Complete genomes of xenobiotic-degrading microorganisms provide valuable resources for researchers to understand molecular mechanisms involved in bioremediation. Despite the well-known ability of Sphingomonas paucimobilis to degrade persistent xenobiotic compounds, a complete genome sequencing is lacking for this organism. In line with this, we report the first complete genome sequence of Sphingomonas paucimobilis (strain AIMST S2), an organophosphate and hydrocarbon-degrading bacterium isolated from oil-polluted soil at Kedah, Malaysia. The genome was derived from a hybrid assembly of short and long reads generated by Illumina HiSeq and MinION, respectively. The assembly resulted in a single contig of 4,005,505 bases which consisted of 3,612 CDS and 56 tRNAs. An array of genes involved in xenobiotic degradation and plant-growth promoters were identified, suggesting its’ potential role as an effective microorganism in bioremediation and agriculture. Having reported the first complete genome of the species, this study will serve as a stepping stone for comparative genome analysis of Sphingomonas strains and other xenobiotic-degrading microorganisms as well as gene expression studies in organophosphate biodegradation.

The IL-2 family of cytokines act via receptor complexes that share the interleukin-2 receptor gamma common (IL-2Rγc) chain to play key roles in lymphopoiesis. Inactivating IL-2Rγc mutations results in severe combined immunodeficiency (SCID) in humans and other species. This study sought to generate an equivalent zebrafish SCID model. The zebrafish il2rga gene was targeted for genome editing using TALENs and presumed loss-of-function alleles analyzed with respect to immune cell development and impacts on intestinal microbiota and tumor immunity. Knockout of zebrafish Il-2rγc.a resulted in a SCID phenotype, including a significant reduction in T cells, with NK cells also impacted. This resulted in dysregulated intestinal microbiota and defective immunity to tumor xenotransplants. Collectively, this establishes a useful zebrafish SCID model.

A simple method for tracing carbon fixation and lipid synthesis in microalgae was developed using a combination of solid-phase extraction (SPE) and negative ion chemical ionisation gas chromatography mass spectrometry (NCI-GC-MS). NCI-GC-MS is an extremely sensitive technique that can produce an unfragmented molecular ion making this technique particularly useful for stable isotope enrichment studies. Derivatisation of fatty acids using pentafluorobenzyl bromide (PFBBr) allows the coupling of the high separation efficiency of GC and the measurement of unfragmented molecular ions for each of the fatty acids by single quadrupole MS. The key is that isotope spectra can be measured without interference from co-eluting fatty acids or other molecules. Pre-fractionation of lipid extracts by SPE allows the measurement of ¹³C isotope incorporation into the three main lipid classes (phospholipids, glycolipids, neutral lipids) in microalgae thus allowing the study of complex lipid biochemistry using relatively straightforward analytical technology. The high selectivity of GC is necessary as it allows the collection of mass spectra for individual fatty acids, including cis/trans isomers, of the PFB-derivatised fatty acids. The combination of solid-phase extraction and GC-MS enables the accurate determination of ¹³C incorporation into each lipid pool. Three solvent extraction protocols that are commonly used in lipidomics were also evaluated and are described here with regard to extraction efficiencies for lipid analysis in microalgae.

A Gram-negative, filamentous aerobic bacterium designated as strain Mgbs1^T was isolated on 12 April 2017 from the subsurface soil and leaf litter substrate at the base of a Koompassia malaccensis tree in a tropical peat swamp forest in the northern regions of the state of Selangor, Malaysia (3° 39′ 04.7′ N 101° 17′ 43.7′′ E). Phylogenetic analyses based on the full 16S rRNA sequence revealed that strain Mgbs1^T belongs to the genus Chitinophaga with the greatest sequence similarity to Chitinophaga terrae KP01^T (97.65 %), Chitinophaga jiangningensis DSM27406^T (97.58 %), and Chitinophaga dinghuensis DHOC24^T (97.17 %). The major fatty acids of strain Mgbs1^T (>10 %) are iso-C_15 : 0, C_16 : 1  ω5c and iso-C_17 : 0 3-OH while the predominant respiratory quinone is menaquinone-7. Strain Mgbs1^T has a complete genome size of 8.03 Mb, with a G+C content of 48.5 mol%. The DNA–DNA hybridization (DDH) score between strain Mgbs1^T and C. jiangningensis DSM27406^T was 15.9 %, while in silico DDH values of strain Mgbs1^T against C. dinghuensis DHOC24^T and C. terrae KP01^T were 20.0 and 19.10% respectively. Concurrently, Average Nucleotide Identity (ANI) scores between strain Mgbs1^T against all three reference strains are 73.2 %. Based on the phenotypic, chemotaxonomic, and phylogenetic consensus, strain Mgbs1^T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga extrema sp. nov. is proposed (=DSM 108835^T=JCM 33276^T).

Mitochondria are central to cellular function, particularly in metabolically active tissues such as skeletal muscle. Nuclear‐encoded RNAs typically localize within the nucleus and cytosol but a small population may also translocate to subcellular compartments such as mitochondria. We aimed to investigate the nuclear‐encoded RNAs that localize within the mitochondria of skeletal muscle cells and tissue. Intact mitochondria were isolated via immunoprecipitation (IP) followed by enzymatic treatments (RNase‐A and proteinase‐K) optimized to remove transcripts located exterior to mitochondria, making it amenable for high‐throughput transcriptomic sequencing. Small RNA sequencing libraries were successfully constructed from as little as 1.8 ng mitochondrial RNA input. Small RNA sequencing of mitochondria from rat myoblasts revealed the enrichment of over 200 miRNAs. Whole‐transcriptome RNA sequencing of enzymatically purified mitochondria isolated by IP from skeletal muscle tissue showed a striking similarity in the degree of purity compared to mitoplast preparations which lack an outer mitochondrial membrane. In summary, we describe a novel, powerful sequencing approach applicable to animal and human tissues and cells that can facilitate the discovery of nuclear‐encoded RNA transcripts localized within skeletal muscle mitochondria.

Understanding the molecular mechanisms of heat tolerance could help to predict the impacts of climate change on our native flora. However, much of our current understanding is derived from Arabidopsis thaliana and select crops exposed to short and intense periods of heat stress. Here, we characterise the transcriptomic response of Wahlenbergia ceracea , a perennial herb found in Australia’s subalpine regions, to sustained moderate warming. We contrasted responses between relatively heat-tolerant and heat-sensitive lines grown under cool (24/15 ºC day/night) or warm (30/20 ºC) temperatures. We observed that sustained warming up-regulated genes related to RNA regulation, including modification and splicing, and down-regulated genes associated with photosynthesis and plastid organization. Interestingly, heat-tolerant lines demonstrated a more pronounced repression of photosynthesis-associated genes, compared to heat-sensitive lines, suggesting that the regulation of the light-harvesting machinery may contribute to photosystem thermal tolerance. Co-expression analyses revealed only weak module-level correlations with direct measures of thermal tolerance. However, stronger associations were evident with chlorophyll content and photosynthetic efficiency, which might indirectly influence thermal tolerance. Prediction of transcription factors targeting warming-responsive genes implicated hormone signaling networks, especially ethylene, in contributing to differences in thermal tolerance. In conclusion, we present genomic resources for transcriptome analyses in W. ceracea and highlight the contrasting gene regulatory patterns between relatively heat-tolerant and heat-sensitive W. ceracea lines experiencing sustained moderate warming.