A phylogeny of Setaria (Poaceae, Panicoideae, Paniceae) and related genera based on the chloroplast gene ndhF

The genus Setaria is the largest genus in the so-called bristle clade, a monophyletic group of panicoid grasses distinguished by the presence of sterile branches, or bristles, in their inflorescences. The clade includes both foxtail millet and pearl millet, the latter an important cereal crop in dry parts of the world. Other members of the clade are weeds that are widespread agricultural pests. Previous molecular phylogenetic studies have suggested that Setaria might not be monophyletic but did not have a large enough sample of species to test this rigorously. In addition, taxonomic studies have suggested a close relationship between Setaria and Paspalidium, with some authors combining them into a single genus, but molecular studies included too few Paspalidium accessions for a meaningful conclusion. Accordingly, we have produced 77 new sequences of the chloroplast gene ndhF for 52 species not in previous analyses. These were added to available sequences for 35 species in 10 genera of the bristle clade and four outgroup taxa. We find that Setaria species fall into several moderately to strongly supported clades that correlate with geography but not with the existing subgeneric classification. Relationships among these clades and among other genera within the bristle clade are unclear. Constraint experiments using the approximately unbiased test reject the monophyly of Pennisetum, Setaria, and Setaria plus Paspalidium, as well as several other groupings, although the test may be overly sensitive and prone to Type I error. The more conservative Shimodaira-Hasegawa test fails to reject monophyly of any of the tested clades.Fil: Kellogg, Elizabeth Anne. University of Missouri; Estados UnidosFil: Aliscioni, Sandra Silvina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Recursos Naturales y Ambiente. Cátedra de Botánica Agrícola; ArgentinaFil: Morrone, Osvaldo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Pensiero, Jose Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional del Litoral. Facultad de Ciencias Agrarias; ArgentinaFil: Zuloaga, Fernando Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; Argentin

A model for estimating the TMDL-related benefits of oyster reef restoration : Harris Creek, Maryland, USA

A user-friendly, web-accessible model has been developed that allows restoration practitioners and resource managers to easily estimate the TMDL-related benefits of oyster reef restoration per unit area, run restoration scenarios in Harris Creek, MD to optimize restoration planning and implementation, and calculate the benefits of the chosen plan. The model is rooted in scientifically defensible data and is readily transferable to systems throughout the Chesapeake Bay and Eastern Shore. The model operates in five vertically well-mixed boxes along the main axis of the creek. Exchanges among creeks are computed using a tidal prism approach and were compared to exchanges provided from a high resolution 3D hydrodynamic model. Watershed inputs for the model were obtained for the Harris Creek sub-watershed from the Phase V Chesapeake Bay Program Watershed Model. The base model simulates daily concentrations over an annual cycle of chlorophyll-a, dissolved inorganic nitrogen (N) and phosphorus (P), dissolved oxygen, total suspended solids, the biomass of benthic microalgae, and the water column and sediment pools of labile organic carbon (C) and associated N and P. Water quality data for model forcing and calibration were obtained from the Chesapeake Bay Program, the Choptank Riverkeeper, the University of Maryland Center for Environmental Science, and the Maryland Department of Natural Resources. An oyster sub-model has been coupled to this base model and computes the volume of water filtered, removal of phytoplankton, suspended solids, and associated nutrients via filtration, recycling of nutrients and consumption of oxygen by oyster respiration, production of feces, N and P accumulation in oyster tissues and shell, oyster-enhanced denitrification, and N and P burial associated with restored reefs. The completed model is served online and operates through a web browser, enabling users to conduct scenario analysis by entering box-specific values for acres restored, restored oyster density, and restored oyster size, as well as the economic value of associated N and P removal

Sparse panicle1 is required for inflorescence development in Setaria viridis and maize.

Setaria viridis is a rapid-life-cycle model panicoid grass. To identify genes that may contribute to inflorescence architecture and thus have the potential to influence grain yield in related crops such as maize, we conducted an N-nitroso-N-methylurea (NMU) mutagenesis of S. viridis and screened for visible inflorescence mutant phenotypes. Of the approximately 2,700 M2 families screened, we identified four recessive sparse panicle mutants (spp1-spp4) characterized by reduced and uneven branching of the inflorescence. To identify the gene underlying the sparse panicle1 (spp1) phenotype, we performed bulked segregant analysis and deep sequencing to fine map it to an approximately 1 Mb interval. Within this interval, we identified disruptive mutations in two genes. Complementation tests between spp1 and spp3 revealed they were allelic, and deep sequencing of spp3 identified an independent disruptive mutation in SvAUX1 (AUXIN1), one of the two genes in the ∼1 Mb interval and the only gene disruption shared between spp1 and spp3. SvAUX1 was found to affect both inflorescence development and root gravitropism in S. viridis. A search for orthologous mutant alleles in maize confirmed a very similar role of ZmAUX1 in maize, which highlights the utility of S. viridis in accelerating functional genomic studies in maize

“Principles of Good Practice” for Academic and Student Affairs Partnership Programs

While academic and student affairs partnership programs have been championed as a means to enhance undergraduate education, research documenting the characteristics of effective part-nership programs is sparse. The Boyer Partnership Assessment Project is a qualitative examination of academic and student affairs partnership programs at 18, diverse institutions. This article identifies seven principles of good practice for creating and sustaining effective partnerships, and discusses the implications of these principles for higher education research and practice

The role of packaged water in meeting global targets on improved water access

Packaged water (as either refill, bottled, or sachet water) has become an important element of water security in many low- and middle-income countries, owing to poor reliability and lack of piped water infrastructure. However, over time and across countries, the Demographic and Health Surveys monitoring program has inconsistently classified packaged water components as either improved or unimproved. Using data collected as part of the Performance Monitoring and Accountability 2020 (PMA2020) surveys on water options in nine study geographies across eight countries, we identified five geographies where packaged water constituted one of several options for 5% or more of users. In this study, four scenarios were designed in which packaged water components were variously classified as either improved or unimproved. Unimproved water use was highest in scenarios where sachet or refill water was classified as an unimproved source. Across the four scenarios, the difference in the use of unimproved water as the main option was highest (65%) in Nigeria (Lagos). That difference increased to 78% when considering all regular options. The development of these scenarios highlights the importance of classifying a source as improved or unimproved in the overall metric that indicates progress at national and international levels.IS

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

The prediction of changes in protein stability and structure resulting from single amino acid substitutions is both a fundamental test of macromolecular modeling methodology and an important current problem as high throughput sequencing reveals sequence polymorphisms at an increasing rate. In principle, given the structure of a wild-type protein and a point mutation whose effects are to be predicted, an accurate method should recapitulate both the structural changes and the change in the folding-free energy. Here, we explore the performance of protocols which sample an increasing diversity of conformations. We find that surprisingly similar performances in predicting changes in stability are achieved using protocols that involve very different amounts of conformational sampling, provided that the resolution of the force field is matched to the resolution of the sampling method. Methods involving backbone sampling can in some cases closely recapitulate the structural changes accompanying mutations but not surprisingly tend to do more harm than good in cases where structural changes are negligible. Analysis of the outliers in the stability change calculations suggests areas needing particular improvement; these include the balance between desolvation and the formation of favorable buried polar interactions, and unfolded state modeling

The draft genome of the C\u3csub\u3e3\u3c/sub\u3e panicoid grass species \u3ci\u3eDichanthelium oligosanthes\u3c/i\u3e

Background: Comparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C3 panicoid grass Dichanthelium oligosanthes from the independent C4 lineages represented by Setaria viridis and Sorghum bicolor occurred approximately 15 million years ago, which is significantly more recent than members of the Bambusoideae, Ehrhartoideae, and Pooideae subfamilies. D. oligosanthes is ideally placed within the panicoid clade for comparative studies of C3 and C4 grasses. Results: We report the assembly of the nuclear and chloroplast genomes of D. oligosanthes, from high-throughput short read sequencing data and a comparative transcriptomics analysis of the developing leaf of D. oligosanthes, S. viridis, and S. bicolor. Physiological and anatomical characterizations verified that D. oligosanthes utilizes the C3 pathway for carbon fixation and lacks Kranz anatomy. Expression profiles of transcription factors along developing leaves of D. oligosanthes and S. viridis were compared with previously published data from S. bicolor, Zea mays, and Oryza sativa to identify a small suite of transcription factors that likely acquired functions specifically related to C4 photosynthesis. Conclusions: The phylogenetic location of D. oligosanthes makes it an ideal C3 plant for comparative analysis of C4 evolution in the panicoid grasses. This genome will not only provide a better C3 species for comparisons with C4 panicoid grasses, but also highlights the power of using high-throughput sequencing to address questions in evolutionary biology

CELLObration

https://dc.ewu.edu/music_performances/1683/thumbnail.jp

Structural and functional differences between porcine brain and budding yeast microtubules

The cytoskeleton of eukaryotic cells relies on microtubules to perform many essential functions. We have previously shown that, in spite of the overall conservation in sequence and structure of tubulin subunits across species, there are differences between mammalian and budding yeast microtubules with likely functional consequences for the cell. Here we expand our structural and function comparison of yeast and porcine microtubules to show different distribution of protofilament number in microtubules assembled in vitro from these two species. The different geometry at lateral contacts between protofilaments is likely due to a more polar interface in yeast. We also find that yeast tubulin forms longer and less curved oligomers in solution, suggesting stronger tubulin:tubulin interactions along the protofilament. Finally, we observed species-specific plus-end tracking activity for EB proteins: yeast Bim1 tracked yeast but not mammalian MTs, and human EB1 tracked mammalian but not yeast MTs. These findings further demonstrate that subtle sequence differences in tubulin sequence can have significant structural and functional consequences in microtubule structure and behavior