Adaptation of soybean to tropical environments for smallholder farmers

There are many traits that influence crop adaption to a new environment so that it can perform as a farmer would prefer. In these chapters, I have shown the influence of the genetic mechanisms behind pod shatter, days to flower, days to maturity, and height for soybean in a tropical environment. We developed two molecular tools to identify the allele status of Pdh1, a gene that influences shatter. Using those tools, we discovered that this genetic source of shatter susceptibility is still prevalent in African breeding materials and released varieties. I also contributed knowledge of the effects of the maturity genes E1, E2, E3 and ELF3 on days to flower and days to maturity. It was discovered that season length can be controlled by choice of the long juvenile trait ELF3 allele. Days to flower is influenced by E1 alleles in a j-1 background, and is influenced by E1, E2, and E3 in a j-x background in some cases. I also discovered that the determinate and indeterminate phenotypes do have different influences on height in this environment, but the gene Dt1 does not affect maturity. The next step is to conduct yield testing to understand how these traits influence yield. In addition, other alleles of ELF3 should be bred into different backgrounds to see if they influence different season lengths as well. Finally, the genetic source of the long juvenile trait in the current African released varieties need to be discovered. Taken together the future data combined with the data presented here can assist a local breeder in Africa to choose the germplasm they want to control their season length or protect yields from pod shatter and ultimately create a new, elite African variety.Includes bibliographical reference

Write Night: How a Writing Accountability Group (WAG) supports scholarly work and connection at a community residency program

Purpose: The purpose of this innovative endeavor was to improve scholarly output and collaboration at the Swedish First Hill Family Medicine residency by establishing a Writing Accountability Group (WAG). Background: While scholarly work during residency training is both required by the ACGME and important for producing physician leaders, many community-based residency programs have no formal structure to support such work and promote collaboration. At our program, faculty worked in functional silos and found it difficult to consistently involve residents in scholarly projects. WAGs have been studied in a variety of settings as a tool to increase scholarly output, improve writing habits, and provide mentorship for junior and senior faculty. Objectives: We aimed to analyze the effectiveness of a WAG in promoting scholarly work and resident scholarly mentorship in a community-based residency program. By reporting this work, we hope to provide inspiration and a roadmap for other faculty to increase scholarly productivity and joy in their work. Implementation/Design: After reviewing the literature regarding WAGs, a faculty member at Swedish First Hill Family Medicine invited other faculty to form a WAG at our community-based residency program. Over the next 18 months, a group of 4-6 faculty met every 2-3 weeks for 90-minute sessions to write, provide peer mentorship regarding scholarly pursuits, and collaborate on scholarly projects. Sessions were held on mutually convenient evenings at a faculty member’s home and over Zoom during the COVID-19 pandemic. Results/Outcomes: To assess the efficacy of the WAG, we measured total scholarly activity in an academic year for the five faculty participants both before (2018-2019) and after (2019-2020) the implementation of the WAG. We used the ACGME template for faculty scholarly activity to identify and categorize different types of activity. The total number of faculty scholarly activities increased from 20 to 44 after the formation of a WAG, representing a 120% increase in our total activity. For scholarly activity that required peer review or conference acceptance, our total number of submissions increased from 14 to 28, yet maintained a similar acceptance rate (79% in 2018-2019, 85% in 2019-2020). While the majority of our scholarly activity consisted of national conference submissions, we also noted increases in publications, podcasts, and other writing submissions. In addition to increased faculty scholarly productivity, our WAG was associated with increases in faculty job satisfaction, faculty collaboration, and resident scholarly activity. Significance: Creation of a WAG provided a structure for faculty scholarly collaboration and accountability for completion of scholarly projects. The WAG also provided a clear point of contact for other faculty and residents interested in scholarly work. In addition to increasing scholarly output and resident participation, our WAG improved wellness among faculty, providing a sense of collaboration and celebration of our scholarly work, particularly important during the COVID-19 pandemic. We plan to continue to evaluate the impact of the WAG in future years to look for sustained improvement.https://digitalcommons.psjhealth.org/swedish_learning_day_posters/1005/thumbnail.jp

Exploring the Life Course Perspective in Maternal and Child Health through Community-Based Participatory Focus Groups: Social Risks Assessment

Little is known about the patterns of risk factors experienced by communities of color and how diverse community contexts shape the health trajectory of women from the early childhood period to the time of their pregnancies. Thus, we conducted a focus group study to identify social risks over the life course that contribute to maternal and child health from the perspective of community members residing in low income urban areas. Ten community-based participatory focus groups were conducted with residents from selected communities in Tampa, Florida, from September to November 2013. We used the life course perspective to illuminate and explain the experiences reported by the interviewees. A total of 78 residents participated in the focus groups. Children and adolescents’ health risks were childhood obesity, lack of physical activity, and low self-esteem. Women’s health risks were low self-esteem, low educational level, low health literacy, inadequate parenting skills, and financial problems. Risks during pregnancy included stress, low self-esteem, inadequate eating patterns, lack of physical activity, healthcare issues, lack of social support, and lack of father involvement during pregnancy. Multiple risk factors contribute to maternal and child health in low income communities in Tampa Bay. The intersection of risk factors in different life periods suggest possible pathways, cumulative, and latent effects, which must be considered in future longitudinal studies and when developing effective maternal and child health programs and policies

Quaternary Structure Defines a Large Class of Amyloid-β Oligomers Neutralized by Sequestration

SummaryThe accumulation of amyloid-β (Aβ) as amyloid fibrils and toxic oligomers is an important step in the development of Alzheimer’s disease (AD). However, there are numerous potentially toxic oligomers and little is known about their neurological effects when generated in the living brain. Here we show that Aβ oligomers can be assigned to one of at least two classes (type 1 and type 2) based on their temporal, spatial, and structural relationships to amyloid fibrils. The type 2 oligomers are related to amyloid fibrils and represent the majority of oligomers generated in vivo, but they remain confined to the vicinity of amyloid plaques and do not impair cognition at levels relevant to AD. Type 1 oligomers are unrelated to amyloid fibrils and may have greater potential to cause global neural dysfunction in AD because they are dispersed. These results refine our understanding of the pathogenicity of Aβ oligomers in vivo

Meta-Analysis of Placental Transcriptome Data Identifies a Novel Molecular Pathway Related to Preeclampsia

Studies using the placental transcriptome to identify key molecules relevant for preeclampsia are hampered by a relatively small sample size. In addition, they use a variety of bioinformatics and statistical methods, making comparison of findings challenging. To generate a more robust preeclampsia gene expression signature, we performed a meta-analysis on the original data of 11 placenta RNA microarray experiments, representing 139 normotensive and 116 preeclamptic pregnancies. Microarray data were pre-processed and analyzed using standardized bioinformatics and statistical procedures and the effect sizes were combined using an inverse-variance random-effects model. Interactions between genes in the resulting gene expression signature were identified by pathway analysis (Ingenuity Pathway Analysis, Gene Set Enrichment Analysis, Graphite) and protein-protein associations (STRING). This approach has resulted in a comprehensive list of differentially expressed genes that led to a 388-gene meta-signature of preeclamptic placenta. Pathway analysis highlights the involvement of the previously identified hypoxia/HIF1A pathway in the establishment of the preeclamptic gene expression profile, while analysis of protein interaction networks indicates CREBBP/EP300 as a novel element central to the preeclamptic placental transcriptome. In addition, there is an apparent high incidence of preeclampsia in women carrying a child with a mutation in CREBBP/EP300 (Rubinstein-Taybi Syndrome). The 388-gene preeclampsia meta-signature offers a vital starting point for further studies into the relevance of these genes (in particular CREBBP/EP300) and their concomitant pathways as biomarkers or functional molecules in preeclampsia. This will result in a better understanding of the molecular basis of this disease and opens up the opportunity to develop rational therapies targeting the placental dysfunction causal to preeclampsia.Peer reviewe

Quantifying evidence toward pathogenicity for rare phenotypes: The case of succinate dehydrogenase genes, SDHB and SDHD.

PURPOSE: The weight of the evidence to attach to observation of a novel rare missense variant in SDHB or SDHD in individuals with the rare neuroendocrine tumors, pheochromocytomas and paragangliomas (PCC/PGL), is uncertain. METHODS: We compared the frequency of SDHB and SDHD very rare missense variants (VRMVs) in 6328 and 5847 cases of PCC/PGL, respectively, with that of population controls to generate a pan-gene VRMV likelihood ratio (LR). Via windowing analysis, we measured regional enrichments of VRMVs to calculate the domain-specific VRMV-LR (DS-VRMV-LR). We also calculated subphenotypic LRs for variant pathogenicity for various clinical, histologic, and molecular features. RESULTS: We estimated the pan-gene VRMV-LR to be 76.2 (54.8-105.9) for SDHB and 14.8 (8.7-25.0) for SDHD. Clustering analysis revealed an SDHB enriched region (ɑɑ 177-260, P = .001) for which the DS-VRMV-LR was 127.2 (64.9-249.4) and an SDHD enriched region (ɑɑ 70-114, P = .000003) for which the DS-VRMV-LR was 33.9 (14.8-77.8). Subphenotypic LRs exceeded 6 for invasive disease (SDHB), head-and-neck disease (SDHD), multiple tumors (SDHD), family history of PCC/PGL, loss of SDHB staining on immunohistochemistry, and succinate-to-fumarate ratio >97 (SDHB, SDHD). CONCLUSION: Using methodology generalizable to other gene-phenotype dyads, the LRs relating to rarity and phenotypic specificity for a single observation in PCC/PGL of a SDHB/SDHD VRMV can afford substantial evidence toward pathogenicity

Mutational heterogeneity in cancer and the search for new cancer genes

Major international projects are now underway aimed at creating a comprehensive catalog of all genes responsible for the initiation and progression of cancer. These studies involve sequencing of matched tumor–normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here, we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false positive findings that overshadow true driver events. Here, we show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumor-normal pairs and discover extraordinary variation in (i) mutation frequency and spectrum within cancer types, which shed light on mutational processes and disease etiology, and (ii) mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and allow true cancer genes to rise to attention

Autophagy Protein Atg3 is Essential for Maintaining Mitochondrial Integrity and for Normal Intracellular Development of Toxoplasma gondii Tachyzoites

Autophagy is a cellular process that is highly conserved among eukaryotes and permits the degradation of cellular material. Autophagy is involved in multiple survival-promoting processes. It not only facilitates the maintenance of cell homeostasis by degrading long-lived proteins and damaged organelles, but it also plays a role in cell differentiation and cell development. Equally important is its function for survival in stress-related conditions such as recycling of proteins and organelles during nutrient starvation. Protozoan parasites have complex life cycles and face dramatically changing environmental conditions; whether autophagy represents a critical coping mechanism throughout these changes remains poorly documented. To investigate this in Toxoplasma gondii, we have used TgAtg8 as an autophagosome marker and showed that autophagy and the associated cellular machinery are present and functional in the parasite. In extracellular T. gondii tachyzoites, autophagosomes were induced in response to amino acid starvation, but they could also be observed in culture during the normal intracellular development of the parasites. Moreover, we generated a conditional T. gondii mutant lacking the orthologue of Atg3, a key autophagy protein. TgAtg3-depleted parasites were unable to regulate the conjugation of TgAtg8 to the autophagosomal membrane. The mutant parasites also exhibited a pronounced fragmentation of their mitochondrion and a drastic growth phenotype. Overall, our results show that TgAtg3-dependent autophagy might be regulating mitochondrial homeostasis during cell division and is essential for the normal development of T. gondii tachyzoites

SNAPSHOT USA 2019 : a coordinated national camera trap survey of the United States

This article is protected by copyright. All rights reserved.With the accelerating pace of global change, it is imperative that we obtain rapid inventories of the status and distribution of wildlife for ecological inferences and conservation planning. To address this challenge, we launched the SNAPSHOT USA project, a collaborative survey of terrestrial wildlife populations using camera traps across the United States. For our first annual survey, we compiled data across all 50 states during a 14-week period (17 August - 24 November of 2019). We sampled wildlife at 1509 camera trap sites from 110 camera trap arrays covering 12 different ecoregions across four development zones. This effort resulted in 166,036 unique detections of 83 species of mammals and 17 species of birds. All images were processed through the Smithsonian's eMammal camera trap data repository and included an expert review phase to ensure taxonomic accuracy of data, resulting in each picture being reviewed at least twice. The results represent a timely and standardized camera trap survey of the USA. All of the 2019 survey data are made available herein. We are currently repeating surveys in fall 2020, opening up the opportunity to other institutions and cooperators to expand coverage of all the urban-wild gradients and ecophysiographic regions of the country. Future data will be available as the database is updated at eMammal.si.edu/snapshot-usa, as well as future data paper submissions. These data will be useful for local and macroecological research including the examination of community assembly, effects of environmental and anthropogenic landscape variables, effects of fragmentation and extinction debt dynamics, as well as species-specific population dynamics and conservation action plans. There are no copyright restrictions; please cite this paper when using the data for publication.Publisher PDFPeer reviewe