High-throughput sequencing reveals the molecular mechanisms determining the stay-green characteristic in soybeans

Senescence is an internally systematized degeneration process leading to death in plants. Leaf yellowing, oneof the most prominent features of plant aging may lead to reduced crop yields. The molecular mechanism ofresponses to senescence in soybean leaves is not completely clear. In our research, two soybean varieties wereselected with different stay-green traits: stay-green variety (BN106) and non-stay-green variety (KF14). RNAsamples extracted from the leaves of two varieties were sequenced and compared using high-throughputsequencing. Six key enzyme genes in chlorophyll degradation pathways were studied to analyze the changes intheir expression at seedling, flowering and maturation stage. Meanwhile, the construction of the genetictransformation process had been constructed to identify the function of putative gene by RNA-interference. Atotal of 4329 DEGs were involved in 52 functional groups and 254 KEGG pathways. Twelve genes encodingsenescence-associated and inducible chloroplast stay-green protein showed significant differential expression.MDCase and PAO have a significant expression in BN106 that may be the key factors affecting the maintenance of green characteristics. In addition, the function of GmSGRs has been identified by genetic transformation. The loss of GmSGRs may cause soybean seeds to change from yellow to green. In summary, ourresults revealed fundamental information about the molecular mechanism of aging in soybeans with differentstay-green characteristics. The work of genetic transformation lays a foundation for putative gene functionstudies that could contribute to postpone aging in soybeans

Minor temperature shifts do not affect chromosomal ploidy but cause transcriptomic changes in Leishmania braziliensis promastigotes in vitro

BACKGROUND The leishmaniases are complex neglected diseases caused by protozoan parasites of the genus Leishmania. Leishmania braziliensis is the main etiological agent of cutaneous leishmaniasis in the New World. In recent studies, genomic changes such as chromosome and gene copy number variations (CNVs), as well as transcriptomic changes have been highlighted as mechanisms used by Leishmania species to adapt to stress situations. OBJECTIVES The aim of this study was to determine the effect of short-term minor temperature shifts in the genomic and transcriptomic responses of L. braziliensis promastigotes in vitro. METHODS Growth curves, genome and transcriptome sequencing of L. braziliensis promastigotes were conducted from cultures exposed to three different temperatures (24ºC, 28ºC and 30ºC) compared with the control temperature (26ºC). FINDINGS Our results showed a decrease in L. braziliensis proliferation at 30ºC, with around 3% of the genes showing CNVs at each temperature, and transcriptomic changes in genes encoding amastin surface-like proteins, heat shock proteins and transport proteins, which may indicate a direct response to temperature stress. MAIN CONCLUSIONS This study provides evidence that L. braziliensis promastigotes exhibit a decrease in cell density, and noticeable changes in the transcriptomic profiles. However, there were not perceptible changes at chromosome CNVs and only ~3% of the genes changed their copies in each treatment.

Transcriptome and Regulatory Network Analyses of CD19-CAR-T Immunotherapy for B-ALL / 基因组蛋白质组与生物信息学报·英文版

Chimeric antigen receptor (CAR) T cell therapy has exhibited dramatic anti-tumor efficacy in clinical trials. In this study, we reported the transcriptome profiles of bone marrow cells in four B cell acute lymphoblastic leukemia (B-ALL) patients before and after CD19-specific CAR-T therapy. CD19-CAR-T therapy remarkably reduced the number of leukemia cells, and three patients achieved bone marrow remission (minimal residual disease negative). The efficacy of CD19-CAR-T therapy on B-ALL was positively correlated with the abundance of CAR and immune cell subpopulations, e.g., CD8 T cells and natural killer (NK) cells, in the bone marrow. Additionally, CD19-CAR-T therapy mainly influenced the expression of genes linked to cell cycle and immune response pathways, including the NK cell mediated cytotoxicity and NOD-like receptor signaling pathways. The regulatory network analyses revealed that microRNAs (e.g., miR-148a-3p and miR-375), acting as oncogenes or tumor suppressors, could regulate the crosstalk between the genes encoding transcription factors (TFs; e.g., JUN and FOS) and histones (e.g., HIST1H4A and HIST2H4A) involved in CD19-CAR-T therapy. Furthermore, many long non-coding RNAs showed a high degree of co-expression with TFs or histones (e.g., FOS and HIST1H4B) and were associated with immune processes. These transcriptome analyses provided important clues for further understanding the gene expression and related mechanisms underlying the efficacy of CAR-T immunotherapy.