The transcriptome analysis on urea response mechanism in the process of ergosterol synthesis by Cordyceps cicadae

Nitrogen source is required for the growth of Cordyceps cicadae and involved in the regulation of metabolite synthesis. In order to further investigate the regulatory effects of nitrogen sources on the ergosterol synthesis by C. cicadae. We first confirmed that urea could significantly increase the ergosterol synthesis. The transcriptome analysis showed that compared with biomass cultured in the control fermentation medium (CFM), 1340 differentially expressed genes (DEGs) were obtained by Gene Ontology (GO) annotation, and 312 DEGs were obtained by Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation from the biomass cultured in CFM + CO(NH2)2. Urea up-regulated D-3-phosphoglycerate dehydrogenase gene transcription level and down-regulated enolase and L-serine/L-threonine ammonialyase gene transcription level, increased serine synthesis, allosterically activate pyruvate kinase, to promote the synthesis of pyruvate and CH3CO ~ SCOA, the primer of ergosterol; Urea increase the genes transcription related with ergosterol synthesis by up-regulating the steroid regulatory element binding protein gene transcription levels. The transcriptome results were provided by those of qRT-PCR. Collectively, our finding provided valuable insights into the regulatory effect of nitrogen source on the ergosterol synthesis by C. cicadae.

Long Non-coding RNAs Responsive to Blast Fungus Infection in Rice

Background Long non-coding RNAs (LncRNAs) have emerged as important regulators in many physiological processes in plant. By high-throughput RNA-sequencing, many pathogen-associated LncRNAs were mapped in various plants, and some of them were proved to be involved in plant defense responses. The rice blast disease caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases in rice. However, M. oryzae-induced LncRNAs in rice is yet to be studied. Findings We investigated rice LncRNAs that were associated with the rice blast fungus. Totally 83 LncRNAs were up-regulated after blast fungus infection and 78 were down-regulated. Of them, the natural antisense transcripts (NATs) were the most abundant. The expression of some LncRNAs has similar pattern with their host genes or neighboring genes, suggesting a cis function of them in regulating gene transcription level. The deferentially expressed (DE) LncRNAs and genes co-expression analysis revealed some LncRNAs were associated with genes known to be involved in pathogen resistance, and these genes were enriched in terpenoid biosynthesis and defense response by Gene Ontology (GO) enrichment analysis. Interestingly, one of up-regulated DE-intronic RNA was derived from a jasmonate (JA) biosynthetic gene, lipoxygenase RLL (LOX-RLL). Levels of JAs were significantly increased after blast fungus infection. Given that JA is known to regulate blast resistance in rice, we suggested that LncRNA may be involved in JA-mediated rice resistance to blast fungus. Conclusions This study identified blast fungus-responsive LncRNAs in rice, which provides another layer of candidates that regulate rice and blast fungus interactions.

Long non-coding RNAs responsive to blast fungus infection in rice

Background Long non-coding RNAs (LncRNAs) have emerged as important regulators in many physiological processes in plant. By high-throughput RNA-sequencing, many pathogen-associated LncRNAs were mapped in various plants, and some of them were proved to be involved in plant defense responses. The rice blast disease caused by Magnaporthe oryzae ( M. oryzae ) is one of the most destructive diseases in rice. However, M. oryzae -induced LncRNAs in rice is yet to be studied. Findings We investigated rice LncRNAs that were associated with the rice blast fungus. Totally 83 LncRNAs were up-regulated after blast fungus infection and 78 were down-regulated. Of them, the natural antisense transcripts (NATs) were the most abundant. The expression of some lncRNAs has similar pattern with their host genes or neighboring genes, suggesting a cis function of them in regulating gene transcription level. The deferentially expressed (DE) LncRNAs and genes co-expression analysis revealed some LncRNAs were associated with genes known to be involved in pathogen resistance, and these genes were enriched in terpenoid biosynthesis and defense response by Gene Ontology (GO) enrichment analysis. Interestingly, one of up-regulated DE-intronic RNA was derived from a jasmonate (JA) biosynthetic gene, lipoxygenase RLL (LOX-RLL). Levels of JAs were significantly increased after blast fungus infection. Given that JA is known to regulate blast resistance in rice, we suggested that LncRNA may be involved in JA-mediated rice resistance to blast fungus. Conclusions This study identified blast fungus-responsive LncRNAs in rice, which provides another layer of candidates that regulate rice and blast fungus interactions.

To be more precise: the role of intracellular trafficking in development and pattern formation

Living cells interpret a variety of signals in different contexts to elucidate functional responses. While the understanding of signalling molecules, their respective receptors and response at the gene transcription level have been relatively well-explored, how exactly does a single cell interpret a plethora of time-varying signals? Furthermore, how their subsequent responses at the single cell level manifest in the larger context of a developing tissue is unknown. At the same time, the biophysics and chemistry of how receptors are trafficked through the complex dynamic transport network between the plasma membrane–endosome–lysosome–Golgi–endoplasmic reticulum are much more well-studied. How the intracellular organisation of the cell and inter-organellar contacts aid in orchestrating trafficking, as well as signal interpretation and modulation by the cells are beginning to be uncovered. In this review, we highlight the significant developments that have strived to integrate endosomal trafficking, signal interpretation in the context of developmental biology and relevant open questions with a few chosen examples. Furthermore, we will discuss the imaging technologies that have been developed in the recent past that have the potential to tremendously accelerate knowledge gain in this direction while shedding light on some of the many challenges.

Long non-coding RNAs responsive to blast fungus infection in rice

Background Long non-coding RNAs (LncRNAs) have emerged as important regulators in many physiological processes in plant. By high-throughput RNA-sequencing, many pathogen-associated lncRNAs were mapped in various plants, and some of them were proved to be involved in plant defense responses. The rice blast disease caused by Magnaporthe oryzae (M. oryzae ) is one of the most destructive diseases in rice. However, M. oryzae-induced lncRNAs in rice is yet to be studied. Findings: We investigated rice lncRNAs that were associated with the rice blast fungus. Totally 83 lncRNAs were up-regulated after blast fungus infection and 78 were down-regulated. Of them, the natural antisense transcripts (NATs) were the most abundant. The expression of some lncRNAs has similar pattern with their host genes or neighboring genes, suggesting a cis function of them in regulating gene transcription level. The deferentially expressed (DE) lncRNAs and genes co-expression analysis revealed some lncRNAs were associated with genes known to be involved in pathogen resistance, and these genes were enriched in terpenoid biosynthesis and defense response by Gene Ontology (GO) enrichment analysis. Interestingly, one of up-regulated DE-intronic RNA was derived from a jasmonate (JA) biosynthetic gene, lipoxygenase RLL (LOX-RLL). Levels of JAs were significantly increased after blast fungus infection. Given that JA is known to regulate blast resistance in rice, we suggested that lncRNA may be involved in JA-mediated rice resistance to blast fungus. Conclusions This study identified blast fungus-responsive lncRNAs in rice, which provides another layer of candidates that regulate rice and blast fungus interactions.

Osmotic and ionic regulation by hololimnetic freshwater crustaceans: a molecular role for gill ion transporters

Owing to their extraordinary niche diversity, the Crustacea are ideal for comprehending the evolution of osmoregulation. The processes that effect systemic hydro-electrolytic homeostasis maintain hemolymph ionic composition via membrane transporters located in highly specialized gill ionocytes. We evaluated physiological and molecular hyper- and hypo-osmoregulatory mechanisms in two phylogenetically distant, freshwater crustaceans, the crab Dilocarcinus pagei and the shrimp Macrobrachium jelskii, when osmotically challenged for up to 10 days. When in distilled water, hemolymph osmolality and [Cl−] increased briefly in D. pagei, stabilizing at initial values, while [Na+] decreased continually. Gill V(H+)-ATPase, Na+/K+-ATPase and Na+/K+/2Cl− gene expressions were unchanged. In M. jelskii, hemolymph osmolality, [Cl−] and [Na+] decreased continually for 12 h, the shrimps no longer surviving. Gill transporter gene expressions increased 2- to 5-fold. After 10-days exposure to brackish water, D. pagei was isosmotic, iso-chloremic and iso-natriuremic. Gill V(H+)-ATPase expression decreased while Na+/K+-ATPase and Na+/K+/2Cl− expressions were unchanged. In M. jelskii, the hemolymph was hypo-regulated, particularly [Cl−]. Transporter expressions initially increased 3- to 12-fold, declining to control values. Gill V(H+)-ATPase expression underlies the ability of D. pagei to survive in fresh water while Na+/K+-ATPase and Na+/K+/2Cl− expressions enable M. jelskii to deal with osmotic challenge. These findings reveal divergent responses in two unrelated crustaceans habiting a similar osmotic niche. While D. pagei has maintained the capacity to tolerate elevated cellular isosmoticity despite its inability to secrete salt, M. jelskii displays clear hypo-osmoregulatory ability. Each species has developed distinct strategies at the transcription and systemic levels during adaptation to fresh water.Summary statementDuring their evolutionary adaptation to fresh water, unrelated hololimnetic crustaceans have developed physiological strategies like tolerating elevated cellular isosmoticity or regulating hypo-osmoregulatory ability at the gene transcription level.

Transcriptome analysis of maize reveals potential key genes involved in the response to belowground herbivore Holotrichia parallela larvae feeding

The larvae of Holotrichia parallela, a destructive belowground herbivore, causes tremendous damages to maize plants. However, little is known if there are any defense mechanisms in maize roots to defend themselves against this herbivore. In the current research, we carried out RNA-sequencing to investigate the changes in gene transcription level in maize roots after H. parallela larvae infestation. A total of 644 up-regulated genes and 474 down-regulated genes was found. In addition, Gene ontology (GO) annotation analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed. Weighted gene co-expression network analysis (WGCNA) indicated that peroxidase genes may be the hub genes that regulate maize defenses to H. parallela larvae attack. We also found 105 transcription factors, 44 hormone-related genes, and 62 secondary metabolism-related genes within differentially expressed genes (DEGs). Furthermore, the expression profiles of 12 DEGs from the transcriptome analysis were confirmed by quantitative real-time PCR experiments. This transcriptome analysis provides insights into the molecular mechanisms of the underground defense in maize roots to H. parallela larvae attack and will help to select target genes of maize for defense against belowground herbivory.

Microbial assembly, interaction, functioning, activity and diversification: a review derived from community compositional data

Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge in studies on marine microbial community composition using high-throughput sequencing methods. Extensive mining of the compositional data has provided exciting new insights into marine microbial ecology from a number of perspectives. Both deterministic and stochastic processes contribute to microbial community assembly but their relative importance in structuring subcommunities, that are categorized by traits such as abundance, functional type and activity, differs. Through correlation-based network analysis, significant progress has been made in unraveling microbial co-occurrence patterns and dynamics in response to environmental changes. Prediction of ecosystem functioning, based on microbial data, is receiving increasing attention, as closely related microbes often share similar ecological traits and microbial diversity often exhibits significant correlations to ecosystem functioning. The ecosystem functioning is likely executed not by the whole community, but rather by an active fraction of a community, which can be inferred from the marker gene transcription level of community members. Furthermore, the huge amount of microbial community data has significantly expanded the tree of life and illuminated microbial phylogenetic divergence and evolutionary history. This review summarizes important findings in microbial assembly, interaction, functioning, activity and diversification, highlighting the interacting roles of different aspects, derived from community compositional data.