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Objective: Soybean seed development is negatively impacted by elevated temperatures during seed fill, which can decrease seed quality and economic value. Prior germplasm screens identified an exotic landrace able to maintain ~ 95% seed germination under stress conditions that reduce germination dramatically (> 50%) for typical soybean seeds. Seed transcriptomic analysis was performed for two soybean lines (a heat-tolerant landrace and a typical high-yielding adapted line) for dry, mature seed, 6-h imbibed seed and germinated seed. Seeds were produced in two environments: a typical Midwestern field and a heat stressed field located in the Midsouth soybean production region., Results: Transcriptomic analysis revealed 23-30K expressed genes in each seed tissue sample, and differentially expressed genes (DEGs) with ≥ twofold gene expression differences (at q-value < 0.05) comprised ~ 5-44% of expressed genes. Gene ontology (GO) enrichment analysis on DEGs revealed enrichment in heat-tolerant seeds for genes annotated for general and temperature-specific stress, as well as protein-refolding. DEGs were also clustered in modules using weighted co-expressed gene network analysis, which were examined for enrichment of GO biological process terms. Collectively, our results provide new and valuable insights into this unique form of genetic abiotic stress tolerance and to soybean seed physiological responses to elevated temperatures.

Cyst nematodes deliver effector proteins into host cells to manipulate cellular processes and establish a metabolically hyperactive feeding site. The novel 30D08 effector protein is produced in the dorsal gland of parasitic juveniles, but its function has remained unknown. We demonstrate that expression of 30D08 contributes to nematode parasitism, the protein is packaged into secretory granules and it is targeted to the plant nucleus where it interacts with SMU2 (homolog of suppressor of mec-8 and unc-52 2), an auxiliary spliceosomal protein. We show that SMU2 is expressed in feeding sites and an smu2 mutant is less susceptible to nematode infection. In Arabidopsis expressing 30D08 under the SMU2 promoter, several genes were found to be alternatively spliced and the most abundant functional classes represented among differentially expressed genes were involved in RNA processing, transcription and binding, as well as in development, and hormone and secondary metabolism, representing key cellular processes known to be important for feeding site formation. In conclusion, we demonstrated that the 30D08 effector is secreted from the nematode and targeted to the plant nucleus where its interaction with a host auxiliary spliceosomal protein may alter the pre-mRNA splicing and expression of a subset of genes important for feeding site formation., (© 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.)

Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease. This pathogen is capable of transferring the T-DNA from its Ti plasmid to the host cell and, then, integrating it into the host genome. To date, this genetic transformation ability has been harnessed as the dominant technology to produce genetically modified plants for both basic research and crop biotechnological applications. However, little is known about the interaction between Agrobacterium tumefaciens and host plants, especially the host responses to Agrobacterium infection and its associated factors. We employed RNA-seq to follow the time course of gene expression in Arabidopsis seedlings infected with either an avirulent or a virulent Agrobacterium strain. Gene Ontology analysis indicated many biological processes were involved in the Agrobacterium-mediated transformation process, including hormone signaling, defense response, cellular biosynthesis, and nucleic acid metabolism. RNAseq and quantitative reverse transcription-polymerase chain reaction results indicated that expression of genes involved in host plant growth and development were repressed but those involved in defense response were induced by Agrobacterium tumefaciens. Further analysis of the responses of transgenic Arabidopsis lines constitutively expressing either the VirE2 or VirE3 protein suggested Vir proteins act to enhance plant defense responses in addition to their known roles facilitating T-DNA transformation.

Countless studies have identified differences between the gut microbiota of humans affected with myriad conditions and healthy individuals, and animal models are commonly used to determine whether those differences are causative or correlative. Recently, concerns have arisen regarding the reproducibility of animal models between institutions and across time. To determine the influence of three common husbandry-associated factors that vary between institutions, groups of weanling mice were placed in either static or ventilated microisolator caging, with either aspen or paperchip bedding, and with one of three commonly used rodent chows, in a fully crossed study design. After thirteen weeks, samples were collected from multiple regions of the gastrointestinal tract and characterized using culture-independent sequencing methods. Results demonstrated that seemingly benign husbandry factors can interact to induce profound changes in the composition of the microbiota present in certain regions of the gut, most notably the cecum, and that those changes are muted during colonic transit. These findings indicate that differences in factors such as caging and bedding can interact to modulate the gut microbiota that in turn may affect reproducibility of some animal models, and that cecal samples might be optimal when screening environmental effects on the gut microbiota.

Our prior work showed that a novel microbiome resides in the seminal vesicles of wild-type and oestrogen receptor α (Esr1) knock-out mice and is impacted by the presence of functional Esr1 genes. The seminal fluid microbiome (SFM) may influence the health and reproductive status of the male, along with that of his partner and offspring. A high-fat diet (HFD) alters metabolites and other factors within seminal fluid and might affect the SFM. Adult (~15 weeks old) male mice were placed for 4 weeks on a control or high-fat diet and seminal fluid and fecal samples were collected, bacterial DNA isolated and subjected to 16s rRNA sequencing. Corynebacterium spp. were elevated in the seminal fluid of HFD males; however, Acinetobacter johnsonii, Streptophyta, Ammoniphilus spp., Bacillus spp. and Propionibacterium acnes were increased in control males. Rikenellaceae was more abundant in the fecal samples from HFD males. However, Bacteroides ovatus and another Bacteroides species, Bilophila, Sutterella spp., Parabacteroides, Bifidobacterium longum, Akkermansia muciniphila and Desulfovibrio spp. were greater in control males. Thus, short-term consumption of a HFD influences the seminal fluid and fecal microbiomes, which may have important health consequence for males and developmental origins of health and disease effects in resulting offspring.

Due to their antimicrobial properties, silver nanoparticles (AgNPs) are being used in non-edible and edible consumer products. It is not clear though if exposure to these chemicals can exert toxic effects on the host and gut microbiome. Conflicting studies have been reported on whether AgNPs result in gut dysbiosis and other changes within the host. We sought to examine whether exposure of Sprague-Dawley male rats for two weeks to different shapes of AgNPs, cube (AgNC) and sphere (AgNS) affects gut microbiota, select behaviors, and induces histopathological changes in the gastrointestinal system and brain. In the elevated plus maze (EPM), AgNS-exposed rats showed greater number of entries into closed arms and center compared to controls and those exposed to AgNC. AgNS and AgNC treated groups had select reductions in gut microbiota relative to controls. Clostridium spp., Bacteroides uniformis, Christensenellaceae, and Coprococcus eutactus were decreased in AgNC exposed group, whereas, Oscillospira spp., Dehalobacterium spp., Peptococcaeceae, Corynebacterium spp., Aggregatibacter pneumotropica were reduced in AgNS exposed group. Bacterial reductions correlated with select behavioral changes measured in the EPM. No significant histopathological changes were evident in the gastrointestinal system or brain. Findings suggest short-term exposure to AgNS or AgNC can lead to behavioral and gut microbiome changes.

Bisphenol A (BPA) is a widely present endocrine disruptor chemical found in many household items. Moreover, this chemical can bioaccumulate in various terrestrial and aquatic sources; thereby ensuring continual exposure of animals and humans. For most species, including humans, diet is considered the primary route of exposure. However, there has been little investigation whether commercial-brands of dog foods contain BPA and potential health ramifications of BPA-dietary exposure in dogs. We sought to determine BPA content within dog food, whether short-term consumption of these diets increases serum concentrations of BPA, and potential health consequences, as assessed by potential hematological, serum chemistry, cortisol, DNA methylation, and gut microbiome changes, in dogs associated with short-term dietary exposure to BPA. Fourteen healthy privately-owned dogs were used in this study. Blood and fecal samples were collected prior to dogs being placed for two-weeks on one of two diets (with one considered to be BPA-free), and blood and fecal samples were collected again. Serum/plasma samples were analyzed for chemistry and hematology profiles, cortisol concentrations, 5-methylcytosine in lymphocytes, and total BPA concentrations. Fecal samples were used for microbiome assessments. Both diets contained BPA, and after two-weeks of being on either diet, dogs had a significant increase in circulating BPA concentrations (pre-samples=0.7±0.15ng/mL, post-samples=2.2±0.15ng/mL, p<0.0001). Elevated BPA concentrations positively correlated with increased plasma bicarbonate concentrations and associated with fecal microbiome alterations. Short-term feeding of canned dog food increased circulating BPA concentrations in dogs comparable to amounts detected in humans, and greater BPA concentrations were associated with serum chemistry and microbiome changes. Dogs, who share our internal and external environments with us, are likely excellent indicators of potential human health concerns to BPA and other environmental chemicals. These findings may also have relevance to aquatic and terrestrial wildlife., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Bisphenol A (BPA) is an endocrine-disrupting chemical (EDC) prevalent in many household items. Rodent models and human epidemiological studies have linked this chemical to neurobehavior impairments. In California mice, developmental exposure to BPA results in sociosexual disorders at adulthood, including communication and biparental care deficits, behaviors that are primarily regulated by the hypothalamus. Thus, we sought to examine the transcriptomic profile in this brain region of juvenile male and female California mice offspring exposed from periconception through lactation to BPA or ethinyl estradiol (EE, estrogen present in birth control pills and considered a positive estrogen control for BPA studies). Two weeks prior to breeding, P 0 females were fed a control diet, or this diet supplemented with 50 mg BPA/kg feed weight or 0.1 ppb EE, and continued on the diets through lactation. At weaning, brains from male and female offspring were collected, hypothalamic RNA isolated, and RNA-seq analysis performed. Results indicate that BPA and EE groups clustered separately from controls with BPA and EE exposure leading to unique set of signature gene profiles. Kcnd3 was downregulated in the hypothalamus of BPA- and EE-exposed females, whereas Tbl2 , Topors , Kif3a , and Phactr2 were upregulated in these groups. Comparison of transcripts differentially expressed in BPA and EE groups revealed significant enrichment of gene ontology terms associated with microtubule-based processes. Current results show that perinatal exposure to BPA or EE can result in several transcriptomic alterations, including those associated with microtubule functions, in the hypothalamus of California mice. It remains to be determined whether these genes mediate BPA-induced behavioral disruptions., (© 2017 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.)

Gut dysbiosis may result in various diseases, such as metabolic and neurobehavioral disorders. Exposure to endocrine disrupting chemicals (EDCs), including bisphenol A (BPA) and ethinyl estradiol (EE), especially during development, may also increase the risk for such disorders. An unexplored possibility is that EDC-exposure might alter the gut microbial composition. Gut flora and their products may thus be mediating factors for the disease-causing effects of these chemicals. To examine the effects of EDCs on the gut microbiome, female and male monogamous and biparental California mice (Peromyscus californicus) were exposed to BPA (50 mg/kg feed weight) or EE (0.1 ppb) or control diet from periconception through weaning. 16s rRNA sequencing was performed on bacterial DNA isolated from fecal samples, and analyses performed for P 0 and F 1 males and females. Both BPA and EE induced generational and sex-dependent gut microbiome changes. Many of the bacteria, e.g. Bacteroides, Mollicutes, Prevotellaceae, Erysipelotrichaceae, Akkermansia, Methanobrevibacter, Sutterella, whose proportions increase with exposure to BPA or EE in the P 0 or F 1 generation are associated with different disorders, such as inflammatory bowel disease (IBD), metabolic disorders, and colorectal cancer. However, the proportion of the beneficial bacterium, Bifidobacterium, was also elevated in fecal samples of BPA- and EE-exposed F 1 females. Intestinal flora alterations were also linked to changes in various metabolic and other pathways. Thus, BPA and EE exposure may disrupt the normal gut flora, which may in turn result in systemic effects. Probiotic supplementation might be an effective means to mitigate disease-promoting effects of these chemicals.

Bacteria harbored in the male reproductive system may influence reproductive function and health of the male and result in developmental origins of adult health and disease (DOHaD) effects in his offspring. Such effects could be due to the seminal fluid, which is slightly basic and enriched with carbohydrates; thereby, creating an ideal habitat for microbes or a potential seminal fluid microbiome (SFM). Using wild-type (WT) and estrogen receptor-alpha (ESR1) knockout (KO) male mice, we describe a unique SFM whose inhabitants differ from gut microbes. The bacterial composition of the SFM is influenced according to whether mice have functional Esr1 genes. Propionibacterium acnes, causative agent of chronic prostatitis possibly culminating in prostate cancer, is reduced in SFM of ESR1 KO compared to WT mice (P ≤ 0.0007). In certain genetic backgrounds, WT mice show a greater incidence of prostate cancer than ESR1 KO, which may be due to increased abundance of P. acnes. Additionally, select gut microbiome residents in ESR1 KO males, such as Lachnospiraceae and Christensenellaceae, might contribute to previously identified phenotypes, especially obesity, in these mutant mice. Understanding how genetics and environmental factors influence the SFM may provide the next frontier in male reproductive disorders and possibly paternal-based DOHaD diseases.

Genetically modified pigs are commonly created via somatic cell nuclear transfer (SCNT). Treatment of reconstructed embryos with histone deacetylase inhibitors (HDACi) immediately after activation improves cloning efficiency. The objective of this experiment was to evaluate the transcriptome of SCNT embryos treated with suberoylanilide hydroxamic acid (SAHA), 4-iodo-SAHA (ISAHA), or Scriptaid as compared to untreated SCNT, in vitro-fertilized (IVF), and in vivo (IVV) blastocyst-stage embryos. SAHA (10 μM) had the highest level of blastocyst development at 43.9%, and all treatments except 10 μM ISAHA had the same percentage of blastocyst development as Scriptaid (p<0.05). Two treatments, 1.0 μM ISAHA and 1.0 μM SAHA, had higher mean cell number than No HDACi treatment (p<0.021). Embryo transfers performed with 10 μM SAHA- and 1 μM ISAHA-treated embryos resulted in the birth of healthy piglets. GenBank accession numbers from up- and downregulated transcripts were loaded into the Database for Annotation, Visualization and Integrated Discovery to identify enriched biological themes. HDACi treatment yielded the highest enrichment for transcripts within the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway, lysosome. The mean intensity of LysoTracker was lower in IVV embryos compared to IVF and SCNT embryos (p<0.0001). SAHA and ISAHA can successfully be used to create healthy piglets from SCNT.

Drought and salinity stress pose threats to agricultural production in drylands. Although breeding and genetic modification techniques have been employed to develop drought- and salt-tolerant crops, these methods are costly and risky. Hence, the potential application of endophytic fungi in dryland agriculture is being explored as a novel approach in improving plant tolerance to environmental stress. In this study, endophytic fungi with growth-promoting effects were isolated, characterized, and evaluated in terms of their ability to confer drought and stress tolerance to their host plants. Seventy-seven growth-promoting endophytic fungi belonging to 20 genera were isolated from barley roots; of these, strain T-2 elicited remarkable effects on plant growth parameters. Phylogenetic analysis revealed that strain T-2 belongs to genus Leptosphaeria, whose members are generally known as plant pathogens. Thus, Leptosphaeria sp. strain T-2 is a novel endophytic fungus that promotes plant growth. Moreover, it alleviated growth inhibition caused drought and salinity stress, as evidenced by the survival and maintained health of lettuce plants inoculated with strain T-2. The results of this study suggest that strain T-2 can be applied as a biofertilizer to improve agricultural production in drylands. Highlights: • Endophytic fungi with growth-promoting effects were isolated and identified. • Phylogenetic analysis revealed fungal strain T-2 belongs to genus Leptosphaeria. • Fungal strain T-2 improved plant growth under drought and salt stress. • Fungal strain T-2 conferred drought and salt stress tolerance to its host plant. • Fungal strain T-2 may be utilized in dryland agriculture. [ABSTRACT FROM AUTHOR]

The merging of physiology and toxicokinetics, or pharmacokinetics, with computational modeling to characterize dosimetry has led to major advances for both the chemical and pharmaceutical research arenas. Driven by the mutual need to estimate internal exposures where in vivo data generation was simply not possible, the application of toxicokinetic modeling has grown exponentially in the past 30 years. In toxicology the need has been the derivation of quantitative estimates of toxicokinetic and toxicodynamic variability to evaluate the suitability of the tenfold uncertainty factor employed in risk assessment decision-making. Consideration of a host of physiologic, ontogenetic, genetic, and exposure factors are all required for comprehensive characterization. Fortunately, the underlying framework of physiologically based toxicokinetic models can accommodate these inputs, in addition to being amenable to capturing time-varying dynamics. Meanwhile, international interest in advancing new approach methodologies has fueled the generation of in vitro toxicity and toxicokinetic data that can be applied in in vitro-in vivo extrapolation approaches to provide human-specific risk-based information for historically data-poor chemicals. This review will provide a brief introduction to the structure and evolution of toxicokinetic and physiologically based toxicokinetic models as they advanced to incorporate variability and a wide range of complex exposure scenarios. This will be followed by a state of the science update describing current and emerging experimental and modeling strategies for population and life-stage variability, including the increasing application of in vitro-in vivo extrapolation with physiologically based toxicokinetic models in pharmaceutical and chemical safety research. The review will conclude with case study examples demonstrating novel applications of physiologically based toxicokinetic modeling and an update on its applications for regulatory decision-making. Physiologically based toxicokinetic modeling provides a sound framework for variability evaluation in chemical risk assessment. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) and Alzheimer's disease-related dementias (ADRDs) are broad-impact multifactorial neurodegenerative diseases. Their complexity presents unique challenges for developing effective therapies. This review highlights research presented at the 2024 Society for Neuroscience meeting which emphasized the gut microbiome's role in AD pathogenesis by influencing brain function and neurodegeneration through the microbiota--gut--brain axis. This emerging evidence underscores the potential for targeting the gut microbiota to treat AD/ADRD. [ABSTRACT FROM AUTHOR]

Water scarcity and soil carbon dioxide elevation in arid regions are considered the most serious factors affecting crop growth and productivity. This study aimed to investigate the impacts of elevated CO2 levels (eCO2 at rates of 700 and 1000 ppm) on agro-physiological attributes to induce drought tolerance in cucumbers by activating the expression of genes related to aquaporin and stress response, which improved the yield of cucumber under two levels of irrigation water conditions [75% and 100% crop evapotranspiration (ETc)]. Therefore, two field experiments were conducted in a greenhouse with controlled internal climate conditions, at the Mohamed Naguib sector of the national company for protected agriculture, during the winter seasons of 2021–2022 and 2022–2023. The treatments included eCO2 in soil under normal and partial root zoon drying (PRD, 100% ETc Full irrigations, and 75% ETc). All the applied treatments were organized as a randomized complete block design (RCBD) and each treatment was replicated six times. Untreated plants were designed as control treatment (CO2 concentration was 400 ppm). The results of this study showed that elevating CO2 at 700 and 1000 ppm in soil significantly increased plant growth parameters, photosynthesis measurements, and phytohormones [indole acetic acid (IAA) and gibberellic acid (GA3)], under partial root-zone drying (75% ETc) and full irrigation conditions (100% ETc). Under PRD condition, eCO2 at 700 ppm significantly improved plant height (13.68%), number of shoots (19.88%), Leaf greenness index (SPAD value, 16.60%), root length (24.88%), fresh weight (64.77%) and dry weight (61.25%) of cucumber plant, when compared to untreated plants. The pervious treatment also increased photosynthesis rate, stomatal conductance, and intercellular CO2 concentration by 50.65%, 15.30% and 12.18%; respectively, compared to the control treatment. Similar findings were observed in nutrient concentration, carbohydrate content, Proline, total antioxidants in the leaf, and nutrients. In contrast, eCO2 at 700 ppm in the soil reduced the values of transpiration rate (6.33%) and Abscisic acid (ABA, 34.03%) content in cucumber leaves compared to untreated plants under both water levels. Furthermore, the results revealed that the gene transcript levels of the aquaporin-related genes (CsPIP1-2 and CsTIP4) significantly increased compared with a well-watered condition. The transcript levels of CsPIP improved the contribution rate of cell water transportation (intermediated by aquaporin’s genes) and root or leaf hydraulic conductivity. The quantitative real-time PCR expression results revealed the upregulation of CsAGO1 stress-response genes in plants exposed to 700 ppm CO2. In conclusion, elevating CO2 at 700 ppm in the soil might be a promising technique to enhance the growth and productivity of cucumber plants in addition to alleviating the adverse effects of drought stresses. [ABSTRACT FROM AUTHOR]

Main Conclusion: The review describes tissue-specific and non-cell autonomous molecular responses regulating the root system architecture and function in plants. Phenotypic plasticity of roots relies on specific molecular and tissue specific responses towards local and microscale heterogeneity in edaphic factors. Unlike gravitropism, hydrotropism in Arabidopsis is regulated by MIZU KUSSIE1 (MIZ1)-dependent asymmetric distribution of cytokinin and activation of Arabidopsis response regulators, ARR16 and ARR17 on the lower water potential side of the root leading to higher cell division and root bending. The cortex specific role of Abscisic acid (ABA)-activated SNF1-related protein kinase 2.2 (SnRK2.2) and MIZ1 in elongation zone is emerging for hydrotropic curvature. Halotropism involves clathrin-mediated internalization of PIN FORMED 2 (PIN2) proteins at the side facing higher salt concentration in the root tip, and ABA-activated SnRK2.6 mediated phosphorylation of cortical microtubule-associated protein Spiral2-like (SP2L) in the root transition zone, which results in anisotropic cell expansion and root bending away from higher salt. In hydropatterning, Indole-3-acetic acid 3 (IAA3) interacts with SUMOylated-ARF7 (Auxin response factor 7) and prevents expression of Lateral organ boundaries-domain 16 (LBD16) in air-side of the root, while on wet side of the root, IAA3 cannot repress the non-SUMOylated-ARF7 thereby leading to LBD16 expression and lateral root development. In root vasculature, ABA induces expression of microRNA165/microRNA166 in endodermis, which moves into the stele to target class III Homeodomain leucine zipper protein (HD-ZIP III) mRNA in non-cell autonomous manner. The bidirectional gradient of microRNA165/6 and HD-ZIP III mRNA regulates xylem patterning under stress. Understanding the tissue specific molecular mechanisms regulating the root responses under heterogeneous and stress environments will help in designing climate-resilient crops., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Substantial mortality of in vitro manipulated porcine embryos is observed during peri-attachment development. Herein we describe our efforts to characterize the transcriptomes of embryonic disc (ED) and trophectoderm (TE) cells from porcine embryos derived from in vivo fertilization, in vitro fertilization (IVF), parthenogenetic oocyte activation (PA), and somatic cell nuclear transfer (SCNT) on days 10, 12, and 14 of gestation. The IVF, PA, and SCNT embryos were generated with in vitro matured oocytes and were cultured overnight in vitro before being transferred to recipient females. Sequencing of cDNA from the resulting embryonic samples was accomplished with the Genome Analyzer IIx platform from Illumina. Reads were aligned to a custom-built swine transcriptome. A generalized linear model was fit for ED and TE samples separately, accounting for embryo type, gestation day, and their interaction. Those genes with significant differences between embryo types were characterized in terms of gene ontologies and KEGG pathways. Transforming growth factor-β signaling was downregulated in the EDs of IVF embryos. In TE cells from IVF embryos, ubiquitin-mediated proteolysis and ErbB signaling were aberrantly regulated. Expression of genes involved in chromatin modification, gene silencing by RNA, and apoptosis was significantly disrupted in ED cells from SCNT embryos. In summary, we have used high-throughput sequencing technologies to compare gene expression profiles of various embryo types during peri-attachment development. We expect that these data will provide important insight into the root causes of (and possible opportunities for mitigation of) suboptimal development of embryos derived from assisted reproductive technologies.

In Neurospora crassa, unpaired genes are silenced by a mechanism called meiotic silencing by unpaired DNA (MSUD). Although some RNA interference proteins are necessary for this process, its requirement of small RNAs has yet to be formally established. Here we report the characterization of small RNAs targeting an unpaired region, using Illumina sequencing.

Using High-Throughput DNA Sequencing (HTS) to examine gene expression is rapidly becoming a -viable choice and is typically referred to as RNA-seq. Often the depth and breadth of coverage of RNA-seq data can exceed what is achievable using microarrays. However, the strengths of RNA-seq are often its greatest weaknesses. Accurately and comprehensively mapping millions of relatively short reads to a reference genome sequence can require not only specialized software, but also more structured and automated procedures to manage, analyze, and visualize the data. Additionally, the computational hardware required to efficiently process and store the data can be a necessary and often-overlooked component of a research plan. We discuss several aspects of the computational analysis of RNA-seq, including file management and data quality control, analysis, and visualization. We provide a framework for a standard nomenclature -system that can facilitate automation and the ability to track data provenance. Finally, we provide a general workflow of the computational analysis of RNA-seq and a downloadable package of scripts to automate the processing.

In vitro embryo culture systems promote development at rates lower than in vivo systems. The goal of this project was to discover transcripts that may be responsible for a decrease of embryo competency in blastocyst-stage embryos cultured in vitro. Gilts were artificially inseminated on the first day of estrus, and on Day 2, one oviduct and the tip of a uterine horn were flushed and the recovered embryos were cultured in porcine zygote medium 3 for 4 days. On Day 6, the gilts were euthanized and the contralateral horn was flushed to obtain in vivo derived embryos. Total RNA was extracted from three pools of 10 blastocysts from each treatment. First and second strand cDNA was synthesized and sequenced using Illumina sequencing. The reads generated were aligned to a custom-built database designed to represent the known porcine transcriptome. A total of 1170 database members were different between the two groups (P < 0.05), and 588 of those had at least a 2-fold difference. Eleven transcripts were subjected to real-time PCR that validated the sequencing. There was an overall decrease in inner cell mass (ICM) and trophectodermal (TE) cell numbers in embryos cultured in vitro; however, no difference in the ICM:TE ratio was found. Interestingly, the transcript SLC7A1 was higher in the in vitro cultured group. This difference disappeared after addition of arginine to the 4-day culture. Illumina sequencing and alignment to a custom transcriptome identified a large number of genes that yield clues on ways to manipulate the culture media to mimic the in vivo environment.

cDNA derived from trophectoderm (TE) and embryonic disc (ED) of a single day 12 porcine embryo was subjected to next-generation sequencing using the Illumina platform. The short sequencing reads from triplicate sequencing runs were aligned to a custom database designed to represent the known porcine transcriptome. As expected, genes involved in epithelial cell function and steroid biosynthesis were more abundant in cells from the TE; genes involved in maintenance of pluripotency and chromatin remodeling were more highly expressed in cells from the ED. Quantitative real-time PCR was used to confirm the validity of the approach. We conclude that gene expression profiles of even extremely small samples (

Development of a porcine germinal vesicle oocyte (GVO) to a 4-cell stage embryo occurs during a transcriptionally silent period when the oocyte/embryo relies on maternally derived mRNA to encode proteins required for development. Regulation of translation and degradation of maternal mRNA is thought to be partially dependent on cytoplasmic polyadenylation elements (CPEs) within the 3' untranslated region of the mRNA. The goal of this study was to determine how CPE sites affect the abundance of mRNA during embryogenesis and parthenogenetic development, and how cordycepin, a 3'-deooxyadenosine (3'-dA) that inhibits poly-(A) tail formation, affects polyadenylation and transcript abundance. Expressed sequence tags (ESTs) from oocytes and 4-cell stage embryos were scanned for the presence of five consensus CPEs. Nineteen different transcripts containing one to three CPEs were selected, and transcript abundance was determined in GVO, metaphase II, 2-cell, and 4-cell stage embryos via real-time PCR while the length of the poly-(A) tail was determined by using a poly-(A) tail PCR (PAT) assays. Real-time PCR was performed on three biological and two technical replicates for each stage. There was no direct correlation between poly-(A) tail length, transcript abundance, and the CPE. In addition, the abundance of some messages was different if the embryo was the result of parthenogenetic activation. Cordycepin prevented polyadenylation of transcripts that normally undergo noticeable polyadenylation. Thus, CPEs may not be the only factors that regulate message stability, and parthenogenetic activation does not result in changes in transcript abundance that mimic in vitro fertilization., ((c) 2010 Wiley-Liss, Inc.)

Background: Previous work showed that the maize primary root adapts to low Psiw (-1.6 MPa) by maintaining longitudinal expansion in the apical 3 mm (region 1), whereas in the adjacent 4 mm (region 2) longitudinal expansion reaches a maximum in well-watered roots but is progressively inhibited at low Psiw. To identify mechanisms that determine these responses to low Psiw, transcript expression was profiled in these regions of water-stressed and well-watered roots. In addition, comparison between region 2 of water-stressed roots and the zone of growth deceleration in well-watered roots (region 3) distinguished stress-responsive genes in region 2 from those involved in cell maturation., Results: Responses of gene expression to water stress in regions 1 and 2 were largely distinct. The largest functional categories of differentially expressed transcripts were reactive oxygen species and carbon metabolism in region 1, and membrane transport in region 2. Transcripts controlling sucrose hydrolysis distinguished well-watered and water-stressed states (invertase vs. sucrose synthase), and changes in expression of transcripts for starch synthesis indicated further alteration in carbon metabolism under water deficit. A role for inositols in the stress response was suggested, as was control of proline metabolism. Increased expression of transcripts for wall-loosening proteins in region 1, and for elements of ABA and ethylene signaling were also indicated in the response to water deficit., Conclusion: The analysis indicates that fundamentally different signaling and metabolic response mechanisms are involved in the response to water stress in different regions of the maize primary root elongation zone.

Regionally distinct elongation responses to water stress in the maize primary root tip have been observed in the past. A genetic basis for such differential responses has been demonstrated. Normalized bar-coded cDNA libraries were generated for four regions of the root tip, 0-3 mm (R1), 3-7 mm (R2), 7-12 mm (R3), and 12-20 mm (R4) from the root apex, and transcript profiles for these regions were sampled. This permitted a correlation between transcript nature and regional location for 15 726 expressed sequence tags (ESTs) that, in approximately equal numbers, derived from three conditions of the root: water stress (water potential: -1.6 MPa) for 5 h and for 48 h, respectively, and well watered (5 h and 48 h combined). These normalized cDNA libraries provided 6553 unigenes. An analysis of the regional representation of transcripts showed that populations were largely unaffected by water stress in R1, correlating with the maintenance of elongation rates under water stress known for R1. In contrast, transcript profiles in regions 2 and 3 diverged in well-watered and water-stressed roots. In R1, transcripts for translation and cell cycle control were prevalent. R2 was characterized by transcripts for cell wall biogenesis and cytoskeleton formation. R3 and R4 shared prevalent groups of transcripts responsible for defence mechanisms, ion transport, and biogenesis of secondary metabolites. Transcripts which were followed for 1, 6, and 48 h of water stress showed distinct region-specific changes in absolute expression and changes in regulated functions.

Background: The frequency and severity of abiotic stress events, especially drought, are increasing due to climate change. The plant root is the most important organ for water uptake and the first to be affected by water limitation. It is therefore becoming increasingly important to include root traits in studies on drought stress tolerance. However, phenotyping under field conditions remains a challenging task. In this study, plants were grown in a hydroponic system with polyethylene glycol as an osmotic stressor and in sand pots to examine the root system of eleven spring barley genotypes. The root anatomy of two genotypes with different response to drought was investigated microscopically. Results: Root diameter increased significantly (p < 0.05) under polyethylene glycol treatment by 54% but decreased significantly (p < 0.05) by 12% under drought stress in sand pots. Polyethylene glycol treatment increased root tip diameter (51%) and reduced diameter of the elongation zone (14%) compared to the control. Under drought stress, shoot mass of plants grown in sand pots showed a higher correlation (r = 0.30) with the shoot mass under field condition than polyethylene glycol treated plants (r = -0.22). Conclusion: These results indicate that barley roots take up polyethylene glycol by the root tip and polyethylene glycol prevents further water uptake. Polyethylene glycol-triggered osmotic stress is therefore unsuitable for investigating root morphology traits in barley. Root architecture of roots grown in sand pots is more comparable to roots grown under field conditions. [ABSTRACT FROM AUTHOR]

There has been much evidence showing the repercussions of prenatal bisphenol A (BPA) exposure with a postnatal high fat-diet (HFD) on offspring's health. However, the information on how the interaction between these two variables affects the gut microbiome is rather limited. Hence, we investigated the impact of a postnatal trans fat diet (TFD) on the gut microbiome of offspring exposed to BPA during the prenatal period in an animal model. Pregnant rats were divided into 5 mg/kg/day BPA, vehicle Tween80 (P80) or control (CTL) drinking water until delivery (N = 6 per group). Then, weaned male pups were further subdivided into three normal diet (ND) groups (CTLND, P80ND, and BPAND) and three TFD groups (CTLTFD, P80TFD, and BPATFD) (n = 6 per group). 180–250 g of faecal samples were collected on days 50 and 100 to assess the composition of the offspring's intestinal flora using next-generation sequencing. The alpha diversity indices of TFD offspring with and without BPA were markedly lower than their ND counterparts (p<0.001–p<0.05). The beta diversity, hierarchical cluster and network analyses of the offspring's microbiome demonstrated that the microbiome species of the TFD group with and without BPA were distinctly different compared to the ND group. Consistently, TFD and ND offspring pairings exhibited a higher number of significantly different species (p<0.0001–p<0.05) compared to those exposed to prenatal BPA exposure and different life stages comparisons, as shown by the multivariate parametric analysis DESeq2. Predictive functional profiling of the offspring's intestinal flora demonstrated altered expressions of genes involved in metabolic pathways. In summary, the gut flora composition of the rat offspring may be influenced by postnatal diet instead of prenatal exposure to BPA. Our data indicate the possibility of perturbed metabolic functions and epigenetic modifications, in offspring that consumed TFD, which may theoretically lead to metabolic diseases in middle or late adulthood. Further investigation is necessary to fully understand these implications. [ABSTRACT FROM AUTHOR]

Background/Aim: The leaves of Laurus nobilis have been used for culinary purposes for many years and have recently been shown to have beneficial effects on human health by altering microbiota composition. However, the effects of L. nobilis on the diversity of microbiomes in the oral cavity and gut remain unknown. Therefore, in this study, we examined the effects of an extract of L. nobilis on the diversity of microbiomes in the oral cavity and gut in mice. Materials and Methods: C57BL/6J mice were randomly divided into two groups and fed a standard diet (SD) and a standard diet containing 5% LAURESH®, a laurel extract (SDL). After 10 weeks, oral swabs and fecal samples were collected. The bacterial DNA extracted from the oral swabs and feces was used for microbiota analysis using 16S rRNA sequencing. The sequencing data were analyzed using the Quantitative Insights into Microbial Ecology 2 in the DADA2 pipeline and 16S rRNA database. Results: The a-diversity of the oral microbiome was significantly greater in the SDL group than in the SD group. The β-diversity of the oral microbiome was also significantly different between the groups. Moreover, the taxonomic abundance analysis showed that five bacteria in the gut were significantly different among the groups. Furthermore, the SDL diet increased the abundance of beneficial gut bacteria, such as Akkermansia sp. Conclusion: Increased diversity of the oral microbiome and proportion of Akkermansia sp. in the gut microbiome induced by L. nobilis consumption may benefit oral and gut health. [ABSTRACT FROM AUTHOR]

Serial Analysis of Gene Expression was used to define number and relative abundance of transcripts in the root tip of well-watered maize seedlings (Zea mays cv FR697). In total, 161,320 tags represented a minimum of 14,850 genes, based on at least two tags detected per transcript. The root transcriptome has been sampled to an estimated copy number of approximately five transcripts per cell. An extrapolation from the data and testing of single-tag identifiers by reverse transcription-PCR indicated that the maize root transcriptome should amount to at least 22,000 expressed genes. Frequency ranged from low copy number (2-5, 68.8%) to highly abundant transcripts (100-->1,200; 1%). Quantitative reverse transcription-PCR for selected transcripts indicated high correlation with tag frequency. Computational analysis compared this set with known maize transcripts and other root transcriptome models. Among the 14,850 tags, 7,010 (47%) were found for which no maize cDNA or gene model existed. Comparing the maize root transcriptome with that in other plants indicated that highly expressed transcripts differed substantially; less than 5% of the most abundant transcripts were shared between maize and Arabidopsis (Arabidopsis thaliana). Transcript categories highlight functions of the maize root tip. Significant variation in abundance characterizes transcripts derived from isoforms of individual enzymes in biochemical pathways.

Progress in understanding the network of mechanisms involved in maize primary root growth maintenance under water deficits is reviewed. These include the adjustment of growth zone dimensions, turgor maintenance by osmotic adjustment, and enhanced cell wall loosening. The role of the hormone abscisic acid (ABA) in maintaining root growth under water deficits is also addressed. The research has taken advantage of kinematic analysis, i.e. characterization of spatial and temporal patterns of cell expansion within the root growth zone. This approach revealed different growth responses to water deficits and ABA deficiency in distinct regions of the root tip. In the apical 3 mm region, elongation is maintained at well-watered rates under severe water deficit, although only in ABA-sufficient roots, whereas the region from 3-7 mm from the apex exhibits maximum elongation in well-watered roots, but progressive inhibition of elongation in roots under water deficit. This knowledge has greatly facilitated discovery of the mechanisms involved in regulating the responses. The spatial resolution with which this system has been characterized and the physiological knowledge gained to date provide a unique and powerful underpinning for functional genomics studies. Characterization of water deficit-induced changes in transcript populations and cell wall protein profiles within the growth zone of the maize primary root is in progress. Initial results from EST and unigene analyses in the tips of well-watered and water-stressed roots highlight the strength of the kinematic approach to transcript profiling.

Identification of mRNAs that are present at early stages of embryogenesis is critical for a better understanding of development. To this end, cDNA libraries were constructed from germinal vesicle-stage oocytes, in vivo-produced four-cell- and blastocyst-stage embryos, and from in vitro-produced four-cell- and blastocyst-stage embryos. Randomly picked clones (10 848) were sequenced from the 3' end and those of sufficient quality (8066, 74%) were clustered into groups of sequence similarity (>95% identity), resulting in 2489 clusters. The sequence of the longest representative expressed sequence tag (EST) of each cluster was compared with GenBank and TIGR. Scores below 200 were considered unique, and 1114 (44.8%) did not have a match in either database. Sequencing from the 5' end yielded 12 of 37 useful annotations, suggesting that one third of the 1114 might be identifiable, still leaving over 700 unique ESTs. Virtual Northerns compared between the stages identified numerous genes where expression appears to change from the germinal vesicle oocyte to the four-cell stage, from the four-cell to blastocyst stage, and between in vitro- and in vivo-derived four-cell- and blastocyst-stage embryos. This is the first large-scale sequencing project on early pig embryogenesis and has resulted in the discovery of a large number of genes as well as possible stage-specific expression. Because many of these ESTs appear to not be in the public databases, their addition will be useful for transcriptional profiling experiments conducted on early pig embryos.

Previous work demonstrated that normal levels of endogenous abscisic acid (ABA) are required to maintain shoot growth in well-watered tomato plants independently of effects of hormone status on plant water balance. The results suggested that the impairment of shoot growth in ABA-deficient mutants is at least partly attributable to increased ethylene production. To assess the extent to which ABA maintains shoot growth by ethylene suppression, the growth of ABA-deficient (aba2-1) and ethylene-insensitive (etr1-1) single- and double-mutants of Arabidopsis was examined. To ensure that the results were independent of effects of hormone status on plant water balance, differential relative humidity regimes were used to achieve similar leaf water potentials in all genotypes and treatments. In aba2-1, shoot growth was substantially inhibited and ethylene evolution was doubled compared with the wild type, consistent with the results for tomato. In the aba2-1 etr1-1 double mutant, in which ABA was equally as deficient as in aba2-1 and shoot growth was shown to be insensitive to ethylene, shoot growth was substantially, although incompletely, restored relative to etr1-1. Treatment with ABA resulted in the complete recovery of shoot growth in aba2-1 relative to the wild type, and also significantly increased the growth of aba2-1 etr1-1 such that total leaf area and shoot fresh weight were not significantly lower than in etr1-1. In addition, ABA treatment of aba2-1 etr1-1 restored the wider leaf morphology phenotype exhibited by etr1-1. The results demonstrate that normal levels of endogenous ABA maintain shoot development, particularly leaf expansion, in well-watered Arabidopsis plants, partly by suppressing ethylene synthesis and partly by another mechanism that is independent of ethylene.

Acclimation of root growth is vital for plants to survive salt stress. Halophytes are great examples of plants that thrive even under severe salinity, but their salt tolerance mechanisms, especially those mediated by root responses, are still largely unknown. We compared root growth responses of the halophyte Schrenkiella parvula with its glycophytic relative species Arabidopsis thaliana under salt stress and performed transcriptomic analysis of S. parvula roots to identify possible gene regulatory networks underlying their physiological responses. Schrenkiella parvula roots do not avoid salt and experience less growth inhibition under salt stress. Salt-induced abscisic acid levels were higher in S. parvula roots compared with Arabidopsis. Root transcriptomic analysis of S. parvula revealed the induction of sugar transporters and genes regulating cell expansion and suberization under salt stress. 14 C-labeled carbon partitioning analyses showed that S. parvula continued allocating carbon to roots from shoots under salt stress while carbon barely allocated to Arabidopsis roots. Further physiological investigation revealed that S. parvula roots maintained root cell expansion and enhanced suberization under severe salt stress. In summary, roots of S. parvula deploy multiple physiological and developmental adjustments under salt stress to maintain growth, providing new avenues to improve salt tolerance of plants using root-specific strategies., (© 2023 The Authors New Phytologist © 2023 New Phytologist Foundation.)

We have characterized the growth responses of Arabidopsis thaliana seedlings to water deficit. To manipulate the water potential, we developed a method whereby the nutrient-agar medium could be supplemented with polyethylene glycol (PEG 8000); PEG was introduced into gelled media by diffusion, which produced media with water potential as low as -1.6 MPa. For dark-grown plants, hypocotyl growth had a hyperbolic dependence on water potential, and was virtually stopped by -1 MPa. In contrast, primary root elongation was stimulated by moderate deficit and even at -1.6 MPa was not significantly less than the control. That these results did not depend on a direct effect of PEG was attested by obtaining indistinguishable results when a dialysis membrane impermeable to PEG was placed between the medium and the seedlings. For light-grown seedlings, moderate deficit also stimulated primary root elongation and severe deficit reduced elongation only partially. These changes in elongation were paralleled by changes in root system dry weight. At moderate deficit, lateral root elongation and initiation were unaffected and at higher stress levels both were inhibited. Primary root diameter increased steadily with time in well-watered controls and under water deficit increased transiently before stabilizing at a diameter that was inversely proportional to the deficit. Along with stimulated primary root elongation, moderate water deficit also stimulated the rate of cell production. Thus, A. thaliana responds to water deficit vigorously, which enhances its use as a model to uncover mechanisms underlying plant responses to water deficit.

Previous work showed that primary root elongation in maize (Zea mays L.) seedlings at low water potentials (psi(w)) requires the accumulation of abscisic acid (ABA) (R.E. Sharp, Y. Wu, G.S. Voetberg, I.N. Saab, M.E. LeNoble [1994] J Exp Bot 45: 1743-1751). The objective of the present study was to determine whether the inhibition of elongation in ABA-deficient roots is attributable to ethylene. At a psi(w) of -1.6 MPa, inhibition of root elongation in dark-grown seedlings treated with fluridone to impose ABA deficiency was largely prevented with two inhibitors of ethylene synthesis (aminooxyacetic acid and aminoethoxyvinylglycine) and one inhibitor of ethylene action (silver thiosulfate). The fluridone treatment caused an increase in the rate of ethylene evolution from intact seedlings. This effect was completely prevented with aminooxyacetic acid and also when ABA was supplied at a concentration that restored the ABA content of the root elongation zone and the root elongation rate. Consistent results were obtained when ABA deficiency was imposed using the vp5 mutant. Both fluridone-treated and vp5 roots exhibited additional morphological symptoms of excess ethylene. The results demonstrate that an important role of ABA accumulation in the maintenance of root elongation at low psi(w) is to restrict ethylene production.

Previous work suggested that an increase in cell wall-loosening contributes to the maintenance of maize (Zea mays L.) primary root elongation at low water potentials ([psi]w). It was also shown that root elongation at low [psi]w requires increased levels of abscisic acid (ABA). In this study we investigated the effects of low [psi]w and ABA status on xyloglucan endotransglycosylase (XET) activity in the root elongation zone. XET is believed to contribute to wall-loosening by reversibly cleaving xyloglucan molecules that tether cellulose microfibrils. The activity of XET per unit fresh weight in the apical 10 mm (encompassing the elongation zone) was constant at high [psi]w but increased by more than 2-fold at a [psi]w of -1.6 MPa. Treatment with fluridone to decrease ABA accumulation greatly delayed the increase in activity at low [psi]w. This effect was largely overcome when internal ABA levels were restored by exogenous application. Spatial distribution studies showed that XET activity was increased in the apical 6 mm at low [psi]w whether expressed per unit fresh weight, total soluble protein, or cell wall dry weight, corresponding to the region of continued elongation. Treatment with fluridone progressively inhibited the increase in activity with distance from the apex, correlating with the pattern of inhibition of elongation. Added ABA partly restored activity at all positions. The increase in XET activity at low [psi]w was due to maintenance of the rate of deposition of activity despite decreased deposition of wall material. The loss of activity associated with decreased ABA was due to inhibition of the deposition of activity. The results demonstrate that increased XET activity is associated with maintenance of root elongation at low [psi]w and that this response requires increased ABA.

Changes in dry matter and water-soluble carbohydrate components, especially fructan, were examined in the basal 25 mm of expanding leaf blades of tall fescue (Festuca arundinacea Schreb.) to assess their roles in plant response to water deficit. Water was withheld from vegetative plants grown in soil in controlled-environment chambers. As stress progressed, leaf elongation rate decreased sooner in the light period than it did in the dark period. The decrease in growth rate in the dark period was associated with a decrease in local relative elongation rates and a shortening of the elongation zone from about 25 mm (control) to 15 mm. Dry matter content of the leaf base increased 23% during stress, due mainly to increased water-soluble carbohydrate near the ligule and to increased water-soluble, carbohydrate-free dry matter at distal positions. Sucrose content increased 258% in the leaf base, but especially (over 4-fold) within 10 mm of the ligule. Hexose content increased 187% in the leaf base. Content of total fructan decreased to 69% of control, mostly in regions farther from the ligule. Fructan hydrolysis could account for the hexose accumulated. Stress caused the osmotic potential to decrease throughout the leaf base, but more toward the ligule. With stress there was 70% less direct contribution of low-degree-of-polymerization fructan to osmotic potential in the leaf base, but that for sucrose and hexose increased 96 and 67%, respectively. Thus, fructan metabolism is involved but fructan itself contributes only indirectly to osmotic adjustment.

Spatial distributions of turgor and longitudinal growth were compared in primary roots of maize (Zea mays L. cv FR27 x FRMo 17) growing in vermiculite at high (-0.02 megapascals) or low (-1.6 megapascals) water potential. Turgor was measured directly using a pressure probe in cells of the cortex and stele. At low water potential, turgor was greatly decreased in both tissues throughout the elongation zone. Despite this, longitudinal growth in the apical 2 millimeters was the same in the two treatments, as reported previously. These results indicate that the low water potential treatment caused large changes in cell wall yielding properties that contributed to the maintenance of root elongation. Further from the apex, longitudinal growth was inhibited at low water potential despite only slightly lower turgor than in the apical region. Therefore, the ability to adjust cell wall properties in response to low water potential may decrease with cell development.

Background: FAR1/FHY3 transcription factors are derived from transposase, which play important roles in light signal transduction, growth and development, and response to stress by regulating downstream gene expression. Although many FAR1/FHY3 members have been identified in various species, the FAR1/FHY3 genes in maize are not well characterized and their function in drought are unknown. Method: The FAR1/FHY3 family in the maize genome was identified using PlantTFDB, Pfam, Smart, and NCBI-CDD websites. In order to investigate the evolution and functions of FAR1 genes in maize, the information of protein sequences, chromosome localization, subcellular localization, conserved motifs, evolutionary relationships and tissue expression patterns were analyzed by bioinformatics, and the expression patterns under drought stress were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Results: A total of 24 ZmFAR members in maize genome, which can be divided into five subfamilies, with large differences in protein and gene structures among subfamilies. The promoter regions of ZmFARs contain abundant abiotic stress-responsive and hormone-respovensive cis-elements. Among them, drought-responsive cis-elements are quite abundant. ZmFARs were expressed in all tissues detected, but the expression level varies widely. The expression of ZmFARs were mostly down-regulated in primary roots, seminal roots, lateral roots, and mesocotyls under water deficit. Most ZmFARs were down-regulated in root after PEG-simulated drought stress. Conclusions: We performed a genome-wide and systematic identification of FAR1/FHY3 genes in maize. And most ZmFARs were down-regulated in root after drought stress. These results indicate that FAR1/FHY3 transcription factors have important roles in drought stress response, which can lay a foundation for further analysis of the functions of ZmFARs in response to drought stress. [ABSTRACT FROM AUTHOR]

Nanotechnology emerged as a critical force in agriculture and the most vital technology. Nanobiotechnology offers significant benefits for farmers to control their output by regulating nutrient use via nano-fertilizers, rationalizing agrochemical use, detecting, and treating disease–host interactions, molecular interactions with nanocarriers (nano biosensors) for plant disease diagnosis, and removing contaminants from water and soil, farm management, and current trends include salinity soil treatment. Nanosensors can also detect pathogens, moisture, fertilizers, and acidity of soil to improve products used to protect the plant, reduce nutrient leakage, and increase yield production due to effective management of nutrients. This section will look at bio-nanosensors based on soil sensors and nano-sensors that can be conjugated with nematode biomarkers to deliver the easy and quick detection of nematode plant diseases. They are also integrating biomarker with nanosensor to improve the vision and application of biosensor technology. According to the Docking test, Selectivity and specificity of the protein (MiPFN3) found specifically in root–knot nematodes and is not present in plants or other organisms. Therefore, inhibiting this protein would be a highly specific and targeted approach for controlling these nematodes, minimizing potential harm to non-target organisms. by generating a random pool of sequences using the shuffle-seq tool. In-silico Aptamer that can interact and inhibit MiPFN3 was designed. Schematic representation to illustrate Plant parasitic nematode diagnostics with nano biosensors as a novel extremely sensitive tool in sustainable agriculture. [ABSTRACT FROM AUTHOR]

The prevalence of metabolic diseases, such as obesity, diabetes, metabolic syndrome and chronic liver diseases among others, has been rising for several years. Epidemiology and mechanistic (in vivo, in vitro and in silico) toxicology have recently provided compelling evidence implicating the chemical environment in the pathogenesis of these diseases. In this review, we will describe the biological processes that contribute to the development of metabolic diseases targeted by metabolic disruptors, and will propose an integrated pathophysiological vision of their effects on several organs. With regard to these pathomechanisms, we will discuss the needs, and the stakes of evolving the testing and assessment of endocrine disruptors to improve the prevention and management of metabolic diseases that have become a global epidemic since the end of last century., (© 2022 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.)

Background: Bisphenol A (BPA) is an environmental contaminant with endocrine-disrupting properties that induce fetal growth restriction (FGR). Previous studies on pregnant ewes revealed that BPA exposure causes placental apoptosis and oxidative stress (OS) and decreases placental efficiency, consequently leading to FGR. Nonetheless, the response of gut microbiota to BPA exposure and its role in aggravating BPA-mediated apoptosis, autophagy, mitochondrial dysfunction, endoplasmic reticulum stress (ERS), and OS of the maternal placenta and intestine are unclear in an ovine model of gestation. Results: Two pregnant ewe groups (n = 8/group) were given either a subcutaneous (sc) injection of corn oil (CON group) or BPA (5 mg/kg/day) dissolved in corn oil (BPA group) once daily, from day 40 to day 110 of gestation. The maternal colonic digesta and the ileum and placental tissue samples were collected to measure the biomarkers of autophagy, apoptosis, mitochondrial dysfunction, ERS, and OS. To investigate the link between gut microbiota and the BPA-induced FGR in pregnant ewes, gut microbiota transplantation (GMT) was conducted in two pregnant mice groups (n = 10/group) from day 0 to day 18 of gestation after removing their intestinal microbiota by antibiotics. The results indicated that BPA aggravates apoptosis, ERS and autophagy, mitochondrial function injury of the placenta and ileum, and gut microbiota dysbiosis in pregnant ewes. GMT indicated that BPA-induced ERS, autophagy, and apoptosis in the ileum and placenta are attributed to gut microbiota dysbiosis resulting from BPA exposure. Conclusions: Our findings indicate the underlying role of gut microbiota dysbiosis and gut-placental axis behind the BPA-mediated maternal intestinal and placental apoptosis, OS, and FGR. The findings further provide novel insights into modulating the balance of gut microbiota through medication or probiotics, functioning via the gut-placental axis, to alleviate gut-derived placental impairment or FGR. DorkkcsjvJM4thb48aSHyr Video Abstract [ABSTRACT FROM AUTHOR]

To explore the fruit-cracking mechanism in nectarine, we compared three cracking-susceptible nectarine varieties ('Huaguang', 'Yanguang', and 'Zaohongzhu') and one cracking-resistant nectarine variety ('Shuguang'). Our findings indicate that 'Shuguang' nectarines exhibited significantly higher levels of calcium, calcium pectinate, total pectin, cellulose, Na2CO3-soluble pectin and CDTA-soluble pectin in the peel compared to 'Huaguang', 'Yanguang', and 'Zaohongzhu'. In contrast, the activities of polygalacturonases, pectinesterases, β-galactosidases, and cellulase were significantly lower in 'Shuguang'. Interestingly, no significant differences were observed in indole-3-acetic acid and gibberellic acid content between 'Shuguang' and the other three cracking-susceptible nectarine varieties. However, the abscisic acid content in 'Shuguang' was significantly lower. Additionally, compared with the three cracking-susceptible nectarine varieties, the expression level of PpPIP1 (encoding the plasma membrane intrinsic protein, which can improve the permeability of plant cell membranes and greatly improve the efficiency of water diffusion across membranes) in flesh was significantly lower, and the expression levels of PpExp1 and PpExp2 (encoding expansins, which play significant roles in loosening and expanding cell wall components) were significantly higher in the peels of cracking-resistant nectarine varieties. These differences can provide a basis for further study of the mechanism of nectarine fruit-cracking. [ABSTRACT FROM AUTHOR]

Background: Drought poses a major threat to agricultural production and thus food security. Understanding the processes shaping plant responses to water deficit is essential for global food safety. Though many studies examined the effect of water deficit on the whole-root level, the distinct functions of each root zone and their specific stress responses remain masked by this approach. Results: In this study, we investigated the effect of water deficit on root development of the spring barley (Hordeum vulgare L.) cultivar Morex and examined transcriptomic responses at the level of longitudinal root zones. Water deficit significantly reduced root growth rates after two days of treatment. RNA-sequencing revealed root zone and temporal gene expression changes depending on the duration of water deficit treatment. The majority of water deficit-regulated genes were unique for their respective root zone-by-treatment combination, though they were associated with commonly enriched gene ontology terms. Among these, we found terms associated with transport, detoxification, or cell wall formation affected by water deficit. Integration of weighted gene co-expression analyses identified differential hub genes, that highlighted the importance of modulating energy and protein metabolism and stress response. Conclusion: Our findings provide new insights into the highly dynamic and spatiotemporal response cascade triggered by water deficit and the underlying genetic regulations on the level of root zones in the barley cultivar Morex, providing potential targets to enhance plant resilience against environmental constraints. This study further emphasizes the importance of considering spatial and temporal resolution when examining stress responses. [ABSTRACT FROM AUTHOR]

The hypocotyl is the embryonic stem connecting the primary root to the cotyledons. Hypocotyl length varies tremendously depending on the conditions. This developmental plasticity and the simplicity of the organ explain its success as a model for growth regulation. Light and temperature are prominent growth-controlling cues, using shared signaling elements. Mechanisms controlling hypocotyl elongation in etiolated seedlings reaching the light differ from those in photoautotrophic seedlings. However, many common growth regulators intervene in both situations. Multiple photoreceptors including phytochromes, which also respond to temperature, control the activity of several transcription factors, thereby eliciting rapid transcriptional reprogramming. Hypocotyl growth often depends on sensing in green tissues and interorgan communication comprising auxin. Hypocotyl auxin, in conjunction with other hormones, determines epidermal cell elongation. Plants facing cues with opposite effects on growth control hypocotyl elongation through intricate mechanisms. We discuss the status of the field and end by highlighting open questions. [ABSTRACT FROM AUTHOR]

Coronary microvascular dysfunction (CMD) is associated with cardiac dysfunction and predictive of cardiac mortality in obesity, especially in females. Clinical data further support that CMD associates with development of heart failure with preserved ejection fraction and that mineralocorticoid receptor (MR) antagonism may be more efficacious in obese female, versus male, HFpEF patients. Accordingly, we examined the impact of smooth muscle cell (SMC)-specific MR deletion on obesity-associated coronary and cardiac diastolic dysfunction in female mice. Obesity was induced in female mice via western diet (WD) feeding alongside littermates fed standard diet. Global MR blockade with spironolactone prevented coronary and cardiac dysfunction in obese females and specific deletion of SMC-MR was sufficient to prevent obesity-associated coronary and cardiac diastolic dysfunction. Cardiac gene expression profiling suggested reduced cardiac inflammation in WD-fed mice with SMC-MR deletion independent of blood pressure, aortic stiffening, and cardiac hypertrophy. Further mechanistic studies utilizing single-cell RNA sequencing of non-cardiomyocyte cell populations revealed novel impacts of SMC-MR deletion on the cardiac cellulome in obese mice. Specifically, WD feeding induced inflammatory gene signatures in non-myocyte populations including B/T cells, macrophages, and endothelium as well as increased coronary VCAM-1 protein expression, independent of cardiac fibrosis, that was prevented by SMC-MR deletion. Further, SMC-MR deletion induced a basal reduction in cardiac mast cells and prevented WD-induced cardiac pro-inflammatory chemokine expression and leukocyte recruitment. These data reveal a central role for SMC-MR signaling in obesity-associated coronary and cardiac dysfunction, thus supporting the emerging paradigm of a vascular origin of cardiac dysfunction in obesity. [ABSTRACT FROM AUTHOR]