Search Results (733)

Soybean (Glycine max) is relatively recalcitrant to genetic manipulations; hence, it is often interrogated with transient means such as virus-induced gene silencing (VIGS). We earlier modified cowpea severe mosaic virus (CPSMV) to develop a soybean-friendly VIGS system referred to as QUIN-FZ. Here we report additional calibrations of this system. We enhanced the intra-bacterial stability of plasmid QUIN, which contained a CPSMV RNA1 cDNA embedded with four introns, by adding a fifth intron, resulting in PENTIN. We separately upgraded the plasmid FZ, which contained a modified CPSMV RNA2 cDNA with a cloning site in the middle of the viral polyprotein, by creating another cloning site within the 3′ untranslated region, leading to ZY. We next used the new PENTIN-ZY system to investigate a putative soybean protein kinase designated QL18. Virus-mediated overexpression of two allelic, 147-amino-acid (aa) protein fragments, derived from two different QL18 orthologs, elicited drastically different responses in soybeans. While the fragment derived from soybean accession OX20-8 prevented the cognate virus from infecting top young leaves in at least 50% of inoculated seedlings, its allelic counterpart derived from soybean accession PI427105B elicited apical necrosis in 100% of soybean seedlings. By examining progeny viruses as well as viruses encoding chimeras of the two fragments, we identified more than a dozen mutations that abrogated these unique phenotypes. Our findings establish the PENTIN-ZY system as a versatile tool for overexpressing small proteins and protein fragments, accelerating their functional characterization. Full article

Zucchini tigre mosaic virus (ZTMV; Potyvirus pepotigris), which infects wax gourd (Benincasa hispida), was first identified in Taiwan in 2017 and designated ZTMV-TW. In this study, mild strains of ZTMV-TW were generated by modifying the pathogenicity factor HC-Pro to develop cross-protection strategies for cucurbit crops. A full-length infectious cDNA clone of ZTMV-TW was cloned in pCAMBIA1304 under the control of the CaMV 35S promoter (ZTMV-TWic). ZTMV-TWic induced typical potyvirus particles, cytoplasmic inclusion bodies, and severe symptoms in wax gourd, pumpkin, and zucchini plants. Conserved motifs of HC-Pro were mutated to generate four single mutants (F7I, R181I, F206L, and D397N) and three double mutants (F7I+F206L, R181I+D397N, and F206L+D397N). Mutants R181I and R181I+D397N caused mild or no symptoms in zucchini, while D397N and F206L+D397N were mild in wax gourd. Cross-protection assays showed that R181I and R181I+D397N provided complete protection against ZTMV-GFP in zucchini, whereas D397N and F206L+D397N conferred high protection in wax gourd. These results demonstrate the feasibility of host-specific mild strain selection for effective ZTMV cross-protection. Full article

Seeds of Paeonia lactiflora Pall. ‘Hangshao’ contain over 20% oil, of which more than 90% are unsaturated fatty acids, showing its high potential as an oil crop. Triacylglycerol (TAG) is the main storage form of fatty acids, and diacylglycerol acyltransferase 2 (DGAT2) is a key enzyme in TAG biosynthesis. In this study, the full-length cDNA of PlDGAT2 (326 amino acids) was cloned. Subcellular localization assays further indicated that it localized in the endoplasmic reticulum. Functional verification showed that silencing PlDGAT2 in herbaceous peony decreased the level of total fatty acids, palmitic acid (C16:0, PA) and α-linolenic acid (C18:3, ALA), but increased linoleic acid (C18:2, LA) in leaves. Overexpressing PlDGAT2 in tobacco elevated the content of total fatty acids, PA, and ALA in seeds, while also enlarging the seed sizes, but it reduced the LA content in tobacco seeds. This study suggests that PlDGAT2 contributes to the accumulation of ALA and total fatty acids, offering a potential gene target for improving the oil quality of herbaceous peony seeds. Full article

DNA cloning traditionally relies on two approaches: restriction endonuclease digestion-ligation, and homologous recombination involving exonucleases, polymerases, and other enzymes. Here, we present a novel cloning method that requires only restriction endonucleases, eliminating the need for exonucleases or polymerases. The linearized cloning vector and the foreign DNA fragment (FDF) containing overlapping sequences were mixed and incubated at the melting temperature of the overlapping DNA sequences for 5 min, then cooled slowly to 0 °C. The mixture was transformed into E. coli and positive transformants were obtained. This cloning method was named DNA ‘breathing’ recombination (DBR) cloning. The overlapping sequence between the linearized vector and the FDF is preferably from 12 to 16 base pairs. Even when the ends of the linearized vector contain mismatches of up to 20 base pairs with the ends of the FDF, the DBR cloning method can still proceed efficiently, enabling truly seamless assembly. Meanwhile, the DBR method supports one-step assembly of multiple fragments. Therefore, the DBR cloning method simplifies experimental operations and reduces experimental costs while maintaining high cloning efficiency. Full article

Ascorbate peroxidase (APX) is a heme-containing enzyme involved in hydrogen peroxide (H₂O₂) detoxification within the ascorbate–glutathione (AsA–GSH) cycle. In this study, the full-length genomic DNA and cDNA of an APX1 gene (VsAPX1) were cloned and characterized from Vicia sativa. The genomic sequence of VsAPX1 is 2425 bp in length and comprises 10 exons separated by nine introns, with the first intron located within the 5′ untranslated region (5′UTR). The corresponding cDNA is 1010 bp long and includes a 61 bp 5′UTR, a 753 bp open reading frame, and a 196 bp 3′UTR. VsAPX1 encodes a predicted cytosolic APX protein of 250 amino acids, with a molecular weight of 27.1 kDa and a theoretical isoelectric point (pI) of 5.60. Bioinformatics analysis revealed that the deduced VsAPX1 protein shares high sequence similarity with cytosolic APX1 proteins from other plant species, contains conserved APX domains, and clusters within the cytosolic APX clade in phylogenetic analysis. Quantitative real-time PCR analysis showed that VsAPX1 expression exhibits transient and moderate changes in response to abiotic stress and phytohormone treatments. Transcript levels increased at early time points following heat stress (42 °C), abscisic acid, and salicylic acid treatments, and after 4 h of jasmonic acid exposure, whereas hydrogen peroxide treatment resulted in a gradual down-regulation of expression. Overall, this study provides the first molecular and expression characterization of a cytosolic APX1 gene from Vicia sativa and establishes a foundation for future functional analyses of antioxidant genes in this species. Full article

The history of stromal-derived factor-1 (SDF-1), alias CXCL12, started serendipitously and relatively late in the cytokine cDNA cloning era (1975–2000) and evolved at the biological level from progenitor cell-specific chemokine in the bone marrow to multifunctional cytokine with growth factor-like and tissue-regenerative activities. This evolution was parallelled by the integration of SDF-1/CXCL12 within the protein families of chemokines, cytokines and cell growth-promoting recombinant products having the potential for clinical applications. Here, we use this central position of CXCL12 as small signaling protein as an example for future developments in regenerative medicine. We provide context about SDF-1 biology within the field of skin wound healing research and how this compares with studies of other cytokines and growth factors. We also discuss whether SDF-1 formulations may be exemplary for other cytokines used for tissue regeneration. Normal skin wound healing is fraught with delays and complications in patients with specific underlying diseases, such as diabetes, hypertension and other elderly-related comorbidities, skin infections and accidental physical insults. Except for platelet-derived growth factor (PDGF), many cytokines, including vascular endothelial growth factor (VEGF) and epidermal growth factor (EGF), have failed so far in clinical studies of skin wound healing. This is in part due to the fact that (i) the biology of tissue regeneration is complex and insufficiently studied, (ii) in vitro approaches hardly mimic in vivo situations and (iii) commonly used animal models of acute and chronic wounding do not perfectly match human skin wound regeneration. A review of critical cells and molecules in normal skin and their actions in wounded tissue and a balanced comparison of the recent literature are preambles for progress in wound repair. We define advantages and limitations of recent approaches and appeal for more research. In particular, the possibilities of cellular immunomodulation mediated by endogenous and exogenous SDF-1/CXCL12 as a key molecule for skin regeneration are reviewed. Furthermore, biomaterials and scaffolds for the delivery and use of cytokines in precision medicine and aspects of their biofabrication are outlined with SDF-1 as an example. Finally, we indicate how applications of dermatological SDF-1 formulations for skin wound healing may be tailored for applications in other acute and chronic inflammatory conditions and regenerative medicine. Thereby, SDF-1/CXCL12 is placed at the crossroads between recombinant products, cytokines, chemokines and growth factors and occupies a central position between regenerative biology and medicine. Full article

Coffea canephora is economically and socially important for small-scale agriculture in Northern Brazil. To identify genotypes adapted to Amazonian edaphoclimatic conditions, clones of the species have been evaluated across multiple locations in Amazonas. Introducing genetically selected materials into comparable environments may promote consistent productivity gains in the short and medium term. In this context, the aim of this study was to assess the genetic diversity of different C. canephora genotypes using microsatellite markers, which will support the development of superior genotypes adapted to Amazon conditions. A total of 43 C. canephora genotypes were analyzed. Leaves were collected for genomic DNA extraction and were standardized and amplified by PCR using microsatellite primers. Genotyping was performed via capillary electrophoresis, allowing for the determination of allele sizes. Genetic structure was inferred, and genetic diversity parameters were estimated. The average observed heterozygosity (H_O = 0.64) exceeded the expected heterozygosity (H_E = 0.53), and the average inbreeding coefficient (f = −0.19) indicated an excess of heterozygotes. The results revealed high genetic variability among the evaluated genotypes. These findings highlight the broad genetic diversity of C. canephora, reinforcing its potential as a genetic basis for selection and the development of cultivars adapted to the environmental conditions of the Amazon. Full article

The purpose of our study is to explore the potential of a transcription factor-based strategy for directly converting mouse fibroblasts into photoreceptor-like cells. The mouse cDNAs of Ascl, Crx, Ngn1, Nrl, and Otx2 were cloned into a modified commercial adenoviral vector. Mouse embryonic fibroblasts (MEFs) were isolated from E13.5 embryos, and mouse postnatal fibroblasts (MPFs) were isolated from three-day-old mice. A pool of adenoviruses containing five genes was prepared to infect MEFs or MPFs once daily for two days. The MEFs or MPFs were incubated in a specific medium supplemented with forskolin and were changed every two days. After 7 or 14 days, the photoreceptor-like cells were assayed via immunofluorescence or polymerase chain reaction with reverse transcription (RT–PCR). The photoreceptor-like cells were then transplanted into adult C57BL/6 mouse retinas and were assessed by immunofluorescence 14 days following transplantation. Screening from a pool of five candidate genes, we reported that a combination of only three factors—Crx, Nrl, and Otx2—was sufficient to convert mouse embryonic and postnatal fibroblasts into photoreceptor-like cells. The induced photoreceptor-like cells expressed photoreceptor-specific proteins such as Recoverin, Rhodopsin, and Opsin and integrated into the outer nuclear layer of the retina following transplantation. This exploratory study provides preliminary evidence that fibroblasts can be directly converted into photoreceptor-like cells, suggesting a cellular model and potential source for future transplantation strategies aimed at retinal repair. Full article

Arapaima gigas growth hormone (ag-GH) cDNA was previously cloned from A. gigas pituitaries. In this work ag-GH has been synthesized using human embryonic kidney 293 cells (HEK293) transiently transfected with the 3.4-TOPO^® vector carrying ag-GH cDNA. The 4th day after transfection, the presence of putative ag-GH was detected via SDS-PAGE and Western blotting in comparison with human GH. Ion exchange purification exhibited a clearly symmetric peak, absent in the control medium. The purified fraction, submitted to high-performance size-exclusion chromatography (HPSEC), SDS-PAGE, and Western blotting, contained an immunoreactive molecule, slightly smaller than hGH as expected. MALDI-TOF-MS determined a high-resolution molecular mass of 21,220 Da versus a theoretical value of 21,150. A phylogenetic analysis positioned ag-GH within basal teleost lineages, consistent with earlier analyses of A. gigas gonadotrophic hormones, reinforcing the structural and functional conservation relevant for its biologic activity. An in vivo bioassay based on the body weight increase of dwarf “little” mice demonstrated a biological activity for ag-GH comparable to that of the international reference preparation of rec-hGH. For two species (H. sapiens and A. gigas) separated by an evolutionary period of >100 million years, such a positive biological correlation is remarkable. Full article

The aquaporin 0 (AQP0)/major intrinsic protein of eye lens (MIP) cDNA was cloned and sequenced. Initial studies of the tissue distribution of mRNA expression proved to be incorrect. Subsequent experiments showed that AQP0 mRNA is expressed strongly in the eye with moderately strong expression in the kidneys and some expression was seen in the brain and muscle tissue, and very low expression in the esophagus/fundic stomach. Another set of PCR reactions with five times the amount of cDNA additionally showed mRNA/cDNA expression in the liver, rectal gland, and a very low level in the intestine. Sporadic expression of different pieces of AQP0 cDNA was seen in various experiments in gill and pyloric stomach. A custom polyclonal antibody was produced against a region near the C-terminal end of the AQP0 protein sequence. The antibody gave a band of around the correct size (for the AQP0 protein) on the Western blot, which also showed a few other higher-molecular-weight bands. The antibody was also used in immunohistochemistry, and in the kidney, it showed staining in the proximal II (PII), intermediate segment I (IS I), and late distal tubule (LDT) parts of the sinus zone region of nephrons as well as some staining in the bundle zone tubule segments, suggesting a role for AQP0 as a water channel. In the rectal gland, the antibody showed weak apical membrane staining in a few secretory tubules near the duct, but also somewhat stronger staining in cells appearing to connect various secretory tubules, suggesting a role in cell–cell adhesion. In the spiral valve intestine side wall and valve flap, after signal amplification, weak antibody staining was seen in the apical and lateral membranes of epithelial cells adjacent to the luminal surface. There was also some staining in the intestinal muscle. In the rectum/colon, staining was seen in a layer of cells underlying the epithelium and in some muscle layers. In the gill, there was very weak staining in secondary lamellae epithelial cells and in connective tissue surrounding blood vessels and blood sinuses. The low level of transcript expression in the rectal gland, gill, and intestinal tissues suggests caution in the interpretation of the immunohistochemical staining in these tissues. Full article

Pepino mosaic virus (PepMV) is a significant threat to global tomato production, with symptom severity varying widely among strains and often leading to significant economic losses. Despite extensive studies on aggressive variants, the molecular determinants of mild symptomatology in field isolates, particularly from Korea, remain underexplored. In this study, we characterized a mildly infecting PepMV isolate from asymptomatic tomato plants during a field survey in Jeonju, South Korea. The full-length genome sequence and phylogenetic analysis classified it as a CH2 strain. A full-length cDNA infectious clone of this isolate was constructed and confirmed to induce no mosaic symptoms in tomato plants. To identify symptom determinants, targeted mutagenesis was performed in the coat protein (CP) open reading frame. Substitution mutations at CP position 236 or combined 6/155 substitutions converted the mild isolate into a severe variant, inducing strong mosaic symptoms and significantly higher viral accumulation (up to tenfold). These results demonstrated that specific CP residues act as key regulators of symptom severity in PepMV CH2 strains and provide defined severe mutants as useful tools for screening resistance in tomatoes. Although the mechanism underlying symptom modulation remains unclear, this work advanced our understanding of molecular differences between mild and severe strains and supported targeted strategies for managing this economically important virus. Full article

Chilli veinal mottle virus (ChiVMV) is an important potyvirus that poses a serious threat to crop production. In this study, small RNA sequencing and molecular cloning were used to obtain the complete genome sequence of a ChiVMV isolate identified in pepper plants in Sichuan (SC1 isolate). Molecular evolutionary and phylogenetic analysis of SC1 and 35 ChiVMV isolates revealed four clades of ChiVMV isolates. Recombination analysis found 23 recombinant events and 28 recombinants, with the SC1 isolate arising from the recombination of the PK isolate from Pakistan and the YNpe isolate from Yunnan, China. A full-length infectious cDNA clone of ChiVMV was constructed and demonstrated to be infectious in both Nicotiana benthamiana and pepper plants. Moreover, a Myc-tag was inserted after NIb, and the derived infectious clone of ChiVMV remained infectious, and NIb-Myc was readily expressed in infected host plants. These reverse genetic tools will promote the study of the function of ChiVMV-encoded proteins, especially the NIb protein, and facilitate basic and translational studies of ChiVMV. Full article

The multidrug and toxic compound extrusion (MATE) protein plays a crucial role in mediating plant responses to aluminum (Al) toxicity. The key candidate gene BnaMATE43b related to Al toxicity stress in rapeseed was identified using GWAS and transcriptome analysis. In this study, the BnaMATE43b gene was cloned and functionally characterized in rapeseed. Compared with wild-type rapeseed (WT), the BnaMATE43b overexpression lines (OE) demonstrated stronger aluminum tolerance, specifically manifested in higher relative elongation of taproots (RETs) and relative total root length (RTRL); under Al toxicity stress, the enzyme activities (SOD and POD) and root activity were significantly increased in the OE lines, whereas the MDA content and relative electrical conductivity were reduced in rapeseed root. Further transcriptome analysis of OE-3 showed that the differentially expressed genes (DEGs) were mainly enriched in zeatin biosynthesis (map00908), glucosinolate biosynthesis (map00966), phenylpropanoid biosynthesis (map00940), and ascorbate and aldarate metabolism (map00053). In addition, the yeast cDNA library of rapeseed was constructed, and twenty-two candidate upstream transcription factors (UTFs) of BnaMATE43b were screened; furthermore, four candidate UTFs were obtained through one-on-one interaction validation and luciferase assays, comprising three bHLH transcription factors (BnaA02g28220D, BnaA06g07840D, and BnaA08g24520D) and one ERF transcription factor (BnaA05g23130D). Collectively, these results suggest that BnaMATE43b could improve Al tolerance in rapeseed by mediating antioxidant enzyme activities and the related metabolic pathway, while the obtained UTFs lay the foundation for further analysis of the gene regulatory network under Al toxicity stress. Full article

Blood-sucking organisms produce various anticoagulant proteins that prevent blood clotting in their prey. Even in well-studied species like Hirudo medicinalis, many such proteins remain unidentified. We previously described a novel cysteine-rich anticoagulant (CRA), a distant homolog of antistasin. Later, we discovered another, much larger homolog in the medicinal leech. Its amino acid sequence is also highly cysteine-rich. Analysis of cysteine patterns showed four antistasin-like domain motifs, with one of them strongly disrupted. Since both antistasin and CRA contain two such domains, the new protein represents a duplicated antistasin-like structure. We cloned its cDNA, expressed the recombinant protein in Escherichia coli, purified it by metal-chelate chromatography, refolded it, and tested its anticoagulant properties. Using standard clinical assays—activated partial thromboplastin time, prothrombin time, and thrombin time—we found that the protein inhibited coagulation in all tests, though to varying degrees. These findings suggest that different antistasin-like anticoagulants in the leech enable it to block both intrinsic and extrinsic coagulation pathways, while hirudin inhibits the final step of clot formation. The combination of different anticoagulant proteins allows the leech to effectively prevent the prey’s blood from clotting during feeding. Full article

Cryptochromes (CRYs) are a conserved class of blue light and near-ultraviolet light receptors that regulate diverse processes, including photomorphogenesis in plants. In the extreme Antarctic environment, ice algae endure intense UV radiation, prolonged darkness, and low temperatures, where cryptochromes play a vital role in light sensing and stress response. In this study, we cloned the complete open reading frame (ORF) of the cryptochrome gene CiCRY-DASH1 from the Antarctic microalga Chlamydomonas sp. ICE-L. Both in vivo and in vitro DNA photorepair assays showed that CiCRY-DASH1 effectively repairs cyclobutane pyrimidine dimer (CPD) and 6-4 photoproducts (6-4PPs) induced by UV radiation. Furthermore, deletion of the N-terminal and C-terminal loop regions, combined with activity assays, revealed that the C-terminal loop region plays a crucial role in photorepair activity. These findings elucidate the adaptive photorepair mechanisms of Antarctic microalgae and establish CiCRY-DASH1 as a valuable genetic resource. Specifically, the high catalytic efficiency and evolutionary robustness of the engineered variants position it as a promising marine bioactive agent for photoprotective therapeutics and a strategic target for constructing microbial chassis to enable sustainable drug biomanufacturing. Full article