University of Georgia

About: University of Georgia is a education organization based out in Athens, Georgia, United States. It is known for research contribution in the topics: Population & Gene. The organization has 41934 authors who have published 93622 publications receiving 3713212 citations. The organization is also known as: UGA & Franklin College.

Genome sequence of mungbean and insights into evolution within Vigna species

Abstract: Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis.

Temperatures of serpentinization of ultramafic rocks based on O 18 /O 16 fractionation between coexisting serpentine and magnetite

Abstract: Five lizardite-chrysotile type serpentinites from California, Guatemala and the Dominican Republic show oxygen isotope fractionations of 15.1 to 12.9 per mil between coexisting serpentine and magnetite (δO18 magnetite=−7.6 to −4.6 per mil relative to SMOW). Nine antigorites (mainly from Vermont and S. E. Pennsylvania) show distinctly smaller fractionations of 8.7 to 4.8 per mil (δO18 magnetite=−2.6 to +1.7 per mil). Two lizardite and chrysotile serpentinites dredged from the Mid-Atlantic Ridge exhibit fractionations of 10.0 and 12.4 per mil (δO18 magnetite=−6.8 and −7.9 per mil, respectively), whereas an oceanic antigorite shows a value of 8.2 per mil (δO18 magnetite=−6.2). These data all clearly indicate that the antigorites formed at higher temperatures than the chrysotilelizardites. Electron microprobe analyses of magnetites from the above samples show that they are chemically homogeneous and essentially pure Fe3O2. However, some magnetites from certain other samples that show a wide variation of Cr content also give very erratic oxygen isotopic results, suggesting non-equilibrium. An approximate serpentine-magnetite geothermometer curve was constructed by (1) extrapolation of observed O18 fractionations between coexisting chlorites and Fe-Ti oxides in low-grade pelitic schists whose isotopic temperatures are known from the quartz-muscovite O18 geothermometer, and (2) estimates of the O18 fractionation factor between chlorite and serpentine (assumed to be equal to unity). This serpentine-magnetite geothermometer suggests approximate equilibrium temperatures as follows: continental lizardite-chrysotile, 85° to 115° C; oceanic lizardite and chrysotile, 130° C and 185° C, respectively; oceanic antigorite, 235° C; and continental antigorites, 220° to 460° C.

Comparison of the methods for profiling glycoprotein glycans--HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study.

Abstract: Mass spectrometry (MS) of glycoproteins is an emerging field in proteomics, poised to meet the technical demand for elucidation of the structural complexity and functions of the oligosaccharide components of molecules. Considering the divergence of the mass spectrometric methods employed for oligosaccharide analysis in recent publications, it is necessary to establish technical standards and demonstrate capabilities. In the present study of the Human Proteome Organisation (HUPO) Human Disease Glycomics/Proteome Initiative (HGPI), the same samples of transferrin and immunoglobulin-G were analyzed for N-linked oligosaccharides and their relative abundances in 20 laboratories, and the chromatographic and mass spectrometric analysis results were evaluated. In general, matrix-assisted laser desorption/ionization (MALDI) time-of-flight MS of permethylated oligosaccharide mixtures carried out in six laboratories yielded good quantitation, and the results can be correlated to those of chromatography of reductive amination derivatives. For underivatized oligosaccharide alditols, graphitized carbon-liquid chromatography (LC)/electrospray ionization (ESI) MS detecting deprotonated molecules in the negative ion mode provided acceptable quantitation. The variance of the results among these three methods was small. Detailed analyses of tryptic glycopeptides employing either nano LC/ESI MS/MS or MALDI MS demonstrated excellent capability to determine site-specific or subclass-specific glycan profiles in these samples. Taking into account the variety of MS technologies and options for distinct protocols used in this study, the results of this multi-institutional study indicate that MS-based analysis appears as the efficient method for identification and quantitation of oligosaccharides in glycomic studies and endorse the power of MS for glycopeptide characterization with high sensitivity in proteomic programs.

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors.

Abstract: Targeting the interaction between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptor is a promising therapeutic strategy. We designed inhibitors using two de novo design approaches. Computer-generated scaffolds were either built around an ACE2 helix that interacts with the spike receptor binding domain (RBD) or docked against the RBD to identify new binding modes, and their amino acid sequences were designed to optimize target binding, folding, and stability. Ten designs bound the RBD, with affinities ranging from 100 picomolar to 10 nanomolar, and blocked SARS-CoV-2 infection of Vero E6 cells with median inhibitory concentration (IC50) values between 24 picomolar and 35 nanomolar. The most potent, with new binding modes, are 56- and 64-residue proteins (IC50 ~ 0.16 nanograms per milliliter). Cryo-electron microscopy structures of these minibinders in complex with the SARS-CoV-2 spike ectodomain trimer with all three RBDs bound are nearly identical to the computational models. These hyperstable minibinders provide starting points for SARS-CoV-2 therapeutics.