Biology subjects

Whittall, J. B.

Publications and source records attributed to Whittall, J. B..

5 recordsLinked to original sources

bioRxiv2026

Purifying selection and phylogenetic discord among microneme proteins in Toxoplasma gondii

In Toxoplasma gondii, microneme proteins (MICs) are secreted components of the apical complex that play central roles in motility, host cell attachment, and invasion. Because proteins at the host-parasite interface are often predicted to evolve rapidly, MICs have been suggested as candidates for adaptive diversification. We tested this expectation using comparative analyses of three relatively understudied microneme proteins, MIC13, MIC12, and MIC16. Coding sequences were assembled from GenBank and ToxoDB, aligned by translation, and analyzed using maximum-likelihood phylogenetics, codon-based tests of selection, and predicted protein structure. MIC13 was represented by 51 sequences, MIC12 by 30, and MIC16 by 34, spanning multiple T. gondii haplogroups and including Hammondia hammondi and Neospora caninum as outgroups. All three genes were highly conserved among T. gondii strains, but their phylogenetic trees were topologically incongruent, indicating that individual MICs do not recover a single shared strain history. Contrary to expectation, no positively selected codons were detected in any gene. Instead, purifying selection was detected at one site in MIC13 and 15 sites in MIC12, while no significant codon-specific selection was detected in MIC16. Several constrained MIC12 sites overlapped annotated EGF and calcium-binding EGF-like domains, consistent with structural conservation of extracellular adhesion modules. AlphaFold prediction of MIC13 supported two sialic acid-binding micronemal adhesive repeat regions, but the single constrained MIC13 site did not overlap these motifs. Together, these results indicate that MIC13, MIC12, and MIC16 are shaped more by sequence conservation and heterogeneous gene histories than by strong recurrent positive selection. These findings refine expectations for microneme evolution in T. gondii and highlight conserved domains that may be important for parasite invasion and future functional study.

evolutionary biology↗

bioRxiv2022

The Universal Endurance Microbiome?

Billions of microbial cells sculpt the gut ecosystem, playing essential roles in human physiology. Since endurance athletes performance is often physiology-limited, understanding the composition and interactions within these athletes gut microbiomes could lead to improved performance. Previous studies describe differences in the relative abundance of bacterial taxa when comparing athletes versus controls or athletes before and after an endurance event, suggesting the existence of an "endurance microbiome". However, there are inconsistencies among studies in which taxa correlate with extended physical exertion. Although these studies employed similar barcoding methods, variation in downstream bioinformatic analyses makes it difficult to determine whether inconsistencies are due to methodological differences or biological factors. Herein, we created a metagenomic bioinformatics workflow reanalyzing four 16S rDNA sequence datasets reflecting endurance athletes gut microbiomes, looking at alpha diversity, changes in relative abundance of gut microbiome genera, changes in pairwise correlations between bacterial genera and compared bacterial association networks. There were no significant differences in alpha diversity between any of the four treatment group comparisons. For relative abundance, there were no consistent differences in all four datasets, and only two genera were significantly different in 50% of the datasets. Although many genera showed changes in pairwise correlations in endurance microbiome samples from individual datasets, none were consistent across datasets. Collectively, these results suggest that either there is no universal endurance microbiome, or that it remains elusive even after controlling for the bioinformatic workflow and statistical analyses. Using this data, a power analysis indicates that sample sizes 150- to 800-fold larger than these published studies would be necessary to detect a 10% difference in relative abundance. Furthermore, 10- to 20-fold more samples will be needed to control for the multitude of covariates (genetic, metabolic, dietary, environmental, and pharmacological factors) that mold the gut microbiome of athletes and non-athletes alike. Im going to work so that its a pure guts race at the end, and if it is, I am the only one who can win it. - Steve Prefontaine

microbiology↗

bioRxiv2020

Proteomic analysis of microtubule inner proteins (MIPs) in Rib72 null Tetrahymena cells reveals functional MIPs

Motile cilia and flagella are built from stable populations of doublet microtubules that comprise their axonemes. Their unique stability is brought about, at least in part, by a network of Microtubule Inner Proteins (MIPs) found in the lumen of their doublet microtubules. Rib72A and Rib72B were identified as microtubule inner proteins (MIPs) in the motile cilia of Tetrahymena thermophila. Loss of these proteins leads to ciliary defects and loss of multiple MIPs. We performed mass spectrometry coupled with proteomic analysis and bioinformatics to identify the MIPs lost in RIB72A/B knockout (KO) Tetrahymena cells. From this analysis we identified a number of candidate MIPs and pursued one, Fap115, for functional characterization. We find that loss of Fap115 results in disrupted cell swimming and aberrant ciliary beating. Cryo-electron tomography reveals that Fap115 localizes to MIP6a in the A-tubule of the doublet microtubules. Overall, our results highlight the complex relationship between MIPs, ciliary structure, and ciliary function.

molecular biology↗

bioRxiv2020

The ITS region provides a reliable DNA barcode for identifying reishi/lingzhi (Ganoderma) from herbal supplements

The dietary supplement industry is a growing enterprise, valued at over $100 billion by 2025 yet, a recent study revealed that up to 60% of herbal supplements may have substituted ingredients not listed on their labels, some with harmful contaminants. Substituted ingredients make rigorous quality control testing a necessary aspect in the production of supplements. Traditionally, species have been verified morphologically or biochemically, but this is not possible for all species if the identifying characteristics are lost in the processing of the material. One approach to validating plant and fungal ingredients in herbal supplements is through DNA barcoding complemented with a molecular phylogenetic analysis. This method provides an efficient, objective, rigorous and repeatable method for species identification. We employed a molecular phylogenetic analysis for species authentication of the commonly used fungal supplement, reishi (Ganoderma lingzhi), by amplifying and sequencing the nuclear ribosomal internal transcribed spacer regions (ITS) with genus-specific primers. PCR of six powdered samples and one dried sample sold as G. lucidum representing independent suppliers produced single, strong amplification products in the expected size-range for Ganoderma. Both best-hit BLAST and molecular phylogenetic analyses using a reference panel assembled from Genbank clearly identified the predominant fungal DNA was G. lingzhi in all seven herbal supplements. We detected variation in ITS among our samples, but all samples still fall within a large clade of G. lingzhi. ITS is a successful and cost-effective method for DNA-based species authentication that could be used in the herbal supplement industry for this and other fungal and plant species that are otherwise difficult to identify.

genetics↗

bioRxiv2020

UV radiation increases flavonoid protection but decreased reproduction in Silene littorea

Plants respond to changes in ultraviolet (UV) radiation via morphological and physiological changes. Among the variety of plant UV-responses, the synthesis of UV-absorbing flavonoids constitutes an effective non-enzymatic mechanism to mitigate photoinhibitory and photooxidative damage caused by UV stress, either reducing the penetration of incident UV radiation or acting as quenchers of reactive oxygen species (ROS). In this study, we designed a UV-exclusion experiment to investigate the effects of UV radiation in Silene littorea. We spectrophotometrically quantified concentrations of both anthocyanins and non-anthocyanin flavonoids (flavones) in petals, calyces, leaves and stems. Furthermore, we analyzed the UV effect on the photosynthetic activity in hours of maximum solar radiation and we tested the impact of UV radiation on male and female reproductive performance. We found that anthocyanin concentrations showed a significant decrease of about 20% with UV-exclusion in petals and stems, and 30% in calyces. Flavone concentrations showed a significant reduction of approximately 25% in calyces and stems, and 12% in leaves. Photochemical efficiency of plants grown under UV stress decreased sharply at maximum light stress, but their ability for recovery after light-stress was not affected. In addition, exposure to UV radiation does not seem to affect ovule production or seed set, but decreases the total seed production per plant and pollen production by 69% and 31%, respectively. Our results demonstrate that UV radiation produced opposite effects on flavonoid accumulation and reproduction in S. littorea. UV stress increased flavonoid concentrations, suggesting a photoprotective role of flavonoids against UV radiation, but had negative consequences for reproduction. We propose that this trade-off helps this species to occupy exposed habitats with high UV radiation.

evolutionary biology↗