7141 research outputs found
Sort by
Deep Learning for Secondary Structure Elements Prediction From Cryo-EM Data
No full textUnderstanding protein structure is vital for drug design and advancing medical knowledge, playing a crucial role in modern medicine. Cryo-Electron Microscopy (Cryo-EM) is a leading method for imaging proteins, yet challenges persist, particularly at mid-level resolutions (4 to 10 angstroms), compromising clarity and hindering the identification of secondary structure elements like Helix, Sheet, and Coils.Artificial Neural Networks (ANNs) emulate human neurons and have been early tools for protein structure prediction. Deep learning, a form of ANN, excels in pattern detection.The Inception architecture, introduced by Google in 2014, addresses computational limitations in deep neural networks by utilizing convolutional filters of varying sizes (1x1, 3x3, and 5x5) simultaneously. This approach captures both local and global features efficiently, proving powerful in pattern detection.We present a novel deep learning framework for annotating secondary structures in intermediate-resolution cryo-EM maps, employing a three-dimensional Inception architecture. Evaluation on diverse datasets, including maps with authentic resolutions, demonstrates its accuracy and robustness. Comparative analysis against state-of-the-art frameworks reveals superior performance across secondary structure elements, with notable F1 scores of 0.657 for helix, 0.712 for coil, and 0.596 for sheet predictions. Certain helix and sheet predictions achieved impressive F1 scores of 0.881
Flatheaded and Roundheaded Borer Management and Phenology in Nursery Systems
No full textFlatheaded borers (Coleoptera: Buprestidae) and longhorn beetles (Coleoptera: Cerambycidae) are common pests in nursery production systems. The goals of this study were to examine characteristics of a pest buprestid [flatheaded appletree borer, Chrysobothris femorata (Olivier)] and cerambycid [tupelo borer, Aegomorphus morrisi (Uhler)]. The experiments included investigations of phenology, and the development of an artificial diet that would aid in rearing beetles for further studies. Stress factors such as mechanical damage and herbicide-stressed-foliage were evaluated for effects on beetle tree attacks and trap captures. Both beetles were successfully reared from artificial diet from older instars; however, flatheaded borer larvae showed less signs of diet feeding compared to longhorn beetle larvae. In the field, adult flatheaded borers were fully developed at ~746 growing degree days (GDD) (base 10°C [50°F]) based on dissections of trees in spring. Different mechanical stress treatments showed that large red maples with a trunk wedge removed had more attacks than girdled or felled trees. Based on the data, higher attacks may be due to the tree still being partially alive and declining more slowly when attacked versus completely dead. When looking at the attractiveness of herbicide-stressed vegetation, vegetation sprayed throughout the summer months did not affect the number of flatheaded borers caught on traps. This study also evaluated different lures commonly used to attract a variety of longhorned beetles for ability to capture tupelo borer; however, the tupelo borer was not trapped using fuscumol or fuscumol acetate. With this information collected better management strategies and practices to reduce flatheaded borer and longhorn beetle attacks within a nursery system can be evaluated
Evaluation of Mung Bean Varieties for Adaptation to Tennessee Growing Conditions
No full textThis study evaluates the adaptability and performance of mung bean varieties across different agricultural settings in Tennessee, incorporating conventional and organic farming practices to enhance crop rotation biodiversity. Trials conducted in Nashville, Memphis, and Carthage focused on assessing the growth and yield of mung bean varieties (AAMU, Berken, Handy Pantry Organic, and OK2000) post-winter wheat rotation with varied planting dates, tillage methods, and row spacing. Despite environmental challenges, such as drought and weed competition, our findings indicate a robust adaptability of mung beans to Tennessee\u27s climate, with significant yield variations based on variety, location, and year. In Nashville during 2023, the Handy Pantry Organic variety demonstrated superior performance in terms of yield and biomass, particularly with later planting dates that minimized weed competition. Soil analysis across locations informed management practices, with Memphis showing a notable yield increase to up to 1,500 lbs./acre under higher seed density and irrigation. planting dates in Nashville impacted the performance of Mung bean with late June significantly outyielding Mid may with a p value of (\u3c0.001). The study identified the critical role of weed management, especially in organic settings like Carthage, affecting the overall yield. Through detailed soil and phenotypic analyses, this research reveals mung bean\u27s potential to contribute significantly to sustainable agriculture in Tennessee, diversifying crop rotations and enhancing production within the state\u27s unique environmental constraints
Dynamics of soil microbial communities involved in carbon cycling along three successional forests in southern China
Get PDFDynamics of plant communities during forest succession have been received great attention in the past decades, yet information about soil microbial communities that are involved in carbon cycling remains limited. Here we investigated soil microbial community composition and carbohydrate degradation potential using metagenomic analysis and examined their influencing factors in three successional subtropical forests in southern China. Results showed that the abundances of soil bacteria and fungi increased (p ≤ 0.05 for both) with forest succession in relation to both soil and litter characteristics, whereas the bacterial diversity did not change (p \u3e 0.05) and the fungal diversity of Shannon-Wiener index even decreased (p ≤ 0.05). The abundances of microbial carbohydrate degradation functional genes of cellulase, hemicellulase, and pectinase also increased with forest succession (p ≤ 0.05 for all). However, the chitinase gene abundance did not change with forest succession (p \u3e 0.05) and the amylase gene abundance decreased firstly in middlesuccession forest and then increased in late-succession forest. Further analysis indicated that changes of functional gene abundance in cellulase, hemicellulase, and pectinase were primarily affected by soil organic carbon, soil total nitrogen, and soil moisture, whereas the variation of amylase gene abundance was well explained by soil phosphorus and litterfall. Overall, we created a metagenome profile of soil microbes in subtropical forest succession and fostered our understanding of microbially-mediated soil carbon cycling
Dissecting the Genetic Diversity of USDA Cowpea Germplasm Collection Using Kompetitive Allele Specific PCR-Single Nucleotide Polymorphism Markers
Get PDFCowpea (Vigna unguiculata L. Walp) is an important grain legume crop of the subtropics, particularly in West Africa, where it contributes to the livelihoods of small-scale farmers. Despite being a drought-resilient crop, cowpea production is hampered by insect pests, diseases, parasitic weeds, and various abiotic stresses. Genetic improvement can help overcome these limitations, and exploring diverse cowpea genetic resources is crucial for cowpea breeding. This study evaluated the genetic diversity of 361 cowpea accessions from the USDA core collection for the species using 102 Kompetitive Allele Specific PCR (KASP) single nucleotide polymorphism (SNP) markers. A total of 102 KASP-SNP was validated in the germplasm panel, and 72 showed polymorphism across the germplasm panel. The polymorphism information content (PIC) of all SNPs ranged from 0.1 to 0.37, with an average of 0.29, while the mean observed heterozygosity was 0.52. The population structure revealed three distinct populations that clustered into two major groups after phylogenetic analysis. Analysis of molecular variance (AMOVA) indicated greater genetic variation within populations than among populations. Although cowpea generally has a narrow genetic diversity, the accessions used in this study exhibited considerable variation across geographical regions, sub-species, and improvement status. These results indicated that the selected KASP genotyping assay can provide robust and accurate genotyping data for application in the selection and management of cowpea germplasm in breeding programs and genebanks
0610181443
No full texthttps://digitalscholarship.tnstate.edu/m-chamberlain-landscapes/1007/thumbnail.jp
Summer Breese
No full texthttps://digitalscholarship.tnstate.edu/m-chamberlain-landscapes/1005/thumbnail.jp