Biology subjects

Triplett, E.

Publications and source records attributed to Triplett, E..

3 recordsLinked to original sources

bioRxiv2022

Eradicating Citrus Greening By Dual Action Targeting of Liberibacter asiaticus and Diaphorina citri.

Huanglongbing (citrus greening) is caused by the unculturable, gram negative bacterium Liberibacter asiaticus and transmitted by the Asian Citrus Psyllid (Diaphorina citri). Prior research demonstrated that the rifampicin-derivative TPR-1 as well as Palisades Therapeutic (PT) compounds PT159 and PT160 were effective at inhibiting growth of the L. cresens, the only culturable model for Las, showing 100% inhibition at 0.5 g mL-1, and 80% inhibition at 0.05 g mL-1. Research with the PT glucocorticoid antagonist compounds demonstrated an inhibition of bacterial growth in L crescens as well, possibly a synergistic addition to TPR-1. A search of the L. asiaticus genome revealed the presence of 3 putative glucocorticoid response elements (GRE). Putative GRE are present in all organisms and may be involved in organism signaling as well as host-pathogen crosstalk. In Drosophila, the estrogen-related receptor (ERR) transcription factor is a master regulator of larval and pupal maturation. ERR binds to GRE promoter elements in the genome to regulate the transcription of pathways involved in glucose metabolism. Null mutations of ERR fail to leave pupation and demonstrate elevated glucose levels when compared to wild-type. Treatment of Drosophila larvae with PT compounds demonstrated developmental delay disruptions in pupation, including premature pupation and increased lethality. Pupae that had been fed PT compounds as larvae showed elevated glucose levels when compared to controls. Sequences identified in Drosophila ERR showed high homology to 2 proteins in D. citri (ERR-like 1 and ERR-like 2), leading us to hypothesize that a glucocorticoid antagonist may disrupt psyllid development. Because these genes and signaling pathways are highly conserved between these taxa, we propose that Drosophila serves as a good model for screening potential compounds for the control of psyllid populations. Collectively, we hypothesize that the dual action of these compounds offers a solution to HLB that can salvage the dying citrus industry in Florida and provide the first effective treatment. By simultaneous targeting of both Las and D. citri, it may be possible to both cure infected trees and block psyllid development in adults feeding on those same trees. Disruption of the psyllids ability to carry Las or cure Las from the psyllid gut are also both substantial possibilities.

plant biology↗

bioRxiv2019

PIME: a package for discovery of novel differences among microbial communities

Massive sequencing of genetic markers, such as the 16S rRNA gene for prokaryotes, allows the comparative analysis of diversity and abundance of whole microbial communities. However, the data used for profiling microbial communities is usually low in signal and high in noise preventing the identification of real differences among treatments. PIME (Prevalence Interval for Microbiome Evaluation) fills this gap by removing those taxa that may be high in relative abundance in just a few samples but have a low prevalence overall. The reliability and robustness of PIME were compare against the existing methods and verified by a number of approaches using 16S rRNA independent datasets. To remove the noise, PIME filters microbial taxa not shared in a per treatment prevalence interval starting at 5% with increments of 5% at each filtering step. For each prevalence interval, hundreds of decision trees are calculated to predict the likelihood of detecting differences in treatments. The best prevalence-filtered dataset is user-selected by choosing the prevalence interval that keeps the majority of the 16S rRNA reads in the dataset and shows the lowest error rate. To obtain the likelihood of introducing bias while building prevalence-filtered datasets, an error detection step based in random permutations is also included. A reanalysis of previews published datasets with PIME uncovered previously missed microbial associations improving the ability to detect important organisms, which may be masked when only relative abundance is considered.

bioinformatics↗

bioRxiv2017

Barriers to Integration of Bioinformatics into Undergraduate Life Sciences Education

Bioinformatics, a discipline that combines aspects of biology, statistics, and computer science, is increasingly important for biological research. However, bioinformatics instruction is rarely integrated into life sciences curricula at the undergraduate level. To understand why, the Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE, \"nibbles\") recently undertook an extensive survey of life sciences faculty in the United States. The survey responses to open-ended questions about barriers to integration were subjected to keyword analysis. The barrier most frequently reported by the ~1,260 respondents was lack of faculty training. Faculty at associates-granting institutions report the least training in bioinformatics and the least integration of bioinformatics into their teaching. Faculty from underrepresented minority groups (URMs) in STEM reported training barriers at a higher rate than others, although the number of URM respondents was small. Interestingly, the cohort of faculty with the most recently awarded PhD degrees reported the most training but were teaching bioinformatics at a lower rate than faculty who earned their degrees in previous decades. Other barriers reported included lack of student interest in bioinformatics; lack of student preparation in mathematics, statistics, and computer science; already overly full curricula; and limited access to resources, including hardware, software, and vetted teaching materials. The results of the survey, the largest to date on bioinformatics education, will guide efforts to further integrate bioinformatics instruction into undergraduate life sciences education.

scientific communication and education↗