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Abstract Background Genomic three-dimensional (3D) spatial organization plays a key role in shaping gene expression and associated chromatin modification, and it is highly sensitive to environmental stress conditions. In microalgae, exposure to nitrogen stress can drive lipid accumulation, yet the associated functional alterations in the spatial organization of the microalgal genome have yet to be effectively characterized. Results Accordingly, the present study employed RNA-seq, Hi-C, and ChIP-seq approaches to explore the relationship between 3D chromosomal architecture and gene expression during lipid accumulation in the marine microalga Nannochloropsis oceanica in response to nitrogen deprivation (ND). These analyses revealed that ND resulted in various changes in chromosomal organization, including A/B compartment transitions, topologically associating domain (TAD) shifts, and the disruption of short-range interactions. Significantly higher levels of gene expression were evident in A compartments and TAD boundary regions relative to B compartments and TAD interior regions, consistent with observed histone modification enrichment in these areas. ND-induced differentially expressed genes (DEGs) were notably enriched in altered TAD-associated regions and regions exhibiting differential genomic contact. These DEGs were subjected to Gene Ontology (GO) term analyses that indicated they were enriched in the ‘fatty acid metabolism’, ‘response to stress’, ‘carbon fixation’ and ‘photosynthesis’ functional categories, in line with the ND treatment conditions used to conduct this study. These data indicate that Nannochloropsis cells exhibit a clear association between chromatin organization and transcriptional activity under nitrogen stress conditions. Pronounced and extensive histone modifications were evident in response to ND. Observed changes in chromatin architecture were linked to shifts in histone modifications and gene expression. Conclusions Overall, the reprogramming of many lipid metabolism-associated genes was evident under nitrogen stress conditions with respect to both histone modifications and chromosomal organization. Together these results revealed that higher-order chromatin architecture represents a new layer that can guide efforts to understand the transcriptional regulation of lipid metabolism in nitrogen-deprived microalgae.

The soil-derived Bacillus toyonensis HSY140 strain was found to produce parasporal crystalline inclusions. Genome sequencing and annotation did not find the three-domain Cry (3d-Cry) and Cyt toxins, but a novel mpp23-like gene (918 bp) containing an ETX/MTX2 domain was detected. Alignment and phylogenetic analysis revealed that the translated Mpp23-like protein had the highest homology to Cry23Aa1 (now named Mpp23Aa1, AAA22333.1). Cloning and expression of the mpp23-like gene into the acrystalliferous Bacillus thuringiensis BMB171 (cry-) generated a recombinant strain able to produce elliptical parasporal crystals with the same shape as those of the HSY140 strain. Finally, bioassay experiments indicated that the expressed Mpp23-like protein did not exhibit any activity to the lepidopteran insects of Plutella xylostella, Helicoverpa armigera, and Spodoptera exigua and the dipteran insect of Aedes aegypti. Altogether, we have characterized for the first time a new toxin, Mpp23-like protein, responsible for the formation of crystalline inclusions in B. toyonensis HSY140 strain. [ABSTRACT FROM AUTHOR]

Normalized difference vegetation index (NDVI) derived from satellites has been ubiquitously utilized in the field of remote sensing. Nevertheless, there are multitudinous contaminations in NDVI time series because of the atmospheric disturbance, cloud cover, sensor failure, and so on. It is crucial to remove the noises prior to further applications. Numerous techniques have been proposed to alleviate this issue in the last few decades. To the best of our knowledge, there hasn’t been a systematical study to summarize and analyze the status of NDVI time series reconstruction techniques since 1980s. As a result, our goal is to recapitulate the current approaches for reconstructing high-quality NDVI time series, followed by an interpretation on the principle, merits and demerits of different kinds of methods. They were mainly classified into temporal-based methods, frequency-based methods and hybrid methods. The evaluation approaches on the quality of NDVI reconstruction were introduced, accompanied with the future development tendency.