The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies.

BACKGROUND: Multiple studies have demonstrated a negative correlation between gene expression and positioning of genes at the nuclear envelope (NE) lined by nuclear lamina, but the exact relationship remains unclear, especially in light of the highly stochastic, transient nature of the gene association with the NE. RESULTS: In this paper, we ask whether there is a causal, systematic, genome-wide relationship between the expression levels of the groups of genes in topologically associating domains (TADs) of Drosophila nuclei and the probabilities of TADs to be found at the NE. To investigate the nature of this possible relationship, we combine a coarse-grained dynamic model of the entire Drosophila nucleus with genome-wide gene expression data; we analyze the TAD averaged transcription levels of genes against the probabilities of individual TADs to be in contact with the NE in the control and lamins-depleted nuclei. Our findings demonstrate that, within the statistical error margin, the stochastic positioning of Drosophila melanogaster TADs at the NE does not, by itself, systematically affect the mean level of gene expression in these TADs, while the expected negative correlation is confirmed. The correlation is weak and disappears completely for TADs not containing lamina-associated domains (LADs) or TADs containing LADs, considered separately. Verifiable hypotheses regarding the underlying mechanism for the presence of the correlation without causality are discussed. These include the possibility that the epigenetic marks and affinity to the NE of a TAD are determined by various non-mutually exclusive mechanisms and remain relatively stable during interphase. CONCLUSIONS: At the level of TADs, the probability of chromatin being in contact with the nuclear envelope has no systematic, causal effect on the transcription level in Drosophila. The conclusion is reached by combining model-derived time-evolution of TAD locations within the nucleus with their experimental gene expression levels.

Effect of Eco-Friendly Application of Bee Honey Solution on Yield, Physio-Chemical, Antioxidants, and Enzyme Gene Expressions in Excessive Nitrogen-Stressed Common Bean (Phaseolus vulgaris L.) Plants.

Excessive use of nitrogen (N) pollutes the environment and causes greenhouse gas emissions; however, the application of eco-friendly plant biostimulators (BSs) can overcome these issues. Therefore, this paper aimed to explore the role of diluted bee honey solution (DHS) in attenuating the adverse impacts of N toxicity on Phaseolus vulgaris growth, yield quality, physio-chemical properties, and defense systems. For this purpose, the soil was fertilized with 100, 125, and 150% of the recommended N dose (RND), and the plants were sprayed with 1.5% DHS. Trials were arranged in a two-factor split-plot design (N levels occupied main plots × DH- occupied subplots). Excess N (150% RND) caused a significant decline in plant growth, yield quality, photosynthesis, and antioxidants, while significantly increasing oxidants and oxidative damage [hydrogen peroxide (H2O2), superoxide (O2•-), nitrate, electrolyte leakage (EL), and malondialdehyde (MDA) levels]. However, DHS significantly improved antioxidant activities (glutathione and nitrate reductases, catalase, ascorbate peroxidase, superoxide dismutase, proline, ascorbate, α-tocopherol, and glutathione) and osmoregulatory levels (soluble protein, glycine betaine, and soluble sugars). Enzyme gene expressions showed the same trend as enzyme activities. Additionally, H2O2, O2•-, EL, MDA, and nitrate levels were significantly declined, reflecting enhanced growth, yield, fruit quality, and photosynthetic efficiency. The results demonstrate that DHS can be used as an eco-friendly approach to overcome the harmful impacts of N toxicity on P. vulgaris plants.

Cytokine Responses during Mycobacterium tuberculosis H37Rv and Ascaris lumbricoides Costimulation Using Human THP-1 and Jurkat Cells, and a Pilot Human Tuberculosis and Helminth Coinfection Study.

BACKGROUND: Helminth infections are widespread in tuberculosis-endemic areas and are associated with an increased risk of active tuberculosis. In contrast to the pro-inflammatory Th1 responses elicited by Mycobacterium tuberculosis (Mtb) infection, helminth infections induce anti-inflammatory Th2/Treg responses. A robust Th2 response has been linked to reduced tuberculosis protection. Several studies show the effect of helminth infection on BCG vaccination and TB, but the mechanisms remain unclear. AIM: To determine the cytokine response profiles during tuberculosis and intestinal helminth coinfection. METHODS: For the in vitro study, lymphocytic Jurkat and monocytic THP-1 cell lines were stimulated with Mtb H37Rv and Ascaris lumbricoides (A. lumbricoides) excretory-secretory protein extracts for 24 and 48 h. The pilot human ex vivo study consisted of participants infected with Mtb, helminths, or coinfected with both Mtb and helminths. Thereafter, the gene transcription levels of IFN-γ, TNF-α, granzyme B, perforin, IL-2, IL-17, NFATC2, Eomesodermin, IL-4, IL-5, IL-10, TGF-ß and FoxP3 in the unstimulated/uninfected controls, singly stimulated/infected and costimulated/coinfected groups were determined using RT-qPCR. RESULTS: TB-stimulated Jurkat cells had significantly higher levels of IFN-γ, TNF-α, granzyme B, and perforin compared to unstimulated controls, LPS- and A. lumbricoides-stimulated cells, and A. lumbricoides plus TB-costimulated cells (p < 0.0001). IL-2, IL-17, Eomes, and NFATC2 levels were also higher in TB-stimulated Jurkat cells (p < 0.0001). Jurkat and THP-1 cells singly stimulated with TB had lower IL-5 and IL-4 levels compared to those singly stimulated with A. lumbricoides and those costimulated with TB plus A. lumbricoides (p < 0.0001). A. lumbricoides-singly stimulated cells had higher IL-4 levels compared to TB plus A. lumbricoides-costimulated Jurkat and THP-1 cells (p < 0.0001). TGF-ß levels were also lower in TB-singly stimulated cells compared to TB plus A. lumbricoides-costimulated cells (p < 0.0001). IL-10 levels were lower in TB-stimulated Jurkat and THP-1 cells compared to TB plus A. lumbricoides-costimulated cells (p < 0.0001). Similar results were noted for the human ex vivo study, albeit with a smaller sample size. CONCLUSIONS: Data suggest that helminths induce a predominant Th2/Treg response which may downregulate critical Th1 responses that are crucial for tuberculosis protection.

Whole-Transcriptome Analysis on the Leaves of Rosa chinensis Jacq. under Exposure to Polycyclic Aromatic Hydrocarbons.

The leaves of plants can be recommended as a cheap and sustainable environmental protection tool to mitigate PAHs with high toxicity in the ambient environment because they can serve as a reactor to remove ambient PAHs. Although previous studies have demonstrated that PAHs exhibit toxicological features, our knowledge about how ambient PAHs influence the leaves of plants is limited regarding the leaves of plants reducing ambient PAHs as a reactor. In this study, 1-year-old Rosa chinensis Jacq. with good growth potential was selected as a model plant. The leaves of Rosa chinensis Jacq. were exposed to 16 types of PAHs in the environmental concentration exposure group (0.1 µg L-1) and high-concentration exposure group (5 µg L-1) for seven days. In comparison, the leaves of Rosa chinensis Jacq. were exposed to de-ionized water and were chosen as the control group. During the exposure periods, the physiological parameters of leaves including, chlorophyll value, water content, temperature and nitrogen, were monitored using a chlorophyll meter. After 7 days of exposure, the leaves in the control and exposure groups were collected and used for whole-transcriptome analysis. Our results demonstrate that significant differentially expressed genes were observed in the leaves of Rosa chinensis Jacq. exposed to individual PAHs at 5 µg L-1 compared to the control group. These differentially expressed genes were involved in seven main pathways using bioinformatic analyses. In contrast, the levels of PAHs at environmentally relevant concentrations had negligible impacts on the physiological parameters and the gene transcription levels of the leaves of Rosa chinensis Jacq. Our results may provide direct evidence to remove ambient PAHs using terrestrial trees without considering the risk of PAHs at environmentally relevant concentrations on the leaves of terrestrial plants.

OsSHMT4 Is Required for Synthesis of Rice Storage Protein and Storage Organelle Formation in Endosperm Cells.

Storage proteins are essential for seed germination and seedling growth, as they provide an indispensable nitrogen source and energy. Our previous report highlighted the defective endosperm development in the serine hydroxymethyltransferase 4 (OsSHMT4) gene mutant, floury endosperm20-1 (flo20-1). However, the alterations in storage protein content and distribution within the flo20-1 endosperm remained unclear. Here, the immunocytochemistry analyses revealed a deficiency in storage protein accumulation in flo20-1. Electron microscopic observation uncovered abnormal morphological structures in protein bodies (PBI and PBII) in flo20-1. Immunofluorescence labeling demonstrated that aberrant prolamin composition could lead to the subsequent formation and deposition of atypical structures in protein body I (PBI), and decreased levels of glutelins and globulin resulted in protein body II (PBII) malformation. Further RNA-seq data combined with qRT-PCR results indicated that altered transcription levels of storage protein structural genes were responsible for the abnormal synthesis and accumulation of storage protein, which further led to non-concentric ring structural PBIs and amorphous PBIIs. Collectively, our findings further underscored that OsSHMT4 is required for the synthesis and accumulation of storage proteins and storage organelle formation in endosperm cells.

Identification and Characterization of a Predominant Hydrophobin in the Edible Mushroom Grifola frondosa.

Hydrophobins (HFBs) are a group of small, secreted amphipathic proteins of fungi with multiple physiological functions and potential commercial applications. In this study, HFB genes of the edible mushroom, Grifola frondosa, were systematically identified and characterized, and their transcriptional profiles during fungal development were determined. In total, 19 typical class I HFB genes were discovered and bioinformatically analyzed. Gene expression profile examination showed that Gf.hyd9954 was particularly highly upregulated during primordia formation, suggesting its major role as the predominant HFB in the lifecycle of G. frondosa. The wettability alteration profile and the surface modification ability of recombinant rGf.hyd9954 were greater than for the Grifola HFB HGFII-his. rGf.hyd9954 was also demonstrated to form the typical class I HFB characteristic-rodlet bundles. In addition, rGf.hyd9954 was shown to possess nanoparticle characteristics and emulsification activities. This research sheds light on the regulation of fungal development and its association with the expression of HFB genes.

GmDREB6, a soybean transcription factor, notably affects the transcription of the NtP5CS and NtCLC genes in transgenic tobacco under salt stress conditions.

Soil is contaminated with salinity, which inhibits plant growth and development and reduces crop yields. The DREB (dehydration responsive element binding protein) gene responds to salt stresses through enhanced transcriptional expression and activation of genes involved in plant salinity resistance. In this study, we present the results of the analysis of the expression of the GmDREB6 transgene, a gene that encodes the soybean DREB6 transcription factor, regulating the transcription of the NtP5CS and NtCLC genes in transgenic tobacco under salt stress conditions. The transcription of GmDREB6, NtP5CS, and NtCLC in transgenic tobacco lines was confirmed by qRT-PCR. Under salt stress conditions, the GmDREB6 gene transcription levels in the transgenic tobacco lines L1 and L9 had increased from 2.40- to 3.22- fold compared with the condition without salinity treatment. Two transgenic lines, L1 and L9, had transcription levels of the P5CS gene that had increased from 1.24- to 3.60- fold compared with WT plants. For the NtCLC gene, under salt stress conditions, the transgenic lines had transcription levels that had increased by 3.65-4.54 (fold) compared with WT plants (P < 0.05). The L1-transgenic tobacco line showed simultaneous expression of both the GmDREB6 transgene and two intrinsic genes, the NtP5CS and NtCLC genes. This study demonstrated that expression of the GmDREB6 gene from soybean increases the transcription levels of the NtP5CS and NtCLC genes in transgenic tobacco plants under salt stress conditions. The analysis results have suggested that the GmDREB6 gene is a potential candidate for improving the salt tolerance of plants, opening up research and development opportunities for salt stress-tolerant crops to respond to climate change and the rise in sea levels.

TMEA: A Thermodynamically Motivated Framework for Functional Characterization of Biological Responses to System Acclimation.

The objective of gene set enrichment analysis (GSEA) in modern biological studies is to identify functional profiles in huge sets of biomolecules generated by high-throughput measurements of genes, transcripts, metabolites, and proteins. GSEA is based on a two-stage process using classical statistical analysis to score the input data and subsequent testing for overrepresentation of the enrichment score within a given functional coherent set. However, enrichment scores computed by different methods are merely statistically motivated and often elusive to direct biological interpretation. Here, we propose a novel approach, called Thermodynamically Motivated Enrichment Analysis (TMEA), to account for the energy investment in biological relevant processes. Therefore, TMEA is based on surprisal analysis, which offers a thermodynamic-free energy-based representation of the biological steady state and of the biological change. The contribution of each biomolecule underlying the changes in free energy is used in a Monte Carlo resampling procedure resulting in a functional characterization directly coupled to the thermodynamic characterization of biological responses to system perturbations. To illustrate the utility of our method on real experimental data, we benchmark our approach on plant acclimation to high light and compare the performance of TMEA with the most frequently used method for GSEA.

The potential association of the transcription levels of the ABO gene with the disease phases in AML patients.

Patients with AML may show ABO blood typing discrepancy, and the expression levels of the ABO antigens may show some alterations with the disease progression. To better understand this phenomenon, the blood samples of 25 AML patients and 25 healthy blood donors were examined. The serological ABO blood types of the patients were determined in different AML stages, and gene sequencing was performed to identify the precise ABO genotypes. Reverse transcription-polymerase chain reaction (RT-PCR) was carried out to detect the transcription levels of the antigens. The genotyping result showed that there were 4 patients with genotype A1O, 5 patients with B1O, and 16 patients with A1B1. RT-PCR results indicated that the transcription levels of the ABO gene in 76% (19/25) of the patients were significantly lower compared with those in controls (p <0.05). After therapy, 3/4 patients with A1O returned to normal A, 4/5 patients with B1O returned to normal B, and 10/16 patients with A1B1 returned to normal AB. The patients who achieved complete remission (CR) showed no difference of transcription levels of the ABO gene from those of controls. The data indicated that the transcription levels of the ABO gene changed with the disease progression, suggesting its potential role in the progression of AML disease.

Regulation of On-Tree Vitamin E Biosynthesis in Olive Fruit during Successive Growing Years: The Impact of Fruit Development and Environmental Cues.

The term vitamin E refers to a group of eight lipophilic compounds known as tocochromanols. The tocochromanols are divided into two groups, that is, tocopherols and tocotrienols, with four forms each, namely α-, ß-, γ-, and δ-. In order to explore the temporal biosynthesis of tocochromanols in olive (Olea europaea cv. 'Koroneiki') fruit during on-tree development and ripening over successive growing years, a combined array of analytical, molecular, bioinformatic, immunoblotting, and antioxidant techniques were employed. Fruits were harvested at eight successive developmental stages [10-30 weeks after flowering (WAF)], over three consecutive years. Intriguingly, climatic conditions affected relative transcription levels of vitamin E biosynthetic enzymes; a general suppression to induction pattern (excluding VTE5) was monitored moving from the 1st to the 3rd growing year, probably correlated to decreasing rainfall levels and higher temperature, particularly at the fruit ripening stage. A gradual diminution of VTE5 protein content was detected during the fruit development of each year, with a marked decrease occurring after 16 WAF. Alpha-tocopherol was the most abundant metabolite with an average percentage of 96.82 ± 0.23%, 91.13 ± 0.95%, and 88.53 ± 0.96% (during the 1st, 2nd, and 3rd year, respectively) of total vitamin E content in 10-30 WAF. The concentrations of α-tocopherol revealed a generally declining pattern, both during the on-tree ripening of the olive fruit and across the 3 years, accompanied by a parallel decline of the total antioxidant capacity of the drupe. Contrarily, all other tocochromanols demonstrated an inverse pattern with lowest levels being recorded during the 1st year. It is likely that, in a defense attempt against water deficit conditions and increased air temperature, transcription of genes involved in vitamin E biosynthesis (excluding VTE5) is up-regulated in olive fruit, probably leading to the blocking/deactivating of the pathway through a negative feedback regulatory mechanism.

Photosynthesis and chloroplast genes are involved in water-use efficiency in common bean.

A recent proposal to mitigate the effects of climatic change and reduce water consumption in agriculture is to develop cultivars with high water-use efficiency. The aims of this study were to characterize this trait as a differential response mechanism to water-limitation in two bean cultivars contrasting in their water stress tolerance, to isolate and identify gene fragments related to this response in a model cultivar, as well as to evaluate transcription levels of genes previously identified. Keeping CO2 assimilation through a high photosynthesis rate under limited conditions was the physiological response which allowed the cultivar model to maintain its growth and seed production with less water. Chloroplast genes stood out among identified genetic elements, which confirmed the importance of photosynthesis in such response. ndhK, rpoC2, rps19, rrn16, ycf1 and ycf2 genes were expressed only in response to limited water availability.