Current challenges and future of agricultural genomes to phenomes in the USA.

Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by improvements in identifying and measuring relevant trait variation in such populations across many environments (phenomics). Identifying the most critical opportunities and challenges in genome to phenome (G2P) research is the focus of this paper. Previously (Genome Biol, 23(1):1-11, 2022), we laid out how Agricultural Genome to Phenome Initiative (AG2PI) will coordinate activities with USA federal government agencies expand public-private partnerships, and engage with external stakeholders to achieve a shared vision of future the AG2PI. Acting on this latter step, AG2PI organized the "Thinking Big: Visualizing the Future of AG2PI" two-day workshop held September 9-10, 2022, in Ames, Iowa, co-hosted with the United State Department of Agriculture's National Institute of Food and Agriculture (USDA NIFA). During the meeting, attendees were asked to use their experience and curiosity to review the current status of agricultural genome to phenome (AG2P) work and envision the future of the AG2P field. The topic summaries composing this paper are distilled from two 1.5-h small group discussions. Challenges and solutions identified across multiple topics at the workshop were explored. We end our discussion with a vision for the future of agricultural progress, identifying two areas of innovation needed: (1) innovate in genetic improvement methods development and evaluation and (2) innovate in agricultural research processes to solve societal problems. To address these needs, we then provide six specific goals that we recommend be implemented immediately in support of advancing AG2P research.

Comprehensive Review on Medicinal Applications of Coumarin-Derived Imine-Metal Complexes.

Coumarins are fused six-membered oxygen-containing benzoheterocycles that join two synthetically useful rings: α-pyrone and benzene. A survey of the literature shows that coumarins and their metal complexes have received great interest from synthetic chemists, medicinal scientists, and pharmacists due to their wide spectrum of biological applications. For instance, coumarin and its derivatives have been used as precursors to prepare a large variety of medicinal agents. Likewise, coumarin-derived imine-metal complexes have been found to display a variety of therapeutic applications, such as antibacterial, antifungal, anticancer, antioxidant, anthelmintic, pesticidal, and nematocidal activities. This review highlights the current synthetic methodologies and known bioactivities of coumarin-derived imine-metal complexes that make this molecule a more attractive scaffold for the discovery of newer drugs.

Preliminary Phytochemical Profile and Bioactivity of Inga jinicuil Schltdl & Cham. ex G. Don.

Several Mesoamerican cultures have used Inga jinicuil as traditional medicine for the treatment of gastrointestinal, inflammatory, and infectious issues. The aims of this contribution were to elucidate the phytochemical profile of the organic extracts from the bark and leaves of I. jinicuil and to assess the anti-inflammatory and antibacterial properties of these extracts. The preliminary chemical profile was determined by HPLC-PDA and GC-MS; the anti-inflammatory activity was evaluated with a mouse ear edema model, whereas the antibacterial activity was screened against several bacteria. The phytochemical profile of both organs (bark and leaves) of I. jinicuil led to the identification of 42 compounds, such as polyphenolic, flavonoids, triterpenes, prenol-type lipids, and aliphatic and non-aliphatic esters. This molecular diversity gave moderate anti-inflammatory activity (67.3 ± 2.0%, dichloromethane bark extract) and excellent antibacterial activity against Pseudomona aeruginosa and methicillin-resistant Sthaphylococcus aureus (MIC values of ˂3.12 and 50 µg/mL, respectively). These results contribute to the chemotaxonomic characterization and the rational use in traditional medicine of Inga jinicuil Schltdl & Cham. ex G. Don.

Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity.

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

Pre-clerkship physical examination assessment rubric.

INTRODUCTION: The physical examination is a core competency in the training of pre-clerkship medical students. It is important to certify proficiency in the physical examination before students start their clinical rotations. Many institutions use home grown assessment tools for this purpose; however, there currently are no validated rubrics designed to assess the performance a head to toe physical examination by a pre-clerkship medical student. The goal of this study is to assess the reliability (inter-rater and intra-rater) of our institutionally developed rubric. METHODS: Clinical faculty with various levels of teaching experience watched videos of students doing a head to toe physical examination and scored the students using our assessment rubric. These scores were evaluated for intra-rater and inter-rater reliability. RESULTS: A total of 15 student videos were reviewed by five faculty members with varying levels of teaching experience. The degree of inter-rater agreement (between raters) for single and average measure was excellent and the degree of intra-rater agreement (same rater twice) for single and average measure was excellent. DISCUSSION: We conclude that our institutionally developed physical examination assessment rubric is a reliable means to certify proficiency in the physical examination before students start their clinical clerkships.

A genetic link between leaf carbon isotope composition and whole-plant water use efficiency in the C4 grass Setaria.

Genetic selection for whole-plant water use efficiency (yield per transpiration; WUEplant ) in any crop-breeding programme requires high-throughput phenotyping of component traits of WUEplant such as intrinsic water use efficiency (WUEi ; CO2 assimilation rate per stomatal conductance). Measuring WUEi by gas exchange measurements is laborious and time consuming and may not reflect an integrated WUEi over the life of the leaf. Alternatively, leaf carbon stable isotope composition (δ13 Cleaf ) has been suggested as a potential time-integrated proxy for WUEi that may provide a tool to screen for WUEplant . However, a genetic link between δ13 Cleaf and WUEplant in a C4 species has not been well established. Therefore, to determine if there is a genetic relationship in a C4 plant between δ13 Cleaf and WUEplant under well watered and water-limited growth conditions, a high-throughput phenotyping facility was used to measure WUEplant in a recombinant inbred line (RIL) population created between the C4 grasses Setaria viridis and S. italica. Three quantitative trait loci (QTL) for δ13 Cleaf were found and co-localized with transpiration, biomass accumulation, and WUEplant . Additionally, WUEplant for each of the δ13 Cleaf QTL allele classes was negatively correlated with δ13 Cleaf , as would be predicted when WUEi influences WUEplant . These results demonstrate that δ13 Cleaf is genetically linked to WUEplant , likely to be through their relationship with WUEi , and can be used as a high-throughput proxy to screen for WUEplant in these C4 species.

An Old Disease With an Unfamiliar Face: A Case Report of Ocular Syphilis.

Syphilis is an infection caused by the bacterium Treponema pallidum. Patients with syphilis can present with a wide range of symptoms depending on the stage of disease. An underappreciated manifestation of syphilis is ocular involvement, which has been increasingly reported in the last several years. Delay in diagnosis and treatment of ocular syphilis can increase the risk of irreversible vision loss. Syphilis can affect almost every structure in the eye; however, most commonly presents with panuveitis. Ocular syphilis is treated similarly to neurosyphilis with prompt initiation of intravenous penicillin G.

Differences in medical student self-evaluations of clinical and professional skills.

BACKGROUND: The skill of self-assessment is critical to medical students. We sought to determine whether there were differences between student self-assessments and their faculty assessments and if they were modified by gender. Additionally, we sought to determine the differences in these assessments between students in a traditional (core) versus an enhanced (SELECT) medical school curriculum. METHODS: In this retrospective study, mid-term and final assessment and feedback forms from the first-year Doctoring 1 course were analyzed from three academic years: 2014-2015 through 2016-2017. Data were abstracted from the forms and de-identified for analysis. Class year, student gender, and class type were also abstracted from this "on the shelf" data from program assessment. The level of agreement between faculty and student assessments was investigated using Wilcoxon signed ranks test. The gender differences (male versus female students) between student assessments and their assessment by their faculty were investigated by using the Kruskal Wallis test. RESULTS: Five hundred and thirty-five student self-assessments were analyzed. Fifty-six percent (301/535) were male while 44% (234/535) were female. Faculty assessments (P-value <0.001) were higher than students and this was not modified by student gender. Compared to the domain of "participation" in the core program, there was no difference between the student/faculty ratings based on student gender (P-value: 0.48); there was a difference in the SELECT program cohort (P-value: 0.02). Specifically, the female students appear to rate themselves lower (female student: mean/standard deviation: 2.07/0.52) compared to their faculty (faculty: mean/standard deviation: 2.42/0.55). CONCLUSION: Faculty consistently assessed the students at a higher rating than the students rated themselves. The level of difference between student self-assessments and their assessment by their faculty was not modified by student gender. With the minor exception of "participation," there was no difference between students in the two different doctoring class curriculums.

Components of Water Use Efficiency Have Unique Genetic Signatures in the Model C4 Grass Setaria.

Plant growth and water use are interrelated processes influenced by genetically controlled morphological and biochemical characteristics. Improving plant water use efficiency (WUE) to sustain growth in different environments is an important breeding objective that can improve crop yields and enhance agricultural sustainability. However, genetic improvement of WUE using traditional methods has proven difficult due to the low throughput and environmental heterogeneity of field settings. To overcome these limitations, this study utilizes a high-throughput phenotyping platform to quantify plant size and water use of an interspecific Setaria italica × Setaria viridis recombinant inbred line population at daily intervals in both well-watered and water-limited conditions. Our findings indicate that measurements of plant size and water use are correlated strongly in this system; therefore, a linear modeling approach was used to partition this relationship into predicted values of plant size given water use and deviations from this relationship at the genotype level. The resulting traits describing plant size, water use, and WUE all were heritable and responsive to soil water availability, allowing for a genetic dissection of the components of plant WUE under different watering treatments. Linkage mapping identified major loci underlying two different pleiotropic components of WUE. This study indicates that alleles controlling WUE derived from both wild and domesticated accessions can be utilized to predictably modulate trait values given a specified precipitation regime in the model C4 genus Setaria.

High-fidelity detection of crop biomass quantitative trait loci from low-cost imaging in the field.

Field-based, rapid, and nondestructive techniques for assessing plant productivity are needed to accelerate the discovery of genotype-to-phenotype relationships in next-generation biomass grass crops. The use of hemispherical imaging and light attenuation modeling was evaluated against destructive harvest measures with respect to their ability to accurately capture phenotypic and genotypic relationships in a field-grown grass crop. Plant area index (PAI) estimated from below-canopy hemispherical images, as well as a suite of thirteen traits assessed by manual destructive harvests, were measured in a Setaria recombinant inbred line mapping population segregating for aboveground productivity and architecture. A significant correlation was observed between PAI and biomass production across the population at maturity (r 2 = .60), as well as for select diverse genotypes sampled repeatedly over the growing season (r 2 = .79). Twenty-seven quantitative trait loci (QTL) were detected for manually collected traits associated with biomass production. Of these, twenty-one were found in four clusters of colocalized QTL. Analysis of image-based estimates of PAI successfully identified all four QTL hot spots for biomass production. QTL for PAI had greater overlap with those detected for traits associated with biomass production than with those for plant architecture and biomass partitioning. Hemispherical imaging is an affordable and scalable method, which demonstrates how high-throughput phenotyping can identify QTL related to biomass production of field trials in place of destructive harvests that are labor, time, and material intensive.

PlantCV v2: Image analysis software for high-throughput plant phenotyping.

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.

Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria.

Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed six controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The non-destructive nature of plant height measurements has enabled us to monitor height throughout the plant life cycle in both field and controlled environments. We find that plant height is reduced under water limitation and high density planting and affected by growth environment (field vs. growth chamber). The results support a model where plant height is a heritable, polygenic trait and that the major genetic loci that influence plant height function independent of growth environment. The identity and contribution of loci that influence height changes dynamically throughout development and the reduction of growth observed in water limited environments is a consequence of delayed progression through the genetic program which establishes plant height in Setaria. In this population, alleles inherited from the weedy S. viridis parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated S. italica parent collectively act to increase plant height later in development.

Grasses suppress shoot-borne roots to conserve water during drought.

Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C4 grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.

Above-Label Doses of Octreotide-LAR in Patients With Metastatic Small Intestinal Carcinoid Tumors.

BACKGROUND: Octreotide LAR is indicated for treatment of malignant carcinoid syndrome and has been studied at doses of 10 to 30 mg intramuscularly every 4 weeks. In clinical practice, higher doses are often prescribed for patients who experience refractory carcinoid syndrome (flushing and/or diarrhea) or tumor growth while on the maximum label-recommended dose. METHODS: We performed a retrospective, longitudinal review of octreotide LAR administration at a tertiary institution to determine the frequency of above-label dosing and outcomes. RESULTS: Three hundred thirty-eight patients were considered evaluable, among whom 100 (30%) underwent at least 1 increase in dose or frequency of octreotide-LAR above the standard label dose. The most common maximum doses were 40 mg every 4 weeks (n = 37 patients), 60 mg every 4 weeks (n = 34), and 30 mg every 3 weeks (n = 18). The indications for dose increase were worsening carcinoid syndrome (n = 60), radiographic progression (n = 33), and rising urine 5-HIAA (n = 6). Of the patients whose doses were increased for refractory carcinoid syndrome, 62% (n = 34) experienced improvement in diarrhea, and 56% (n = 28) experienced improvement in flushing. CONCLUSIONS: In conclusion, octreotide LAR is commonly prescribed in doses or schedules above the recommended dose and frequency. Patients with refractory carcinoid syndrome appear to experience a clinical benefit from this change. Prospective data may be used to further evaluate this strategy.

Control of cell proliferation, endoreduplication, cell size, and cell death by the retinoblastoma-related pathway in maize endosperm.

The endosperm of cereal grains is one of the most valuable products of modern agriculture. Cereal endosperm development comprises different phases characterized by mitotic cell proliferation, endoreduplication, the accumulation of storage compounds, and programmed cell death. Although manipulation of these processes could maximize grain yield, how they are regulated and integrated is poorly understood. We show that the Retinoblastoma-related (RBR) pathway controls key aspects of endosperm development in maize. Down-regulation of RBR1 by RNAi resulted in up-regulation of RBR3-type genes, as well as the MINICHROMOSOME MAINTENANCE 2-7 gene family and PROLIFERATING CELL NUCLEAR ANTIGEN, which encode essential DNA replication factors. Both the mitotic and endoreduplication cell cycles were stimulated. Developing transgenic endosperm contained 42-58% more cells and ∼70% more DNA than wild type, whereas there was a reduction in cell and nuclear sizes. In addition, cell death was enhanced. The DNA content of mature endosperm increased 43% upon RBR1 down-regulation, whereas storage protein content and kernel weight were essentially not affected. Down-regulation of both RBR1 and CYCLIN DEPENDENT KINASE A (CDKA);1 indicated that CDKA;1 is epistatic to RBR1 and controls endoreduplication through an RBR1-dependent pathway. However, the repressive activity of RBR1 on downstream targets was independent from CDKA;1, suggesting diversification of RBR1 activities. Furthermore, RBR1 negatively regulated CDK activity, suggesting the presence of a feedback loop. These results indicate that the RBR1 pathway plays a major role in regulation of different processes during maize endosperm development and suggest the presence of tissue/organ-level regulation of endosperm/seed homeostasis.

Prognostic validity of the American Joint Committee on Cancer staging classification for midgut neuroendocrine tumors.

PURPOSE: The American Joint Committee on Cancer (AJCC) staging manual has introduced a TNM staging classification for jejunal-ileal (midgut) neuroendocrine tumors (NETs). This classification has not been validated in a population consisting solely of midgut NETs. The purpose of this study was to test the prognostic validity of the classification in such a population. METHODS: Patients with jejunal and ileocecal NETs who were treated at the Moffitt Cancer Center between 2000 and 2010 were assigned stages (I through IV). Kaplan-Meier analyses for overall survival (OS) were performed on the basis of TNM stage and pathologic grade. Multivariate modeling was performed using Cox proportional hazards regression. RESULTS: We identified 691 patients with jejunal-ileocecal NETs. The AJCC classification in aggregate was highly prognostic for OS (P < .001). Five-year OS rates for stages I through IV were 100%, 100%, 91%, and 72%, respectively. The survival difference between stages III and IV was significant (P < .001); the difference between stages I/II versus III was not statistically significant (P = .1). Among patients with stage IIIB tumors, 5-year survival rates were 95% for resectable tumors versus 78% for unresectable mesenteric tumors (P = .02). A proliferative threshold of five mitoses per 10 high-power fields (HPF) was of greater prognostic value than a threshold of two mitoses per 10 HPF for discriminating between low- and intermediate-grade tumors. CONCLUSION: Stage I and II midgut NETs are associated with identical survival rates. Stage IIIB tumors are heterogeneous, with significant differences in survival observed between resectable mesenteric lymph nodes versus unresectable masses in the root of the mesentery. A higher mitotic cutoff of five per 10 HPF may lead to improved prognostic differentiation between low- and intermediate-grade tumors. Revisions to the current AJCC staging and grading classification may be warranted.