Biology subjects

Gardner, P.

Publications and source records attributed to Gardner, P..

4 recordsLinked to original sources

bioRxiv2024

Temperature and host plant ecotype drive nitrogen fixation, but not nodule community composition, in hairy

Hairy vetch (Vicia villosa Roth) is a commonly grown cover crop throughout the U.S., which can contribute nitrogen for subsequent cash crops through biological nitrogen fixation (BNF) in association with Rhizobium leguminosarum biovar viciae (Rlv) bacteria. Hairy vetch is one of the few cover crops sufficiently cold-tolerant to over-winter in the Upper Midwestern U.S. However, nitrogen contributions by hairy vetch vary across locations, potentially due to cold impacts on the legume/rhizobia symbiosis. The traditional route to improve BNF in legumes involves selecting superior rhizobia strains to create more effective inoculants to apply at planting, but inoculants often fail to compete and survive in agricultural soils. Instead, this study tested the effects of temperature and host plant ecotype on hairy vetch BNF and Rlv community composition in nodules, with the goal of potentially identifying vetch ecotypes able to select beneficial Rlv strains from the soil community. Four hairy vetch ecotypes trapped Rlv from three Minnesota soils, at warm or cold temperatures. Vetch ecotype was a key driver of BNF and nodule formation under warm and cold conditions. However, temperature and plant ecotype did not drive Rlv community composition in nodules, and Rlv community composition did not affect plant productivity. Taken together, these results suggest that the best strategy to improve BNF at low temperatures in hairy vetch likely depends on breeding for improved biomass accumulation and nitrogen fixation in host plants, rather than focusing on host plant selection of beneficial rhizobia.

plant biology↗

bioRxiv2019

The tuatara genome: insights into vertebrate evolutionfrom the sole survivor of an ancient reptilian order

The tuatara (Sphenodon punctatus), the only living member of the archaic reptilian order Rhynchocephalia (Sphenodontia) once widespread across Gondwana, is an iconic and enigmatic terrestrial vertebrate endemic to New Zealand. A key link to the now extinct stem reptiles from which dinosaurs, modern reptiles, birds and mammals evolved, the tuatara provides exclusive insights into the ancestral amniotes. The tuatara genome, at [~]5 Gbp, is among the largest vertebrate genomes assembled. Analysis of this genome and comparisons to other vertebrates reinforces the uniqueness of the tuatara. Phylogenetic analyses indicate tuatara diverged from the snakes and lizards [~]250 MYA. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Genome sequence analysis identifies expansions of protein, non-protein-coding RNA families, and repeat elements, the latter of which show an extraordinary amalgam of reptilian and mammalian features. Sequencing of this genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. It also provides important insights into both the technical challenges and the cultural obligations associated with genome sequencing.

genomics↗

bioRxiv2018

Anticancer Drug Impact on DNA - A Study by Neutron Spectrocopy, Synchrotron-based FTIR and EXAFS

A complementary structural and dynamical information on drug-DNA interplay has been achieved at a molecular level, for Pt/Pd-drugs, allowing a better understanding of their pharmacodynamic profile. The interaction of two cisplatin-like dinuclear Pt(II) and Pd(II) complexes with DNA was studied through a multidisciplinary experimental approach, using quasi-elastic neutron scattering (QENS) techniques coupled to synchrotron-based extended X-ray absorption fine structure (SR-EXAFS) and Fourier-Transform Infrared Spectroscopy-Attenuated Total Reflectance (SR-FTIR-ATR). The drug impact on DNAs dynamical profile, via its hydration layer, was provided by QENS, a drug-triggered enhanced mobility having been revealed. Additionally, an onset of anharmonicity was detected for dehydrated DNA, at room temperature. Far- and mid-infrared measurements allowed the first simultaneous detection of the drugs and its primary pharmacological target, as well as the drug-prompted changes in DNAs conformation that mediate cytotoxicity in DNA extracted from drug-exposed human triple negative breast cancer cells (MDA-MB-231), a low prognosis type of cancer. The local environment of the absorbing Pd(II) and Pt(II) centers in the drugs adducts with adenine, guanine and glutathione was attained by EXAFS.

biophysics↗

bioRxiv2016

A meta-analysis of bioinformatics softwarebenchmarks reveals that publication-bias undulyinfluences software accuracy

BackgroundComputational biology provides widely used and powerful software tools for testing and making inferences about biological data. In the face of rapidly increasing volumes of data, heuristic methods that trade software speed for accuracy may be employed. We are have studied these trade-offs using the results of a large number of independent software benchmarks, and evaluated whether external factors are indicative of accurate software. MethodWe have extracted accuracy and speed ranks from independent benchmarks of different bioinformatic software tools, and evaluated whether the speed, author reputation, journal impact, recency and developer efforts are indicative of accuracy. ResultsWe found that software speed, author reputation, journal impact, number of citations and age are all unreliable predictors of software accuracy. This is unfortunate because citations, author and journal reputation are frequently cited reasons for selecting software tools. However, GitHub-derived records and high version numbers show that the accurate bioinformatic software tools are generally the product of many improvements over time, often from multiple developers. DiscussionWe also find that the field of bioinformatics has a large excess of slow and inaccurate software tools, and this is consistent across many sub-disciplines. Meanwhile, there are few tools that are middle-of-road in terms of accuracy and speed trade-offs. We hypothesise that a form of publication-bias influences the publication and development of bioinformatic software. In other words, software that is intermediate in terms of both speed and accuracy may be difficult to publish - possibly due to author, editor and reviewer practices. This leaves an unfortunate hole in the literature as the ideal tools may fall into this gap. For example, high accuracy tools are not always useful if years of CPU time are required, while high speed is not useful if the results are also inaccurate.

bioinformatics↗