvoviral virus-like particles (VLPs) as vaccines and as logistical platforms for vaccine deployment are well studied. However, no single experimental report on the role of VP1 in the assembly and stability of BPV-VLPs is available. Furthermore, the self-assembly, integrity and stability of the VLPs of recombinant BPV VP2 in comparison to VP1 VP2 Cap proteins using any expression method has not been studied previously. In this study, we experimentally evaluated the self-assembling ability with which BPV virus-like particles (VLPs) could be synthesized from a single structural protein (VP2) and by integrating both VP2 and VP1 amino acid sequences. METHODS: In silico and experimental cloning methods were carried out. His-tagged and without-His-tag VP2 and V1VP2-encoding amino acid sequences were cloned and inserted into pFastbacdual, and insect cell-generated recombinant protein was evaluated by SDS‒PAGE and western blot. Period of infectivity and expression level were determined by IFA. The integrity and stability of the BPV VLPs were evaluated by transmission electron microscopy. The secondary structure of the BPV VLPs from both VP2 and V1VP2 was analyzed by circular dichroism. RESULTS: Our findings show that VP2 alone was equally expressed and purified into detectable proteins, and the stability at different temperatures and pH values was not appreciably different between the two kinds of VLPs. Furthermore, BPV-VP2 VLPs were praised for their greater purity and integrity than BPV-VP1VP2 VLPs, as indicated by SDS‒PAGE. Therefore, our research demonstrates that the function of VP1 has no bearing on the stability or integrity of BPV-VLPs. CONCLUSIONS: In summary, incredible physiochemically stable BPV VP2-derived VLPs have been found to be promising candidates for the development of multivalent vaccines and immunodiagnostic kits against enteric viruses and to carry heterogeneous epitopes for various economically important livestock diseases.

Feruloyl Glyceride Mitigates Tomato Postharvest Rot by Inhibiting Penicillium expansum Spore Germination and Enhancing Suberin Accumulation.

Postharvest rot, caused by Penicillium expansum, in tomatoes poses significant economic and health risks. Traditional control methods, such as the use of fungicides, raise concerns about pathogen resistance, food safety, and environmental impact. In search of sustainable alternatives, plant secondary metabolites, particularly phenolic compounds and their derivatives, have emerged as promising natural antimicrobials. Among these, feruloyl glyceride (FG), a water-soluble derivative of ferulic acid, stands out due to its antioxidant properties, antibacterial properties, and improved solubility. In this study, we provide evidence demonstrating FG is capable of inhibiting the spore germination of P. expansum and effectively reducing the incidence rate of Penicillium rot of tomatoes, without compromising quality. Electron microscopy observations combined with metabolite and transcriptomic analyses revealed that FG treatments resulted in enhanced suberin accumulation through promoting the expression of suberin synthesis related genes and, consequently, inhibited the growth and expansion of P. expansum on the fruits. This work sheds light on the mechanisms underlying FG's inhibitory effects, allowing its potential application as a natural and safe alternative to replace chemical fungicides for postharvest preservation.

The mRNA Vaccine Expressing Single and Fused Structural Proteins of Porcine Reproductive and Respiratory Syndrome Induces Strong Cellular and Humoral Immune Responses in BalB/C Mice.

PRRS is a viral disease that profoundly impacts the global swine industry, causing significant economic losses. The development of a novel and effective vaccine is crucial to halt the rapid transmission of this virus. There have been several vaccination attempts against PRRSV using both traditional and alternative vaccine design development approaches. Unfortunately, there is no currently available vaccine that can completely control this disease. Thus, our study aimed to develop an mRNA vaccine using the antigens expressed by single or fused PRRSV structural proteins. In this study, the nucleotide sequence of the immunogenic mRNA was determined by considering the antigenicity of structural proteins and the stability of spatial structure. Purified GP5 protein served as the detection antigen in the immunological evaluation. Furthermore, cellular mRNA expression was detected by immunofluorescence and western blotting. In a mice experiment, the Ab titer in serum and the activation of spleen lymphocytes triggered by the antigen were detected by ELISA and ICS, respectively. Our findings demonstrated that both mRNA vaccines can significantly stimulate cellular and humoral immune responses. More specifically, the GP5-mRNA exhibited an immunological response that was similar to that of the commercially available vaccine when administered in high doses. To conclude, our vaccine may show promising results against the wild-type virus in a natural host.

Discovery and vertical transmission analysis of Dabieshan Tick Virus in Haemaphysalis longicornis ticks from Chengde, China.

Introduction: Ticks are important blood-sucking ectoparasites that can transmit various pathogens, posing significant threats to the wellbeing of humans and livestock. Dabieshan tick virus (DBTV) was initially discovered in 2015 in Haemaphysalis longicornis ticks from the Dabieshan mountain region in Hubei Province, China. In recent years, DBTV has been discovered in various regions of China, including Shandong, Zhejiang, Liaoning, Hubei, Yunnan, and Guizhou Provinces. However, the researches on tick-borne transmission of DBTV are scarce. Methods: This study utilized the small RNA sequencing (sRNA-seq) method to identify tick-associated viruses in ticks collected from Chengde in Hebei Province and Yongcheng in Henan Province, leading to the discovery of a new DBTV strain in Hebei. The complete coding genome of DBTV Hebei strain was obtained through RNA-seq and Sanger sequencing. Furthermore, the transmission experiment of DBTV in H. longicornis was examined in laboratory for the first time. Results: DBTV was detected in newly molted adult H. longicornis ticks collected in Chengde, Hebei Province. Additionally, DBTV was also detected in both unfed nymphs and engorged females of H. longicornis collected from Chengde, with a positive rate of 20% and 56.25%, respectively. The complete coding genome of DBTV (OP682840 and OP716696) were obtained, and phylogenetic analysis revealed that the DBTV Hebei strain clustered with previously reported DBTV strains. Furthermore, this virus was observed in engorged females, eggs, and larvae of the subsequent generation. Discussion: It is necessary to expand the scope of DBTV investigation, particularly in northern China. This study demonstrated that DBTV can be transmitted from engorged females to larvae of the next generation. Moreover, the detection of DBTV in unfed nymphs and adults (which moulted from engorged nymphs) collected from the filed of Chengde suggests that H. longicornis serves as a potential transmission host and reservoir for DBTV through transstadial and transovarial transmission. However, there remains a lack of research on the isolation and pathogenicity of DBTV, highlighting the need for further studies to mitigate potential harm to the health of animals and humans.

Dimensional Regulation from 1D/3D to 2D/3D of Perovskite Interfaces for Stable Inverted Perovskite Solar Cells.

Constructing low-dimensional/three-dimensional (LD/3D) perovskite solar cells can improve efficiency and stability. However, the design and selection of LD perovskite capping materials are incredibly scarce for inverted perovskite solar cells (PSCs) because LD perovskite capping layers often favor hole extraction and impede electron extraction. Here, we develop a facile and effective strategy to modify the perovskite surface by passivating the surface defects and modulating surface electrical properties by incorporating morpholine hydriodide (MORI) and thiomorpholine hydriodide (SMORI) on the perovskite surface. Compared with the PI treatment that we previously developed, the one-dimensional (1D) perovskite capping layer derived from PI is transformed into a two-dimensional (2D) perovskite capping layer (with MORI or SMORI), achieving dimension regulation. It is shown that the 2D SMORI perovskite capping layer induces more robust surface passivation and stronger n-N homotype 2D/3D heterojunctions, achieving a p-i-n inverted solar cell with an efficiency of 24.55%, which retains 87.6% of its initial efficiency after 1500 h of operation at the maximum power point (MPP). Furthermore, 5 × 5 cm2 perovskite mini-modules are presented, achieving an active-area efficiency of 22.28%. In addition, the quantum well structure in the 2D perovskite capping layer increases the moisture resistance, suppresses ion migration, and improves PSCs' structural and environmental stability.

Haplotype-resolved genome assembly provides insights into evolutionary history of the Actinidia arguta tetraploid.

Actinidia arguta, known as hardy kiwifruit, is a widely cultivated species with distinct botanical characteristics such as small and smooth-fruited, rich in beneficial nutrients, rapid softening and tolerant to extremely low temperatures. It contains the most diverse ploidy types, including diploid, tetraploid, hexaploid, octoploid, and decaploid. Here we report a haplotype-resolved tetraploid genome (A. arguta cv. 'Longcheng No.2') containing four haplotypes, each with 40,859, 41,377, 39,833 and 39,222 protein-coding genes. We described the phased genome structure, synteny, and evolutionary analyses to identify and date possible WGD events. Ks calculations for both allelic and paralogous genes pairs throughout the assembled haplotypic individuals showed its tetraploidization is estimated to have formed ~ 1.03 Mya following Ad-α event occurred ~ 18.7 Mya. Detailed annotations of NBS-LRRs or CBFs highlight the importance of genetic variations coming about after polyploidization in underpinning ability of immune responses or environmental adaptability. WGCNA analysis of postharvest quality indicators in combination with transcriptome revealed several transcription factors were involved in regulating ripening kiwi berry texture. Taking together, the assembly of an A. arguta tetraploid genome provides valuable resources in deciphering complex genome structure and facilitating functional genomics studies and genetic improvement for kiwifruit and other crops.

"Whole-Body" Fluorination for Highly Efficient and Ultra-Stable All-Inorganic Halide Perovskite Quantum Dots.

Inherent "soft" ionic lattice nature of halide perovskite quantum dots (QDs), triggered by the weak Pb-X (X=Cl, Br, I) bond, is recognized as the primary culprit for their serious instability. A promising way is to construct exceedingly strong ionic interaction inside the QDs and increase their crystal cohesive energy by substituting the interior X- with highly electronegative F- , however, which is challenging and hitherto remains unreported. Here, a "whole-body" fluorination strategy is proposed for strengthening the interior bonding architecture of QDs, wherein the F- are uniformly distributed throughout the whole nanocrystal encompassing both the interior lattice and surface, successfully stabilizing their "soft" crystal lattice and passivating surface defects. This approach effectively mitigates their intrinsic instability issues including light-induced phase segregation. As a result, light-emitting devices based on these QDs exhibit exceptional efficiency and remarkable stability.

Modulating the Dipole Moment of Secondary Ammonium Spacers for Efficient 2D Ruddlesden-Popper Perovskite Solar Cells.

Layered two-dimensional (2D) perovskites are emerging as promising optoelectronic materials owing to their excellent environmental stability. Regulating the dipole moment of organic spacers has the potential to reduce the exciton binding energy (Eb ) of 2D perovskites and improve their photovoltaic performance. Here, we developed two azetidine-based secondary ammonium spacers with different electron-withdrawing groups, namely 3-hydroxyazatidine (3-OHAz) and 3,3-difluoroazetidine (3,3-DFAz) spacers, for 2D Ruddlesden-Popper (RP) perovskites. It was found that the large dipole moment of the fluorinated dipole spacer could effectively enhance the interaction between organic spacers and inorganic layers, leading to improved charge dissociation in 2D RP perovskite. In contrast to 3-OHAz spacer, the 2D perovskite using 3,3-DFAz as spacer also shows improved film quality, optimized energy level alignment, and reduced exciton binding energy. As a result, the 2D perovskite (n=4) device based on 3,3-DFAz yields an outstanding efficiency of 19.28 %, surpassing that of the 3-OHAz-Pb device (PCE=11.35 %). The efficiency was further improved to 19.85 % when using mixed A-site cation of MA0.95 FA0.05 . This work provides an effective strategy for modulating the energy level alignment and reducing the Eb by regulating the dipole moment of organic spacers, ultimately enabling the development of high-performance 2D perovskite solar cells.

Reduction of renal activity retention of radiolabeled albumin binding domain­derived affinity proteins using a non­residualizing label strategy compared with a cleavable glycine­leucine­glycine­lysine­linker.

The feasibility of targeted imaging and therapy using radiolabeled albumin­binding domain­derived affinity proteins (ADAPTs) has been demonstrated. However, high renal uptake of radioactivity limits the maximum tolerated dose. Successful reduction of renal retention of radiolabeled Fab fragments has been demonstrated by incorporating a cleavable linker between the targeting agent and the radiometal chelator. The present study investigated if the introduction of a glycine­leucine­glycine­lysine (GLGK)­linker would reduce the kidney uptake of radiolabeled ADAPT6 and also compared it with the non­residualizing [125I]I­[(4­hydroxyphenyl)ethyl]maleimide ([125I]I­HPEM) labeling strategy. GLGK was site­specifically coupled to human epidermal growth factor receptor 2 (HER2)­targeting ADAPT6. Conjugates without the cleavable linker were used as controls and all constructs were labeled with lutetium­177 (177Lu). [125I]I­HPEM was coupled to ADAPT6 at the C­terminus. Biodistribution of all constructs was evaluated in NMRI mice 4 h after injection. Specific binding to HER2­expressing cells in vitro was demonstrated for all constructs. No significant difference in kidney uptake was observed between the [177Lu]Lu­2,2',2",2"'­(1,4,7,10­tetraazacyclododecane­1,4,7,10­tetrayl)tetraacetic acid­GLGK­conjugates and the controls. The renal activity of [125I]I­HPEM­ADAPT6 was significantly lower compared with all other constructs. In conclusion, the incorporation of the cleavable GLGK­linker did not result in lower renal retention. Therefore, the present study emphasized that, in order to achieve a reduction of renal retention, alternative molecular design strategies may be required for different targeting agents.

Agrobacterium rhizogenes-mediated marker-free transformation and gene editing system revealed that AeCBL3 mediates the formation of calcium oxalate crystal in kiwifruit.

The transformation and gene editing of the woody species kiwifruit are difficult and time-consuming. The fast and marker-free genetic modification system for kiwifruit has not been developed yet. Here, we establish a rapid and efficient marker-free transformation and gene editing system mediated by Agrobacterium rhizogenes for kiwifruit. Moreover, a removing-root-tip method was developed to significantly increase the regeneration efficiency of transgenic hairy roots. Through A. rhizogenes-mediated CRISPR/Cas9 gene editing, the editing efficiencies of CEN4 and AeCBL3 achieved 55 and 50%, respectively. And several homozygous knockout lines for both genes were obtained. Our method has been successfully applied in the transformation of two different species of kiwifruit (Actinidia chinensis 'Hongyang' and A.eriantha 'White'). Next, we used the method to study the formation of calcium oxalate (CaOx) crystals in kiwifruit. To date, little is known about how CaOx crystal is formed in plants. Our results indicated that AeCBL3 overexpression enhanced CaOx crystal formation, but its knockout via CRISPR/Cas9 significantly impaired crystal formation in kiwifruit. Together, we developed a fast maker-free transformation and highly efficient CRISPR-Cas9 gene editing system for kiwifruit. Moreover, our work revealed a novel gene mediating CaOx crystal formation and provided a clue to elaborate the underlying mechanisms.

Single-Crystal-Assisted In Situ Phase Reconstruction Enables Efficient and Stable 2D/3D Perovskite Solar Cells.

Perovskite solar cells (PSCs) that incorporate both two-dimensional (2D) and three-dimensional (3D) phases possess the potential to combine the high stability of 2D PSCs with the superior efficiency of 3D PSCs. Here, we demonstrated in situ phase reconstruction of 2D/3D perovskites using a 2D perovskite single-crystal-assisted method. A gradient phase distribution of 2D RP perovskites was formed after spin-coating a solution of the 2D Ruddlesden-Popper (RP) perovskite single crystal, (DFP)2PbI4, onto the 3D perovskite surface, followed by thermal annealing. The resulting film exhibits much reduced trap density, increased carrier mobility, and superior water resistance. As a result, the optimized 2D/3D PSCs achieved a champion efficiency of 24.87% with a high open-circuit voltage (VOC) of 1.185 V. This performance surpasses the control 3D perovskite device, which achieved an efficiency of 22.43% and a VOC of 1.129 V. Importantly, the unencapsulated device demonstrates significantly enhanced operational stability, preserving over 97% of its original efficiency after continuous light irradiation for 1500 h. Moreover, the extrapolated T80 lifetimes surpass 5700 h. These findings pave the way for rational regulation of the gradient phase distribution at the interface between 2D and 3D perovskites by employing 2D RP perovskite crystals to achieve stable and efficient PSCs.

Transcriptome analysis of long non-coding RNA and mRNA Profiles in VSV-infected BHK-21 Cells.

BACKGROUND: Vesicular stomatitis virus (VSV) is a typical non-segmented negative-sense RNA virus of the genus Vesiculovirus in the family Rhabdoviridae. VSV can infect a wide range of animals, including humans, with oral blister epithelial lesions. VSV is an excellent model virus with a wide range of applications as a molecular tool, a vaccine vector, and an oncolytic vector. To further understand the interaction between VSV and host cells and to provide a theoretical basis for the application prospects of VSV, we analyzed the expression of host differentially expressed genes (DEGs) during VSV infection using RNA-Seq. RESULTS: Our analyses found a total of 1015 differentially expressed mRNAs and 161 differentially expressed LncRNAs in BHK-21 cells infected with VSV for 24 h compared with controls. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment showed that the differentially expressed lncRNAs and their target genes were mainly concentrated in pathways related to apoptosis, cancer, disease, and immune system activation, including the TNF, P53, MAPK, and NF-kappaB signaling pathways. The differentially expressed lncRNA can modulate immune processes by regulating genes involved in these signaling transmissions. Ten randomly selected DEGs, namely, Il12rb2, F2, Masp2, Mcl1, FGF18, Ripk1, Fas, BMF, POLK, and JAG1, were validated using RT-qPCR. As predicted through RNA-Seq analysis, these DEGs underwent either up- or downregulation, suggesting that they may play key regulatory roles in the pathways mentioned previously. CONCLUSIONS: Our study showed that VSV infection alters the host metabolic network and activates immune-related pathways, such as MAPK and TNF. The above findings provide unique insights for further study of the mechanism of VSV-host interactions and, more importantly, provide a theoretical basis for VSV as an excellent vaccine carrier.