RNA-Seq time-course analysis of neural precursor cell transcriptome in response to herpes simplex Virus-1 infection.

The neurogenic niches within the central nervous system serve as essential reservoirs for neural precursor cells (NPCs), playing a crucial role in neurogenesis. However, these NPCs are particularly vulnerable to infection by the herpes simplex virus 1 (HSV-1). In the present study, we investigated the changes in the transcriptome of NPCs in response to HSV-1 infection using bulk RNA-Seq, compared to those of uninfected samples, at different time points post infection and in the presence or absence of antivirals. The results showed that NPCs upon HSV-1 infection undergo a significant dysregulation of genes playing a crucial role in aspects of neurogenesis, including genes affecting NPC proliferation, migration, and differentiation. Our analysis revealed that the CREB signaling, which plays a crucial role in the regulation of neurogenesis and memory consolidation, was the most consistantly downregulated pathway, even in the presence of antivirals. Additionally, cholesterol biosynthesis was significantly downregulated in HSV-1-infected NPCs. The findings from this study, for the first time, offer insights into the intricate molecular mechanisms that underlie the neurogenesis impairment associated with HSV-1 infection.

GC-MS-based metabonomic analysis of silkworm haemolymph reveals four-stage metabolic responses to nucleopolyhedrovirus infection.

Silkworm, Bombyx mori, an economically significant insect, plays a crucial role in silk production. However, silkworm breeding is highly susceptible to various pathogens, particularly the Bombyx mori nucleopolyhedrovirus (BmNPV), which poses a serious threat. Recent metabonomic studies have provided insights into the metabolic changes associated with BmNPV infection. BmNPV infection has obvious temporal characteristics. However, few studies have investigated the silkworms infected in different periods. This study employed gas chromatography-mass spectrometry (GC-MS) to perform a comprehensive analysis of haemolymph metabolites in silkworms at 48, 72, 96 and 120 h post-infection (h.p.i.). Through the integration of time-course analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, the study revealed distinct four-stage metabolic characteristics in the silkworm's response to BmNPV infection. At Stage 1 (48 h.p.i.), silkworms activate antioxidant defence mechanisms, with significant enrichment in metabolic pathways involving key antioxidants such as glutathione, to mitigate oxidative stress induced by viral invasion. By Stage 2 (72 h.p.i.), pathways related to amino acid metabolism and protein synthesis become active, indicating an increase in protein synthesis. In Stage 3 (96 h.p.i.), energy metabolism and substance transport pathways are significantly upregulated to support the rapid viral replication and the enhanced locomotor behaviour of silkworm. Finally, at Stage 4 (120 h.p.i.), there is a further enhancement of pathways related to energy metabolism, nucleic acid synthesis, and substance transport, which align with peak viral assembly and release. These findings contribute to an in-depth understanding of the biochemical basis of silkworm resistance to NPV.

Magnitude and time course of insulin resistance accumulation with the risk of cardiovascular disease: an 11-years cohort study.

BACKGROUND: The risk of cardiovascular disease (CVD) depended on the magnitude and exposure duration of insulin resistance (IR). This study aimed to investigate the associations of cumulative metabolic score for IR (cumMETS-IR) with incident CVD, and to further explore the modulated effects of time course of METS-IR accumulation. METHODS: We enrolled 47,270 participants without CVD and underwent three examinations during 2006-2010 from the Kailuan study. CumMETS-IR from 2006 to 2010 were calculated as the mean values of METS-IR between consecutive examinations multiplying by time intervals between visits. Time course of METS-IR accumulation was calculated as the slope of METS-IR versus time. Hazard ratios (HRs) and 95% confidence intervals (CIs) for CVD risk were calculated with multivariable-adjusted Cox regressions. RESULTS: During a median follow-up of 10.99 years, we identified 3184 cases of incident CVD. The risk of incident CVD increased with increasing cumMETS-IR (HR, 1.77; 95% CI 1.58-1.98 for the Q4 versus Q1 group), exposure duration (HR, 1.60; 95% CI 1.45-1.77 for 6 years versus 0 years), and cumulative burden (HR, 1.49; 95% CI 1.37-1.61 for burden ≥ 0 versus < 0). A positive slope was associated with 14% higher risk of CVD (HR, 1.14; 95% CI 1.07-1.22). When combining cumMETS-IR and slope, those with cumMETS-IR ≥ median (142.78) and slope ≥ 0 had the highest risk of CVD (HR,1.38; 95% CI 1.25-1.53). CONCLUSIONS: The risk of CVD increased with elevated cumMETS-IR and an increasing trend over time, emphasizing the importance of maintaining optimal METS-IR levels across life span.

Time course of the triglyceride glucose index accumulation with the risk of cardiovascular disease and all-cause mortality.

BACKGROUND: Future risk of cardiovascular disease (CVD) and mortality is associated with cumulative amount TyG index (cumTyG) exposure, while whether time course of TyG accumulation modulates the risk remains unclear. This study sought to examine the associations of cumTyG index accumulation time course with the risk of CVD and all-cause mortality. METHODS: We enrolled 51,734 participants free of CVD and underwent three examinations at year 2006, 2008, and 2010. CumTyG from baseline to the third examination was calculated. Time course of cumTyG accumulation was calculated as the slope of TyG versus time from 2006 to 2010, or as splinting the overall TyG index accumulation into early (cumTyG06 - 08) and late accumulation (cumTyG08 - 10). Participants were categorized by the combination of cumTyG < or ≥ median (34.44 × years) and a negative or positive TyG slope. RESULTS: During a median follow-up of 9.04 years, we identified 3,602 incident CVD cases and 3,165 deaths. The risk of CVD and all-cause mortality increased with decreased TyG slope, the corresponding adjusted hazard ratio (aHR) with 95% confidence interval (CI) was 1.11 (1.04-1.19) and 1.18 (1.10-1.26) for patients with a negative TyG slope, respectively. Consistently, a later accumulation of TyG index was not associated with the risk of CVD and all-cause mortality after adjustment for an early accumulation. When considering the combination of cumTyG index and time course, participants with a cumTyG ≥ median and a negative TyG slope had elevated risk of CVD (aHR, 1.37; 95% CI, 1.24-1.51) and all-cause mortality (aHR, 1.28; 95% CI, 1.15-1.43). Additionally, the association was more prominent in young adults. CONCLUSION: Early TyG index accumulation resulted in a greater risk of CVD and all-cause mortality than later TyG later accumulation with the same overall cumulative exposure, emphasizing the importance of optimal TyG index control earlier in life.

Dynamic changes in the food-cue processing of obese adolescents: A controlled eye-tracking study from a dual-system perspective.

Adolescent obesity is a growing global health problem. Studies have demonstrated that exposure to food cues plays a role in both the development and the persistence of obesity. Understanding how visual attention changes dynamically in response to food cues may explain how they contribute to obesity. The primary aims were to evaluate attentional bias for food cues and conduct a time-course analysis of obese adolescents' food-cue processing. We also investigated the roles of inhibition, cognitive flexibility, and eating styles in their visual attention to food stimuli. A total of 60 age- and gender-matched 12-16-year-olds (n = 30, obese group; n = 30, control group; M = 13.9 years, SD = 1.26) were included in this study's sample. The participants viewed a series of high-calorie and low-calorie food images along with nonfood images in the free exploration paradigm during eye-tracking. Time-course analysis of the proportion of fixations on images of food and high-calorie foods determined that the attentional processing of the two groups differed, especially in later stages. The obese group had higher Stroop Interference and Trail Making Test-B scores than the control group, but these executive functions' scores did not affect their proportions of fixations on food and high-calorie food images over time. Higher Perceptual Reasoning Index scores led to a decrease in the proportions of fixations on high-calorie food images over time in the obese group, and this was particularly noticeable after about 4000 ms. This study found that time-course analysis of visual attention to food cues allows us to understand how it changes dynamically over larger time intervals. Future studies should provide knowledge about maintained attention for food cues and their relationship with top-down factors in obese adolescents.

Analysis of intestinal immunity and flora in a collagen-induced mouse arthritis model: differences during arthritis progression.

Intestinal immunity and flora are reported to be associated with the onset of rheumatoid arthritis. However, differences in the intestinal immunity and flora dynamics between the initial peak and relapse of arthritis have not been investigated. Here we analyzed the lymphocyte populations in different lymphoid tissues, the IgA in feces, and the intestinal flora at the initial peak and the relapse phase of arthritis in a collagen-induced arthritis (CIA) mouse model. In this model compared with the control group, the percentage of RORγt+CD4+ T cells in the mesenteric lymph nodes (mLN) was increased at the initial peak but decreased at the relapse stage of arthritis, and the opposite changes were observed in the spleen. The percentage of Foxp3+CD4+ T cells was unchanged at the initial peak in both tissues but increased only in the mLN at the relapse stage. The IgA in feces increased with the progression of arthritis, and bacterial analysis revealed that some specific bacterial families were changed at the peak and relapse stages of arthritis. Finally, the immune dynamics under different arthritic conditions were examined by integrating these factors using principal component analysis (PCA). PCA showed that the immunological and intestinal flora profiles were different between the initial peak and the relapse of the arthritis. Our findings suggest that the intestinal immunity and the environment change drastically with the progress of arthritis.

In vitro versus in vivo models of kidney fibrosis: Time-course experimental design is crucial to avoid misinterpretations of gene expression data.

BACKGROUND: In vitro models are common tools in nephrology research. However, their validity has rarely been scrutinized. MATERIALS AND METHODS: Considering the critical role of transforming growth factor (TGF)-ß and hypoxia pathways in kidney fibrosis, kidney-derived cells were exposed to TGF-ß and/or hypoxic conditions and the expression levels of some genes related to these two signaling pathways were quantified in a time-course manner. Furthermore, a unilateral ureteral obstruction mouse model was generated, and the expressions of the same genes were assessed. RESULTS: In all in vitro experimental groups, the expression of the genes was noisy with no consistent pattern. However, in the animal model, TGF-ß pathway-related genes demonstrated considerable overexpression in the ureteral obstruction group compared with the sham controls. Interestingly, hypoxia pathway genes had prominent fluctuations with very similar patterns in both animal groups, suggesting a periodical pattern not affected by the intervention. CONCLUSION: The findings of this study suggest that in vitro findings should be interpreted cautiously and if possible are substituted or supported by animal models that are more consistent and reliable. Furthermore, we underscore the importance of time-course evaluation of both case and control groups in gene expression studies to avoid misconceptions caused by gene expression noise or intrinsic rhythms.

The gene expression and immunohistochemical time-course of diphenylcyclopropenone-induced contact allergy in healthy humans following repeated epicutaneous challenges.

The gene expression time-course of repeated challenge of contact allergy (CA) remains largely unknown. Therefore, using diphenylcyclopropenone (DPCP) as model allergen in healthy humans we set out to examine: (i) the monotonous and complex gene expression time-course trajectories following repeated DPCP challenges to find the predominant gene expression pattern, (ii) the time-course of cell infiltration following repeated DPCP challenges and (iii) the transcriptome of a repeated CA exposure model. We obtained punch biopsies from control and DPCP-exposed skin from ten DPCP sensitized individuals at 5-6 monthly elicitation challenges. Biopsies were used for microarray gene expression profiling, histopathology and immunohistochemical staining. Validation of microarray data by qRT-PCR was performed on 15 selected genes. Early gene expression time points were also validated in an independent data set. An increasing and decreasing trend in gene expression followed by a plateau was predominantly observed during repeated DPCP challenges. Immune responses reached a plateau after two challenges histopathologically, immunohistochemically and in the time-course gene expression analysis. Transcriptional responses over time revealed a Th1/Th17 polarization as three upstream regulators (IFN-γ, IL-1 and IL-17) activated most of the top upregulated genes. Of the latter genes, 9 of 10 were the same throughout the time course. Excellent correlations between array and PCR data were observed. The transcriptional responses to DPCP over time followed a monotonous pattern. This response pattern confirms and supports the newly reported clinical time-course observations in de novo-sensitized individuals showing a plateau response, and thus, there is concordance between clinical response, histopathology, immunohistochemistry and microarray gene expression in volunteers de novo-sensitized to DPCP.

Pupillary dilation response to the auditory food words in adolescents with obesity without binge eating disorder.

Childhood obesity is a growing global public health problem. Studies suggest that environmental cues contribute to developing and maintaining obesity. We aimed to evaluate pupillary changes to auditory food words vs. nonfood words and to conduct a dynamic temporal analysis of pupil size changes in adolescents with obesity without binge eating disorder by comparing healthy-weight adolescents. In this study, a total of 63 adolescents aged 12-18 years (n = 32, obesity group (OG); n = 31, control group (CG)) were included. In an auditory paradigm, participants were presented with a series of high and low-calorie food and nonfood words. A binocular remote eye-tracking device was used to measure pupil diameter. Generalized additive mixed models (GAMMs) were used for dynamic temporal analysis of pupillometry data. The results of GAMM analysis indicated that CG had larger pupil dilation than the OG while listening to auditory food words. CG had larger pupil dilation in food words than in nonfood words. However, the OG had a similar pupillary response in food and nonfood words. Pupil dilation response to higher-calorie foods was extended over the later stages of the time period (after 2000 ms) in the OG. In summary, our findings indicated that individuals with obesity had lower pupil dilation to auditory food words compared to normal-weight peers. Adolescents with obesity had prolonged pupillary dilation in higher calories of food words. The individual psychological factors affecting the dynamic changes of pupil responses to food cues in adolescents with obesity should be examined in further studies.

Inhibition of anaerobic digestion by various ammonia sources resulted in subtle differences in metabolite dynamics.

The impact of ammonia on anaerobic digestion performance and microbial dynamics has been extensively studied, but the concurrent effect of anions brought by ammonium salt should not be neglected. This paper studied this effect using metabolomics and a time-course statistical framework. Metabolomics provides novel perspectives to study microbial processes and facilitates a more profound understanding at the metabolic level. The advanced statistical framework enables deciphering the complexity of large metabolomics data sets. More specifically, a series of lab-scale batch reactors were set up with different ammonia sources added. Samples of nine time points over the degradation were analyzed with liquid chromatography-mass spectrometry. A filtering procedure was applied to select the promising metabolomic peaks from 1262 peaks, followed by modeling their intensities across time. The metabolomic peaks with similar time profiles were clustered, evidencing the correlation of different biological processes. Differential analysis was performed to seek the differences in metabolite dynamics caused by different anions. Finally, tandem mass spectrometry and metabolite annotation provided further information on the molecular structure and possible metabolic pathways. For example, the consumption of 5-aminovaleric acid, a short-chain fatty acid obtained from l-lysine degradation, was slowed down by phosphates. Overall, by investigating the effect of anions on anaerobic digestion, our study demonstrated the effectiveness of metabolomics in providing detailed information in a set of samples from different experimental conditions. With the statistical framework, the approach enables capturing subtle differences in metabolite dynamics between samples while accounting for the differences caused by time variations.

Temporal dynamics of positive emotion regulation: insights from facial electromyography.

Introduction: Emotion regulation (ER) is a complex process that manifests gradually over time. This study investigated the temporal dynamics of ER in modifying positive emotions in terms of both negative affect (NA) and positive affect (PA) dimensions. Methods: After participants had been exposed to pleasant pictures for 8,000 ms, they received instructions to either continue viewing the picture (no regulation) or reappraise it with a neutral meaning (neutralize goal) or negative meaning (transform goal) for another 8,000 ms. We obtained corrugator supercilii and zygomaticus major electromyography (EMG) as objective measures of NA and PA. Results: For the no-regulation condition, upon instruction onset, we observed maintained low levels of corrugator and high levels of zygomaticus EMG reactivity, indicating sustained PA activation. Compared to the no-regulation condition, for the neutralize goal, we observed no change in corrugator reactivity, which remained at a low level, while zygomaticus reduction started at 1,000 ms after instruction onset, indicating decreased PA and generation of a neutral emotional state. For the transform goal, we observed corrugator increase and zygomaticus decrease both starting at 1,500 ms after instruction onset and co-existing throughout the regulation period. These results indicate increased NA and decreased PA, relating to generation of a negative emotional state. The transform goal differed from the neutralize goal in terms of corrugator increase starting at 2,500 ms after instruction onset. Albeit simultaneous onset of changes on corrugator and zygomaticus reactivity under the transform goal, model-fitting analyses indicated that the best-fitting trajectory was one that first emphasized PA reduction until, at 3,000 ms, it turned into primary NA increase. Discussion: These distinct temporal patterns highlight the possibility of effecting one-dimensional PA change with the neutralize goal and sequential two-dimensional change (first decreasing PA, then increasing NA) with the transform goal. This research sheds light on the time course of emotional change brought about by different regulatory goals.

Long-term adaptation of Saccharomyces cerevisiae to the burden of recombinant insulin production.

High-level production of heterologous proteins is likely to impose a metabolic burden on the host cell and can thus affect various aspects of cellular physiology. A data-driven approach was applied to study the secretory production of a human insulin analog precursor (IAP) in Saccharomyces cerevisiae during prolonged cultivation (80 generations) in glucose-limited aerobic chemostat cultures. Physiological characterization of the recombinant cells involved a comparison with cultures of a congenic reference strain that did not produce IAP, and time-course analysis of both strains aimed at identifying the metabolic adaptation of the cells towards the burden of IAP production. All cultures were examined at high cell density conditions (30 g/L dry weight) to increase the industrial relevance of the results. The burden of heterologous protein production in the recombinant strain was explored by global transcriptome analysis and targeted metabolome analysis, including the analysis of intracellular amino acid pools, glycolytic metabolites, and TCA intermediates. The cellular re-arrangements towards IAP production were categorized in direct responses, for example, enhanced metabolism of amino acids as precursors for the formation of IAP, as well as indirect responses, for example, changes in the central carbon metabolism. As part of the long-term adaptation, a metabolic re-modeling of the IAP-expressing strain was observed, indicating an augmented negative selection pressure on glycolytic overcapacity, and the emergence of mitochondrial dysfunction. The evoked metabolic re-modeling of the cells led to less optimal conditions with respect to the expression and processing of the target protein and thus decreased the cellular expression capacity for the secretory production of IAP during prolonged cultivation.

Early signaling of inflammation in patients following traumatic injury with accurately estimated time of injury by profiling C-reactive protein levels.

BACKGROUND: Despite its widespread use, the precise dynamics of CRP response in clinical practice remain poorly defined. We employed a novel quadratic model to explore the time-course analysis of CRP values in trauma patients with known precise time of injury. METHODS: Relevant data on all adult patients admitted to our hospital following traumatic incidents between January 1st 2010 to December 31, 2020 were retrospectively collected. Those with a documented time of injury and who underwent CRP evaluation within the first 24 h since injury were studied. RESULTS: Based on the findings from our annual health check-up center, we established a reference upper normal CRP value of 12.99 mg/L. Within the first 7 h after injury, the CRP levels of 8-9% of the 1545 study patients exceeded the reference threshold. The proportion of patients with CRP levels > 12.99 mg/L increased to 18.5% at 8-9 h later and rose sharply to 91.6% at 22-24 h later. Our quadratic model yielded the equation: CRP = 5.122-0.528xTime + 0.139xTime 2. It accounted for > 40% of the variance in CRP levels (R2 = 42.4%). CONCLUSIONS: Clear and prominent CRP elevations following atraumatic event are detected only 9-12 h following the insult. This novel finding has crucial implications for accurate CRP assessment of inflammatory responses to physical injuries.

Understanding the transcriptomic response of Lactiplantibacillus pentosus LPG1 during Spanish-style green table olive fermentations.

Lactiplantibacillus pentosus (Lbp. pentosus) is a species of lactic acid bacteria with a great relevance during the table olive fermentation process, with ability to form non-pathogenic biofilms on olive epidermis. The objective of this work is to deepen into the genetic mechanisms of adaptation of Lpb. pentosus LPG1 during Spanish-style green table olive fermentations, as well as to obtain a better understanding of the mechanisms of adherence of this species to the fruit surface. For this purpose, we have carried out a transcriptomic analysis of the differential gene expression of this bacterium during 60 days of fermentation in both brine and biofilms ecosystems. In brines, it was noticed that a total of 235 genes from Lpb. pentosus LPG1 were differentially expressed during course of fermentation and grouped into 9 clusters according to time-course analysis. Transport and metabolism of carbohydrates and amino acids, energy production, lactic acid and exopolysaccharide synthesis genes increased their expression in the planktonic cells during course of fermentation. On the other hand, expression of genes associated to stress response, bacteriocin synthesis and membrane protein decreased. A total of 127 genes showed significant differential expression between Lpb. pentosus LPG1 planktonic (brine) and sessile (biofilms) cells at the end of fermentation process (60 days). Among the 64 upregulated genes in biofilms, we found genes involved in adhesion (strA), exopolysaccharide production (ywqD, ywqE, and wbnH), cell shape and elongation (MreB), and well as prophage excision. Deeping into the genetic bases of beneficial biofilm formation by Lpb. pentosus strains with probiotic potential will help to turn this fermented vegetable into a carrier of beneficial microorganisms to the final consumers.

Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.

Background: Single-cell RNA sequencing (scRNA-seq) technologies have rapidly developed in recent years. The droplet-based single cell platforms enable the profiling of gene expression in tens of thousands of cells per sample. The goal of a typical scRNA-seq analysis is to identify different cell subpopulations and their respective marker genes. Additionally, trajectory analysis can be used to infer the developmental or differentiation trajectories of cells. Methods: This article demonstrates a comprehensive workflow for performing trajectory inference and time course analysis on a multi-sample single-cell RNA-seq experiment of the mouse mammary gland. The workflow uses open-source R software packages and covers all steps of the analysis pipeline, including quality control, doublet prediction, normalization, integration, dimension reduction, cell clustering, trajectory inference, and pseudo-bulk time course analysis. Sample integration and cell clustering follows the Seurat pipeline while the trajectory inference is conducted using the monocle3 package. The pseudo-bulk time course analysis uses the quasi-likelihood framework of edgeR. Results: Cells are ordered and positioned along a pseudotime trajectory that represented a biological process of cell differentiation and development. The study successfully identified genes that were significantly associated with pseudotime in the mouse mammary gland. Conclusions: The demonstrated workflow provides a valuable resource for researchers conducting scRNA-seq analysis using open-source software packages. The study successfully demonstrated the usefulness of trajectory analysis for understanding the developmental or differentiation trajectories of cells. This analysis can be applied to various biological processes such as cell development or disease progression, and can help identify potential biomarkers or therapeutic targets.

Child emotion lability is associated with within-task changes of autonomic activity during a mirror-tracing task.

Adaptive biological and emotional stress responding are both critical for healthy human development. However, the complex associations between the two are not fully understood. The current study addresses this gap in research by studying associations of child emotion regulation and lability with within-task changes in the biological stress response during a mirror-tracing task. Participants were 59 families including two parents and a child between 5 and 12 years old (52.2% female). Parents reported on family demographics and completed the Emotion Regulation Checklist. Child skin conductance level (SCL) and respiratory sinus arrhythmia (RSA) were recorded during a baseline task and during a 3-minute mirror-tracing task. Within-task patterns of SCL and RSA during the task were estimated with multilevel modeling (measures within persons). The emotion regulation subscale was unrelated to any facet of SCL/RSA time courses. However, lower emotion lability was related to SCL patterns that changed less during the task and were overall lower. For RSA, lower emotion lability was related to higher initial RSA that significantly decreased during the task. These findings suggest that higher child emotion lability may promote increased physiological arousal of target organs during challenging activities.

Dual RNA-Seq Profiling Unveils Mycoparasitic Activities of Trichoderma atroviride against Haploid Armillaria ostoyae in Antagonistic Interaction Assays.

Armillaria ostoyae, a species among the destructive forest pathogens from the genus Armillaria, causes root rot disease on woody plants worldwide. Efficient control measures to limit the growth and impact of this severe underground pathogen are under investigation. In a previous study, a new soilborne fungal isolate, Trichoderma atroviride SZMC 24276 (TA), exhibited high antagonistic efficacy, which suggested that it could be utilized as a biocontrol agent. The dual culture assay results indicated that the haploid A. ostoyae-derivative SZMC 23085 (AO) (C18/9) is highly susceptible to the mycelial invasion of TA. In the present study, we analyzed the transcriptome of AO and that of TA in in vitro dual culture assays to test the molecular arsenal of Trichoderma antagonism and the defense mechanisms of Armillaria. We conducted time-course analysis and functional annotation and analyzed enriched pathways and differentially expressed genes including biocontrol-related candidate genes from TA and defense-related candidate genes from AO. The results indicated that TA deployed several biocontrol mechanisms when confronted with AO. In response, AO initiated multiple defense mechanisms to protect against the fungal attack. To our knowledge, the present study offers the first transcriptome analysis of a biocontrol fungus attacking AO. Overall, this study provides insights that aid the further exploration of plant pathogen-biocontrol agent interaction mechanisms. IMPORTANCE Armillaria species can survive for decades in the soil on dead woody debris, develop rapidly under favorable conditions, and harmfully infect newly planted forests. Our previous study found Trichoderma atroviride to be highly effective in controlling Armillaria growth; therefore, our current work explored the molecular mechanisms that might play a key role in Trichoderma-Armillaria interactions. Direct confrontation assays combined with time course-based dual transcriptome analysis provided a reliable system for uncovering the interactive molecular dynamics between the fungal plant pathogen and its mycoparasitic partner. Furthermore, using a haploid Armillaria isolate allowed us to survey the deadly prey-invading activities of the mycoparasite and the ultimate defensive strategies of its prey. Our current study provides detailed insights into the essential genes and mechanisms involved in Armillaria defense against Trichoderma and the genes potentially involved in the efficiency of Trichoderma to control Armillaria. In addition, using a sensitive haploid Armillaria strain (C18/9), with its complete genome data already available, also offers the opportunity to test possible variable molecular responses of Armillaria ostoyae toward diverse Trichoderma isolates with various biocontrol abilities. Initial molecular tests of the dual interactions may soon help to develop a targeted biocontrol intervention with mycoparasites against plant pathogens.

Multi-time scale transcriptomic analysis on the dynamic process of tamoxifen resistance development in breast cancer cell lines.

BACKGROUND: Approximately 30% of breast cancer patients develop endocrine resistance after tamoxifen therapy. There still lacks a comprehensive understanding on the mechanism of tamoxifen resistance. This study aims to explore the dynamic process of ER + breast cancer resistance to tamoxifen through the time course transcriptomic analysis. METHODS: The transcriptome profiles of human breast cancer cell line MCF-7 treated with tamoxifen at different time scales were collected from LINCS, SRA and GEO databases. Differentially expressed genes (DEGs) were identified in the short-term tamoxifen treatment and tamoxifen-resistant cell lines. The time course analysis was used to explore the dynamic development of tamoxifen resistance using the transcriptome profiles of tamoxifen-cultured MCF-7 for 1-12 weeks. RESULTS: After the short-term treatment of MCF-7 with tamoxifen for 6 h or 24 h, the expression level of gene PRSS23 was significantly reduced. However, its expression recovered in the resistant cell lines. The time course analysis identified 9 clusters of the DEGs based on the temporal trend of their expression levels. Gene PRSS23 belongs to cluster 2 in which the expression levels were significantly down-regulated in the first 4 weeks but gradually recovered afterwards. Functional enrichment analysis of the DEGs in cluster 2 showed that they are significantly enriched in DNA replication, mismatch repair and cell cycle pathways. Their specific role in the resistance development needs to be further explored. The protein-protein interaction network analysis indicates that gene PRSS23 participates in the drug resistance by regulating multiple tamoxifen drug targets. CONCLUSIONS: The acquired drug resistance in ER + breast cancer is a complex and dynamic biological process. PRSS23 plays an important role in the development of resistance and is a potential target for overcoming resistance.

Implicitly learning when to be ready: From instances to categories.

There is growing appreciation for the role of long-term memory in guiding temporal preparation in speeded reaction time tasks. In experiments with variable foreperiods between a warning stimulus (S1) and a target stimulus (S2), preparation is affected by foreperiod distributions experienced in the past, long after the distribution has changed. These effects from memory can shape preparation largely implicitly, outside of participants' awareness. Recent studies have demonstrated the associative nature of memory-guided preparation. When distinct S1s predict different foreperiods, they can trigger differential preparation accordingly. Here, we propose that memory-guided preparation allows for another key feature of learning: the ability to generalize across acquired associations and apply them to novel situations. Participants completed a variable foreperiod task where S1 was a unique image of either a face or a scene on each trial. Images of either category were paired with different distributions with predominantly shorter versus predominantly longer foreperiods. Participants displayed differential preparation to never-before seen images of either category, without being aware of the predictive nature of these categories. They continued doing so in a subsequent Transfer phase, after they had been informed that these contingencies no longer held. A novel rolling regression analysis revealed at a fine timescale how category-guided preparation gradually developed throughout the task, and that explicit information about these contingencies only briefly disrupted memory-guided preparation. These results offer new insights into temporal preparation as the product of a largely implicit process governed by associative learning from past experiences.

Cherry Blossom Forecast Based on Transcriptome of Floral Organs Approaching Blooming in the Flowering Cherry (Cerasus × yedoensis) Cultivar 'Somei-Yoshino'.

To gain insights into the genetic mechanisms underlying blooming and petal movement in flowering cherry (Cerasus × yedoensis), we performed time-course RNA-seq analysis of the floral buds and open-flowers of the most popular flowering cherry cultivar, 'Somei-Yoshino.' Independent biological duplicate samples of floral buds and open-flowers were collected from 'Somei-Yoshino' trees grown at three different locations in Japan. RNA-seq reads obtained from floral bud and open-flower samples collected in the current study (in 2019) and in a previous study (in 2017) were aligned against the genome sequence of 'Somei-Yoshino' to quantify gene transcript levels. Clustering analysis of RNA-seq reads revealed dynamic changes in the transcriptome, with genes in seven modules predominantly expressed at specific time points, ranging from 5 weeks before flowering to 2 weeks after flowering. Based on the identified gene modules and Gene Ontology (GO) terms enriched at different floral stages, we speculate that the genetic mechanisms underlying petal movement and flower opening in cherry involve the processes of development, cell wall organization, reproduction, and metabolism, which are executed by genes encoding transcription factors, phytohormones, transporters, and polysaccharide metabolic enzymes. Furthermore, we established a statistical model for cherry bloom forecasting, based on gene expression levels as RNA markers at different time points before flowering.