Expansions to the MGDrivE suite for simulating the efficacy of novel gene-drive constructs in the control of mosquito-borne diseases

OBJECTIVE

The MGDrivE (MGDrivE 1 and MGDrivE 2) modeling framework provides a flexible and expansive environment for testing the efficacy of novel gene-drive constructs for the control of mosquito-borne diseases. However, the existing model framework did not previously support several features necessary to simulate some types of intervention strategies. Namely, current MGDrivE versions do not permit modeling of small molecule inducible systems for controlling gene expression in gene drive designs or the inheritance patterns of self-eliminating gene drive mechanisms.

RESULTS

Here, we demonstrate a new MGDrivE 2 module that permits the simulation of gene drive strategies incorporating small molecule-inducible systems and self-eliminating gene drive mechanisms. Additionally, we also implemented novel sparsity-aware sampling algorithms for improved computational efficiency in MGDrivE 2 and supplied an analysis and plotting function applicable to the outputs of MGDrivE 1 and MGDrivE 2.

Saturated fat, the estimated absolute risk and certainty of risk for mortality and major cancer and cardiometabolic outcomes: an overview of systematic reviews

OBJECTIVE

To assess the impact of reducing saturated fat or fatty foods, or replacing saturated fat with unsaturated fat, carbohydrate or protein, on the risk of mortality and major cancer and cardiometabolic outcomes in adults.

METHODS

We searched MEDLINE, EMBASE, CINAHL, and references of included studies for systematic reviews and meta-analyses (SRMAs) of randomized controlled trials (RCTs) and observational studies in adults published in the past 10 years. Eligible reviews investigated reducing saturated fat or fatty foods or replacing saturated fat with unsaturated fat, carbohydrate or protein, on the risk of cancer and cardiometabolic outcomes and assessed the certainty of evidence for each outcome using, for example, the GRADE (Grading of Recommendations, Assessment, Development, and Evaluations) approach. We assessed the quality of SRMAs using a modified version of AMSTAR-2. Results were summarized as absolute estimates of effect together with the certainty of effects using a narrative synthesis approach.

RESULTS

We included 17 SRMAs (13 reviews of observational studies with follow-up 1 to 34 years; 4 reviews of RCTs with follow-up 1 to 17 years). The quality of two-thirds of the SRMAs was critically low to moderate; the main limitations included deficient reporting of study selection, absolute effect estimates, sources of funding, and a priori subgroups to explore heterogeneity. Our included reviews reported > 100 estimates of effect across 11 critically important cancer and cardiometabolic outcomes. High quality SRMAs consistently and predominantly reported low to very low certainty evidence that reducing or replacing saturated fat was associated with a very small risk reduction in cancer and cardiometabolic endpoints. The risk reductions where approximately divided, some being statistically significant and some being not statistically significant. However, based on 2 moderate to high quality reviews, we found moderate certainty evidence for a small but important effect that was statistically significant for two outcomes (total mortality events [20 fewer events per 1000 followed] and combined cardiovascular events [16 fewer per 1000 followed]). Conversely, 4 moderate to high quality reviews showed very small effects on total mortality, with 3 of these reviews showing non-statistically significant mortality effects.

CONCLUSION

Systematic reviews investigating the impact of SFA on mortality and major cancer and cardiometabolic outcomes almost universally suggest very small absolute changes in risk, and the data is based primarily on low and very low certainty evidence.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO CRD42020172141.

Dietary supplementation with L-citrulline improves placental angiogenesis and embryonic survival in gilts

This study was conducted with gilts as an animal model to test the hypothesis that dietary supplementation with L-citrulline (Cit) improves placental angiogenesis and embryonic survival. Between Days 14 and 25 of gestation, each gilt was fed a corn- and soybean-meal-based diet (2 kg/day) supplemented with 0.4% Cit or an isonitrogenous amount of L-alanine (Control). On Day 25 of gestation, gilts were hysterectomized to obtain conceptuses. Amniotic and allantoic fluids and placentae were analyzed for NOx [stable oxidation products of nitric oxide (NO)], polyamines, and amino acids (AAs). Placentae were also analyzed for syntheses of NO and polyamines; concentrations of AAs and related metabolites; and the expression of angiogenic factors and aquaporins (AQPs). Compared to the control group, Cit supplementation increased (P < 0.01) the number of viable fetuses by 2.0 per litter, the number and diameter of placental blood vessels (21% and 24%, respectively), placental weight (15%), and total allantoic and amniotic fluid volumes (20% and 47%, respectively). Cit supplementation also increased (P < 0.01) enzymatic activities of GTP-cyclohydrolase-1 (32%) and ornithine decarboxylase (27%) in placentae; syntheses of NO (29%) and polyamines (26%); concentrations of NOx (19%), tetrahydrobiopterin (28%), polyamines (22%), cAMP (26%), and cGMP (24%) in placentae; total amounts of NOx (22-40%), polyamines (23-40%), AAs (16-255%), glucose (22-44%), and fructose (22-43%) in allantoic and amniotic fluids. Furthermore, Cit supplementation increased (P < 0.05) placental mRNA levels for angiogenic factors (eNOS [84%], GTP-CH1 [55%], PGF [61%], VEGFA120 [26%], and VEGFR2 [137%], as well as AQPs - AQP1 [105%], AQP3 [53%], AQP5 [77%], AQP8 [57%], and AQP9 [31%]). Collectively, dietary Cit supplementation enhanced placental NO and polyamine syntheses as well as angiogenesis to improve conceptus development and survival.

Effectiveness of fluralaner treatment regimens for the control of canine Chagas disease: A mathematical modeling study

BACKGROUND

Canine Chagas disease is caused by the protozoan parasite Trypanosoma cruzi and transmitted by insect triatomine vectors known as kissing bugs. The agent can cause cardiac damage and long-term heart disease and death in humans, dogs, and other mammals. In laboratory settings, treatment of dogs with systemic insecticides has been shown to be highly efficacious at killing triatomines that feed on treated dogs.

METHOD

We developed compartmental vector-host models of T. cruzi transmission between the triatomine and dog population accounting for the impact of seasonality and triatomine migration on disease transmission dynamics. We considered a single vector-host model without seasonality, and model with seasonality, and a spatially coupled model. We used the models to evaluate the effectiveness of the insecticide fluralaner with different durations of treatment regimens for reducing T. cruzi infection in different transmission settings.

RESULTS

In low and medium transmission settings, our model showed a marginal difference between the 3-month and 6-month regimens for reducing T. cruzi infection among dogs. The difference increases in the presence of seasonality and triatomine migration from a sylvatic transmission setting. In high transmission settings, the 3-month regimen was substantially more effective in reducing T. cruzi infections in dogs than the other regimens. Our model showed that increased migration rate reduces fluralaner effectiveness in all treatment regimens, but the relative reduction in effectiveness is minimal during the first years of treatment. However, if an additional 10% or more of triatomines killed by dog treatment were eaten by dogs, treatment could increase T. cruzi infections in the dog population at least during the first year of treatment.

CONCLUSION

Our analysis shows that treating all peridomestic dogs every three to six months for at least five years could be an effective measure to reduce T. cruzi infections in dogs and triatomines in peridomestic transmission settings. However, further studies at the local scale are needed to better understand the potential impact of routine use of fluralaner treatment on increasing dogs' consumption of dead triatomines.

Technical note: Evaluation of sampling methods for methane concentration from in vitro fermentation

The objectives of this multipart study were 1) to assess the efficacy of sampling methods of methane concentration ([CH4]) of headspace gas produced during in vitro gas production (IVGP) fermentation, 2) to verify whether headspace [CH4] sampled from an exetainer has the same [CH4] as the headspace of IVGP bottles, 3) to measure relative humidity (RH) within an IVGP bottle, and 4) to compare [CH4] on a dry-gas (DG) basis when accounting for water vapor pressure (Pw). The original IVGP protocol recommends placing bottles on ice (0 °C) for 30 min to stop fermentation (ICE). A laboratory protocol recommends placing the bottles in the refrigerator (4 to 6 °C) to slow fermentation for 48 h and subsequently allowing the bottles to return to ambient temperature before sampling (FRIDGE). This study evaluated the previous methods against a direct sampling of the headspace gas after incubation (DIRECT). Rumen inoculum from four rumen-cannulated beef steers was combined and homogenized before incubating the fermentable substrate of ground alfalfa hay. After 48 h of IVGP incubation, each bottle was randomly assigned to a treatment protocol. The pressure (P), volume (V), and temperature (T) of headspace gas in each bottle were recorded. Headspace gas was then thoroughly mixed, and 12 mL gas was removed into an evacuated exetainer for [CH4] sampling via gas chromatography (EXET; Objective 1). Eight bottles from ICE and FRIDGE were randomly selected to follow EXET, whereas the remaining bottles had [CH4] directly measured from their headspace (BOTT; Objective 2). Five diets of differing feed composition and nutrient densities were used with a blank to test the RH of the IVGP slurry (Objective 3). Using RH, [CH4] was transformed to a DG basis to account for Pw (Objective 4). Statistical analysis was completed using a random coefficients model. There were no differences between EXET and BOTT (P = 0.28). The RH of the IVGP slurry was 100% (P = 1.00), confirming that IVGP gas is saturated with water vapor. The P, V, and T differed among treatments (P < 0.01). The [CH4] of DIRECT, ICE, and FRIDGE were different (P < 0.01). Dry-gas P, V, and [CH4] differed among treatments (P < 0.01). As the methods differ in their assessment of [CH4], there is no clear recommendation. Instead, to present a more accurate [CH4], P, V, and T should be measured when sampling headspace gas and equations presented should be used to remove volume inflation due to water vapor and present [CH4] on a DG basis.

Optimization of Prime Editing in Rice, Peanut, Chickpea, and Cowpea Protoplasts by Restoration of GFP Activity

Precise editing of the plant genome has long been desired for functional genomic research and crop breeding. Prime editing is a newly developed precise editing technology based on CRISPR-Cas9, which uses an engineered reverse transcriptase (RT), a catalytically impaired Cas9 endonuclease (nCas9), and a prime editing guide RNA (pegRNA). In addition, prime editing has a wider range of editing types than base editing and can produce nearly all types of edits. Although prime editing was first established in human cells, it has recently been applied to plants. As a relatively new technique, optimization will be needed to increase the editing efficiency in different crops. In this study, we successfully edited a mutant GFP in rice, peanut, chickpea, and cowpea protoplasts. In rice, up to 16 times higher editing efficiency was achieved with a dual pegRNA than the single pegRNA containing vectors. Edited-mutant GFP protoplasts have also been obtained in peanut, chickpea, and cowpea after transformation with the dual pegRNA vectors, albeit with much lower editing efficiency than in rice, ranging from 0.2% to 0.5%. These initial results promise to expedite the application of prime editing in legume breeding programs to accelerate crop improvement.

No Evidence of SARS-CoV-2 Among Flies or Cockroaches in Households Where COVID-19 Positive Cases Resided

Flies and other arthropods mechanically transmit multiple pathogens and a recent experimental study demonstrated house flies, Musca domestica L. (Diptera: Muscidae), can mechanically transmit SARS-CoV-2. The purpose of this study was to explore the possibility of mechanical transmission of SARS-CoV-2 by domestic insects and their potential as a xenosurveillance tool for detection of the virus. Flies were trapped in homes where at least one confirmed human COVID-19 case(s) resided using sticky and liquid-baited fly traps placed inside and outside the home in the Texas counties of Brazos, Bell, and Montgomery, from June to September 2020. Flies from sticky traps were identified, pooled by taxa, homogenized, and tested for the presence of SARS-CoV-2 RNA using quantitative reverse transcription PCR (RT-qPCR). Liquid traps were drained, and the collected fluid similarly tested after RNA concentration. We processed the contents of 133 insect traps from 40 homes, which contained over 1,345 individual insects of 11 different Diptera families and Blattodea. These individuals were grouped into 243 pools, and all tested negative for SARS-CoV-2 RNA. Fourteen traps in seven homes were deployed on the day that cat or dog samples tested positive for SARS-CoV-2 RNA by nasal, oral, body, or rectal samples. This study presents evidence that biting and nonbiting flies and cockroaches (Blattodea) are not likely to contribute to mechanical transmission of SARS-CoV-2 or be useful in xenosurveillance for SARS-CoV-2.

Phenomic data-facilitated rust and senescence prediction in maize using machine learning algorithms

Current methods in measuring maize (Zea mays L.) southern rust (Puccinia polyspora Underw.) and subsequent crop senescence require expert observation and are resource-intensive and prone to subjectivity. In this study, unoccupied aerial system (UAS) field-based high-throughput phenotyping (HTP) was employed to collect high-resolution aerial imagery of elite maize hybrids planted in the 2020 and 2021 growing seasons, with 13 UAS flights obtained from 2020 and 17 from 2021. In total, 36 vegetation indices (VIs) were extracted from mosaicked aerial images that served as temporal phenomic predictors for southern rust scored in the field and senescence as scored using UAS-acquired mosaic images. Temporal best linear unbiased predictors (TBLUPs) were calculated using a nested model that treated hybrid performance as nested within flights in terms of rust and senescence. All eight machine learning regressions tested (ridge, lasso, elastic net, random forest, support vector machine with radial and linear kernels, partial least squares, and k-nearest neighbors) outperformed a general linear model with both higher prediction accuracies (92-98%) and lower root mean squared error (RMSE) for rust and senescence scores (linear model RMSE ranged from 65.8 to 2396.5 across all traits, machine learning regressions RMSE ranged from 0.3 to 17.0). UAS-acquired VIs enabled the discovery of novel early quantitative phenotypic indicators of maize senescence and southern rust before being detectable by expert annotation and revealed positive correlations between grain filling time and yield (0.22 and 0.44 in 2020 and 2021), with practical implications for precision agricultural practices.

Transcriptome profiling of two rice genotypes under mild field drought stress during grain-filling stage

Drought is one of the most critical abiotic stresses that threaten crop production worldwide. This stress affects the rice crop in all stages of rice development; however, the occurrence during reproductive and grain-filling stages has the most impact on grain yield. Although many global transcriptomic studies have been performed during the reproductive stage in rice, very limited information is available for the grain-filling stage. Hence, we intend to investigate how the rice plant responds to drought stress during the grain-filling stage and how the responses change over time under field conditions. Two rice genotypes were selected for RNA-seq analysis: '4610', previously reported as a moderately tolerant breeding line, and Rondo, an elite indica rice cultivar susceptible to drought conditions. Additionally, 10 agronomic traits were evaluated under normal irrigated and drought conditions. Leaf tissues were collected during grain-filling stages at two time points, 14 and 21 days after the drought treatment, from both the drought field and normal irrigated field conditions. Based on agronomic performances, '4610' was less negatively affected than Rondo under mild drought conditions, and expression profiling largely aligned with the phenotypic data. The transcriptomic data indicated that, in general, '4610' had much earlier responses than its counterpart in mitigating the impact of drought stress. Several key genes and gene families related to drought stress or stress-related conditions were found differentially expressed in this study, including transcription factors, drought tolerance genes and reactive oxygen species scavengers. Furthermore, this study identified novel differentially expressed genes (DEGs) without function annotations that may play roles in drought tolerance-related functions. Some of the important DEGs detected in this study can be targeted for future research.

Delivery of selenium using chitosan nanoparticles: Synthesis, characterization, and antioxidant and growth effects in Nile tilapia (Orechromis niloticus)

This study aimed to elucidate the effects of selenium-loaded chitosan nanoparticles used as a dietary supplement on Nile tilapia (Oreochromis niloticus) antioxidant and growth responses. First, chitosan-based nanoparticles containing selenium (Se) were synthesized using the ionotropic gelation method and their physicochemical characteristics, controlled release profile, and antioxidant activity properties were investigated. Thereafter, the effects on glutathione peroxidase and antioxidant activities (by radical scavenging activity), growth, and whole-body composition of Nile tilapia were evaluated when they were fed with Se-loaded chitosan nanoparticles and compared with other selenium dietary supplements. Se-loaded chitosan nanoparticles showed high entrapment efficiency (87%), spherical shape, smooth surface, and broad size distribution. The controlled release of Se consisted of an initial burst followed by a gradual release over 48 h. Se-loaded nanoparticles presented significantly higher antioxidant activity compared to free Se. A 60-day feeding trial was conducted to compare the effects of supplementing different dietary Se sources, including selenomethionine (as organic source), sodium selenite (as inorganic source), and Se-loaded chitosan nanoparticles (Se-Nano and Se-Nano x1.5) on antioxidant and growth responses of Nile tilapia. A basal diet without Se supplementation was used as the control. The dietary supplementations with different Se sources (free and encapsulated selenium) lead to significant improvements in final weight and feed efficiency of Nile tilapia fingerlings. However, dietary treatments did not affect whole-body protein and lipid content. Diets containing Se-Nano and Se-Nano x1.5 were more effective than sodium selenite and selenomethionine in preventing oxidative stress and improving antioxidant activity in Nile tilapia. Overall, Se-loaded nanoparticles presented a great potential as an efficient source for delivering dietary Se to Nile tilapia, directly affecting the growth performance, feed efficiency, oxidative stress, and antioxidant activity of this species.

Inclusion of quebracho tannin extract in a high-roughage cattle diet alters digestibility, nitrogen balance, and energy partitioning

Condensed tannins (CT) might improve animal and system-level efficiency due to enhanced protein efficiency and reduced CH4. This study evaluated the impact of quebracho tannin (QT) extract fed at 0%, 1.5%, 3%, and 4.5% of dry matter (DM), within a roughage-based diet on apparent digestibility of DM, organic matter (OM), fibrous fractions, and N retention and energy partitioning of growing steers (236 ± 16 kg BW). A Latin rectangle design with eight animals and four periods was used to determine the whole-animal exchange of CO2, O2, and CH4 as well as the collection of total feces and urine over a 48-h period, using two open-circuit, indirect calorimetry respiration chambers. Following the removal of steers from respiration chambers, rumen inoculum was collected to determine ruminal parameter, including volatile fatty acids (VFA) and ammonia. Animals were fed a 56.5% roughage diet at 1.7% BW (dry matter basis). Dry matter and gross energy intakes were influenced by the level of QT inclusion (P ≤ 0.036). Digestibility of DM, OM, and N was reduced with QT inclusion (P < 0.001), and fiber digestibility was slightly impacted (P > 0.123). QTs altered the N excretion route, average fecal N-to-total N ratio excreted increased 14%, and fecal N-to-urinary N ratio increased 38% (P < 0.001) without altering the retained N. Increased fecal energy with QT provision resulted in reduced dietary digestible energy (DE) concentration (Mcal/kg DM; P = 0.024). There were no differences in urinary energy (P = 0.491), but CH4 energy decreased drastically (P = 0.007) as QT inclusion increased. Total ruminal VFA concentration did not differ across treatments, but VFA concentration increased linearly with QT inclusion (P = 0.049). Metabolizable energy (ME) was not affected by the QT rate, and the conversion efficiency of DE-to-ME did not differ. Heat energy decreased (P = 0.013) with increased QT provision likely due to changes in the DE intake, but there was no difference in retained energy. There were no differences for retained energy or N per CO2 equivalent emission produced (P = 0.774 and 0.962, respectively), but improved efficiency for energy retention occurred for 3% QT. We concluded that QT provided up to 4.5% of dry matter intake (about 3.51% of CT, dry matter basis) does not affect N and energy retention within the current setting. Feeding QT reduced energy losses in the form of CH4 and heat, but the route of energy loss appears to be influenced by the rate of QT inclusion.

Unmanned aerial systems-based remote sensing for monitoring sorghum growth and development

Unmanned Aerial Vehicles and Systems (UAV or UAS) have become increasingly popular in recent years for agricultural research applications. UAS are capable of acquiring images with high spatial and temporal resolutions that are ideal for applications in agriculture. The objective of this study was to evaluate the performance of a UAS-based remote sensing system for quantification of crop growth parameters of sorghum (Sorghum bicolor L.) including leaf area index (LAI), fractional vegetation cover (f_c) and yield. The study was conducted at the Texas A&M Research Farm near College Station, Texas, United States. A fixed-wing UAS equipped with a multispectral sensor was used to collect image data during the 2016 growing season (April–October). Flight missions were successfully carried out at 50 days after planting (DAP; 25 May), 66 DAP (10 June) and 74 DAP (18 June). These flight missions provided image data covering the middle growth period of sorghum with a spatial resolution of approximately 6.5 cm. Field measurements of LAI and f_c were also collected. Four vegetation indices were calculated using the UAS images. Among those indices, the normalized difference vegetation index (NDVI) showed the highest correlation with LAI, f_c and yield with R² values of 0.91, 0.89 and 0.58 respectively. Empirical relationships between NDVI and LAI and between NDVI and f_c were validated and proved to be accurate for estimating LAI and f_c from UAS-derived NDVI values. NDVI determined from UAS imagery acquired during the flowering stage (74 DAP) was found to be the most highly correlated with final grain yield. The observed high correlations between UAS-derived NDVI and the crop growth parameters (f_c, LAI and grain yield) suggests the applicability of UAS for within-season data collection of agricultural crops such as sorghum.

Roles of dietary glycine, proline, and hydroxyproline in collagen synthesis and animal growth

Glycine, proline, and hydroxyproline (Hyp) contribute to 57% of total amino acids (AAs) in collagen, which accounts for one-third of proteins in animals. As the most abundant protein in the body, collagen is essential to maintain the normal structure and strength of connective tissue, such as bones, skin, cartilage, and blood vessels. Mammals, birds, and fish can synthesize: (1) glycine from threonine, serine, choline, and Hyp; (2) proline from arginine; and (3) Hyp from proline residues in collagen, in a cell- and tissue-specific manner. In addition, livestock (e.g., pigs, cattle, and sheep) produces proline from glutamine and glutamate in the small intestine, but this pathway is absent from birds and possibly most fish species. Results of the recent studies indicate that endogenous synthesis of glycine, proline, and Hyp is inadequate for maximal growth, collagen production, or feed efficiency in pigs, chickens, and fish. Although glycine, proline and Hyp, and gelatin can be used as feed additives in animal diets, these ingredients except for glycine are relatively expensive, which precludes their inclusion in practical rations. Alternatively, hydrolyzed feather meal (HFM), which contains 9% glycine, 5% Hyp, and 12% proline, holds great promise as a low cost but abundant dietary source of glycine, Hyp, and proline for ruminants and nonruminants. Because HFM is deficient in most AAs, future research efforts should be directed at improving the bioavailability of its AAs and the balance of AAs in HFM-supplemented diets. Finally, HFM may be used as a feed additive to prevent or ameliorate connective tissue disorders in domestic and aquatic animals.

Amino acids and mammary gland development: nutritional implications for milk production and neonatal growth

Milk is synthesized by mammary epithelial cells of lactating mammals. The synthetic capacity of the mammary gland depends largely on the number and efficiency of functional mammary epithelial cells. Structural development of the mammary gland occurs during fetal growth, prepubertal and post-pubertal periods, pregnancy, and lactation under the control of various hormones (particularly estrogen, growth hormone, insulin-like growth factor-I, progesterone, placental lactogen, and prolactin) in a species- and stage-dependent manner. Milk is essential for the growth, development, and health of neonates. Amino acids (AA), present in both free and peptide-bound forms, are the most abundant organic nutrients in the milk of farm animals. Uptake of AA from the arterial blood of the lactating dam is the ultimate source of proteins (primarily β-casein and α-lactalbumin) and bioactive nitrogenous metabolites in milk. Results of recent studies indicate extensive catabolism of branched-chain AA (leucine, isoleucine and valine) and arginine to synthesize glutamate, glutamine, alanine, aspartate, asparagine, proline, and polyamines. The formation of polypeptides from AA is regulated not only by hormones (e.g., prolactin, insulin and glucocorticoids) and the rate of blood flow across the lactating mammary gland, but also by concentrations of AA, lipids, glucose, vitamins and minerals in the maternal plasma, as well as the activation of the mechanistic (mammalian) target rapamycin signaling by certain AA (e.g., arginine, branched-chain AA, and glutamine). Knowledge of AA utilization (including metabolism) by mammary epithelial cells will enhance our fundamental understanding of lactation biology and has important implications for improving the efficiency of livestock production worldwide.