Nathan J. Ricks’s research while affiliated with University of Utah and other places
What is this page?
This page lists works of an author who doesn't have a ResearchGate profile or hasn't added the works to their profile yet. It is automatically generated from public (personal) data to further our legitimate goal of comprehensive and accurate scientific recordkeeping. If you are this author and want this page removed, please let us know.
Malate is a key intermediate in the citric acid cycle, an enzymatic cascade that is central to cellular energy metabolism and that has been applied to make biofuel cells. To enable real-time sensing of malate levels, we have engineered a genetically encoded, protein-based fluorescent biosensor called Malon specifically responsive to malate by performing structure-based mutagenesis of the Cache-binding domain of the Citron GFP-based biosensor. Malon demonstrates high specificity and fluorescence activation in response to malate, and has been applied to monitor enzymatic reactions in vitro. Furthermore, we successfully incorporated Malon into redox polymer hydrogels and bacterial cells, enabling analysis of malate levels in these materials and living systems. These results show the potential for fluorescent biosensors in enzymatic cascade monitoring within biomaterials and present Malon as a novel tool for bioelectronic devices.
As plant-microbe interactions are both ubiquitous and critical in shaping plant fitness, patterns of plant adaptation to their local environment may be influenced by these interactions. Identifying the contribution of soil microbes to plant adaptation may provide insight into the evolution of plant traits and their microbial symbioses. To this end, we assessed the contribution of soil microbes to plant salinity adaptation by growing 10 populations of Bromus tectorum, collected from habitats differing in their salinity, in the greenhouse under either high-salinity or nonsaline conditions and with or without soil microbial partners. Across two live soil inoculum treatments, we found evidence for adaptation of these populations to their home salinity environment. However, when grown in sterile soils, plants were slightly maladapted to their home salinity environment. As plants were on average more fit in sterile soils, pathogenic microbes may have been significant drivers of plant fitness herein. Consequently, we hypothesized that the plant fitness advantage in their home salinity may have been due to increased plant resistance to pathogenic attack in those salinity environments. Our results highlight that plant-microbe interactions may partially mediate patterns of plant adaptation as well as be important selective agents in plant evolution.
We examine the 4 recognized varieties of Penstemon scariosus that constitute a complex of related taxa that share overlapping morphological characters: namely varieties albifluvis, cyanomontanus, garrettii, and scariosus. Modern taxonomic descriptions and associated keys are not in complete agreement on how to clearly delineate these varieties. It is particularly important to understand the taxonomic circumscription of variety albifluvis, since it is being considered for listing under the Endangered Species Act. To address the taxonomic position of taxa in this species complex , we examine the genetic structure of 66 accessions of P. scariosus, representing the 4 known varieties, across its entire known geographic range using 10 SSR (microsatellite) markers. We also examine plant morphology of these taxa from 264 herbarium specimens. The results of our molecular and morphological studies give rise to 4 conclusions. First, due to the genetic distinctiveness of P. scariosus var. albifluvis and its geographical isolation, we consider conserving its original status at the species level. Second, our molecular study suggests that the geographic area for var. cyanomontanus is much larger than previously understood, consisting of plants and populations with or without the characteristic glandular hairs that have been used to identify that taxon. Third, both our molecular and morphometric data suggest that varieties garrettii and scariosus are not reliably separable and should be considered the same taxon. Finally, our molecular data reveal a distinct genotype from the Tabby Mountain, Utah, area that has not previously been given taxonomic recognition. We describe this new taxon and provide a taxonomic key to separate this new variety from the other members of the species complex. RESUMEN.-Examinamos las cuatro variedades reconocidas de Penstemon scariosus que comprenden un complejo de taxones relacionados que comparten caracteres morfológicos superpuestos: las variedades albifluvis, cyanomontanus, gar-rettii y scariosus. Las descripciones taxonómicas modernas y las claves asociadas no están completamente de acuerdo en cómo delimitar claramente estas variedades. Resulta especialmente importante entender la circunscripción taxonómica de la variedad albifluvis, debido a que se ha considerado su inclusión en la Ley de Especies Amenazadas. Para abordar la posi-ción taxonómica de los taxones en este complejo de especies, examinamos la estructura genética de 66 registros de P. scar-iosus que representan las cuatro variedades reconocidas dentro de su área de distribución geográfica conocida, utilizando diez marcadores SSR (microsatélites). También examinamos la morfología vegetal de estos taxones a partir de 264 especímenes de herbario. Los resultados de nuestros estudios moleculares y morfológicos dan lugar a cuatro conclusiones. En primer lugar, debido al carácter genético distintivo de P. scariosus var. albifluvis y a su aislamiento geográfico, consid-eramos conservar su estado original a nivel de especie. En segundo lugar, nuestro estudio molecular sugiere que el área geográfica de la var. cyanomontanus es mucho mayor de lo que se conocía hasta ahora, y que consta de plantas y pobla-ciones con o sin tricomas glandulares característicos que se han utilizado para identificar ese taxón. En tercer lugar, tanto nuestros datos moleculares como morfométricos sugieren que las variedades garrettii y scariosus no se pueden separar de forma confiable y deberían considerarse el mismo taxón. Por último, nuestros datos moleculares revelan un genotipo dis-tinto de la zona de Tabby Mountain, UT, que no ha sido reconocido taxonómicamente con anterioridad. Describimos este nuevo taxón y proporcionamos una clave taxonómica para separar esta nueva variedad de los otros miembros del complejo de especies. This is an open access article distributed under the terms of the Creative Commons Attribution License CC BY-NC 4.0, which permits unrestricted noncommercial use and redistribution provided that the original author and source are credited.
The Hypr cGAMP signaling pathway was discovered via the function of the riboswitch. In this study, we show the development of a method for affinity capture followed by sequencing to identify non-coding RNA regions that bind nucleotide signals such as cGAMP. The RNAseq of affinity-captured cGAMP riboswitches from the Geobacter sulfurreducens transcriptome highlights general challenges that remain for this technique. Furthermore, by applying riboswitch reporters in vivo, we identify new growth conditions and transposon mutations that affect cGAMP levels in G. sulfurreducens. This work reveals an extensive regulatory network and supports a second functional cGAMP synthase gene in G. sulfurreducens. The activity of the second synthase was validated using riboswitch-based fluorescent biosensors, and is the first known example of an active enzyme with a variant GGDDF motif.
Cheatgrass (Bromus tectorum L.) is an invasive annual grass (Poaceae) that has colonized large portions of the Intermountain West. Cheatgrass stand failures have been observed throughout the invaded region, the cause of which may be related to the presence of several species of pathogenic fungi in the soil or surface litter. In this metabarcoding study, we compared the fungal communities between sites that have and have not experienced stand failure. Samples were taken from the soil and surface litter near Winnemucca, Nevada, and in Skull Valley, Utah. Our results show distinct fungal communities associated with stand failure based on both geography and sample type. In both the Winnemucca and Skull Valley surface litter, there was an elevated abundance of the endophyte Ramimonilia apicalis in samples that had experienced a stand failure. Winnemucca surface litter stand failure samples had an increased abundance of a potential pathogen in the genus Comoclathris. Skull Valley surface litter stand failure samples had an increased abundance of an undescribed new species in the Rustroemiaceae family which is responsible for the so‐called bleach blonde syndrome in cheatgrass, while the soils had an increased abundance of potential pathogens in the genera Olpidium and Monosporascus. Metabarcoding via targeted ITS sequencing was used to characterize fungal communities in cheatgrass soils affected by stand failure in multiple areas. Analysis of the data confirmed key differences in the overall community composition between native communities and those affected by stand failure. Several identified fungal pathogens warrant further investigation to determine whether they are causal agents of stand failure.
... This is the basis of the holobiont theory, a theory that postulates that multicellular hosts work in symbiosis with their microbiome [71][72][73], and the contribution of the microbiome to the host needs to be considered over evolutionary space. This hardcoding of mechanisms through which plants can manipulate their microbiome may serve as part of adaptation to their environment to provide them with a fitness advantage [72,74]. Importantly, we identify several key remaining questions that challenge the importance of this host genome-microbiome coevolution. ...
... Mutations affecting OmcS assembly allowed easier detection of PilA pili and OmcE polymers, while pilA-N mutations in previous studies decreased production of OmcS polymers. Given the importance of PilA in controlling omcS, omcB, omcAHG, omcOP and pgcA expression via PilS/PilR-dependent and cyclic di-GMP/ cyclic AMP-GMP-dependent regulatory networks 49,50,78 , changes in type IV pilin subunits should always be expected to affect electron transfer phenotypes and production of conductive appendages in Geobacter experiments. ...
... Future research should further explore these interrelationships, potentially employing metagenomic analyses to examine functional diversity in conjunction with phylogenetic structure. 38,39 Apart from these, some environment and plant-specific fungal genera were also identified in the rumen contents of both yak groups, including Comoclathris, Rachicladosporium, Lambertella, Gelasinospora, Cosmospora, and Ustilago, [40][41][42][43][44] suggesting that the abundance difference between DLf and PLf yak groups may not have a significant relationship with the number of ribs. ...
... All the analyzed breeds exhibited the same predominant bacterial phyla, Firmicutes and Bacteroidota, which is consistent with previous studies in cattle and other ruminants, such as goats [4,52], alpacas [53,54], and cattle [3,55]. Firmicutes, known for their role in fermentation of complex carbohydrates and the production of short-chain fatty acids, are crucial for the digestive efficiency of ruminants [56]. ...
... Molecular genetic studies showed that P. semeniperda exhibits high levels of genetic diversity and regional genetic differentiation, even at the ITS locus, which is most often monomorphic at the species level [79]. It was later demonstrated that strains with different ITS haplotypes are strongly genetically differentiated and likely represent cryptic species [80]. ...
... These nSSRs have already been tested in >50 Penstemon species in studies of genetic diversity and relatedness (e.g. Broderick 2010, Dockter et al. 2013, Rodríguez-Peña et al. 2018, Ksiazek-Mikenas et al. 2019) and used in other Penstemon population genetic studies (Kramer et al. 2011, Becker 2013, Wolfe et al. 2014, 2016, Redecker 2017, Crump et al. 2020, Kucera et al. 2022. While single nucleotide polymorphisms (SNP) markers are becoming increasingly common in population genetics studies, nSSRs remain valuable and widely used molecular tools (Hodel et al. 2016, Szatmári et al. 2021. ...
... Here we report the assembled and annotated plastomes of P. cyaneus, P. dissectus, P. palmeri, P. personatus, and P. rostriflorus, representing the Habroanthus, Dissecti, Penstemon, Cryptostemon, and Saccanthera subgenera, respectively. We include the previously published plastome of P. fruticosus [35] in our analyses to represent the basal subgenus, Dasanthera, thus including representatives from all recognized Penstemon subgenera. We had three primary objectives to guide our studies of Penstemon plastomes. ...
... With the rapid progress of sequencing technologies several LAB strains were sequenced, and genome assembled, to explore their diversity and applications. Among them, the genome of several species from genera Weissella was recently investigated [7,8]. Along with the probiotic capacity, some strains produced bacteriocins with a narrow antimicrobial spectrum [9,10]. ...
... Often, geography is used to assist in the delimitation of taxa (Holmgren 1984, Neese and Atwood 2016, Holmgren 2017). More recently, researchers have used molecular techniques to examine Penstemon genetic diversity and taxonomy (Wolfe and Randle 2001, Datwyler and Wolfe 2004, Wolfe et al. 2006, Kramer and Fant 2007, Johnson et al. 2016, Wessinger et al. 2016, Rodríguez-Peña et al. 2018, Stone et al. 2019, Crump et al. 2020. Our laboratory has developed simple sequence repeat (SSR) markers for P. scariosus that have demonstrated usefulness in several other species of Penstemon (Dockter et al. 2013, Johnson et al. 2016, Crump et al. 2020. ...
... We used fluorescently labeled primer pairs that were created for 9 SSR markers in Penstemon (Table 2) and which were identified by Anderson et al. (2016), and we followed PCR amplification steps and analysis as described therein. We used Geneious 8.0.5 (Kearse et al. 2012) to score the output generated from the ABI 3730xl (Applied Biosystems, Carlsbad, CA, USA) at Brigham Young University's DNA Sequencing Center (Provo, UT, USA) for the population genetic structure study (Fig. 4A, B). ...
![Fig. 8. Eigenvector plot showing the first 3 components of the principal component analysis (PCA) of our 241 Penstemon scariosus accessions based on 9 morphometric characters (plant height, corolla length, sepal length, anther-sac length, verticillasters per thyrse, average number of flowers per verticillaster, total number of flowers per thyrse, distal-most cauline leaf width, and width of bract subtending proximal-most verticillaster [Table 1, Figs. 7, 9]) illustrating morphological relationships among accessions. DNA accessions include samples from P. scariosus var. albifluvis (alb), var. cyanomontanus (cya), var. scariosus (sca), and Tabby Mtn. (Tab). The lengths of the axes represent the proportion of the variance explained for each principal component.](https://www.researchgate.net/profile/Mikel-Stevens/publication/366286952/figure/fig5/AS:11431281107465255@1671068460943/Eigenvector-plot-showing-the-first-3-components-of-the-principal-component-analysis-PCA_Q320.jpg)
