Comparative Analysis of Physiological, Enzymatic, and Transcriptomic Responses Revealed Mechanisms of Salt Tolerance and Recovery in Tritipyrum

Salt stress results in the severe decline of yield and quality in wheat. In the present study, salt-tolerant Tritipyrum (“Y1805”) and salt-sensitive wheat “Chinese Spring” (“CS”) were selected from 121 wheat germplasms to test their physiological, antioxidant enzyme, and transcriptomic responses and mechanisms against salt stress and recovery. 56 chromosomes were identified in “Y1805” that comprised A, B, and D chromosomes from wheat parent and E chromosomes from Thinopyrum elongatum, adding to salt-tolerant trait. Salt stress had a greater inhibitory effect on roots than on shoots, and “Y1805” demonstrated stronger salt tolerance than “CS.” Compared with “CS,” the activities of superoxide dismutase and catalase in “Y1805” significantly increased under salt stress. “Y1805” could synthesize more proline and soluble sugars than “CS.” Both the net photosynthetic rate and chlorophyll a/b were affected by salt stress, though the level of damage in “Y1805” was significantly less than in “CS.” Transcriptome analysis showed that the differences in the transcriptional regulatory networks of “Y1805” were not only in response to salt stress but also in recovery. The functions of many salt-responsive differentially expressed genes were correlated closely with the pathways “peroxisome,” “arginine and proline metabolism,” “starch and sucrose metabolism,” “chlorophyll and porphyrin metabolism,” and “photosynthesis.”

Transcriptomic responses of the human kidney to acute injury at single cell resolution

Background: Acute kidney injury (AKI) occurs frequently in critically ill patients and is associated with adverse outcomes. Cellular mechanisms underlying AKI and kidney cell responses to injury remain incompletely understood. Methods: We performed single-nuclei transcriptomics, bulk transcriptomics, molecular imaging studies, and conventional histology on kidney tissues from 8 individuals with severe AKI (stage 2 or 3 according to Kidney Disease: Improving Global Outcomes (KDIGO) criteria). Specimens were obtained within 1-2 hours after individuals had succumbed to critical illness associated with respiratory infections, with 4 of 8 individuals diagnosed with COVID-19. Control kidney tissues were obtained post-mortem or after nephrectomy from individuals without AKI. Results: High-depth single cell-resolved gene expression data of human kidneys affected by AKI revealed enrichment of novel injury-associated cell states within the major cell types of the tubular epithelium, in particular in proximal tubules, thick ascending limbs and distal convoluted tubules. Four distinct, hierarchically interconnected injured cell states were distinguishable and characterized by transcriptome patterns associated with oxidative stress, hypoxia, interferon response, and epithelial-to-mesenchymal transition, respectively. Transcriptome differences between individuals with AKI were driven primarily by the cell type-specific abundance of these four injury subtypes rather than by private molecular responses. AKI-associated changes in gene expression between individuals with and without COVID-19 were similar. Conclusion: The study provides an extensive resource of the cell type-specific transcriptomic responses associated with critical illness-associated AKI in humans, highlighting recurrent disease-associated signatures and inter-individual heterogeneity. Personalized molecular disease assessment in human AKI may foster the development of tailored therapies.

Gill Transcriptomic Responses to Toxin-producing Alga Prymnesium parvum in Rainbow Trout

The gill of teleost fish is a multifunctional organ involved in many physiological processes, including protection of the mucosal gill surface against pathogens and other environmental antigens by the gill-associated lymphoid tissue (GIALT). Climate change associated phenomena, such as increasing frequency and magnitude of harmful algal blooms (HABs) put extra strain on gill function, contributing to enhanced fish mortality and fish kills. However, the molecular basis of the HAB-induced gill injury remains largely unknown due to the lack of high-throughput transcriptomic studies performed on teleost fish in laboratory conditions. We used juvenile rainbow trout (Oncorhynchus mykiss) to investigate the transcriptomic responses of the gill tissue to two (high and low) sublethal densities of the toxin-producing alga Prymnesium parvum, in relation to non-exposed control fish. The exposure time to P. parvum (4–5 h) was sufficient to identify three different phenotypic responses among the exposed fish, enabling us to focus on the common gill transcriptomic responses to P. parvum that were independent of dose and phenotype. The inspection of common differentially expressed genes (DEGs), canonical pathways, upstream regulators and downstream effects pointed towards P. parvum-induced inflammatory response and gill inflammation driven by alterations of Acute Phase Response Signalling, IL-6 Signalling, IL-10 Signalling, Role of PKR in Interferon Induction and Antiviral Response, IL-8 Signalling and IL-17 Signalling pathways. While we could not determine if the inferred gill inflammation was progressing or resolving, our study clearly suggests that P. parvum blooms may contribute to the serious gill disorders in fish. By providing insights into the gill transcriptomic responses to toxin-producing P. parvum in teleost fish, our research opens new avenues for investigating how to monitor and mitigate toxicity of HABs before they become lethal.

Larval Transcriptomic Responses of a Stony Coral, Acropora Tenuis, During Initial Contact with the Native Symbiont, Symbiodinium Microadriaticum

Although numerous dinoflagellate species (Family Symbiodiniaceae) are present in coral reef environments, Acropora corals tend to select a single species, Symbiodinium microadriaticum, in early life stages, even though this species is rarely found in mature colonies. In order to identify molecular mechanisms involved in initial contact with native symbionts, we analyzed transcriptomic responses of Acropora tenuis larvae at 1, 3, 6, 12, and 24 h after their first contact, together with inoculation using non-native symbionts, including the non-symbiotic S. natans and the occasional symbiont, S. tridacnidorum. Some gene expression changes were detected in larvae inoculated with non-native symbionts 1 h post-inoculation (hpi)), but those returned to baseline levels afterward. In contrast, we found that the number of differentially expressed genes gradually increased in relation to inoculation time when larvae were exposed to native symbionts. As a specific response to native symbionts, upregulation of pattern recognition receptor-like and transporter genes, and suppression of cellular function genes related to immunity and apoptosis, were exclusively observed. These findings indicate that coral larvae recognize differences between symbionts, and when the appropriate symbionts infect, they coordinate gene expression to establish stable mutualism.

Transcriptomic responses of Galapagos finches to avian pox virus infection

Emerging pathogens can have devastating effects on naive hosts, but disease outcomes often vary among hosts. Comparing the cellular response of different host species to infection can provide insight into mechanisms of host defense and the basis of host susceptibility to disease. Here, we used RNA-seq to characterize the transcriptomic response of Darwin's finches to avian poxvirus, which is introduced to the Galapagos Islands. We tested whether gene expression differs between infected and uninfected birds, and whether transcriptomic differences were related either to known antiviral mechanisms and/or the co-option of the host cellular environment by the virus. We compared two species, the medium ground finch (Geospiza fortis) and the vegetarian finch (Platyspiza crassirostris), to determine whether related species have similar responses to the same novel pathogen. We found that medium ground finches had a strong transcriptomic response to infection, upregulating genes involved in the innate immune response including interferon production, inflammation, and other immune signaling pathways. In contrast, vegetarian finches had a more limited response to infection. Our results also revealed evidence of viral manipulation of the host's cellular function and metabolism, providing insight into the ways in which poxviruses affect their hosts. Many of the transcriptomic responses to infection mirrored known processes seen in model and in-vitro studies of poxviruses indicating that many pathways of host defense against poxviruses are conserved among vertebrates and present even in hosts without a long evolutionary history with the virus. At the same time, the variation we observed between closely related species indicates that some endemic species of Galapagos finch may be more susceptible to avian pox than others.

RNA-sequencing elucidates drug-specific mechanisms of antibiotic tolerance and resistance in M. abscessus

Mycobacterium abscessus is an opportunistic pathogen notorious for its resistance to most classes of antibiotics and low cure rates. M. abscessus carries an array of mostly unexplored defence mechanisms. A deeper understanding of antibiotic resistance and tolerance mechanisms is pivotal in development of targeted therapeutic regimens. We provide the first description of all major transcriptional mechanisms of tolerance to all antibiotics recommended in current guidelines, using RNA sequencing-guided experiments. M. abscessus ATCC 19977 bacteria were subjected to sub-inhibitory concentrations of clarithromycin, amikacin, tigecycline, cefoxitin and clofazimine for 4- and 24-hours, followed by RNA sequencing. To confirm key mechanisms of tolerance suggested by transcriptomic responses, we performed time-kill kinetic analysis using bacteria after pre-exposure to clarithromycin, amikacin or tigecycline for 24-hours and we constructed isogenic knockout and knockdown strains. To assess strain specificity, pan-genome analysis of 35 strains from all three subspecies was performed. Mycobacterium abscessus shows both drug-specific and common transcriptomic responses to antibiotic exposure. Ribosome-targeting antibiotics clarithromycin, amikacin and tigecycline elicit a common response characterized by upregulation of ribosome structural genes, the WhiB7 regulon and transferases, accompanied by downregulation of respiration through NuoA-N. Exposure to any of these drugs decreases susceptibility to ribosome-targeting drugs from multiple classes. The cytochrome bd-type quinol oxidase contributes to clofazimine tolerance in M. abscessus and the sigma factor sigH but not anti-sigma factor MAB_3542c is involved in tigecycline resistance. The observed transcriptomic responses are not strain-specific, as all genes involved in tolerance, except erm(41), are found in all included strains.