Project description:Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics (the study of the whole protein complement of a microbial community) can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. Here we present a systematic investigation of variables concerning database construction and annotation, and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. Taxonomic and functional results were revealed to be strongly database-dependent, especially when dealing with mouse samples. As a striking example, in mouse the Firmicutes/Bacteroidetes ratio varied up to 10-fold depending on the database used. Finally, we provide recommendations regarding metagenomic sequence processing aimed at maximizing gut metaproteome characterization, and contribute to identify an optimized pipeline for metaproteomic data analysis.
Project description:In this study, RNA-seq based comparative transcriptome analysis was used to study the genetic response of maize silk to pollen tube penetration and in comparison to the fungal invasion of Fusarium graminearum and Ustilago maydis. RNA-seq libraries of 8 tissues were generated from leaf, root, seed, pollen tube, silk, pollinated silk, infected silk with Fusarium and infected silk with Ustilago.
Project description:We used tomato pollen in order to identify pollen stage-specific small non-coding RNAs (sncRNAs) and their target mRNAs. We further deployed elevated temperatures to discern stress responsive sncRNAs. For this purpose high throughput sncRNA-sequencing was performed for three-replicated sncRNAs libraries derived from tomato tetrad, post-meiotic, and mature pollen under control and heat stress conditions.
Project description:In tomato, there are seven ethylene receptors, ETR1, ETR2, ETR3, ETR4, ETR5, ETR6, and ETR7. In our laboratory, we have ETR3, ETR4, and ETR7, loss-of-function single mutants, in this study we compare the pollen tube length of ETR mutant KO with WT and NR (never rip) gain of function mutant. We found the pollen tube length in ETR3, ETR4, and ETR7 (KO) was more than WT; on the other hand, NR was less than WT, and the treatment by ethylene (ET) increase the length of pollen tube in all ETRs KO and WT but not in NR. The treatment by MCP-1 decreases the pollen tube length slightly in WT, 20% in ETR (KO) and no effect in NR. In conclusion, our results suggest that ethylene receptors (ETRs) in the active state inhibit pollen tube growth; therefore the ethylene is an essential factor for male gametophyte growth.
Project description:The expression analysis had two goals: (1) look at relative transcription within mature pollen grains (2) compare expression in the stigma during pollination with either compatible or in-compatible pollen. Two pairwise comparisons, (i) unpollinated stigma vs. stigma pollinated with compatible pollen, and (ii) unpollinated stigma vs stigma pollinated with incompatible pollen. The genotype where stigma samples were harvested from is F1-30, and this is also the pollen source during an incompatible pollination reaction. The compatible pollen source is the variety Foxtrot (heterogeneous populations).