Agricultural Research Service - Northeast Area

Many studies have demonstrated that the cotton in warm environments is vulnerable to water-limitations thus reducing the yield. A number of plant traits have been recommended to ameliorate the effects of water deficits on plant growth and yield. Limitation on maximum transpiration rate (TR) under high vapor pressure deficit (VPD), usually occurs during midday, is often considered as a water conservation trait. The genotypes with this trait are desirable in high VPD environments where water deficits commonly develop in the later part of the growing season. Our objective of the study was to find the genotypic variation for the trait limited TR under high VPD and also to study leaf temperature, water potential, photosynthesis, and stomatal conductance responses. Also, our objective was also to study the structural changes in the stomatal traits when exposed to long term high VPD conditions and involvement in such responses. In the present study, 17 cotton genotypes were studied for their (TR) response to various VPD environments under well irrigated conditions. Out of 17, eight genotypes limited TR after approximately 2 kPa VPD and rest of them increased their TR with increased VPD. Five selected genotypes with different TR response to increasing VPD were further studied for gas exchange and stomatal properties. All genotypes, irrespective of exhibiting limited TR at high VPD, reduced stomatal conductance, photosynthesis and water potential at high VPD of 3.3 kPa. The genotypes with limited TR modified their stomatal traits mostly on the adaxial surface with frequent and small stomata under high VPD. The genotypes with limited TR also exhibited an increase in epidermal cell expansion and stomatal index at contrasting VPD gradients to effectively balance the liquid and vapor phase conductance to limit TR at high VPD.

Current language in the Food Safety Modernization Act Produce Safety Rule states no objection to a 90- or 120-day interval between application of untreated BSAAO and harvest of crops to minimize transfer of pathogens to produce intended for human consumption with the intent to limit potential cases of foodborne illness. This regional multiple season, multiple location field trial determined survival durations of Escherichia coli in soils amended with manure to determine whether this interval is appropriate. Spatiotemporal factors influence survival durations of E. coli more than amendment type, total amount of E. coli present, organic or conventional soil management, and depth of manure application. Overall, these data show poultry litter may support extended survival of E. coli compared to horse manure or dairy manure, but spatiotemporal factors like site and season may have more influence than manure type in supporting survival of E. coli beyond 90 days in amended soils in the Mid-Atlantic United States.

Irrigation water contaminated with Salmonella enterica and Listeria monocytogenes may provide a route of contamination of raw or minimally processed fruits and vegetables. While previous work has surveyed specific and singular types of agricultural irrigation water for bacterial pathogens, few studies have simultaneously surveyed different water sources repeatedly over an extended period of time. This study quantified S. enterica and L. monocytogenes levels (MPN/L) at 6 sites, including river waters: tidal freshwater river (MA04, n = 34), non-tidal freshwater river, (MA05, n = 32), one reclaimed water holding pond (MA06, n = 25), two pond water sites (MA10, n = 35; MA11, n = 34), and one produce wash water site (MA12, n = 10) from September 2016-October 2018. Overall, 50% (84/168) and 31% (53/170) of sampling events recovered S. enterica and L. monocytogenes, respectively. Results showed that river waters supported significantly (p < 0.05) greater levels of S. enterica than pond or reclaimed waters. The non-tidal river water sites (MA05) with the lowest water temperature supported significantly greater level of L. monocytogenes compared to all other sites; L. monocytogenes levels were also lower in winter and spring compared to summer seasons. Filtering 10 L of water through a modified Moore swab (MMS) was 43.5 (Odds ratio, p < 0.001) and 25.5 (p < 0.001) times more likely to recover S. enterica than filtering 1 L and 0.1 L, respectively; filtering 10 L was 4.8 (p < 0.05) and 3.9 (p < 0.05) times more likely to recover L. monocytogenes than 1L and 0.1 L, respectively. Work presented here shows that S. enterica and L. monocytogenes levels are higher in river waters compared to pond or reclaimed waters in the Mid-Atlantic region of the U.S., and quantitatively shows that analyzing 10 L water is more likely recover pathogens than smaller samples of environmental waters.

Foodborne infections are a significant cause of morbidity and mortality worldwide, and foodborne parasitic diseases, though not as widespread as bacterial and viral infections, are common on all continents and in most ecosystems, including arctic, temperate, and tropical regions. Outbreaks of disease resulting from foodstuffs contaminated by parasitic protozoa have become increasingly recognized as a problem in the United States and globally. Increased international trade in food products has made movement of these organisms across national boundaries more frequent, and the risks associated with infections have become apparent in nations with well-developed food safety apparatus in place.

This study was designed to determine the relative importance of income, wealth, and family characteristics in explaining the decision to save, the level of saving in house holds, and the patterns of saving in several types of families. Data from the 1972 ‐1973 Consumer Expenditure Survey were analyzed using multiple regression and difference of means tests. The results supported the general hypotheses that the decision to save and the level of saving are influenced by income, wealth, and family characteristics and that saving patterns vary among different types of families. The findings suggest that while income is the primary determinant of families' initial decision to save, their level of saving is best explained by their current wealth position.

ABSTRACT Research has shown that it is possible to measure the soil moisture of the upper soil layer using microwave remote sensing. This type of areal measurement, if obtained on a routine basis from a space platform, could have value in hydrological simulations for stream-flow forecasting, irrigation scheduling, and drought monitoring. Possible applications of these data in modelling include parameter calibration and system updating. Conventional point measurements of soil properties and precipitation do not always represent the areal distribution. Periodic measurements of areal soil moisture could be used to correct errors in model simulations of state variables caused by parameter estimates and input data. The possibility of using remotely sensed estimates of soil moisture was tested in an experiment conducted on several small basins located in Oklahoma using the USDA Hydrograph Laboratory Model of watershed hydrology. Periodic soil moisture samples obtained using conventional methods were used to represent the type of data remote sensing could provide. These data were used to evaluate the utility of periodic soil moisture measurements for system updating. Analyses indicated the potential value of the data and supported its evaluation on a larger scale.

The PCBs tested with caged White Leghorn hens were Aroclors 1221, 1232, 1242, 1248, 1254, 1268, 5542 and BP-6 fed at the 20 p.p.m. level. In addition, 1242, 1248 and 1254 were also fed at the 2 p.p.m. level. None of these pollutants exerted any adverse effects on adult body weight gain, livability, egg weight, egg shell thickness or fertility after 9 weeks of PCB feeding. Egg production was significantly reduced by 1232, 1242, 1248, 1254 and BP-6, all at the 20 p.p.m. level. Feed consumption per hen-day was significantly reduced by 20 p.p.m. 1242, 1248, 1254 and BP-6. Hatchability of fertile eggs was significantly affected by the 20 p.p.m. level of 1232, 1242, 1248 and 1254; the hatchability of eggs laid by hens fed 20 p.p.m. 1248 declined to 1.8% by the 9th week of feeding, as compared with 95% for the control group. Progeny growth was significantly depressed by the feeding of 1232, 1242, 1248, 1254 and BP-6 in the maternal diet; only one PCB (Aroclor 1248) in the maternal diet produced a significant increase in mortality of progeny.

We evaluated the effect of applying different sets of 16S rRNA primers on bacterial composition, diversity, and predicted function in chicken ceca. Cecal contents from Ross 708 birds at 1, 3, and 5 weeks of age were collected for DNA isolation. Eight different primer pairs targeting different variable regions of the 16S rRNA gene were employed. DNA sequences were analyzed using open-source platform QIIME2 and the Greengenes database. PICRUSt2 was used to determine the predicted function of bacterial communities. Changes in bacterial relative abundance due to 16S primers were determined by GLMs. The average PCR amplicon size ranged from 315 bp (V3) to 769 bp (V4-V6). Alpha- and beta-diversity, taxonomic composition, and predicted functions were significantly affected by the primer choice. Beta diversity analysis based on Unweighted UniFrac distance matrix showed separation of microbiota with four different clusters of bacterial communities. Based on the alpha- and beta-diversity and taxonomic composition, variable regions V1-V3(1) and (2), and V3-V4 and V3-V5 were in most consensus. Our data strongly suggest that selection of particular sets of the 16S rRNA primers can impact microbiota analysis and interpretation of results in chicken as was shown previously for humans and other animal species.

Heat-treated poultry pellets (HTPP) often are used by fruit and vegetable growers as a slow-release fertilizer. However, contamination of soil on farms may occur through contaminated irrigation water or scat from wild animals. Here, we show that the presence of HTPP in soil led to increased S. Newport survival in soil and to greater likelihood of its transfer to and survival on spinach plants. There were no significant differences in survival durations of WT and Δ rpoS mutant isolates of S. Newport. The statistically similar populations recovered by plate count and estimated by PMA-qPCR for both strains in the amended and unamended soils in this study indicate that all viable populations of S. Newport in soils were culturable.

The biphenyls tested with caged White Leghorn pullets were polychlorinated biphenyl (PCBs) Aroclors 1232, 1242, 1248, 1254 and 1016 and polybrominated biphenyl (PBB) PBP-6 at the 5, 10 and 20 p.p.m. levels. These pollutants exerted no adverse effects on egg production, egg weight, egg shell thickness, feed consumption, adult body weight changes, livability and fertility after 8 weeks of biphenyl feeding, irrespective of biphenyl level or compound. Hatchability of fertile eggs as a result of biphenyl feeding was significantly affected by 10 or 20 p.p.m. and by three PCB compounds (Aroclors 1232, 1242, 1248). The hatchability (%) of eggs laid by pullets fed 10 and 20 p.p.m. declined to 78 and 45, respectively, for Aroclor 1232, 48 and 5 for Aroclor 1242 and 40 and 5 for Aroclor 1248 after 6 weeks of biphenyl feeding, as compared with 90 for the control group. The most common embryonic abnormality was edema in the neck and rump areas. Biphenyl supplementation in the maternal diet also caused a shift in the peak pattern of embryonic death. Progeny growth as a result of biphenyl in the maternal diet was significantly depressed by 10 or 20 p.p.m. and by Aroclors 1242 and 1248. The level of the three PCBs found to be toxic to chickens appears to lie somewhere between 5 and 10 p.p.m.

This study aimed at developing a predictive model that captures the influences of a variety of agricultural and environmental variables and is able to predict the concentrations of enteric bacteria in soil amended with untreated Biological Soil Amendments of Animal Origin (BSAAO) under dynamic conditions. We developed and validated a Random Forest model using data from a longitudinal field study conducted in mid-Atlantic United States investigating the survival of Escherichia coli O157:H7 and generic E. coli in soils amended with untreated dairy manure, horse manure, or poultry litter. Amendment type, days of rain since the previous sampling day, and soil moisture content were identified as the most influential agricultural and environmental variables impacting concentrations of viable E. coli O157:H7 and generic E. coli recovered from amended soils. Our model results also indicated that E. coli O157:H7 and generic E. coli declined at similar rates in amended soils under dynamic field conditions.The Random Forest model accurately predicted changes in viable E. coli concentrations over time under different agricultural and environmental conditions. Our model also accurately characterized the variability of E. coli concentration in amended soil over time by providing upper and lower prediction bound estimates. Cross-validation results indicated that our model can be potentially generalized to other geographic regions and incorporated into a risk assessment for evaluating the risks associated with application of untreated BSAAO. Our model can be validated for other regions and predictive performance also can be enhanced when data sets from additional geographic regions become available.

Surface water is used for irrigation by farmers. However, surface waters may be a source of bacterial foodborne pathogens which contaminate fresh produce intended for human consumption. Proposed but not finalized standards for microbial quality of irrigation water through the Produce Safety Rule (PSR) of the Food Safety Modernization Act (FSMA) in the US emphasize the need for effective reduction of levels of pathogens in surface water intended to be used on fruit and vegetable crops. This study evaluated a zero-valent iron (ZVI)-sand filtration system to reduce E. coli populations in pond water and those transferred to growing spinach plants in a field trial. Six filtration events were conducted with the same ZVI-sand or sand (S) laboratory filtration systems. Filtration systems were constructed by connecting 4 PVC pipes (1.25 L) together. ZVI-sand filters contained 50% ZVI/ 50% sand (0.43-0.60 mm particle size), while sand filters contained 100% sand (0.45-55 mm particle size). In each event, autoclaved pond water (PW) inoculated with E. coli (ca. 4 log CFU/ml) – 8 L - was pumped (1 L/min) through each filter followed by uninoculated autoclaved PW (15 L) with samples taken throughout the filtering process for enumeration of E. coli. Data were fit to a linear model to determine reductions of E. coli levels. ZVI-sand filtration removed significantly (p < 0.05) more E. coli (1.1 log CFU) compared to sand filtration. For ZVI-sand-filtered water, there was a statistically significant (p < 0.05) difference of E. coli removal from early trials (trials 1-3, average removal 96%) than in later trials (trial 4-6, average removal 44%), suggesting that age of the ZVI-sand filters influences E. coli inactivation. Overall, ZVI-sand and sand filtration reduced E. coli populations by 70% and -10%, respectively, indicating that ZVI filtration lowered or inactivated E. coli populations while sand filters accumulated E. coli. Field trials showed that soil and spinach plant samples irrigated with ZVI-sand-filtered water had significantly lower E. coli levels than soils irrigated with sand-filtered water or unfiltered control water. Overall, ZVI-sand filtration significantly reduced E. coli populations in water compared to sand filtration.

UNLABELLED: We examined gene expression of whole blood cells (WBC) from 11 healthy elderly volunteers participating on a Phase I open label study before and after oral treatment with Lactobacillus rhamnosus GG-ATCC 53103 (LGG)) using RNA-sequencing (RNA-Seq). Elderly patients (65-80 yrs) completed a clinical assessment for health status and had blood drawn for cellular RNA extraction at study admission (Baseline), after 28 days of daily LGG treatment (Day 28) and at the end of the study (Day 56) after LGG treatment had been suspended for 28 days. Treatment compliance was verified by measuring LGG-DNA copy levels detected in host fecal samples. Normalized gene expression levels in WBC RNA were analyzed using a paired design built within three analysis platforms (edgeR, DESeq2 and TSPM) commonly used for gene count data analysis. From the 25,990 transcripts detected, 95 differentially expressed genes (DEGs) were detected in common by all analysis platforms with a nominal significant difference in gene expression at Day 28 following LGG treatment (FDR<0.1; 77 decreased and 18 increased). With a more stringent significance threshold (FDR<0.05), only two genes (FCER2 and LY86), were down-regulated more than 1.5 fold and met the criteria for differential expression across two analysis platforms. The remaining 93 genes were only detected at this threshold level with DESeq2 platform. Data analysis for biological interpretation of DEGs with an absolute fold change of 1.5 revealed down-regulation of overlapping genes involved with Cellular movement, Cell to cell signaling interactions, Immune cell trafficking and Inflammatory response. These data provide evidence for LGG-induced transcriptional modulation in healthy elderly volunteers because pre-treatment transcription levels were restored at 28 days after LGG treatment was stopped. To gain insight into the signaling pathways affected in response to LGG treatment, DEG were mapped using biological pathways and genomic data mining packages to indicate significant biological relevance. TRIAL REGISTRATION: ClinicalTrials.gov NCT01274598.

BACKGROUND: Heat stress (HS) has negative effects on poultry productivity, health and welfare resulting in economic losses. Broiler chickens are particularly susceptible to HS due to their high metabolic rate and rapid growth. The commensal intestinal bacterial populations have an important physiological role in the host and could ameliorate the negative effect of HS on the host. Thus, the aim of this study was to compare changes in the ileal (IL) microbiota in four different broiler lines during HS. RESULTS: Day-old broiler chicks from Giant Jungle Fowl (JF), Athens Canadian Random Bred (ACRB), 1995 Random Bred (L1995), and Modern Random Bred (L2015) lines were raised under thermoneutral (TN) conditions until day (d) 28. On d 29 birds were subjected to TN (24 °C) or chronic cyclic HS (8 h/d, 36 °C) condition till d 56. On d 56 two birds per pen were euthanized, and IL luminal content (IL-L) and mucosal scrapings (IL-M) were collected for bacterial DNA isolation. Libraries were constructed using V3-V4 16S rRNA primers and sequenced using MiSeq. DNA sequences were analyzed using QIIME2 platform and SILVA 132 database for alpha and beta diversity, and taxonomic composition, respectively. Functional property of microbiota was predicted using the PICRUSt 2 pipeline and illustrated with STAMP software. Shannon index was significantly elevated in IL-M under HS. β-diversity PCoA plots revealed separation of microbial community of L2015-TN from JF-TN, JF-HS, ACRB-TN, and ACRB-HS in the IL-M. PERMANOVA analysis showed a significant difference between microbial community of L1995-HS compared to ACRB-HS and JF-TN, L1995-TN compared to ACRB-HS and JF-TN, L2015-HS compared to ACRB-HS and ACRB-TN, L2015-HS compared to JF-TN, L2015-TN compared to ACRB-HS and JF-TN, and ACRB-HS compared to JF-TN in the IL-L. The impact of HS on microbial composition of IL-M was more prominent compared to IL-L with 12 and 2 taxa showing significantly different relative abundance, respectively. Furthermore, differences in microbiota due to the genetic line were more prominent in IL-M than IL-L with 18 and 8 taxa showing significantly different relative abundance, respectively. Unlike taxonomy, predicted function of microbiota was not affected by HS. Comparison of L2015 with JF or ACRB showed significant changes in predicted function of microbiota in both, IL-M and IL-L. Differences were most prominent between L2015 and JF; while there was no difference between L2015 and L1995. CONCLUSIONS: These data indicate the genetic line × temperature effect on the diversity and composition of IL microbiota. Moreover, the data showcase the effect of host genetics on the composition of IL microbiota and their predicted function. These data are of critical importance for devising nutritional strategies to maintain GIT microbial balance and alleviate the negative effects of HS on broiler chickens' performance and health.

Journal Article Chromosome Numbers and Interspecific Hybrids Among New Guinea Impatiens Species Get access TORU ARISUMI TORU ARISUMI United States Department of Agriculture, Agricultural Research Service, Northeastern Region, Agricultural Research Center, Plant Genetics and Germplasm Institute, Ornamentals LaboratoryBeltsville, Md. 20705 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 64, Issue 2, March 1973, Pages 77–79, https://doi.org/10.1093/oxfordjournals.jhered.a108358 Published: 01 March 1973

Dietary habits have been linked with variability of gut microbiota composition and disease risk. The aim of this study was to evaluate the effect of feeding a cocoa powder with or without a probiotic on the composition and function of the fecal microbiome of pigs. Four groups of 8 pigs each were fed a standard growth diet supplemented with cocoa powder, Lactobacillus rhamnosus (LGG), cocoa powder + LGG, or an equal amount of fiber similar to that found in cocoa powder (control group). Fecal samples were collected prior to and 4 wk after initiation of the dietary intervention. Microbiota composition was determined after amplification of the first 2 variable regions of the 16S ribosomal DNA (rDNA). Predictions of metagenomic function were calculated using 16S rDNA sequence data through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). After 4 wk of treatment, bacterial abundance analysis demonstrated a prebiotic effect of cocoa powder on endogenous Bifidobacteriaceae and Lactobacillaceae and increased abundance of saccharolytic butyrate-producing bacteria like Roseburia. An increased bacterial evenness, Shannon diversity index, and diverse metabolic profile were detected in microbiomes of pigs fed the cocoa powder + LGG (P < 0.05) but not in pigs in the other 3 groups. The data generated from this work demonstrated that 4-wk dietary treatment with cocoa powder alone or in combination with LGG probiotic had an impact on the composition and function of the fecal microbiota of healthy pigs.

Introduction Antimicrobial peptides (AMPs) are promising alternatives to traditional antibiotics for combating plant pathogenic bacteria in agriculture and the environment. However, identifying potent AMPs through laborious experimental assays is resource-intensive and time-consuming. To address these limitations, this study presents a bioinformatics approach utilizing machine learning models for predicting and selecting AMPs active against plant pathogenic bacteria. Methods N-gram representations of peptide sequences with 3-letter and 9-letter reduced amino acid alphabets were used to capture the sequence patterns and motifs that contribute to the antimicrobial activity of AMPs. A 5-fold cross-validation technique was used to train the machine learning models and to evaluate their predictive accuracy and robustness. Results The models were applied to predict putative AMPs encoded by intergenic regions and small open reading frames (ORFs) of the citrus genome. Approximately 7% of the 10,000-peptide dataset from the intergenic region and 7% of the 685,924-peptide dataset from the whole genome were predicted as probable AMPs. The prediction accuracy of the reported models range from 0.72 to 0.91. A subset of the predicted AMPs was selected for experimental test against Spiroplasma citri , the causative agent of citrus stubborn disease. The experimental results confirm the antimicrobial activity of the selected AMPs against the target bacterium, demonstrating the predictive capability of the machine learning models. Discussion Hydrophobic amino acid residues and positively charged amino acid residues are among the key features in predicting AMPs by the Random Forest Algorithm. Aggregation propensity appears to be correlated with the effectiveness of the AMPs. The described models would contribute to the development of effective AMP-based strategies for plant disease management in agricultural and environmental settings. To facilitate broader accessibility, our model is publicly available on the AGRAMP (Agricultural Ngrams Antimicrobial Peptides) server.

Six major fresh produce crops were periodically sampled at wholesale, studied in retail stores, and purchased for consumptability during their respective seasons in the Greater New York area from 1966 to 1969. The condition of each crop in wholesale samples was compared with that found in retail stores 2 or 3 days later. Losses in retail stores were categorized and measured. Purchased retail store samples were held for varying times at room temperatures (or 70F .) or at 38t o 40t o simulate consumer holding before they were examined for defects resulting in loss of edible tissue. Retail and consumer losses in each commodity for the completed study follow.

This research applied a new 1-step methodology to directly construct a tertiary model that describes the growth of Clostridium perfringens in cooked turkey meat under dynamically cooling conditions. The kinetic parameters of the growth models were determined by numerical analysis and optimization using multiple dynamic growth curves. The models and kinetic parameters were validated using independent growth curves obtained under various cooling conditions. The results showed that the residual errors (ε) of the predictions followed a Laplace distribution that is symmetric with respect to ε = 0. For residual errors, 90.6% are within ±0.5 Log CFU/g and 73.4% are ±0.25 Log CFU/g for all growth curves used for validation. For relative growth <1.0 Log CFU/g, 88.9% of the residual errors are within ±0.5 Log CFU/g, and 63.0% are within ±0.25 Log CFU/g. For relative growth of <2.0 Log CFU/g, 92.7% of the residual errors are within ±0.5 Log CFU/g, and 70.3% are within ±0.25 Log CFU/g. The scale and distribution of residual errors clearly suggests that the models and estimated kinetic parameters are reasonably accurate in predicting the growth of C. perfringens. Monte Carlo simulation was used to estimate the probabilities of >1.0 and 2.0 Log CFU/g relative growth of C. perfringens in the final products at the end of cooling. This probabilistic process analysis approach provides a new alternative for estimating and managing the risk of a product and can help the food industry and regulatory agencies assess the safety of cooked meat in the event of cooling deviation.

Two stereoisomeric zingiberenols in ginger were identified as (3R,6R,7S)-1,10-bisaboladien-3-ol (2) and (3S,6R,7S)-1,10-bisaboladien-3-ol (5). Absolute configurations were assigned by utilizing 1,10-bisaboladien-3-ol stereoisomers and two gas-chromatography columns: a 25 m Hydrodex-β-6TBDM and 60 m DB-5MS. The C-6 and C-7 absolute configurations in both zingiberenols match those of zingiberene present abundantly in ginger rhizomes. Interestingly, zingiberenol 2 has recently been identified as a male-produced sex pheromone of the rice stink bug, Oebalus poecilus, thus indicating that ginger plants may be a potential source of the sex pheromone of this bug.