USDA National Research Articles

Eating Competence in First-Generation Students at a Northeastern, Public University

Abstract Objectives To assess differences in eating competence (EC) between first-generation students (FG) and students with 1 + parents who graduated from college (non-FG), in students 18–24 years old, at a large, northeastern, public university. Methods Data were collected between 2015–2020 from the College Health and Nutrition Assessment Survey, an ongoing, cross-sectional study at a northeastern university. Participants (n = 1974) completed the Eating Competence Satter Inventory (ecSI 2.0TM) and self-reported education status of both parents through an online survey (Qualtrics) during the 3rd or 4th week of classes. ecSI scores range from 0–48; eating competence was defined as ≥32. Subgroups within the ecSI include Eating Attitudes, Food Acceptance, Food Regulation and Contextual Skills. FG was defined if both parents did not obtain a college degree. ANCOVA evaluated differences between mean ecSI scores of FG vs. non-FG (n = 1478); age, gender, race, Pell Grant status, dining hall usage, athlete status, and available kitchen served as covariates. Results In this sample, 64.9% of participants were female students, 25.2% were FG, and had a mean age of 19.0 ± 0.02 years. FG students (n = 496) had modestly lower mean ecSI scores than non-FG students (32.9 ± 0.4 vs. 34.0 ± 0.3, P = 0.03. Subscale scores for Food Acceptance (0–9), Food Regulation (0–9) and Contextual Skills (0–12) were lower in FG students compared to non-FG students (5.1 ± 0.1 vs. 5.4 ± 0.7, P = 0.03, 6.4 ± 0.1 vs. 6.6 ± 0.1, P = 0.05, and 10.4 ± 0.1 vs. 10.9 ± 0.1, P = 0.003 respectively). Conclusions Results suggest FG students have lower EC scores than their non-FG counterparts; subscales suggest where FG students may need more support to achieve more favorable weight and health outcomes. More research in diverse communities of college students will help address the needs of FG students and strengthen outcomes for campus communities. Funding Sources New Hampshire Agriculture Experiment Stations and the USDA National Institute of Food and Agriculture Hatch Project.

Field resistance to wheat stem rust in durum wheat accessions deposited at the USDA National Small Grains Collection.

Wheat stem rust, caused by Puccinia graminis f. sp. tritici, is a re‐emerging disease, posing a significant threat to durum wheat production worldwide. The limited number of stem rust resistance genes in modern cultivars compels us to identify and incorporate new effective genes in durum wheat breeding programs. We evaluated 8,245 spring durum wheat accessions deposited at the USDA National Small Grains Collection (NSGC) for resistance in field stem rust nurseries in Debre Zeit, Ethiopia and St. Paul, MN (USA). A higher level of disease development was observed at the Debre Zeit nursery compared with St. Paul, and the effective alleles of Sr13 in this nursery did not display the level of resistance observed at the St. Paul nursery. Four hundred and ninety‐one (∽6%) accessions exhibited resistant to moderately susceptible responses after three field evaluations at Debre Zeit and two at St. Paul. Nearly 70% of these accessions originated from Ethiopia, Mexico, Egypt, and USA. Eight additional countries, namely Portugal, Turkey, Italy, Canada, Chile, Australia, Syria, and Tunisia contributed to 19% of the resistant to moderately susceptible entries. Among the 491 resistant to moderately susceptible accessions, 53.8% (n = 265) were landraces, and 28.4% (n = 139) and 11.4% (n = 55) were breeding lines and cultivars, respectively. Breeding lines and cultivars displayed a higher level and frequency of resistance than the landraces. We concluded that a large number of durum wheat accessions from diverse origins deposited at the NSGC can be exploited for diversifying and improving stem rust resistance in wheat.

Three datasets for nutrition environment measures of food outlets located in the Lower Mississippi Delta region of the United States.

This data note provides details of a research database containing 266 food outlets located in five rural towns in the Lower Mississippi Delta region of Mississippi, whose nutrition environments were measured from 2016 to 2018. The food outlet types include grocery stores, convenience stores, full-service restaurants, and fast food restaurants. The purpose of this publication is to describe the three datasets for external researchers who may be interested in making use of them. The datasets are available from the USDA National Agricultural Library's Ag Data Commons under a CC0 1.0 Universal License: https://doi.org/10.15482/USDA.ADC/1503704.

83 MicroRNA574-3p Influences Porcine Oocyte Maturation and Regulates Abundance of Proteins Critical to Early Embryo Development

Abstract MicroRNA are small non-coding RNA involved in post-transcriptional gene regulation impacting oocyte maturation and embryo development. MIR574-3p abundance decreases during oocyte in vitro maturation (IVM) and blastocyst development. The study objective was to evaluate the role of MIR574-3p during porcine oocyte maturation and early embryo development. To assess the function of MIR574-3p during these processes, denuded GV stage oocytes injected with MIR574-3p mimic (MIR574-3p-M), MIR574-3p inhibitor (MIR574-3p-I) or negative control oligo (NC) underwent IVM for 42 hours. The number of MII arrested oocytes was decreased (P = 0.06) in the MIR574-3p-M group (67.7 ± 1.4%) as compared to the NC group (76.1 ± 1.3%), whereas maturation was not affected by MIR574-3p-I (75.6 ± 1.5%) as compared to the NC group (73.1 ± 3.6%). MII arrested oocytes were parthenogenetically activated and cultured for 7 days. Neither mimic nor inhibitor affected the cleavage or blastocyst rate. Using LC-MS/MS we evaluated changes in global protein abundance in injected oocytes after 42 hours of IVM. We identified 971 proteins in MIR574-3p-M injected oocytes, of which 57 were differentially abundant as compared to the control group. In MIR574-3p-I injected oocytes, 1007 proteins were identified, of which 107 were differentially abundant as compared to the control group. Overall, MIR574-3p-M upregulated proteins critical to membrane binding mediating sperm receptors on the zona pellucida, while it downregulated intranuclear activity such as nucleotide biosynthesis, mitotic spindle assembly and orientation; whereas MIR574-3p-I induced upregulation of proteins involved in the processes between and including protein biosynthesis and metabolism, while downregulating proteins critical to ATP, RNA, DNA and protein binding. These data suggest artificially increasing MIR574-3p abundance during IVM alters the oocyte proteome and influences meiotic progression to MII. Project was supported by Agriculture and Food Research Initiative Competitive Grant no. 2017-67015-26459 from the USDA National Institute of Food and Agriculture.

174 What Quality and Fertility Should We Expect When Using Semen Cryopreservation and AI with Livestock? a Comparison Across Species

Abstract Assisted reproductive technologies (ART) can be used across most agricultural species and will result in some degree of fertility when employed correctly. Still, conversations with agricultural producers and scientists (corporate, academic, governmental) repeatedly reveal that they do not know what success rates they should anticipate when using some ARTs, specifically semen cryopreservation and artificial insemination, with agricultural species (beef and dairy cattle, goats, pigs, poultry, sheep). These perceptions hinder ART application within the agricultural and scientific communities. Understanding these expected results is a critical component that is used to guide the USDA National Animal Germplasm Program laboratory operations for collecting, freezing and using germ plasm (semen, eggs, embryos, DNA, tissues, organs, cells), has consequently resulted in growth of the national collection, and provided tools, technologies, and educational opportunities for agricultural producers with documented success. Therefore, the intent of this presentation is to provide an overview of what results should be expected when using semen cryopreservation and artificial insemination across livestock species, explain the factors that influence successful use of these ARTs, which should encourage a more broad acceptance of their use with all agricultural species, and discuss opportunities for research and optimization that will improve fertility when using these technologies.

Histone Lysine Demethylase 1A Is a Master Regulator of Genes Necessary for Trophoblast Cell Proliferation

Histone lysine demethylase 1A is a master regulator of genes necessary for trophoblast cell proliferation.A proper functioning placenta is critical for pregnancy, fetal growth and development and postnatal health. Trophoblast cell proliferation and differentiation is critical for placental development and function. Recently we demonstrated that the histone lysine demethylase KDM1A binds to androgen receptor (AR) in human and sheep trophoblast cells, and targets the same promoter region of vascular endothelial growth factor A (VEGFA), suggesting a role for KDM1A and AR in early placental angiogenesis. The goal of this study was to determine the function of KDM1A during early placental development. We hypothesized that KDM1A regulates genes that are necessary for trophoblast cell proliferation, and early placental development. To this end, both in vitro and in vivo approaches were used in this study. ACH-3P cells (human first trimester trophoblast cells (CT and EVT) fused with the choriocarcinoma cell line AC1-1) were used, and a KDM1A knock out (KO) cell line was generated using CRISPR-Cas 9 based genome editing. KDM1A KO in ACH-3P cells led to significant (P<0.05) reduction in AR and VEGFA. Furthermore, factors important for cell proliferation and trophoblast cell development high mobility group AT-hook 1 (HMGA1), LIN28, and MYC protooncogene (cMYC) were significantly (P<0.05) lower in KDM1A KO ACH-3P cells. Cell proliferation assays revealed a significant (P<0.05) reduction in KDM1A KO ACH-3P cells compared to scramble controls. An in vivo experiment was conducted to demonstrate a role for KDM1A in placental development, using the sheep as a model. Day 9 hatched blastocysts were flushed and infected with a Lenti-CRISPRv2 KDM1A target construct (n=4) to knockout KDM1A specifically in the trophectoderm, or with SC (n=5). Infected embryos were transferred to recipient ewes and embryos were collected at gestational day 16. Data suggests that KDM1A KO in trophoblast cells is necessary for conceptus elongation. Current experiments are ongoing to determine the effects of KDM1A and AR knockdown using shRNA lentiviral target vectors on conceptus elongation and pregnancy. Collectively these results indicate that KDM1A plays a central role in regulating genes necessary for trophoblast cell proliferation.This project was supported by Agriculture and Food Research Initiative Competitive Grant no. 2019-67015-29000 from the USDA National Institute of Food and Agriculture.

Genetic fingerprinting identifies apple (Malus domestica Borkh.) fruit cultivars in historic orchards on public lands

The National Historic Preservation Act of 1966 mandates that historic resources, including orchards, on federal lands be evaluated for potential significance. Evaluations include assessments and documentation of an orchard’s layout and location, as well as the architecture, ages, conditions, and cultivars of trees. These factors may reveal an orchard’s history and uniqueness and determine an orchard’s historic importance. Fruit tree cultivar identities are a key piece of this puzzle. They reveal information about an orchard’s use, origin, and uniqueness. In the past, historic preservationists relied on pomologists to identify cultivars based primarily on the phenotypic traits of the tree. DNA fingerprinting technologies, in combination with high-quality reference cultivar collections, have dramatically improved the accuracy of heritage cultivar identification. We demonstrate the utility of using DNA technologies for cultivar identifications on federal lands using examples from trees in orchards of Redwood National and State Parks and the Eldorado National Forest. A total of 87 historic apple trees from these locations were genotyped and cultivar names were determined for 35 trees, using a reference set of 1319 apple cultivars from the USDA National Plant Germplasm System, Washington State University, Seed Savers Exchange, and Temperate Orchard Conservancy. Some of the trees that were not identified may be cultivars that are not included in the reference sets and others may be unique trees derived from seeds. The information derived from genetic fingerprinting analyses will aid in the determination of the historic significance of orchards on public lands.

Phenological corrections to a field-scale, ET-based crop stress indicator: An application to yield forecasting across the U.S. Corn Belt

Soil moisture deficiency is a major factor in determining crop yields in water-limited agricultural production regions. Evapotranspiration (ET), which consists of crop water use through transpiration and water loss through direct soil evaporation, is a good indicator of soil moisture availability and vegetation health. ET therefore has been an integral part of many yield estimation efforts. The Evaporative Stress Index (ESI) is an ET-based crop stress indicator that describes temporal anomalies in a normalized evapotranspiration metric as derived from satellite remote sensing. ESI has demonstrated the capacity to explain regional yield variability in water-limited regions. However, its performance in some regions where the vegetation cycle is intensively managed appears to be degraded due to interannual phenological variability. This investigation selected three study sites across the U.S. Corn Belt – Mead, NE, Ames, IA and Champaign, IL – to investigate the potential operational value of 30-m resolution, phenologically corrected ESI datasets for yield prediction. The analysis was conducted over an 8-year period from 2010 to 2017, which included both drought and pluvial conditions as well as a broad range in yield values. Detrended yield anomalies for corn and soybean were correlated with ESI computed using annual ET curves temporally aligned based on (1) calendar date, (2) crop emergence date, and (3) a growing degree day (GDD) scaled time axis. Results showed that ESI has good correlations with yield anomalies at the county scale and that phenological corrections to the annual temporal alignment of the ET timeseries improve the correlation, especially when the time axis is defined by GDD rather than the calendar date. Peak correlations occur in the silking stage for corn and the reproductive stage for soybean – phases when these crops are particularly sensitive to soil moisture deficiencies. Regression equations derived at the time of peak correlation were used to estimate yields at county scale using a leave-one-out cross-validation strategy. The ESI-based yield estimates agree well with the USDA National Agricultural Statistics Service (NASS) county-level crop yield data, with correlation coefficients ranging from 0.79 to 0.93 and percent root-mean-square errors of 5–8%. These results demonstrate that remotely sensed ET at high spatiotemporal resolution can convey valuable water stress information for forecasting crop yields across the Corn Belt if interannual phenological variability is considered.

First report of leaf blight caused by Phytophthora ramorum on periwinkle (Vinca minor) in Washington State, USA.

Phytophthora ramorum (Werres, De Cock & Man in't Veld) was recovered from symptomatic foliage of periwinkle at a botanical garden in WA in March 2015. Symptoms were tan colored lesions with a dark brown margin visible on both surfaces of the leaf and were found on wounds or around leaf margins. Periwinkle is native to Europe and is commonly used for ground cover in ornamental landscapes. It is known to be invasive in US forests near the urban/wildland interface. Potential spread of P. ramorum into WA forests is of regulatory concern, as well as long distance spread to other states via nursery stock (7 CFR §301.92-2). Phytophthora ramorum was isolated from symptomatic foliage by excising leaf pieces 4-6 mm in diameter and surface-sterilizing in 0.6% sodium hypochlorite followed by two rinses in sterile water. Leaf pieces were plated on PARP medium (Ferguson and Jeffers 1999) and after 2-3 days at 20°C, slow-growing dense colonies with coralloid hyphae were isolated onto V8 agar. Colony morphology and chlamydospore production were consistent with descriptions of P. ramorum (Werres et al. 2001), except that the isolate was slower growing and had irregular, non-wildtype morphology (Elliott et al. 2018) compared to other isolates of P. ramorum. ITS and COX1 regions of mycelial DNA was amplified and sequenced to confirm the identity of P. ramorum using primers ITS1/ITS4 (White et al. 1990) and COX1F1/COX1R1 (Van Poucke et al. 2012). Sequences were submitted to GenBank (accession nos. ITS MT031975, COX1 MT031974). BLAST results showed at least 98% similarity with sequences of P. ramorum (ITS, MN540640 [98%]; COX1, EU124920 [100%]), and belonged to the NA1 clonal lineage. Pathogenicity of P. ramorum to periwinkle was confirmed by completing Koch's Postulates. Inoculum was grown on V8 agar plates at 20°C for two weeks until sporangia were abundant. A zoospore suspension was produced by flooding plates with 7 ml sterile water, incubating for 2 hours at 5°C, then for an additional hour at 24°C. Zoospores were observed under the microscope and quantified with a hemocytometer, then diluted to 2 x 105 zoospores/ml. A 10 µl droplet of inoculum was placed at one wounded and one unwounded site on six leaves on each of four plants. In addition, a set of four plants was inoculated by dipping foliage on one branch per plant into the zoospore suspension for 30 seconds. A set of four control plants were mock inoculated in the same manner using sterile water. The trial was repeated once. Inoculated plant materials were incubated in a moist chamber for 3-5 days and free moisture was present on foliage upon removal. Plants were held in a biocontainment chamber (USDA-APHIS permit # 65857) at 20C and symptom development assessed after 7 days (Figure S1). . Symptoms developed on foliage inoculated using both methods in both trials. Phytophthora ramorum was isolated once from droplet inoculated foliage at a wounded site on one plant. Reisolation onto PARP and then V8 agar was conducted from surface-sterilized symptomatic tissue and the presence of P. ramorum confirmed by observation of colony morphology and chlamydospore production. The presence of P. ramorum was also confirmed with DNA extraction from symptomatic foliage from plants from each of the two trials followed by PCR and sequencing of the COX1 gene (EU124920, 100%) (Figure S2). None of the water-inoculated controls were positive for P. ramorum. Low isolation success could be attributed to reduced pathogenicity due to being a non-wildtype isolate. Acknowledgements This work was supported by the USDA National Institute of Food and Agriculture, McIntire-Stennis project 1019284 and USDA APHIS Cooperative Agreement AP17PPQS&T00C070.

Cost-effective options for increasing consumption of under-consumed food groups and nutrients in the USA.

To identify the most cost-effective options/contributors of under-consumed food groups and nutrients in the USA. Twenty-four-hour dietary recall data were used for the dietary sources of under-consumed food groups and nutrients. Costs were estimated using USDA National Food Price Database 2001-2004 after adjustments for inflation using Consumer Price Index. National Health and Nutrition Examination Survey, 2013-2016. A total of 10 112 adults aged 19+ years. Top five cost-effective options for food groups were apple and citrus juice, bananas, apples, and melons for fruit; baked/boiled white potatoes, mixtures of mashed potatoes, lettuce, carrots and string beans for vegetables; oatmeal, popcorn, rice, yeast breads and pasta/noodles/cooked grains for whole grain; and reduced-fat, low-fat milk, flavoured milk and cheese for dairy. Top five cost-effective sources of under-consumed nutrients were rice, tortillas, pasta/noodles/cooked grains, rolls and buns, and peanut butter-jelly sandwiches for Mg; grits/cooked cereals, low- and high-sugar ready-to-eat (RTE) cereal, rolls and buns, and rice for Fe; low- and high-sugar RTE cereals, rice, protein and nutritional powders, and rolls and buns for Zn; carrots, margarine, other red and orange vegetables, liver and organ meats, butter and animal fats for vitamin A; and citrus juice, other fruit juice, vegetable juice, mustard and other condiments, and apple juice for vitamin C. Apple/citrus juice, white potatoes/carrots, oatmeal, RTE cereals and milk were the most cost-effective food sources of multiple under-consumed food groups and nutrients and can help promote healthy eating habits at minimal cost.

The Quality of the Food Retail Environment When Consumers May Be Mobile

AbstractUsing USDA's National Household Food Acquisition and Purchase Survey (FoodAPS), we estimated block group‐level spending‐weighted mean distance to the retailers where consumers actually shop (3.9 miles overall; 7.0 miles in rural areas and 3.0 miles in urban areas). Holding constant retailer type, every 10% increase in travel distance was associated with a 3.5% decrease in the food‐at‐home spending share. If consumers travel farther to get food, it may signal that they lack satisfactory options at closer distances. Spending‐weighted mean travel distance could support measures of food retail gaps that are consistent both with consumers' revealed preferences and retailers' incentives.

Agricultural Injuries among Farmers and Ranchers in the Central United States during 2011-2015

ABSTRACT The high risk of occupational fatalities in agriculture is well documented, but information on non-fatal injuries is lacking due to challenges in injury surveillance. This surveillance study explored the frequency, characteristics, and risk factors for non-fatal injuries among farmers and ranchers in the central United States. The Central States Center for Agricultural Safety and Health (CS-CASH), in collaboration with the USDA National Agricultural Statistics Service (NASS), conducted annual surveys (n = 34,777 sent) during 2011–2015 covering a seven-state region (Iowa, Kansas, Minnesota, Missouri, North Dakota, Nebraska, and South Dakota). The average response rate was 32% in the five consecutive annual surveys. The average injury incidence rate was 7.0 injuries/100 operators per year. Most injuries (89%) occurred during agricultural work. The most frequent sources of injury were livestock (22%), machinery (13%), and hand tools (12%). Risk factors for injury included: male gender, younger age (vs. 65+ years), farming as the primary occupation, greater work time, greater land area, ranch (vs. farm), organic farming, internet access, and production of several types of crops and animals. Most injuries (56%) required a doctor visit, and 12% required hospitalization. The average medical costs were $1,936 out of pocket and $8,043 paid by insurance. The combined average costs for most serious injuries were $7,858. Most injuries (66%) resulted in some lost time from agricultural work, and 13% were serious, resulting in more than 30 days of lost work time. The non-fatal injury rate for self-employed farmers and ranchers was higher than that of hired agricultural workers reported by the Bureau of Labor Statistics. This result reaffirms farming/ranching as a dangerous occupation and emphasizes the need for efforts to prevent agricultural injuries, especially those associated with identified injury sources and risk factors.

Nutritional quality of retail food purchases is not associated with participation in the Supplemental Nutrition Assistance Program for nutrition-oriented households.

The Supplemental Nutrition Assistance Program (SNAP) provides millions of low-income Americans food benefits and other forms of nutrition assistance. Evidence indicates that SNAP reduces food insecurity. However, there is a concern that the food benefit may increase the demand for less healthy foods more than healthier foods, thereby reducing the overall nutritional quality of the participant's food basket. This paper aims to examine the association of SNAP participation with the nutritional quality of food-at-home purchases of low-income households and to investigate the potential heterogeneity among consumers with different levels of nutrition attitude. This analysis used food purchase data from the USDA National Household Food Acquisition and Purchase Survey (FoodAPS). Our study sample included 2,218 low-income households, of which 1,184 are SNAP participants, and 1,034 are income-eligible nonparticipants. Multivariate regressions were performed to explore the SNAP-nutritional quality association. A household's nutrition attitude was measured using its response to a question on whether the household searched for nutrition information online in the last 2 months. Households that affirmed they had an online nutrition search were treated as nutrition-oriented households (21.2% of the low-income sample), and households that did not were considered less nutrition-oriented households (78.8%). For robustness, we also created an alternative nutrition attitude measure based on reported use of the nutrition facts label. We found that among less nutrition-oriented households, SNAP participants had a statistically significant 0.097 points (p = 0.018) lower Guiding Stars rating than low-income nonparticipants. However, there was no significant SNAP-nutritional quality association among nutrition-oriented households. In conclusion, SNAP participation was associated with lower nutritional quality of food purchases among less nutrition-oriented households, but not among nutrition-oriented households. The results suggest that the intended nutritional benefits of restrictions on purchases of healthy foods may not reach the subgroup of nutrition-oriented SNAP participants.

The National Animal Health Monitoring System's perspective on respiratory disease in dairy cattle.

In 1991, USDA's National Animal Health Monitoring System (NAHMS) conducted its first dairy study, a baseline assessment that focused on the health and management of heifer calves. During the study, producers ranked respiratory disease among the top two most common health problems affecting dairy calves. Over the last 25 years, U.S. dairy producers have participated in six NAHMS studies, yielding a rich repository of information that has helped identify needs for research, extension, and education in the dairy industry. NAHMS' most recent dairy study, conducted in 2014, provides the latest estimates on dairy cattle health and includes another in-depth look at heifer-calf health. While overall mortality in calves has decreased, bovine respiratory disease (BRD) remains an important cause of morbidity in calves. This raises the concern that BRD mitigation may be at a standstill on dairies. Research and on-farm experience have done much to elucidate the challenges associated with detection and perceived impacts of this complex disease. Continued development and implementation of new methods for monitoring health and detecting disease will provide additional tools to upend stalemating factors associated with BRD control, helping the dairy industry 'turn a corner' on this important disease.

372 The timing of pregnancy losses in beef cattle

Abstract Pregnancy loss in beef cattle causes both management and economic challenges to a producer. Recent studies have been conducted to quantify reproductive failures that occur during fertilization, early embryonic development, and late embryonic/early fetal development periods of gestation in beef cattle. Minimizing reproductive inefficiency, specifically embryonic mortality (EM), is vital. Although fertilization rates are reportedly high in beef cattle, significant developmental failure occurs within the first 7 days of gestation. Approximately 28.4% of embryos will not develop past day 7 of gestation with most embryonic losses occurring before day 4. By the conclusion of the first month of gestation, 47.9% of cows submitted to a single insemination at day 0 will not be pregnant. Overall, late embryonic/fetal development between days 32 to 60 and 100 is 5.8% with a range of 3.2 to 42.7%. This talk will highlight some of the work our group is focusing on to determine timing and detection of pregnancy loss during these pivotal periods of pregnancy loss and potential management aspects to mitigate reproductive inefficiency. This was supported by Agriculture and Food Research Initiative Competitive Grant no. 2017-67015-26457 from the USDA National Institute of Food and Agriculture.

PSIII-42 Genome-wide expression profile of trophoblastic cells during late pregnancy in ewes

Abstract During pregnancy, the placenta plays a pivotal role in fetal-maternal communication. Despite the known involvement of trophoblast mononuclear (MNC) and binuclear (BNC) cells in placentation and fetal development, the regulatory mechanisms underlying the gene expression in these cells and their role in pregnancy have not been fully elucidated. Thus, a genome-wide expression profile analysis of MNC and BNC from ovine placentomes on day 90 and 130 of pregnancy was performed to identify differentially expressed genes (DEG) and regulatory pathways. After tissue separation, enzymatic digestion, and elutriation, MNC and BNC were obtained, and the total RNA was isolated and sequenced (n = 2 ewes/day). Differential expression analysis was carried out with DESeq2 after library quality control and read mapping using FastQC and STAR, respectively. Among six pairwise contrasts possible, herein, we focused on the one between MNC and BNC on day 130. Accordingly, we identified 514 genes upregulated and 161 downregulated in BNC (adj.Pval &amp;lt; 0.05). Interestingly, we found nine DE long intergenic noncoding RNAs (lincRNA). Although the function of lincRNAs remains under investigation, its transcription has been associated with gene expression regulation in utero. The DEGs functional over-representation analysis included Rap1 and PI3k-Akt signaling pathways as up-regulated in BNC (adj.Pval. &amp;lt; 0.05). These pathways are activated by extracellular signals and are involved in cell proliferation and differentiation, morphogenesis, and energy metabolism. Furthermore, we identified PLA2G10 gene that codes a phospholipase protein involved in the production of prostaglandins, which have been associated with placental blood flow. These findings suggest an intricate and complex network underlying gene expression between cells and time points that are essential for the fetal-maternal placenta relationship. This project was supported by Agriculture and Food Research Initiative Competitive Grant n. 2016-67016-24884 from the USDA National Institute of Food and Agriculture.

Is Standardization Necessary for Sharing of a Large Mid-Infrared Soil Spectral Library?

Recent developments in diffuse reflectance soil spectroscopy have increasingly focused on building and using large soil spectral libraries with the purpose of supporting many activities relevant to monitoring, mapping and managing soil resources. A potential limitation of using a mid-infrared (MIR) spectral library developed by another laboratory is the need to account for inherent differences in the signal strength at each wavelength associated with different instrumental and environmental conditions. Here we apply predictive models built using the USDA National Soil Survey Center–Kellogg Soil Survey Laboratory (NSSC-KSSL) MIR spectral library (n = 56,155) to samples sets of European and US origin scanned on a secondary spectrometer to assess the need for calibration transfer using a piecewise direct standardization (PDS) approach in transforming spectra before predicting carbon cycle relevant soil properties (bulk density, CaCO3, organic carbon, clay and pH). The European soil samples were from the land use/cover area frame statistical survey (LUCAS) database available through the European Soil Data Center (ESDAC), while the US soil samples were from the National Ecological Observatory Network (NEON). Additionally, the performance of the predictive models on PDS transfer spectra was tested against the direct calibration models built using samples scanned on the secondary spectrometer. On independent test sets of European and US origin, PDS improved predictions for most but not all soil properties with memory based learning (MBL) models generally outperforming partial least squares regression and Cubist models. Our study suggests that while good-to-excellent results can be obtained without calibration transfer, for most of the cases presented in this study, PDS was necessary for unbiased predictions. The MBL models also outperformed the direct calibration models for most of the soil properties. For laboratories building new spectroscopy capacity utilizing existing spectral libraries, it appears necessary to develop calibration transfer using PDS or other calibration transfer techniques to obtain the least biased and most precise predictions of different soil properties.

Standardized Recipes and Their Influence on the Environmental Impact Assessment of Mixed Dishes: A Case Study on Pizza

Food and diet life cycle assessment (LCA) studies offer insights on the environmental performance and improvement potential of food systems and dietary patterns. However, the influence of ingredient resolution in food-LCAs is often overlooked. To address this, four distinct decomposition methods were used to determine ingredients for mixed dishes and characterize their environmental impacts, using the carbon footprint of the U.S. daily pizza intake as a case study. Pizza-specific and daily pizza intake carbon footprints varied substantially between decomposition methods. The carbon footprint for vegetarian pizza was 0.18–0.45 kg CO2eq/serving, for meat pizza was 0.56–0.73 kg CO2eq/serving, and for currently consumed pizzas in the U.S. (26.3 g/person/day; 75 pizzas types) was 0.072–0.098 kg CO2eq/person/day. These ranges could be explained by differences in pizza coverage, ingredient resolution, availability of ingredient environmental information, and ingredient adjustability for losses between decomposition methods. From the approaches considered, the USDA National Nutrient Database for Standard Reference, which reports standardized food recipes in relative weights, appears to offer the most appropriate and useful food decompositions for food-LCAs. The influence and limitations of sources of reference flows should be better evaluated and acknowledged in food and diet LCAs.

Three datasets for nutrition environment measures of food outlets located in the Lower Mississippi Delta region of the United States

This data note provides details of a research database containing 266 food outlets located in five rural towns in the Lower Mississippi Delta region of Mississippi, whose nutrition environments were measured from 2016 to 2018. The food outlet types include grocery stores, convenience stores, full-service restaurants, and fast food restaurants. The purpose of this publication is to describe the three datasets for external researchers who may be interested in making use of them. The datasets are available from the USDA National Agricultural Library’s Ag Data Commons under a CC0 1.0 Universal License: https://doi.org/10.15482/USDA.ADC/1503704.

Optimization of in vitro germination and cryopreservation conditions for preserving date palm pollen in the USDA National Plant Germplasm System

Date palm (Phoenix dactylifera L.) is a staple crop across arid and semi-arid regions around the world. Both genebanks and date palm breeders benefit by having clearly defined methods for the long-term preservation of pollen. Methods were developed to cryopreserve pollen from date palm trees in the USDA-ARS National Plant Germplasm System. First, in vitro pollen germination conditions were optimized using five cultivars. Then, date palm pollen equilibrated over saturated salt solutions of Ca(NO3)2 or MgCl2 at 23 °C (46% and 33% RH, respectively) or in a room set at 23% RH and 5 °C. Pollen was kept at these conditions for one to 56 days and then placed into liquid nitrogen vapor (LNV). Viability was assessed for fresh, moisture-equilibrated (non-LNV and LNV-exposed), and pollen stored in LNV for 9 months. The highest level of in vitro pollen germination was observed for date palm cultivar Thoory BC3 (60 ± 2%) when it was rehydrated for 2 h and then incubated at 23 °C on Marquard medium with 15% sucrose. Viability remained stable for pollen that was stored in LNV for 9 months. In addition, pollen also remained viable if it was cooled to and warmed from LNV for up to 60 cycles. These data suggest that date palm pollen can be successfully placed in genebank cryostorage. Using optimized in vitro germination conditions, date palm pollen can survive at least 9 months in LNV and can be cooled to and warmed from LNV at least 60 times.