Transcript Abundance Of Genes Research Articles

The common house spider, Parasteatoda tepidariorum, maintains silk gene expression on sub-optimal diet.

Cobweb weaving spiders and their relatives spin multiple task-specific fiber types. The unique material properties of each silk type result from differences in amino acid sequence and structure of their component proteins, primarily spidroins (spider fibrous proteins). Amino acid content and gene expression measurements of spider silks suggest some spiders change expression patterns of individual protein components in response to environmental cues. We quantified mRNA abundance of three spidroin encoding genes involved in prey capture in the common house spider, Parasteatoda tepidariorum (Theridiidae), fed different diets. After 10 days of acclimation to the lab on a diet of mealworms, spiders were split into three groups: (1) individuals were immediately dissected, (2) spiders were fed high-energy crickets, or (3) spiders were fed low-energy flies, for 1 month. All spiders gained mass during the acclimation period and cricket-fed spiders continued to gain mass, while fly-fed spiders either maintained or lost mass. Using quantitative PCR, we found no significant differences in the absolute or relative abundance of dragline gene transcripts, major ampullate spidroin 1 (MaSp1) and major ampullate spidroin 2 (MaSp2), among groups. In contrast, prey-wrapping minor ampullate spidroin (MiSp) gene transcripts were significantly less abundant in fly-fed than lab-acclimated spiders. However, when measured relative to Actin, cricket-fed spiders showed the lowest expression of MiSp. Our results suggest that house spiders are able to maintain silk production, even in the face of a low-quality diet.

Loss of COMT activity reduces lateral root formation and alters the response to water limitation in sorghum brown midrib (bmr) 12 mutant.

Lignin is a key target for modifying lignocellulosic biomass for efficient biofuel production. Brown midrib 12 (bmr12) encodes the sorghum caffeic acid O-methyltransferase (COMT) and is one of the key enzymes in monolignol biosynthesis. Loss of function mutations in COMT reduces syringyl (S) lignin subunits and improves biofuel conversion rate. Although lignin plays an important role in maintaining cell wall integrity of xylem vessels, physiological and molecular consequences due to loss of COMT on root growth and adaptation to water deficit remain unexplored. We addressed this gap by evaluating the root morphology, anatomy and transcriptome of bmr12 mutant. The mutant had reduced lateral root density (LRD) and altered root anatomy and response to water limitation. The wild-type exhibits similar phenotypes under water stress, suggesting that bmr12 may be in a water deficit responsive state even in well-watered conditions. bmr12 had increased transcript abundance of genes involved in (a)biotic stress response, gibberellic acid (GA) biosynthesis and signaling. We show that bmr12 is more sensitive to exogenous GA application and present evidence for the role of GA in regulating reduced LRD in bmr12. These findings elucidate the phenotypic and molecular consequences of COMT deficiency under optimal and water stress environments in grasses.

The expression of the acarbose biosynthesis gene cluster in Actinoplanes sp. SE50/110 is dependent on the growth phase

BackgroundActinoplanes sp. SE50/110 is the natural producer of the diabetes mellitus drug acarbose, which is highly produced during the growth phase and ceases during the stationary phase. In previous works, the growth-dependency of acarbose formation was assumed to be caused by a decreasing transcription of the acarbose biosynthesis genes during transition and stationary growth phase.ResultsIn this study, transcriptomic data using RNA-seq and state-of-the-art proteomic data from seven time points of controlled bioreactor cultivations were used to analyze expression dynamics during growth of Actinoplanes sp. SE50/110. A hierarchical cluster analysis revealed co-regulated genes, which display similar transcription dynamics over the cultivation time. Aside from an expected metabolic switch from primary to secondary metabolism during transition phase, we observed a continuously decreasing transcript abundance of all acarbose biosynthetic genes from the early growth phase until stationary phase, with the strongest decrease for the monocistronically transcribed genes acbA, acbB, acbD and acbE. Our data confirm a similar trend for acb gene transcription and acarbose formation rate.Surprisingly, the proteome dynamics does not follow the respective transcription for all acb genes. This suggests different protein stabilities or post-transcriptional regulation of the Acb proteins, which in turn could indicate bottlenecks in the acarbose biosynthesis. Furthermore, several genes are co-expressed with the acb gene cluster over the course of the cultivation, including eleven transcriptional regulators (e.g. ACSP50_0424), two sigma factors (ACSP50_0644, ACSP50_6006) and further genes, which have not previously been in focus of acarbose research in Actinoplanes sp. SE50/110.ConclusionIn conclusion, we have demonstrated, that a genome wide transcriptome and proteome analysis in a high temporal resolution is well suited to study the acarbose biosynthesis and the transcriptional and post-transcriptional regulation thereof.

The agrochemical S-metolachlor disrupts molecular mediators and morphology of the swim bladder: Implications for locomotor activity in zebrafish (Danio rerio)

Metolachlor herbicides are derived from the chloroacetamide chemical family of which there are the S- and R-metolachlor isomers. S-metolachlor is a selective herbicide that inhibits cell division and mitosis via enzyme interference. The herbicide is used globally in agriculture and studies report adverse effects in aquatic organisms; however, there are no studies investigating sub-lethal effects of S-metolachlor on swim bladder formation, mitochondrial ATP production, nor light–dark preference behaviors in fish. These endpoints are relevant for larval locomotor activity and metabolism. To address these knowledge gaps, we exposed zebrafish embryos/larvae to various concentrations of S-metolachlor (0.5–50 µM) over early development. S-metolachlor affected survival, hatching percentage, and increased developmental deformities at concentrations of 50 µM and above. Exposure levels as high as 200 µM for 24 and 48 h did not alter oxygen consumption rates in zebrafish, and there were no changes detected in endpoints related to mitochondrial oxidative phosphorylation. We observed impairment of swim bladder inflation at 50 µM in 6 dpf larvae. To elucidate mechanisms related to this, we measured relative transcript abundance for genes associated with the swim bladder (smooth muscle alpha (α)-2 actin, annexin A5, pre-B-cell leukemia homeobox 1a). Smooth muscle alpha (α)-2 actin mRNA levels were reduced in fish exposed to 50 µM while annexin A5 mRNA levels were increased in abundance, corresponding to reduced swim bladder size in larvae. A visual motor response test revealed that larval zebrafish exhibited some hyperactivity in the light with exposure to the herbicide and only the highest dose tested (50 µM) resulted in hypoactivity in the dark cycle. Regression analysis indicated that there was a positive relationship between surface area of the swim bladder and distance traveled, and the size of the swim bladder explained ~10–14% in the variation for total distance moved. Lastly, we tested larvae in a light dark preference test, and we did not detect any altered behavioral response to any concentration tested. Here we present new data on sublethal endpoints associated with exposure to the herbicide S-metolachlor and demonstrate that this chemical may disrupt transcripts associated with swim bladder formation and morphology, which could ultimately affect larval zebrafish activity. These data are expected to contribute to further risk assessment guidelines for S-metolachlor in aquatic ecosystems.

MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information.

The rapid assignment of genotypes to phenotypes has been a historically challenging process. The discovery of genes encoding biosynthetic pathway enzymes for defined plant specialized metabolites has been informed and accelerated by the detection of gene clusters. Unfortunately, biosynthetic pathway genes are commonly dispersed across chromosomes or reside in genes clusters that provide little predictive value. More reliably, transcript abundance of genes underlying biochemical pathways for plant specialized metabolites display significant coregulation. By rapidly identifying highly coexpressed transcripts, it is possible to efficiently narrow candidate genes encoding pathway enzymes and more easily predict both functions and functional associations. Mutual Rank (MR)-based coexpression analyses in plants accurately demonstrate functional associations for many specialized metabolic pathways; however, despite the clear predictive value of MR analyses, the application is uncommonly used to drive new pathway discoveries. Moreover, many coexpression databases aid in the prediction of both functional associations and gene functions, but lack customizability for refined hypothesis testing. To facilitate and speed flexible MR-based hypothesis testing, we developed MutRank, an R Shiny web-application for coexpression analyses. MutRank provides an intuitive graphical user interface with multiple customizable features that integrates user-provided data and supporting information suitable for personal computers. Tabular and graphical outputs facilitate the rapid analyses of both unbiased and user-defined coexpression results that accelerate gene function predictions. We highlight the recent utility of MR analyses for functional predictions and discoveries in defining two maize terpenoid antibiotic pathways. Beyond applications in biosynthetic pathway discovery, MutRank provides a simple, customizable and user-friendly interface to enable coexpression analyses relating to a breadth of plant biology inquiries. Data and code are available at GitHub: https://github.com/eporetsky/MutRank.

The Inherited MDS Gene DDX41 Is Essential for Ribosomal RNA Processing through Regulation of Snorna Biogenesis

Germline mutations in the DEAD-box RNA helicase gene DDX41 cause inherited susceptibility to Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML). These patients have normal hematopoietic indices into adulthood and present with MDS at a median age of 61 years, slightly younger than the general MDS patient population (71 years). Germline DDX41 mutations are always heterozygous and are typically frame-shift mutations, causing loss of function of the protein. More than half of these patients acquire a second-hit mutation in the healthy DDX41 allele in their disease clones. Greater than 80% of the second-hit mutations cause the amino acid substitution R525H, which results in loss of helicase activity. Multiple functions have been ascribed to DDX41, such as functioning as an innate immune sensor, a component of the RNA spliceosome, and a regulator of ribosomal RNA processing; however, its role in the pathogenesis of MDS remains poorly understood. To mimic the DDX41 mutations in human patients, we generated conditional mouse models of the most common DDX41 mutations, D140fs and R525H. We found that DDX41 is essential for the viability and function of hematopoietic stem and progenitor cells (HSPCs) and that R525H mutations render DDX41 inactive. We have also reported that mice with biallelic DDX41 mutations develop progressive anemia, dysplasia, and marrow failure. HSPCs lacking wild-type Ddx41 have dysfunctional ribosomes and reduced protein translation, leading to cycle arrest and apoptosis. As a mechanistic basis for the ribosome defect in Ddx41-deficient HSPCs, we found that loss of Ddx41 causes a profound increase in unprocessed snoRNA transcripts, which likely interrupts their cellular function. Importantly, we did not observe a change in host gene transcript abundance, and thus it is unlikely that the defects observed in Ddx41-deficient cells are caused by loss of the protein products of the host genes. SnoRNAs regulate ribosomal RNA (rRNA) by catalyzing post-transcriptional modifications, including methylation and pseudouridylation. Since the majority of the snoRNAs that were found to be unprocessed in Ddx41-deficient HSPCs were from the SNORA family, which is involved in pseudouridylation, we quantified the abundance of pseudouridine at specific sites in ribosomal RNA and found it to be reduced in Ddx41-deficient HSPCs. Utilizing global high-throughput sequencing approaches to analyze DDX41 binding to RNAs, we found that DDX41 preferentially binds to snoRNAs relative to all other types of RNA in the cells. Thus, DDX41 binds to snoRNAs and is essential for snoRNA processing, snoRNA-mediated rRNA pseudouridylation, and protein translation in HSPCs. These findings provide critical mechanistic insight into the protein translation defect that we and others have observed in DDX41-deficient cells and uncover the basis of ineffective hematopoiesis in MDS patients with DDX41 mutations. Disclosures Starczynowski: Tolero Therapeutics: Research Funding; Kurome Therapeutics: Consultancy, Current equity holder in private company, Research Funding; Captor Therapeutics: Consultancy.

The caffeoyl-CoA O-methyltransferase gene SNP replacement in Russet Burbank potato variety enhances late blight resistance through cell wall reinforcement.

Metabolic pathway gene editing in tetraploid potato enhanced resistance to late blight. Multiallelic mutation correction of a caffeoyl-CoA O-methyltransferase gene increased accumulation of resistance metabolites in Russet Burbank potato. Late blight of potato is a devastating disease worldwide and requires weekly applications of fungicides to manage. Genetic improvement is the best option, but the self-incompatibility and inter-specific incompatibility makes potato breeding very challenging. Immune receptor gene stacking has increased resistance, but its durability is limited. Quantitative resistance is durable, and it mainly involves secondary cell wall thickening due to several metabolites and their conjugates. Deleterious mutations in biosynthetic genes can hinder resistance metabolite biosynthesis. Here a probable resistance role of the StCCoAOMT gene was first confirmed by an in-planta transient overexpression of the functional StCCoAOMT allele in late blight susceptible Russet Burbank (RB) genotype. Following this, a precise single nucleotide polymorphism (SNP) mutation correction of the StCCoAOMT gene in RB potato was carried out using CRISPR-Cas9 mediated homology directed repair (HDR). The StCCoAOMT gene editing increased the transcript abundance of downstream biosynthetic resistance genes. Following pathogen inoculation, several phenylpropanoid pathway genes were highly expressed in the edited RB plants, as compared to the non-edited. The disease severity (fold change = 3.76) and pathogen biomass in inoculated stems of gene-edited RB significantly reduced (FC = 21.14), relative to non-edited control. The metabolic profiling revealed a significant increase in the accumulation of resistance-related metabolites in StCCoAOMT edited RB plants. Most of these metabolites are involved in suberization and lignification. The StCCoAOMT gene, if mutated, can be edited in other potato cultivars to enhance resistance to late blight, provided it is associated with other functional genes in the metabolic pathway network.

Treatment of Penicillium chrysogenum extracts (PDMP) restricts the spread of Tobacco mosaic virus by priming callose deposition in Nicotiana benthamiana

Plants are often primed to enhanced resistance upon recognizing certain microbes and microbial metabolites/molecules. We investigated the effect of PDMP, the peptides extract of dry mycelia of Penicillium chrysogenum, on defense of Nicotiana benthamiana to Tobacco mosaic virus (TMV). The 30B vector harboring the green fluorescent protein gene (30B:GFP) was used to monitor virus movement. Movement of the virus vector was limitied in PDMP-pretreated tobacco, in which significant callose accumulation was observed after challenge inoculation with the TMV vector. Callose accumulation was absent in plants pretreated with both the PDMP and callose synthesis inhibitor, resulting in elimination of PDMP-induced inhibition of TMV spread. Transcripts of the defense-related genes were significantly accumulated after challenge inoculation with TMV in PDMP-pretreated tobacco. Interestingly, PDMP treatment or TMV inoculation alone did neither induce callose deposition, nor enhance the transcript abundance of the defense-related genes, indicating that PDMP was more likely to promote tobacco to a primed state than induce defense responses directly. The primed callose accumulation plays a crucial role in restricting TMV spread in PDMP-pretreated tobacco. The present results provide evidence of PDMP can promote N. benthamiana to a primed state of enhance defense against TMV.

Ageing and ovarian stimulation modulate the relative levels of transcript abundance of oocyte DNA repair genes during the germinal vesicle-metaphase II transition in mice.

Oocyte quality and reproductive outcome are negatively affected by advanced maternal age, ovarian stimulation and method of oocyte maturation during assisted reproduction; however, the mechanisms responsible for these associations are not fully understood. The aim of this study was to compare the effects of ageing, ovarian stimulation and in-vitro maturation on the relative levels of transcript abundance of genes associated with DNA repair during the transition of germinal vesicle (GV) to metaphase II (MII) stages of oocyte development. The relative levels of transcript abundance of 90 DNA repair-associated genes was compared in GV-stage and MII-stage oocytes from unstimulated and hormone-stimulated ovaries from young (5-8-week-old) and old (42-45-week-old) C57BL6 mice. Ovarian stimulation was conducted using pregnant mare serum gonadotropin (PMSG) or anti-inhibin serum (AIS). DNA damage response was quantified by immunolabeling of the phosphorylated histone variant H2AX (γH2AX). The relative transcript abundance in DNA repair genes was significantly lower in MII oocytes compared to GV oocytes in young unstimulated and PMSG stimulated but was higher in AIS-stimulated mice. Interestingly, an increase in the relative level of transcript abundance of DNA repair genes was observed in MII oocytes from older mice in unstimulated, PMSG-stimulated and AIS-stimulated mice. Decreased γH2AX levels were found in both GV oocytes (82.9%) and MII oocytes (37.5%) during ageing in both ovarian stimulation types used (PMSG/AIS; p < 0.05). In conclusion, DNA repair relative levels of transcript abundance are altered by maternal age and the method of ovarian stimulation during the GV-MII transition in oocytes.

How Do Novel M-Rootstock (Vitis Spp.) Genotypes Cope with Drought?

Most of the vineyards around the world are in areas characterized by seasonal drought, where water deficits and high temperatures represent severe constraints on the regular grapevine growth cycle. Although grapevines are well adapted to arid and semi-arid environments, water stress can cause physiological changes, from mild to irreversible. Screening of available Vitis spp. genetic diversity for new rootstock breeding programs has been proposed as a way for which new viticulture challenges may be faced. In 2014, novel genotypes (M-rootstocks) were released from the University of Milan. In this work, the behavior of M1, M3 and M4 in response to decreasing water availabilities (80%, 50% and 20% soil water content, SWC) was investigated at the physiological and gene expression levels, evaluating gas exchange, stem water potential and transcript abundances of key genes related to ABA (abscisic acid) biosynthesis (VvZEP, VvNCED1 and VvNCED2) and signaling (VvPP2C4, VvSnRK2.6 and VvABF2), and comparing them to those of cuttings of nine commercial rootstocks widely used in viticulture. M-rootstocks showed a change at physiological levels in severe water-stressed conditions (20% soil water content, SWC), reducing the stomatal conductance and stem water potential, but maintaining high photosynthetic activity. Water use efficiency was high in water-limiting conditions. The transcriptional changes were observed at 50% SWC, with an increment of transcripts of VvNCED1 and VvNCED2 genes. M-rootstocks showed similar behavior to 1103P and 110R rootstocks, two highly tolerant commercial genotypes. These rootstocks adopted a tolerant strategy to face water-stressed conditions.

Comparative transcriptome of reproductive axis in Chinese indigenous sheep with different FecB genotypes and prolificacies

In the present study, there were 128, 263, and 139 differentially expressed genes (DEGs) from the ovary, pituitary, and hypothalamus, respectively, with the FecB B+/FecB ++ genotype. Results indicated that there was a synchronized, and differential increase in mRNA transcript abundances for genes encoding for ovarian steroidogenesis-signaling proteins in the ovary, TGF-β-signaling in hypothalamus, cAMP-signaling-transduction, and dopaminergic-synapse pathways in the pituitary. The values for these variables were associated with mean prolificacy in indigenous sheep and results provided indications for candidate regulator proteins that coordinate processes related to prolificacy in ewes. Furthermore, the results when there was evaluation of the FecB-genotype-specific co-expression modules implied that CYP17 was the hub gene connecting the pathways and for modulation of folliculogenesis and ovulation in the ewe with the FecB B+ genotype.

Genome-Wide Identification, Expression Profiling, and Evolution of Phosphate Transporter Gene Family in Green Algae.

Phosphorus (P) is an essential nutrient for plant growth and development. Phosphate transporters (PHTs) are trans-membrane proteins that mediate the uptake and translocation of phosphate (Pi) in green plants. The PHT family including PHT1, PHT2, PHT3 and PHT4 subfamilies are well-studied in land plants; however, PHT genes in green algae are poorly documented and not comprehensively identified. Here, we analyzed the PHTs in a model green alga Chlamydomonas reinhardtii and found 25 putative PHT genes, which can be divided into four subfamilies. The subfamilies of CrPTA, CrPTB, CrPHT3, and CrPHT4 contain four, eleven, one, and nine genes, respectively. The structure, chromosomal distribution, subcellular localization, duplication, phylogenies, and motifs of these genes were systematically analyzed in silico. Expression profile analysis showed that CrPHT genes displayed differential expression patterns under P starvation condition. The expression levels of CrPTA1 and CrPTA3 were down-regulated, while the expression of most CrPTB genes was up-regulated under P starvation, which may be controlled by CrPSR1. The transcript abundance of most CrPHT3 and CrPHT4 genes was not significantly affected by P starvation except CrPHT4-3, CrPHT4-4, and CrPHT4-6. Our results provided basic information for understanding the evolution and features of the PHT family in green algae.

Melatonin slightly alleviates the effect of heat shock on bovine oocytes and resulting blastocysts

Heat stress is associated with increased production of reactive oxygen species (ROS) and disruption of bovine oocyte function. Here, we examined whether the antioxidant melatonin can alleviate the deleterious effects of heat stress on oocyte developmental competence. Cumulus-oocyte complexes were matured for 22 h at 38.5 °C (control) or for 22 h at 41.5 °C (heat shock) with or without 1.0 × 10−7 M melatonin. At the end of maturation, a subgroup of oocytes was examined for nuclear and cytoplasmic maturation, ROS level and mitochondrial membrane potential. A second subgroup of oocytes underwent fertilization (18 h), and putative zygotes were cultured in an incubator equipped with a time-lapse system for ∼190 h. Cleavage rate and the proportion of blastocysts, as well as embryo kinetics were recorded. Expanded blastocysts were collected and their transcript abundance was evaluated. Heat shock increased ROS and reduced the proportion of oocytes that resumed meiosis and reached the metaphase-II stage. Exposing oocytes to heat shock with melatonin alleviated these effects to some extent, expressed by a marginal reduction in ROS level and increased proportion of metaphase-II stage oocytes. Neither the distribution of oocyte cortical granules nor polarization of the mitochondrial membrane differed between control and heat-shocked oocytes cultured with or without melatonin. Heat shock reduced the proportion of embryos that cleaved and developed to blastocysts, characterized by alterations in kinetics of the developed embryos expressed by a delay in the first cleavage, second cleavage and blastocyst formation for heat-shock vs. control groups. Melatonin did not restore the competence or kinetics of embryos developed from heat-shocked oocytes. However, expanded blastocysts developed from heat-shocked oocytes treated with melatonin expressed a higher transcript abundance of genes associated with mitochondrial function, relative to the control and heat-shock group. In summary, melatonin improved the oxidative status of heat-shocked oocytes to some extent and had a beneficial effect on maternal mitochondrial transcripts in the developed blastocysts.

Improvement of in vitro proliferation of cockerel spermatogonial stem cells using different combinations of growth factors

ABSTRACT 1. This study examined whether in vitro proliferation and maintenance of cockerel spermatogonial stem cells (SSCs) could be improved by adding different combinations of growth factors (GFs), including glial cell line-derived neurotrophic factor (GDNF), basic fibroblast growth factor (bFGF) or leukaemia inhibitory factor (LIF) into the culture medium. 2. The SSCs were isolated from the testes of immature cockerels. For short-term cultures, a medium supplemented with different combinations of GFs for 7 d in 5 replicates was used. The groups were classified as follows: without GF (control group); with GDNF (G group); with GDNF and bFGF (GF group); and with GDNF, bFGF and LIF (GFL group). The number of colonies and cells per colony, as well as the transcript abundance of STRA8 and OCT4 genes, was determined 7 d after the initial culturing. Immunofluorescence staining of SSEA-1, SSEA-3 and VASA protein markers, besides periodic acid-Schiff (PAS) staining, was carried out. 3. The number of colonies and cells per colony increased in the G, GF and GFL groups, compared to the control group (P < 0.01); however, the highest proliferation and colony formation were observed in the GFL group. The positive immunofluorescence staining of SSEA-1, SSEA-3 and VASA protein markers, as well as PAS staining, confirmed the self-renewal and colonisation of cockerel SSCs. The proliferation results were supported by the increased STRA8 and OCT4 transcript abundance in the treated groups (G, GF and GLF), compared to the control group. The SSC proliferation was associated with the higher transcript abundance of STAR8 and OCT4 genes in the GFL group, compared to the G and GF groups (P < 0.01). 4. The results showed that proliferation and colony-forming capacity of cockerel SSCs were positively improved by GDNF, bFGF and LIF. However, the most significant effect was observed when the medium was supplemented with LIF in combination with GDNF and bFGF.

Molecular Assessment of Genes Linked to Immune Response Traits of Honey Bees in Conventional and Organically Managed Apiaries.

Simple SummaryHoney bees play a critical role in agriculture as they provide pollination services to many agricultural crops. However, honey bee populations continue to decline due to exposure to pesticides, habitat destruction, pests, diseases and beekeeping practices. In this study, we assessed selected biological parameters associated with honey bee health in two beekeeping practices (organic and conventional). We compared total protein content in young worker bees from organically and conventionally managed apiaries. We also assessed differential gene expression at two levels of Varroa mite infestations (0% and 5%) in selected genes involved in nutrition and cellular defense (vitellogenin (Vg), malvolio (Mvl), prophenoloxidase (PPO)-, genes involved in lifespan (superoxide dismutase (Sod 1), superoxide dismutase 2 (Sod2)) and immune function genes (immune deficiency (Imd), spaetzle (Spz). Total soluble protein in young adult worker bees was similar in both beekeeping practices. The genes PPO, Vg and Mvl were upregulated in young adult bees with no mite infestations from organically managed apiaries and could mount an immune response through Spz and Sod 1 when challenged by 5% Varroa mite infestation levels. Overall, these findings provide useful insights into the genetic response of honey bees under two beekeeping practices and could help improve honey bee health.Honey bees are of great economic importance, not only for honey production but also for crop pollination. However, honey bee populations continue to decline mainly due to exposure to pesticides, pathogens and beekeeping practices. In this study, total soluble protein was measured, total RNA was extracted and first-strand cDNAs were generated. Quantitative PCR was used to assess the relative expression (transcript abundances) of immune function-related genes in honey bees collected from organically and conventionally managed hives. Honey bees collected from conventionally managed hives with 0% Varroa mite infestation levels displayed an upregulated expression of the prophenoloxidase gene (cellular defense). Similarly, honey bees collected from organically managed hives had increased levels of the vitellogenin gene (immune function and longevity). The gene expression for malvolio (sucrose responsiveness) was highest in organically managed hives with 0% Varroa mite infestations. Young adult bees collected from organically managed hives with 5% Varroa mite infestation levels had upregulated expressions of the gene spaetzle, whereas bees from similarly infested, conventionally managed hives did not, suggesting that honey bees from organically managed hives could mount an immune response. In young adult bees collected from organically managed hives only, the expression of the immune deficiency gene (antimicrobial defense) was upregulated. The relative gene expression for superoxide dismutase 1 increased in young adult bees collected from hives with 5% Varroa mite infestation levels as expected. However, for superoxide dismutase 2, there was a high level of gene expression in adult bees from both conventionally managed hives with 0% Varroa mite infestation levels and organically managed hives with 5% Varroa mite infestations. The gene CYP9Q3 (pesticide detoxification) that metabolizes coumaphos and fluvalinate was upregulated in adult bees collected from organically managed bees. Overall, these findings provide useful insights into the genetic response of honey bees to some environmental stressors and could be an important component of best beekeeping practices that intend to enhance honey bee health.

A New “Business as Usual” Climate Scenario and the Stress Response of the Caribbean Coral Montastraea cavernosa

The climate change related decline of shallow (&lt;30 m) coral reef ecosystems has been driven by the significant mortality of scleractinian corals caused primarily by the phenomenon known as “coral bleaching”. Despite pervasive phase shifts and macroalgal dominance on many coral reefs some coral species have persisted on many reefs. One of those species is Montastraea cavernosa which has been categorized as resilient to a range of biotic and abiotic insults. Here we present the results of a thermal stress and ocean acidification experiment on M. cavernosa, both its brown and orange color morphs, closely representing predictions from the Representative Concentration Pathway (RCP) 6.0 scenario in the year 2100. We assessed the community response of the microbiome, and the molecular responses of critical pathways in the host by quantifying transcript abundances of genes encoding fluorescent proteins, heat shock proteins, antioxidant enzymes and regulators of apoptosis. After a 12 d acclimatization experiment no visible bleaching was observed in any treatment, and the excitation pressure on photosystem II of the symbiotic Symbiodiniaceae, while lower under the combined effects of thermal stress and ocean acidification, was not significantly different than control samples. Only minor, but significant, changes in the prokaryotic microbiome were observed when exposed to RCP 6.0 predicted ocean acidification conditions. At the end of the experiment, the host heat shock protein 90 (HSP 90) showed an increase in transcript abundance under the interactive effects of thermal stress and ocean acidification compared to high temperatures alone, but these treatment groups were not significantly different than treatments under normal temperatures. While Bax, an activator of apoptosis, was significantly higher under thermal stress alone compared to control samples. Taken together, M. cavernosa, exhibits persistence, resistance and resilience generally, and when experimentally exposed to the more realistic RCP 6.0 climate model conditions.

Global analysis of SBP gene family in Brachypodiumdistachyon reveals its association with spike development

SQUAMOSA-promoter binding like proteins (SBPs/SPLs) are plant specific transcription factors targeted by miR156 and involved in various biological pathways, playing multi-faceted developmental roles. This gene family is not well characterized in Brachypodium. We identified a total of 18 SBP genes in B.distachyon genome. Phylogenetic analysis revealed that SBP gene family in Brachypodium expanded through large scale duplication. A total of 10 BdSBP genes were identified as targets of miR156. Transcript cleavage analysis of selected BdSBPs by miR156 confirmed their antagonistic connection. Alternative splicing was observed playing an important role in BdSBPs and miR156 interaction. Characterization of T-DNA Bdsbp9 mutant showed reduced plant growth and spike length, reflecting its involvement in the spike development. Expression of a majority of BdSBPs elevated during spikelet initiation. Specifically, BdSBP1 and BdSBP3 differentially expressed in response to vernalization. Differential transcript abundance of BdSBP1,BdSBP3,BdSBP8,BdSBP9,BdSBP14,BdSBP18 and BdSBP23 genes was observed during the spike development under high temperature. Co-expression network, protein–protein interaction and biological pathway analysis indicate that BdSBP genes mainly regulate transcription, hormone, RNA and transport pathways. Our work reveals the multi-layered control of SBP genes and demonstrates their association with spike development and temperature sensitivity in Brachypodium.

Nanoparticle treatment of maize analyzed through the metatranscriptome: compromised nitrogen cycling, possible phytopathogen selection, and plant hormesis

BackgroundThe beneficial use of nanoparticle silver or nanosilver may be confounded when its potent antimicrobial properties impact non-target members of natural microbiomes such as those present in soil or the plant rhizosphere. Agricultural soils are a likely sink for nanosilver due to its presence in agrochemicals and land-applied biosolids, but a complete assessment of nanosilver’s effects on this environment is lacking because the impact on the natural soil microbiome is not known. In a study assessing the use of nanosilver for phytopathogen control with maize, we analyzed the metatranscriptome of the maize rhizosphere and observed multiple unintended effects of exposure to 100 mg kg−1 nanosilver in soil during a growth period of 117 days.ResultsWe found several unintended effects of nanosilver which could interfere with agricultural systems in the long term. Firstly, the archaea community was negatively impacted with a more than 30% decrease in relative abundance, and as such, their involvement in nitrogen cycling and specifically, nitrification, was compromised. Secondly, certain potentially phytopathogenic fungal groups showed significantly increased abundances, possibly due to the negative effects of nanosilver on bacteria exerting natural biocontrol against these fungi as indicated by negative interactions in a network analysis. Up to 5-fold increases in relative abundance have been observed for certain possibly phytopathogenic fungal genera. Lastly, nanosilver exposure also caused a direct physiological impact on maize as illustrated by increased transcript abundance of aquaporin and phytohormone genes, overall resulting in a stress level with the potential to yield hormetically stimulated plant root growth.ConclusionsThis study indicates the occurrence of significant unintended effects of nanosilver use on corn, which could turn out to be negative to crop productivity and ecosystem health in the long term. We therefore highlight the need to include the microbiome when assessing the risk associated with nano-enabled agriculture.8o2Ktf3WjN9uvowsG6Jw_6Video

Biodegradation of Pesticides at the Limit: Kinetics and Microbial Substrate Use at Low Concentrations.

The objective of our study was to test whether limited microbial degradation at low pesticide concentrations could explain the discrepancy between overall degradability demonstrated in laboratory tests and their actual persistence in the environment. Studies on pesticide degradation are often performed using unrealistically high application rates seldom found in natural environments. Nevertheless, biodegradation rates determined for higher pesticide doses cannot necessarily be extrapolated to lower concentrations. In this context, we wanted to (i) compare the kinetics of pesticide degradation at different concentrations in arable land and (ii) clarify whether there is a concentration threshold below which the expression of the functional genes involved in the degradation pathway is inhibited without further pesticide degradation taking place. We set up an incubation experiment for four weeks using 14C-ring labeled 2-methyl-4-chlorophenoxyacetic acid (MCPA) as a model compound in concentrations from 30 to 20,000 μg kg–1 soil. To quantify the abundance of putative microorganisms involved in MCPA degradation and their degradation activity, tfdA gene copy numbers (DNA) and transcripts (mRNA) were determined by quantitative real-time PCR. Mineralization dynamics of MCPA derived-C were analyzed by monitoring 14CO2 production and 14C assimilation by soil microorganisms. We identified two different concentration thresholds for growth and activity with respect to MCPA degradation using tfdA gene and mRNA transcript abundance as growth and activity indices, respectively. The tfdA gene expression started to increase between 1,000 and 5,000 μg MCPA kg–1 dry soil, but an actual increase in tfdA sequences could only be determined at a concentration of 20,000 μg. Accordingly, we observed a clear shift from catabolic to anabolic utilization of MCPA-derived C in the concentration range of 1,000 to 5,000 μg kg–1. Concentrations ≥1,000 μg kg–1 were mainly associated with delayed mineralization, while concentrations ≤1,000 μg kg–1 showed rapid absolute dissipation. The persistence of pesticides at low concentrations cannot, therefore, be explained by the absence of functional gene expression. Nevertheless, significant differences in the degradation kinetics of MCPA between low and high pesticide concentrations illustrate the need for studies investigating pesticide degradation at environmentally relevant concentrations.

Evolutionary network genomics of wood formation in a phylogenetic survey of angiosperm forest trees.

Wood formation was present in early angiosperms, but has been highly modified through evolution to generate the anatomical diversity seen in extant angiosperm lineages. In this project, we modeled changes in gene coexpression relationships associated with the evolution of wood formation in a phylogenetic survey of 13 angiosperm tree species. Gravitropic stimulation was used as an experimental treatment to alter wood formation and also perturb gene expression. Gene transcript abundances were determined using RNA sequencing of developing wood tissues from upright trees, and from the top (tension wood) and bottom (opposite wood) tissues of gravistimulated trees. A network-based approach was employed to align gene coexpression networks across species based on orthologous relationships. A large-scale, multilayer network was modeled that identified both lineage-specific gene coexpression modules and modules conserved across multiple species. Functional annotation and analysis of modules identified specific regulatory processes associated with conserved modules, including regulation of hormones, protein phosphorylation, meristem development and epigenetic processes. Our results provide novel insights into the evolution and development of wood formation, and demonstrate the ability to identify biological processes and genes important for the evolution of a foundational trait in nonmodel, undomesticated forest trees.