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opencc-by-4.0Apr 2023View details →

Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung

Code and data for the preprint "Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung".  Metagenomic analysis  - uses `<a href="https://github.com/ropensci/targets">targets</a>` (workflow manager) and `<a href="https://github.com/rstudio/renv">renv</a>` (environment manager) R packages.  - calling `targets::tar_make()`, once the environment is configured using renv and a separate project has been created (with the exact file structure including the data), should run the entire pipeline, creating a _targets folder with all the .rds files  - independent objects can be explored using `targets::tar_load(obj)` or `targets::tar_read(plot)`  <a href="https://books.ropensci.org/targets/">Targets user manual </a>for more information. Preprocessing/QC scripts can be provided upon reasonable request.

dryad32/100

Warming and grazing independently and interactively impact plant defenses and palatability

The ecological impacts of multiple stressors are hard to predict but important to understand. When multiple stressors influence foundation species, the effects can cascade throughout the ecosystem. Gulf of Mexico seagrass ecosystems are currently experiencing a suite of novel stressors, including warmer water temperatures and increased herbivory due to tropicalization and conservation efforts. We investigated the impact of warming temperatures and grazing history on plant performance, morphology, and palatability by integrating a mesocosm study using the seagrass Thalassia testudinum with feeding trials using the sea urchin Lytechinus variegatus. Warming temperatures negatively impacted T. testudinum tolerance traits, reducing belowground biomass by 34%, productivity by 74%, shoot density by 10%, and the number of leaves per plant by 24%, and negatively impacted resistance traits through 13% lower toughness of young leaves and a trend for reduced leaf carbon:nitrogen. Lytechinus variegatus individuals preferred to consume plants grown under heated conditions, which supports findings of enhanced palatability. Simulated turtle grazing impacted more plant traits than grazing by other herbivores, potentially diminishing plant resilience to future disturbances through reduced rhizome non-structural carbohydrate concentrations and increasing palatability through reduced fiber content and 23% lower leaf carbon:phosphorus. Simulated turtle, simulated parrotfish, and urchin grazing reduced leaf carbon:nitrogen by 11%, also potentially increasing nutritive value. Interactions between warming temperatures and grazers on plant traits were additive for 16 out of 19 response variables. However, the stressors non-additively impacted the number of leaves per plant, fiber content, and epiphyte load. We suggest that the impacts of grazers on leaf turnover rate and leaf age may vary based on water temperature, potentially driving these interactions. Overall, increased temperatures and grazing pressure will likely reduce seagrass resilience, structure, and biomass, potentially impacting feedback systems and producing negative consequences for seagrass cover, associated species, and ecosystem services.

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opencc-by-4.0Dec 2022View details →

Salivary chemical barrier proteins in Oral Squamous Cell Carcinoma – Alterations in the defense mechanism of the oral cavity

Oral squamous cell carcinoma (OSCC) is one of the most frequent type of head and neck cancers. Despite the genetic and environmental risk factors, OSCC is also associated with microbial infections and/or dysbiosis. The secreted saliva serves as the chemical barrier of the oral cavity and since OSCC can alter the protein composition of saliva, our aim was to analyze the effect of OSCC on the salivary chemical barrier proteins. Publicly available datasets regarding the analysis of salivary proteins from patients with OSCC and controls were collected and examined in order to identify differentially expressed chemical barrier proteins. The network analysis and gene onthology (GO) classification of the differentially expressed chemical barrier proteins were performed, as well. 127 proteins showing different expression pattern between the OSCC and control groups were found. The protein-protein interaction network of up- and down-regulated proteins were constructed and analyzed. The main hub proteins (IL-6, IL-1B, IL-8, TNF, APOA1, APOA2, APOB, APOC3, APOE, and HP) were identified and the enriched GO terms were examined. Our study highlighted the importance of the chemical barrier of saliva in the development of OSCC.

Fig. 4 in Suspension cell secretome of the grain legume Lathyrus sativus (grasspea) reveals roles in plant development and defense responses

Fig. 4. Physicochemical assessment of the grasspea suspension secretome (GSS), including pI (A), molecular weight (in kDa) (B), and hydrophilicity (C), with respect to MSS, DSS and LSS (MSS corresponds to the monocot suspension secretome, DSS to the dicot suspension secretome and LSS to the lower plant suspension secretome).

Fig. 2 in Suspension cell secretome of the grain legume Lathyrus sativus (grasspea) reveals roles in plant development and defense responses

Fig. 2. Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments.

Fig. 3 in Suspension cell secretome of the grain legume Lathyrus sativus (grasspea) reveals roles in plant development and defense responses

Fig. 3. Overview of total grasspea suspension secreted (GSS) proteins and prediction of mode of secretion and (A) localization using multiple tools (B). Comparison of shared and distinct GSS proteins, first (C) with respect to total in vitro secretome (IVS) and in planta secretome (IPS) and second (D) compared to the in vitro suspension culture secretome reported in monocots, dicots, and lower plants, abbreviated as MSS, DSS and LSS, respectively (MSS corresponds to monocot suspension secretome, DSS to dicot suspension secretome and LSS to lower plant suspension secretome).

Fig. 1 in Suspension cell secretome of the grain legume Lathyrus sativus (grasspea) reveals roles in plant development and defense responses

Fig. 1. Schematic representation of the experimental design and workflow of the establishment of the grasspea suspension secretome (GSS). Proteomic profiling was accomplished by generating suspension culture and sequential assessment of physicochemical properties and protein identification.

Fig. 6 in Suspension cell secretome of the grain legume Lathyrus sativus (grasspea) reveals roles in plant development and defense responses

Fig. 6. Localization validation of endochitinase (S597) and G-type lectin S-receptor-like serine threonine kinase (S718). The panels include (A) expression of YFPtagged S597 in onion epidermal cells, (B) plasmolysis of S597-transformed onion peel (C), expression of YFP-tagged S718 in onion peel cells and (D) plasmolyzed onion peel cells expressing YFP-tagged S718. A pSITE3CA empty vector control was also monitored besides the target genes (E).

Fig. 6 in α-Linolenic acid in Papilio machaon larvae regurgitant induces a defensive response in Apiaceae

Fig. 6. Accumulation of specialized metabolites in S. divaricata treated with α-LA or water for 5 days. Contents in fresh plants are shown. Values are presented as means ± SE with n = 3 plants per group. The differences were analyzed using Student's t-test. The significance was set at *P <0.05 compared with water treatment (control).

Fig. 5 in α-Linolenic acid in Papilio machaon larvae regurgitant induces a defensive response in Apiaceae

Fig. 5. GC–MS TIC chromatograms of extracts of S. divaricata treated with water (1) or α-LA (2) for 5 days.

Fig. 4 in α-Linolenic acid in Papilio machaon larvae regurgitant induces a defensive response in Apiaceae

Fig. 4. Time course of induction of volatile components by α-LA or water treatment. In the enlarged chromatograms from 4 to 5 min, the ion with m/z 69 was extracted to monitor the amount of cis-3-hexenal. GC–MS XIC chromatograms of S. divaricata treated with α-LA (A) or water (D), C. japonica treated with α-LA (B) or water (E), and P. crispum treated with α-LA (C) or water (F).

Fig. 3 in α-Linolenic acid in Papilio machaon larvae regurgitant induces a defensive response in Apiaceae

Fig. 3. Time course of induction of volatile components by α-LA or water treatment. GC–MS TIC chromatograms of S. divaricata treated with α-LA (A) or water (D), C. japonica treated with α-LA (B) or water (E), and P. crispum treated with α-LA (C) or water (F).

Fig. 2 in α-Linolenic acid in Papilio machaon larvae regurgitant induces a defensive response in Apiaceae

Fig. 2. Structure elucidation of FAs in the regurgitant of P. machaon hippocrates. GC–MS TIC chromatograms of the regurgitant of P. machaon hippocrates larvae feeding on A. acutiloba (1) and G. littoralis (2). GC–MS TIC chromatograms of standard mixture (3).

Fig. 1 in α-Linolenic acid in Papilio machaon larvae regurgitant induces a defensive response in Apiaceae

Fig. 1. LC–MS total ion current (TIC) chromatograms and extracted-ion current (XIC) chromatograms of the regurgitant of P. machaon hippocrates larvae feeding on A. acutiloba (A) and G. littoralis (B). TIC chromatograms of methanol extracts derived from the leaves of A. actiloba (C) and G. littoralis (D). (1) TIC positive ion mode; (2) TIC negative ion mode; (3) m/z 423.2853 ([M + H]+ of volicitin [N-(17-hydroxylinolenoyl)-L-glutamine]); (4) m/z 407.2904 ([M+H]+ of N-linolenoyl-Lglutamine); (5) m/z 409.2823 ([M+H]+ of N-linolenoyl-L-glutamic acid); (6) m/z 421.2708 ([M–H]–of volicitin [N-(17-hydroxylinolenoyl)-L-glutamine]); (7) m/z 405.2759 ([M–H]– of N-linolenoyl-L-glutamine); (8) m/z 407.2677 ([M–H]– of N-linolenoyl-L-glutamic acid).

Fig. 3 in Involvement of OsRIP1, a ribosome-inactivating protein from rice, in plant defense against Nilaparvata lugens

Fig. 3. Average biomass per surviving insect. Every day of the feeding experiment, the average weight per surviving insect was determined by weighing separate feeding cages with and without the surviving insects and dividing the difference in mass by the number of insects in that cage. This was done for the three repeats per treatment and the averages and standard errors are represented. Statistical differences on day 3 are represented by asterisks (*: p ≤ 0.05, **: p ≤ 0.01, ***: p ≤ 0.001).

Fig. 2 in Involvement of OsRIP1, a ribosome-inactivating protein from rice, in plant defense against Nilaparvata lugens

Fig. 2. Effect of different concentrations of OsRIP1 compared on N. lugens survival and development. 30 insects (three cages with each 10 insects) were fed with artificial diet, supplemented with either different concentrations of OsRIP1 (0.75 μM, 1.5 μM or 3 μM), BSA (3 μM) or buffer only, for 3 days. Every day the artificial diet was refreshed, the surviving insects were counted and the developmental stage of each insect was assessed. Letters (a, b, c) denote statistical differences observed between treatments. (Jonckheere-Terpstra test with pairwise multiple comparisons, p <0.05).

Fig. 4 in Involvement of OsRIP1, a ribosome-inactivating protein from rice, in plant defense against Nilaparvata lugens

Fig. 4. Effect of OsRIP1 on translation in a cell-free transcription/translation system based on insect cell extract. The dose dependent effect of recombinant OsRIP1 on the translation of luciferase was assessed using a luminometer. Percentage of translation (= percentage of luciferase activity) is shown as a function of OsRIP1 concentration. BSA was used as a control. Data of two independent replicates are shown.

Fig. 1. Transcript levels for OsRIP1 in Involvement of OsRIP1, a ribosome-inactivating protein from rice, in plant defense against Nilaparvata lugens

Fig. 1. Transcript levels for OsRIP1 in rice shoots after high (A) or low (B) infestation with N. lugens. Expression of OsRIP1 in BPH infested seedlings was determined at different timepoints (3, 5, 6, 9 or 13 days post infestation (dpi)), relative to the transcript levels in mock treated plants. Bars represent mean expression values from three independent biological replicates (normalized to three reference genes), error bars indicate standard errors. Asterisks indicate statistically significant differences compared to expression levels in mock treated plants (*p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001).