Gene loss and genome rearrangement in the plastids of five Hemiparasites in the family Orobanchaceae

BACKGROUND

The chloroplast genomes (plastome) of most plants are highly conserved in structure, gene content, and gene order. Parasitic plants, including those that are fully photosynthetic, often contain plastome rearrangements. These most notably include gene deletions that result in a smaller plastome size. The nature of gene loss and genome structural rearrangement has been investigated in several parasitic plants, but their timing and contributions to the adaptation of these parasites requires further investigation, especially among the under-studied hemi-parasites.

RESULTS

De novo sequencing, assembly and annotation of the chloroplast genomes of five photosynthetic parasites from the family Orobanchaceae were employed to investigate plastome dynamics. Four had major structural rearrangements, including gene duplications and gene losses, that differentiated the taxa. The facultative parasite Aureolaria virginica had the most similar genome content to its close non-parasitic relative, Lindenbergia philippensis, with similar genome size and organization, and no differences in gene content. In contrast, the facultative parasite Buchnera americana and three obligate parasites in the genus Striga all had enlargements of their plastomes, primarily caused by expansion within the large inverted repeats (IRs) that are a standard plastome feature. Some of these IR increases were shared by multiple investigated species, but others were unique to particular lineages. Gene deletions and pseudogenization were also both shared and lineage-specific, with particularly frequent and independent loss of the ndh genes involved in electron recycling.

CONCLUSIONS

Five new plastid genomes were fully assembled and compared. The results indicate that plastome instability is common in parasitic plants, even those that retain the need to perform essential plastid functions like photosynthesis. Gene losses were slow and not identical across taxa, suggesting that different lineages had different uses or needs for some of their plastome gene content, including genes involved in some aspects of photosynthesis. Recent repeat region extensions, some unique to terminal species branches, were observed after the divergence of the Buchnera/Striga clade, suggesting that this otherwise rare event has some special value in this lineage.

The Impact of Plant-Based Non-Dairy Alternative Milk on the Dairy Industry

Vegetarians have claimed and actively promoted the advantages of plant-based alternative milks as the best option for human nutrition and health, compared to the natural dairy milk. However, numerous scientific evidences and reports have demonstrated that the natural milk possesses more beneficial nutrients and bioactive components than artificially manufactured plant-derived milks. The biochemical and nutritional advantages and functionalities of natural dairy milk cannot be replaced by man-made or crafted plant-based beverage products. On the other hand, the tremendous increase in production and consumption of the plant-based alternative milks in recent years has led a serious business downturn in traditional roles and stability of the dairy industry, especially in the major dairy producing Western countries. Although plant-based milk alternatives may have some benefits on nutrition and health of certain consumers, the plant-derived alternative milks may not overshadow the true values of natural milk. Milk is not a high fat and high cholesterol food as animal meat products. Unlike plant-based alternative milks, natural milk contains many bioactive as well as antiappetizing peptides, which can reduce body weight. It has proven that taking low-fat, cultured and lactase treated milk and dairy products with other diversified nutritionally balanced diets have been shown to be healthier dietary option than plant-based milk/foods alone.

A simple plant high-molecular-weight DNA extraction method suitable for single-molecule technologies

BACKGROUND

High-molecular-weight and pure DNA is crucial for high-quality results from 3rd generation DNA Analyzers and optical mapping technologies. Conventional nuclei isolation methods for preparing high-molecular-weight genomic DNA from plant tissues include the preparation of protoplasts or embedding nuclei in an agarose matrix with subsequent manipulations via electro-elution or pulsed-field gel electrophoresis.

RESULTS

In this method, plant nuclei are isolated by physically grinding tissues and reconstituting the intact nuclei in a unique Nuclear Isolation Buffer (NIB). The plastid DNAs are released from organelles and eliminated with an osmotic buffer by washing and centrifugation. The purified nuclei are then lysed and further cleaned by organic extraction, and the genomic DNA is precipitated with a high concentration of CTAB. The highly pure, high molecular weight gDNA is extracted from the nuclei, dissolved in a high pH buffer, allowing for stable long-term storage.

CONCLUSIONS

This method is unique and avoids the use of embedding in agarose, which dramatically reduces time (4-8 h versus days), complexity, and materials cost. This procedure can be used on essentially any plant species and tissue stage. Here we describe a case study and a simple method to rapidly prepare high molecular weight gDNA from Upland cotton, blackgrass, and strawberry suitable for single-molecule sequencing.

Discovery of three loci increasing resistance to charcoal rot caused by Macrophomina phaseolina in octoploid strawberry

Charcoal rot caused by Macrophomina phaseolinais an increasing economic problem in annualized strawberry production systems around the world. Currently there are no effective postfumigation chemical controls for managing charcoal rot, and no information is available on the genetic architecture of resistance to M. phaseolina in strawberry (Fragaria ×ananassa). In this study, three multiparental discovery populations and two validation populations were inoculated at planting and evaluated for mortality in three consecutive growing seasons. Genome-wide SNP genotyping and pedigree-based analysis with FlexQTL™ software were performed. Two large-effect quantitative trait loci (QTL) increasing charcoal rot resistance were discovered and validated in cultivated germplasm. FaRMp1 was located on linkage group 2A in the interval 20.4to 24.9 cM, while FaRMp2 was located on linkage group 4B in the interval 41.1to 61.2 cM. Together these QTLs explained 27% and 17% of the phenotypic variance in two discovery populations consisting of elite breeding germplasm. For both QTLs, the resistant allele showed some evidence of partial dominance, but no significant interaction was detected between the two loci. As the dosage of resistant alleles increased from 0 to 4 across the two QTLs, mortality decreased regardless of the combination of alleles.A third locus, FaRMp3 on 4D, was discovered in FVC 11-58, a reconstituted F.×ananassa originating from diverse F. virginiana and F. chiloensis accessions. This locus accounted for 44% of phenotypic variation in four segregating crosses. These findings will form the basis for DNA-informed breeding for resistance to charcoal rot in cultivated strawberry.

Reconstructing systematic persistent impacts of promotional marketing with empirical nonlinear dynamics

An empirical question of long-standing interest is how price promotions affect a brand’s sale shares in the fast-moving consumer-goods market. We investigated this question with concurrent promotions and sales records of specialty beer brands pooled over Tesco stores in the UK. Most brands were continuously promoted, rendering infeasible a conventional approach of establishing impact against an off-promotion sales baseline, and arguing in favor of a dynamics approach. Moreover, promotion/sales records were volatile without easily-discernable regularity. Past work conventionally attributed volatility to the impact of exogenous random shocks on stable markets, and reasoned that promotions have only an ephemeral impact on sales shares in stationary mean-reverting stochastic markets, or a persistent freely-wandering impact in nonstationary markets. We applied new empirical methods from the applied sciences to uncover an overlooked alternative: ‘systematic persistence’ in which promotional impacts evolve systematically in an endogenously-unstable market governed by deterministic-nonlinear dynamics. We reconstructed real-world market dynamics from the Tesco dataset, and detected deterministic-nonlinear market dynamics. We used reconstructed market dynamics to identify a complex network of systematic interactions between promotions and sales shares among competing brands, and quantified/characterized the dynamics of these interactions. For the majority of weeks in the study, we found that: (1) A brand’s promotions drove down own sales shares (a possibility recognized in the literature), but ‘cannibalized’ sales shares of competing brands (perhaps explaining why brands were promoted despite a negative marginal impact on own sales shares); and (2) Competitive interactions between brands owned by the same multinational brewery differed from those with outside brands. In particular, brands owned by the same brewery enjoyed a ‘mutually-beneficial’ relationship in which an incremental increase in the sales share of one marginally increased the sales share of the other. Alternatively, the sales shares of brands owned by different breweries preyed on each other’s market shares.

A survey of antimicrobial use practices of Tennessee beef producers

BACKGROUND

Inappropriate antimicrobial use (AMU) is a key modifiable factor that leads to the development of antimicrobial resistance (AMR). The objectives of this study were to determine the following among Tennessee beef cattle producers: (1) the opinions on factors driving AMU (2) opinions on alternatives to antimicrobials, (3) the knowledge and perceptions regarding AMU and AMR, and (4) the preferred avenues for receiving information on prudent AMU. A survey questionnaire was made available to participants both in print and online from January 26, 2018 through May 11, 2018. The questions targeted the producers' demographics and their AMU practices; factors driving producer's choice of antimicrobials; perceptions, opinions and concerns about AMU and AMR in cattle production. Ordinal logistic regression was used to test for associations between the captured demographic information and producers' degree of concern about AMR.

RESULTS

Overall, 231 beef producers responded to all or some of the survey questions. More than 60% of the participants mentioned that they kept up-to-date written records on antimicrobial purchases and AMU. Regarding extra-label use, 169 (84.1%) of the 201 respondents did not practice extra-label AMU. Profitability of the beef operation was a key factor influencing the decisions of many producers to use antimicrobials for disease management and prevention on their farms. Of the 228 producers who completed the question on the rating of their degree of concern about AMR, 50 (21.9%) reported that they were very concerned about AMR, 133 (58.3%) were moderately concerned, and 36 (15.8%) reported that they were not concerned about AMR. Nine producers (4%) did not rate their degree of concern about AMR because they were not familiar with what antimicrobial resistance meant. The inferential analyses suggested that younger beef producers were significantly less concerned about AMR when compared to the older ones (P = 0.019). Regarding avenues for receiving information on prudent AMU, no single medium was most preferred by all the respondents.

CONCLUSIONS

There is a need to promote the use of written antimicrobial treatment protocols among beef producers in Tennessee. Continued training for beef producers on infection prevention and control and prudent AMU is needed.

Peripheral blood basophils are the main source for early interleukin-4 secretion upon in vitro stimulation with Culicoides allergen in allergic horses

Interleukin-4 (IL-4) is a key cytokine secreted by type 2 T helper (Th2) cells that orchestrates immune responses during allergic reactions. Human and mouse studies additionally suggest that basophils have a unique role in the regulation of allergic diseases by providing initial IL-4 to drive T cell development towards the Th2 phenotype. Equine Culicoides hypersensitivity (CH) is a seasonal immunoglobulin E (IgE)-mediated allergic dermatitis in horses in response to salivary allergens from Culicoides (Cul) midges. Here, we analyzed IL-4 production in peripheral blood mononuclear cells (PBMC) of CH affected (n = 8) and healthy horses (n = 8) living together in an environment with natural Cul exposure. During Cul exposure when allergic horses had clinical allergy, IL-4 secretion from PBMC after stimulation with Cul extract was similar between healthy and CH affected horses. In contrast, allergic horses had higher IL-4 secretion from PBMC than healthy horses during months without allergen exposure. In addition, allergic horses had increased percentages of IL-4⁺ cells after Cul stimulation compared to healthy horses, while both groups had similar percentages of IL-4⁺ cells following IgE crosslinking. The IL-4⁺ cells were subsequently characterized using different cell surface markers as basophils, while very few allergen-specific CD4⁺ cells were detected in PBMC after Cul extract stimulation. Similarly, IgE crosslinking by anti-IgE triggered basophils to produce IL-4 in all horses. PMA/ionomycin consistently induced high percentages of IL-4⁺ Th2 cells in both groups confirming that T cells of all horses studied were capable of IL-4 production. In conclusion, peripheral blood basophils produced high amounts of IL-4 in allergic horses after stimulation with Cul allergens, and allergic horses also maintained higher basophil percentages throughout the year than healthy horses. These new findings suggest that peripheral blood basophils may play a yet underestimated role in innate IL-4 production upon allergen activation in horses with CH. Basophil-derived IL-4 might be a crucial early signal for immune induction, modulating of immune responses towards Th2 immunity and IgE production.

Invasive grass indirectly alters seasonal patterns in seed predation

Invasive species threaten ecosystems globally, but their impacts can be cryptic when they occur indirectly. Invader phenology can also differ from that of native species, potentially causing seasonality in invader impacts. Yet, it is unclear if invader phenology can drive seasonal patterns in indirect effects. We used a field experiment to test if an invasive grass (Imperata cylindrica) caused seasonal indirect effects by altering rodent foraging and seed predation patterns through time. Using seeds from native longleaf pine (Pinus palustris), we found seed predation was 25% greater, on average, in invaded than control plots, but this effect varied by season. Seed predation was 24-157% greater in invaded plots during spring and autumn months, but invasion had no effect on seed predation in other months. One of the largest effects occurred in October when longleaf pine seeds are dispersed, suggesting potential effects on tree regeneration. Thus, seasonal patterns in indirect effects from invaders may cause underappreciated impacts on ecological communities.

Large-Sample Genome-Wide Association Study of Resistance to Retained Placenta in U.S. Holstein Cows

A genome-wide association study of resistance to retained placenta (RETP) using 632,212 Holstein cows and 74,747 SNPs identified 200 additive effects with p-values < 10-8 on thirteen chromosomes but no dominance effect was statistically significant. The regions of 87.61-88.74 Mb of Chr09 about 1.13 Mb in size had the most significant effect in LOC112448080 and other highly significant effects in CCDC170 and ESR1, and in or near RMND1 and AKAP12. Four non-ESR1 genes in this region were reported to be involved in ESR1 fusions in humans. Chr23 had the largest number of significant effects that peaked in SLC17A1, which was involved in urate metabolism and transport that could contribute to kidney disease. The PKHD1 gene contained seven significant effects and was downstream of another six significant effects. The ACOT13 gene also had a highly significant effect. Both PKHD1 and ACOT13 were associated with kidney disease. Another highly significant effect was upstream of BOLA-DQA2. The KITLG gene of Chr05 that acts in utero in germ cell and neural cell development, and hematopoiesis was upstream of a highly significant effect, contained a significant effect, and was between another two significant effects. The results of this study provided a new understanding of genetic factors underlying RETP in U.S. Holstein cows.

The Composition and Function of Bacterial Communities Associated with the Northern Root-Knot Nematode (Meloidogyne hapla) Populations Showing Parasitic Variability

The co-existence of microbial communities and Meloidogyne hapla populations showing high, medium, and low levels of parasitic variability (PV) in mineral and muck soils with different soil health conditions in Michigan vegetable production fields is established. However, if PV relates or not to bacterial communities is unknown. This study characterized bacterial communities present on and in the body of nine M. hapla field and greenhouse sub-populations isolated from the mineral and muck fields. We utilized a high throughput sequencing of 16S rDNA. Results showed a variable composition (or abundance) of 65 genera in the field and 61 genera in the greenhouse isolates, with 12 genera of unknown and the rest belonging to 14 known functional groups. The medium- and low-PV populations shared more bacterial composition than either one with the high-PV population. Thus, laying a foundation for an in-depth understanding of if the observed associations have any role in cause-and-effect relationships with M. hapla PV.

Recent advances in understanding of the mechanisms of RNA interference in insects

We highlight the recent 5 years of research that contributed to our understanding of the mechanisms of RNA interference (RNAi) in insects. Since its first discovery, RNAi has contributed enormously as a reverse genetic tool for functional genomic studies. RNAi is also being used in therapeutics, as well as agricultural crop and livestock production and protection. Yet, for the wider application of RNAi, improvement of its potency and delivery technologies is needed. A mechanistic understanding of every step of RNAi, from cellular uptake of RNAi trigger molecules to targeted mRNA degradation, is key for developing an efficient strategy to improve RNAi technology. Insects provide an excellent model for studying the mechanism of RNAi due to species-specific variations in RNAi efficiency. This allows us to perform comparative studies in insect species with different RNAi sensitivity. Understanding the mechanisms of RNAi in different insects can lead to the development of better strategies to improve RNAi and its application to manage agriculturally and medically important insects.

Fast analysis of biobank-size data and meta-analysis using the BGLR R-package

Analyzing human genomic data from biobanks and large-scale genetic evaluations often requires fitting models with a sample size exceeding the number of DNA markers used (n>p). For instance, developing polygenic scores for humans and genomic prediction for genetic evaluations of agricultural species may require fitting models involving a few thousand SNPs using data with hundreds of thousands of samples. In such cases, computations based on sufficient statistics are more efficient than those based on individual genotype-phenotype data. Additionally, software that admits sufficient statistics as inputs can be used to analyze data from multiple sources jointly without the need to share individual genotype-phenotype data. Therefore, we developed functionality within the BGLR R-package that generates posterior samples for Bayesian shrinkage and variable selection models from sufficient statistics. In this article, we present an overview of the new methods incorporated in the BGLR R-package, demonstrate the use of the new software through simple examples, provide several computational benchmarks, and present a real-data example using data from the UK-Biobank, All of Us, and the Hispanic Community Health Study/Study of Latinos cohort demonstrating how a joint analysis from multiple cohorts can be implemented without sharing individual genotype-phenotype data, and how a combined analysis can improve the prediction accuracy of polygenic scores for Hispanics-a group severely under-represented in genome-wide association studies data.

Ginger Polyphenols Reverse Molecular Signature of Amygdala Neuroimmune Signaling and Modulate Microbiome in Male Rats with Neuropathic Pain: Evidence for Microbiota-Gut-Brain Axis

Emerging evidence shows that the gut microbiota plays an important role in neuropathic pain (NP) via the gut-brain axis. Male rats were divided into sham, spinal nerve ligation (SNL), SNL + 200 mg GEG/kg BW (GEG200), and SNL + 600 mg GEG/kg BW (GEG600) for 5 weeks. The dosages of 200 and 600 mg GEG/kg BW for rats correspond to 45 g and 135 g raw ginger for human daily consumption, respectively. Both GEG groups mitigated SNL-induced NP behavior. GEG-supplemented animals had a decreased abundance of Rikenella, Muribaculaceae, Clostridia UCG-014, Mucispirillum schaedleri, RF39, Acetatifactor, and Clostridia UCG-009, while they had an increased abundance of Flavonifactor, Hungatella, Anaerofustis stercorihominis, and Clostridium innocuum group. Relative to sham rats, Fos and Gadd45g genes were upregulated, while Igf1, Ccl2, Hadc2, Rtn4rl1, Nfkb2, Gpr84, Pik3cg, and Abcc8 genes were downregulated in SNL rats. Compared to the SNL group, the GEG200 group and GEG600 group had increases/decreases in 16 (10/6) genes and 11 (1/10) genes, respectively. GEG downregulated Fos and Gadd45g genes and upregulated Hdac2 genes in the amygdala. In summary, GEG alleviates NP by modulating the gut microbiome and reversing a molecular neuroimmune signature.

Advances in Mechanisms of Anaphylaxis in Wheat Allergy: Utility of Rodent Models

Wheat is a staple and nutritious food that is consumed globally. However, it is identified as a major allergenic food because of its capacity to trigger life-threatening systemic anaphylaxis. The specific mechanisms that underlie this systemic anaphylaxis in wheat allergy are incompletely understood. As a result, several rodent models have been developed to study anaphylaxis in wheat allergies. In this paper, we have conducted a comprehensive review of wheat-induced anaphylaxis using Google Scholar and PubMed databases with relevant keywords. The following objectives were addressed: (1) to determine the complexity of wheat-induced anaphylaxis; (2) to summarize the role of genetic susceptibility in wheat anaphylaxis; (3) to identify the environmental factors involved in the development of wheat anaphylaxis; (4) to map the current status of mechanisms involved in wheat anaphylaxis; (5) to identify the approaches, strengths, and limitations of rodent models of wheat anaphylaxis; and (6) to identify challenges and opportunities in this area of science. Our findings provide a comprehensive updated critical resource for the future research agenda in wheat allergy-associated anaphylaxis, particularly using rodent models as attractive pre-clinical tools.