Search Results (5)

Plant-specific transcription factors known as SQUAMOSA promoter binding protein-like (SPL) genes are essential for development, growth, and abiotic stress responses. While the SPL gene family has been extensively studied in various plant species, a systematic characterization in Zanthoxylum bungeanum (Zb) is lacking. This study used transcriptomic and bioinformatics data to conduct a thorough genomic identification and expression investigation of the ZbSPL gene family. Eight subfamilies including 73 ZbSPL members were identified, most of which are predicted to be localized in the nucleus. Ka/Ks ratio analysis indicates that most ZbSPL genes have undergone purifying selection. According to evolutionary research, segmental duplication is a major factor in the amplification of the ZbSPL gene family. Gene structures, conserved motifs, and domains were found to be highly conserved among paralogs. Cis-element research revealed that ZbSPLs may be implicated in hormone and abiotic stress responses. Codon usage pattern analysis showed that the ZbSPL gene family was more inclined to A/T base endings; the higher the A/T content, the stronger the preference of the codons; and the use pattern was mainly affected by natural selection. Additionally, 36 ZbSPLs were found to be potential targets of miR156. RNA-seq demonstrated that SPL genes in Zb are differentially expressed in response to distinct abiotic stressors. Two ZbSPL genes (ZbSPL10 and ZbSPL17) were implicated in the response to salt stress, while four ZbSPL genes (ZbSPL06, ZbSPL43, ZbSPL60, and ZbSPL61) showed response to drought stress, based on a qRT-PCR investigation of the ZbSPL genes under various abiotic stress conditions. This study will help us gain a deeper understanding of the functions of ZbSPLs and lay a genetic foundation for future breeding of high-quality, highly abiotic resistant varieties of Z. bungeanum. Full article

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating biological heterogeneity at the single-cell level in human systems and model organisms. Recent advances in scRNA-seq have enabled the pooling of cells from multiple samples into single libraries, thereby increasing sample throughput while reducing technical batch effects, library preparation time, and the overall cost. However, a comparative analysis of scRNA-seq methods with and without sample multiplexing is lacking. In this study, we benchmarked methods from two representative platforms: Parse Biosciences (Parse; with sample multiplexing) and 10x Genomics (10x; without sample multiplexing). By using peripheral blood mononuclear cells (PBMCs) obtained from two healthy individuals, we demonstrate that demultiplexed scRNA-seq data obtained from Parse showed similar cell type frequencies compared to 10x data where samples were not multiplexed. Despite relatively lower cell capture affecting library preparation, Parse can detect rare cell types (e.g., plasmablasts and dendritic cells) which is likely due to its relatively higher sensitivity in gene detection. Moreover, a comparative analysis of transcript quantification between the two platforms revealed platform-specific distributions of gene length and GC content. These results offer guidance for researchers in designing high-throughput scRNA-seq studies. Full article

Sphingosine-1-phosphate lyase insufficiency syndrome (SPLIS) is an inborn error of metabolism caused by inactivating mutations in SGPL1, the gene encoding sphingosine-1-phosphate lyase (SPL), an essential enzyme needed to degrade sphingolipids. SPLIS features include glomerulosclerosis, adrenal insufficiency, neurological defects, ichthyosis, and immune deficiency. Currently, there is no cure for SPLIS, and severely affected patients often die in the first years of life. We reported that adeno-associated virus (AAV) 9-mediated SGPL1 gene therapy (AAV-SPL) given to newborn Sgpl1 knockout mice that model SPLIS and die in the first few weeks of life prolonged their survival to 4.5 months and prevented or delayed the onset of SPLIS phenotypes. In this study, we tested the efficacy of a modified AAV-SPL, which we call AAV-SPL 2.0, in which the original cytomegalovirus (CMV) promoter driving the transgene is replaced with the synthetic “CAG” promoter used in several clinically approved gene therapy agents. AAV-SPL 2.0 infection of human embryonic kidney (HEK) cells led to 30% higher SPL expression and enzyme activity compared to AAV-SPL. Newborn Sgpl1 knockout mice receiving AAV-SPL 2.0 survived ≥ 5 months and showed normal neurodevelopment, 85% of normal weight gain over the first four months, and delayed onset of proteinuria. Over time, treated mice developed nephrosis and glomerulosclerosis, which likely resulted in their demise. Our overall findings show that AAV-SPL 2.0 performs equal to or better than AAV-SPL. However, improved kidney targeting may be necessary to achieve maximally optimized gene therapy as a potentially lifesaving SPLIS treatment. Full article

Astrocytes are critical players in brain health and disease. Sphingosine-1-phosphate (S1P), a bioactive signaling lipid, is involved in several vital processes, including cellular proliferation, survival, and migration. It was shown to be crucial for brain development. Its absence is embryonically lethal, affecting, inter alia, the anterior neural tube closure. However, an excess of S1P due to mutations in S1P-lyase (SGPL1), the enzyme responsible for its constitutive removal, is also harmful. Of note, the gene SGPL1 maps to a region prone to mutations in several human cancers and also in S1P-lyase insufficiency syndrome (SPLIS) characterized by several symptoms, including peripheral and central neurological defects. Here, we investigated the impact of S1P on astrocytes in a mouse model with the neural−targeted ablation of SGPL1. We found that SGPL1 deficiency, and hence the accumulation of its substrate, S1P, causes the elevated expression of glycolytic enzymes and preferentially directs pyruvate into the tricarboxylic acid (TCA) cycle through its receptors (S1PR_2,4). In addition, the activity of TCA regulatory enzymes was increased, and consequently, so was the cellular ATP content. The high energy load activates the mammalian target of rapamycin (mTOR), thus keeping astrocytic autophagy in check. Possible consequences for the viability of neurons are discussed. Full article

The joint use of baculoviruses and synthetic insecticides for integrated pest management requires the study of the additive, synergistic or antagonistic effects among them on pest mortality. Droplet bioassays were conducted with Autographa californica multiple nucleopolyhedrovirus (AcMNPV), Spodoptera littoralis nucleopolyhedrovirus (SpliNPV) and seven insecticides (azadirachtin, Bacillus thuringiensis, cyantraniliprole, emamectin, metaflumizone, methoxyfenozide and spinetoram) on Spodoptera exigua and Spodoptera littoralis. The lethal concentrations LC₅₀ and LC₉₅ were calculated through probit regressions. Then, the sequential feeding of insecticides and nucleopolyhedroviruses was studied. Larvae were provided with the LC₅₀ of one insecticide, followed by the LC₅₀ of one nucleopolyhedrovirus 24 h later. The inverse order was also conducted. The insecticide LC₅₀ and LC₉₅ were higher for S. littoralis than for S. exigua. AcMNPV showed greater toxicity on S. exigua than SpliNPV on S. littoralis. Emamectin showed synergy with AcMNPV when the chemical was applied first, and metaflumizone and AcMNPV were synergistic regardless of the order of application, both from the first day of evaluation. SpliNPV was synergistic with azadirachtin and emamectin when it was applied first, but synergy was reached after 12–13 days. Excellent control is possible with the LC₅₀ of azadirachtin, emamectin and metaflumizone in combination with nucleopolyhedroviruses, and merits further study as a means of controlling lepidopteran pests. Full article