Optimization of Fermentation Process for New Anti-Inflammatory Glycosylceramide Metabolite from Aspergillus sp.

A novel ceramide compound, named Aspercerebroside A (AcA), was successfully isolated from the ethyl acetate layer of the marine symbiotic fungus Aspergillus sp. AcA exhibited notable anti-inflammatory activity by effectively inhibiting the production of nitric oxide (NO) in RAW 264.7 cells at concentrations of 30 µg/mL and 40 µg/mL, offering a promising avenue for the treatment of inflammatory diseases. To optimize the yield of glycosylceramide (AcA), a series of techniques, including single-factor experiments, orthogonal experiments, and response surface optimization, were systematically employed to fine-tune the composition of the fermentation medium. Initially, the optimal carbon source (sucrose), nitrogen source (yeast extract powder), and the most suitable medium salinity (14 ppt) were identified through single-factor experiments. Subsequently, orthogonal experiments, employing an orthogonal table for planning and analyzing multifactor experiments, were conducted. Finally, a mathematical model, established using a Box-Behnken design, comprehensively analyzed the interactions between the various factors to determine the optimal composition of the fermentation medium. According to the model's prediction, when the sucrose concentration was set at 37.47 g/L, yeast extract powder concentration at 19.66 g/L, and medium salinity at 13.31 ppt, the predicted concentration of glycosylceramide was 171.084 µg/mL. The experimental results confirmed the model's accuracy, with the actual average concentration of glycosylceramide under these conditions measured at 171.670 µg/mL, aligning closely with the predicted value.

Insights into brain perceptions of the different taste qualities and hedonic valence of food via scalp electroencephalogram.

Investigating brain activity is essential for exploring taste-experience related cues. The paper aimed to explore implicit (unconscious) emotional or physiological responses related to taste experiences using scalp electroencephalogram (EEG). We performed implicit measures of tastants of differing perceptual types (bitter, salty, sour and sweet) and intensities (low, medium, and high). The results showed that subjects were partially sensitive to different sensory intensities, i.e., for high intensities, taste stimuli could induce activation of different rhythm signals in the brain, with α and θ bands possibly being more sensitive to different taste types. Furthermore, the neural representations and corresponding sensory qualities (e.g., "sweet: pleasant" or "bitter: unpleasant") of different tastes could be discriminated at 250-1,500 ms after stimulus onset, and different tastes exhibited distinct temporal dynamic differences. Source localization indicated that different taste types activate brain areas associated with emotional eating, reward processing, and motivated tendencies, etc. Overall, our findings reveal a larger sophisticated taste map that accounted for the diversity of taste types in the human brain and assesses the emotion, reward, and motivated behavior represented by different tastes. This study provided basic insights and a perceptual foundation for the relationship between taste experience-related decisions and the prediction of brain activity.

Control of the antitumour activity and specificity of CAR T cells via organic adapters covalently tethering the CAR to tumour cells.

On-target off-tumour toxicity limits the anticancer applicability of chimaeric antigen receptor (CAR) T cells. Here we show that the tumour-targeting specificity and activity of T cells with a CAR consisting of an antibody with a lysine residue that catalytically forms a reversible covalent bond with a 1,3-diketone hapten can be regulated by the concentration of a small-molecule adapter. This adapter selectively binds to the hapten and to a chosen tumour antigen via a small-molecule binder identified via a DNA-encoded library. The adapter therefore controls the formation of a covalent bond between the catalytic antibody and the hapten, as well as the tethering of the CAR T cells to the tumour cells, and hence the cytotoxicity and specificity of the cytotoxic T cells, as we show in vitro and in mice with prostate cancer xenografts. Such small-molecule switches of T-cell cytotoxicity and specificity via an antigen-independent 'universal' CAR may enhance the control and safety profile of CAR-based cellular immunotherapies.

Brain activity differences between susceptible and non-susceptible populations under visually induced motion sickness based on sensor-space and source-space analyses.

The neural mechanisms underlying visually induced motion sickness (VIMS) in different susceptible populations are unclear, as it is not clear how brain activity changes in different susceptible populations during the vection section (VS). This study aimed to analyze the brain activity changes in different susceptible populations during VS. Twenty subjects were included in this study and divided into the VIMS-susceptible group (VIMSSG) and VIMS-resistant group (VIMSRG) based on a motion sickness questionnaire. 64-channel electroencephalogram (EEG) data from these subjects during VS were collected. The brain activities during VS for VIMSSG and VIMSRG were analyzed with time-frequency based sensor-space analysis and EEG source imaging based source-space analysis. Under VS, delta and theta energies were significantly increased in VIMSSG and VIMSRG, while alpha and beta energies were only significantly increased in VIMSRG. Also, the superior and middle temporal were activated in VIMSSG and VIMSRG, while lateral occipital, supramarginal gyrus, and precentral gyrus were activated only in VIMSSG. The spatiotemporal differences in brain activity observed between VIMSSG and VIMSRG may be attributed to the different susceptibility of participants in each group and the different severity of MS symptoms experienced. Long-term vestibular training can effectively improve the ability of anti-VIMS. The knowledge gained from this study helps advance understanding of the neural mechanism of VIMS in different susceptible populations.

The potential roles of gut microbiome in anal fistula.

Anal fistula is a common proctological disease, but the thorough mechanisms of the anal fistula formation are still unclear. An increasing number of studies have revealed the crucial role of gut microbiota in intestinal diseases. We used 16S rRNA gene sequencing to analyze the intestinal microbiome in order to determine whether there are differences in the microbiome between anal fistula patients and healthy individuals. The microbiome samples were extracted by repeatedly wiping the rectal wall with intestinal swab. Before this operation, the whole intestine of all participants was irrigated and the score of the Boston bowel preparation scale reached 9. The biodiversity of gut microbiome of rectum revealed significant difference between anal fistula patients and healthy individuals. 36 discriminative taxa were identified by LEfSe analysis between two groups. At the phylum level, Synergistetes was enriched in anal fistula patients, while Proteobacteria was higher in healthy individuals. We also found that at the genus level, Blautia, Faecalibacterium, Ruminococcus, Coprococcus, Bacteroides, Clostridium, Megamonas and Anaerotruncus were highly enriched in anal fistula patients, while the microbiome of healthy individuals was enriched with Peptoniphilus and Corynebacterium. Spearman correlations showed the extensive and close association among genera and species. Finally, a diagnostic prediction model was constructed by random forest classifier, and the area under curve (AUC) reached 0.990. This study gave an important hint for analyzing gut microbiome of rectum in anal fistula patient.Keypoints.We use the 16S rRNA gene sequencing to test the microbiome samples extracted from the intestinal swab. This is the first study to explore the gut microbiome of rectum using this workflow. We also found the distinct gut microbiome of rectum differences between anal fistula patients and healthy individuals.

The effect of TENS on sleep: A pilot study.

BACKGROUND: Insomnia is the second most common neuropsychiatric disorder, but the current treatments are not very effective. There is therefore an urgent need to develop better treatments. Transcutaneous electrical nerve stimulation (TENS) may be a promising means of treating insomnia. OBJECTIVE: This work aims to explore whether and how TENS modulate sleep and the effect of stimulation waveforms on sleep. METHODS: Forty-five healthy subjects participated in this study. Electroencephalography (EEG) data were recorded before and after four mode low-frequency (1 Hz) TENS with different waveforms, which were formed by superimposing sine waves of different high frequencies (60-210 Hz) and low frequencies (1-6 Hz). The four waveform modes are formed by combining sine waves of varying frequencies. Mode 1 (M1) consists of a combination of high frequencies (60-110 Hz) and low frequencies (1-6 Hz). Mode 2 (M2) is made up of high frequencies (60-210 Hz) and low frequencies (1-6 Hz). Mode 3 (M3) consists of high frequencies (110-160 Hz) and low frequencies (1-6 Hz), while mode 4 (M4) is composed of high frequencies (160-210 Hz) and low frequencies (1-6 Hz). For M1, M3 and M4, the high frequency portions of the stimulus waveforms account for 50%, while for M2, the high frequency portion of the waveform accounts for 65%. For each mode, the current intensities ranged from 4 mA to 7 mA, with values for each participant adjusted according to individual tolerance. During stimulation, the subjects were stimulated at the greater occipital nerve by the four mode TENS. RESULTS: M1, M3, and M4 slowed down the frequency of neural activity, broadened the distribution of theta waves, and caused a decrease in activity in wakefulness-related regions and an increase in activity in sleep-related regions. However, M2 has the opposite modulation effect. CONCLUSION: These results indicated that low-frequency TENS (1 Hz) may facilitate sleep in a waveform-specific manner. Our findings provide new insights into the mechanisms of sleep modulation by TENS and the design of effective insomnia treatments.

Economic growth and household energy footprint inequality in China.

There are significant differences in energy footprints among individual households. This study uses an environmentally extended input-output approach to estimate the per capita household energy footprint (PCHEF) of 10 different income groups in China's 30 provinces and analyzes the heterogeneity of household consumption categories, and finally measures the energy equality of households in each province by measuring the energy footprint Gini coefficient (EF-Gini). It is found that the energy footprint of the top 10% income households accounted for about 22% of the national energy footprint in 2017, while the energy footprint of the bottom 40% income households accounted for only 24%. With the growth of China's economy, energy footprint inequality has declined spatially and temporally. Firstly, wealthier coastal regions have experienced greater convergence in their energy footprint than poorer inland regions. Secondly, China's household EF-Gini has declined from 0.38 in 2012 to 0.36 in 2017. This study shows that China's economic growth has not only raised household income levels, but also reduced energy footprint inequality.

Effect of microgravity on mechanical loadings in lumbar spine at various postures: a numerical study.

The aim of this study was to quantitatively analyze the mechanical change of spinal segments (disc, muscle, and ligament) at various postures under microgravity using a full-body musculoskeletal modeling approach. Specifically, in the lumbar spine, the vertebra were modeled as rigid bodies, the intervertebral discs were modeled as 6-degree-of-freedom joints with linear force-deformation relationships, the disc swelling pressure was deformation dependent, the ligaments were modeled as piecewise linear elastic materials, the muscle strength was dependent on its functional cross-sectional area. The neutral posture and the "fetal tuck" posture in microgravity (short as "Neutral 0G" and "Fetal Tuck 0G", in our simulation, the G constant was set to 0 for simulating microgravity), and for comparison, the relaxed standing posture in 1G and 0G gravity (short as "Neutral 1G" and "Standing 0G") were simulated. Compared to values at Neutral 1G, the mechanical response in the lower spine changed significantly at Neutral 0G. For example, the compressive forces on lumbar discs decreased 62-70%, the muscle forces decreased 55.7-92.9%, while disc water content increased 7.0-10.2%, disc height increased 2.1-3.0%, disc volume increased 6.4-9.3%, and ligament forces increased 59.5-271.3% at Neutral 0G. The fetal tuck 0G reversed these changes at Neutral 0G back toward values at Neutral 1G, with magnitudes much larger than those at Neutral 1G. Our results suggest that microgravity has significant influences on spinal biomechanics, alteration of which may increase the risks of disc herniation and degeneration, muscle atrophy, and/or ligament failure.

Evaluation method of ex vivo porcine liver reduced scattering coefficient during microwave ablation based on temperature.

The principle of microwave ablation (MWA) is to cause irreversible damage (protein coagulation, necrosis, etc.) to tumor cells at a certain temperature by heating, thereby destroying the tumor. We have long used functional near-infrared spectroscopy (fNIRs) to monitor clinical thermal ablation efficacy. After a lot of experimental verification, it can be found that there is a clear correlation between the reduced scattering coefficient and the degree of tissue damage. During the MWA process, the reduced scattering coefficient has a stable change. Therefore, both temperature (T) and reduced scattering coefficient ( µ s ' ) are related to the thermal damage of the tissue. This paper mainly studies the changing law of T and µ s ' during MWA and establishes a relationship model. The two-parameter simultaneous acquisition system was designed and used to obtain the T and µ s ' of the ex vivo porcine liver during MWA. The correlation model between T and µ s ' is established, enabling the quantitative estimation of µ s ' of porcine liver based on T. The maximum and the minimum relative errors of µ s ' are 79.01 and 0.39%, respectively. Through the electromagnetic simulation of the temperature field during MWA, 2D and 3D fields of reduced scattering coefficient can also be obtained using this correlation model. This study contributes to realize the preoperative simulation of the optical parameter field of microwave ablation and provide 2D/3D therapeutic effect for clinic.

Phenotype Identification of HeLa Cells Knockout CDK6 Gene Based on Label-Free Raman Imaging.

Identifying cell phenotypes is essential for understanding the function of biological macromolecules and molecular biology. We developed a noninvasive, label-free, single-cell Raman imaging analysis platform to distinguish between the cell phenotypes of the HeLa cell wild type (WT) and cyclin-dependent kinase 6 (CDK6) gene knockout (KO) type. Via large-scale Raman spectral and imaging analysis, two phenotypes of the HeLa cells were distinguished by their intrinsic biochemical profiles. A significant difference was found between the two cell lines: large lipid droplets formed in the knockout HeLa cells but were not observed in the WT cells, which was confirmed by Oil Red O staining. The band ratio of the Raman spectrum of saturated/unsaturated fatty acids was identified as the Raman spectral marker for HeLa cell WT or gene knockout type differentiation. The interaction between organelles involved in lipid metabolism was revealed by Raman imaging and Lorentz fitting, where the distribution intensity of the mitochondria and the endoplasmic reticulum membrane decreased. At the same time, lysosomes increased after the CDK6 gene knockout. The parameters obtained from Raman spectroscopy are based on hierarchical cluster analysis and one-way ANOVA, enabling highly accurate cell classification.

Effect of lumbar muscle atrophy on the mechanical loading change on lumbar intervertebral discs.

The objective of this study was to quantitatively analyze the effect of lumbar spinal muscle atrophy on the compressive (perpendicular to the upper surface of the disc) and shear (parallel to the upper surface of the disc in the anterior-posterior direction) forces change on lumbar intervertebral discs using a full body musculoskeletal modeling approach. Muscles atrophy was modeled with reduction of the functional cross-sectional area (FCSA) of the muscles. Compressive and shear forces under two levels of lumbar muscle atrophy (20% and 40%) at eight daily postures (lying on back, seating slouched, seating straight, standing, standing flexed (36°), standing lift a 20 kg weight close to chest, standing lift a 20 kg weight flexed (38°), and standing lift a 20 kg weight with arm stretched) were analyzed. There was small increase in compressive forces on lumbar discs with muscle atrophy at most postures except lying and sitting straight. The maximum increase of compressive forces on lumbar discs were 23 N (6%), 28 N (5%), 34 N (2%), 71 N (6%), 89 N (4%), and 190 N (10%) with 20% atrophy, and 66 N (19%), 77 N (12%), 98 N (6%), 169 N (14%), 256 N (12%), 501 N (24%) with 40% atrophy at seating slouched, standing, standing flexed, standing lift close, standing lift flexed, and standing stretched arm, respectively. The shear force did not change significantly on lumbar discs with muscle atrophy. This study is important for understanding the biomechanical mechanisms of how lumbar muscle atrophy may affect the lumbar IVD health.

Research Progress of Raman Spectroscopy and Raman Imaging in Pharmaceutical Analysis.

The analytical investigation of the pharmaceutical process monitors the critical process parameters of the drug, beginning from its development until marketing and post-marketing, and appropriate corrective action can be taken to change the pharmaceutical design at any stage of the process. Advanced analytical methods, such as Raman spectroscopy, are particularly suitable for use in the field of drug analysis, especially for qualitative and quantitative work, due to the advantages of simple sample preparation, fast, non-destructive analysis speed and effective avoidance of moisture interference. Advanced Raman imaging techniques have gradually become a powerful alternative method for monitoring changes in polymorph distribution and active pharmaceutical ingredient distribution in drug processing and pharmacokinetics. Surface-enhanced Raman spectroscopy (SERS) has also solved the inherent insensitivity and fluorescence problems of Raman, which has made good progress in the field of illegal drug analysis. This review summarizes the application of Raman spectroscopy and imaging technology, which are used in the qualitative and quantitative analysis of solid tablets, quality control of the production process, drug crystal analysis, illegal drug analysis, and monitoring of drug dissolution and release in the field of drug analysis in recent years.

A comparison of directed functional connectivity among fist-related brain activities during movement imagery, movement execution, and movement observation.

Brain-computer interface (BCI) has been widely used in sports training and rehabilitation training. It is primarily based on action simulation, including movement imagery (MI) and movement observation (MO). However, the development of BCI technology is limited due to the challenge of getting an in-depth understanding of brain networks involved in MI, MO, and movement execution (ME). To better understand the brain activity changes and the communications across various brain regions under MO, ME, and MI, this study conducted the fist experiment under MO, ME, and MI. We recorded 64-channel electroencephalography (EEG) from 39 healthy subjects (25 males, 14 females, all right-handed) during fist tasks, obtained intensities and locations of sources using EEG source imaging (ESI), computed source activation modes, and finally investigated the brain networks using spectral Granger causality (GC). The brain regions involved in the three motor conditions are similar, but the degree of participation of each brain region and the network connections among the brain regions are different. MO, ME, and MI did not recruit shared brain connectivity networks. In addition, both source activation modes and brain network connectivity had lateralization advantages.

Biomimetic integrated olfactory sensory and olfactory bulb systems in vitro based on a chip.

A variety of mammalian or insect behaviors rely on the recognition of relevant odor stimuli. The olfactory system detects and translates complex olfactory stimuli (odors) through the unique and reproducible dynamic ensembles of neuronal activities. This process is involved in various types of neurons of olfactory parts, thereby encoding olfactory information or predicting progression in some neuropsychiatric diseases. In this paper, we constructed a biomimetic model including olfactory sensing system and olfactory bulb processing system to map olfactory-associated ensembles of neuronal activity. The olfactory receptor neurons (ORNs) and olfactory bulb (OB) neurons were primarily cultured and the immunofluorescence images were performed to identify the types of neurons. Diacetyl solution was used as an odor stimulus, and the spike bursts and random spike firing patterns of concentration-dependent excitatory responses were obtained from the ORNs network. The spike waveform and feature parameters were extracted including the spike number and interval in per burst to program the stimulation unit and sequences. The sequences containing odor information were applied to the OB neuronal network for the simulation of the primary olfactory processing. The response pattern and change rule of the OB neuronal network were consistent with the OB neurons affected by the neurotransmitter, which is the carrier of olfactory information transmission in vivo. This biomimetic integrated olfactory sensory and processing system can serve as a novel model for studying the physiological and pathological mechanisms of olfaction, and the pharmacological application in vitro.

Inhibition of MEIS3 Generates Cetuximab Resistance through c-Met and Akt.

INTRODUCTION: Although cetuximab has been widely used in the treatment of colon cancer, a large number of patients eventually develop drug resistance. Therefore, it is essential to clarify the mechanism of drug resistance. METHODS: In this study, we combined in silico analysis and a single guide RNA (sgRNA) library to locate cetuximab-sensitive genes. Cell proliferation, apoptosis, and cell cycle were assessed to validate the change in cetuximab sensitivity. Finally, western blotting was performed to detect changes in epidermal growth factor (EGFR) upstream and downstream genes. RESULTS: Using in silico analysis and the sgRNA library, MEIS3 was confirmed as the cetuximab-sensitive gene. Further experiments indicated that the expression of MEIS3 could determine the level of cetuximab. Meanwhile, MEIS3-inhibited cells were sensitive to mesenchymal epithelial transition factor (c-Met) and protein kinase B (Akt) inhibitors, which is related to the change in phosphorylation of c-Met and degradation of Akt. CONCLUSION: MEIS3 modified the sensitivity to cetuximab through c-Met and Akt.

Effect of intervertebral disc degeneration on mechanical and electric signals at the interface between disc and vertebra.

Intervertebral disc (IVD) degeneration is significantly correlated with the changes in structure and material properties of adjacent vertebral bone, possibly through mechanical and electrical interactions. However, the mechanisms underlying the alteration of the mechanical and electrical environment at the disc-vertebra interface related with disc degeneration have not been well studied. The objective of this study was to numerically investigate the long-term distributions of mechanical and electrical signals on the disc-vertebra interface with disc degeneration. A three-dimensional finite element model of a human lumbar IVD was used to study the mechanical and electric signals at the interface between disc and vertebral body. The disc degeneration was simulated by reducing the nutrition levels on the nucleus pulposus (NP)-vertebra interface and on the annulus fibrosus (AF) periphery to 30% and 60% of its normal values, respectively. In the simulation, the total external mechanical load applied to the disc-vertebra segment was assumed unchanged during disc degeneration. The simulation results showed that the compressive stress of solid matrix changed by up to ~37 kPa on the NP-vertebra interface, while it increased by up to ~32 kPa on the AF-vertebra interface. The shear stress increased by up to ~37 kPa with disc degeneration. The absolute value of the electric potential on the disc-vertebra interface of the disc slightly decreased with the disc degeneration (~0.5 mV). The knowledge of these spatial and temporal variations of the mechanical stresses and electric potential on the disc-vertebra interface is important for understanding the vertebrae adaptation and remodeling during disc degeneration.

Molecular Regulation of Circadian Chromatin.

Circadian rhythms are generated by transcriptional negative feedback loops and require histone modifications and chromatin remodeling to ensure appropriate timing and amplitude of clock gene expression. Circadian modifications to histones are important for transcriptional initiation and feedback inhibition serving as signaling platform for chromatin-remodeling enzymes. Current models indicate circadian-regulated facultative heterochromatin (CRFH) is a conserved mechanism at clock genes in Neurospora, Drosophila, and mice. CRFH consists of antiphasic rhythms in activating and repressive modifications generating chromatin states that cycle between transcriptionally permissive and nonpermissive. There are rhythms in histone H3 lysine 9 and 27 acetylation (H3K9ac and H3K27ac) and histone H3 lysine 4 methylation (H3K4me) during activation; while deacetylation, histone H3 lysine 9 methylation (H3K9me) and heterochromatin protein 1 (HP1) are hallmarks of repression. ATP-dependent chromatin-remodeling enzymes control accessibility, nucleosome positioning/occupancy, and nuclear organization. In Neurospora, the rhythm in facultative heterochromatin is mediated by the frequency (frq) natural antisense transcript (NAT) qrf. While in mammals, histone deacetylases (HDACs), histone H3 lysine 9 methyltransferase (KMT1/SUV39), and components of nucleosome remodeling and deacetylase (NuRD) are part of the nuclear PERIOD complex (PER complex). Genomics efforts have found relationships among rhythmic chromatin modifications at clock-controlled genes (ccg) revealing circadian control of genome-wide chromatin states. There are also circadian clock-regulated lncRNAs with an emerging function that includes assisting in chromatin dynamics. In this review, we explore the connections between circadian clock, chromatin remodeling, lncRNAs, and CRFH and how these impact rhythmicity, amplitude, period, and phase of circadian clock genes.

BMAL1 associates with chromosome ends to control rhythms in TERRA and telomeric heterochromatin.

The circadian clock and aging are intertwined. Disruption to the normal diurnal rhythm accelerates aging and corresponds with telomere shortening. Telomere attrition also correlates with increase cellular senescence and incidence of chronic disease. In this report, we examined diurnal association of White Collar 2 (WC-2) in Neurospora and BMAL1 in zebrafish and mice and found that these circadian transcription factors associate with telomere DNA in a rhythmic fashion. We also identified a circadian rhythm in Telomeric Repeat-containing RNA (TERRA), a lncRNA transcribed from the telomere. The diurnal rhythm in TERRA was lost in the liver of Bmal1-/- mice indicating it is a circadian regulated transcript. There was also a BMAL1-dependent rhythm in H3K9me3 at the telomere in zebrafish brain and mouse liver, and this rhythm was lost with increasing age. Taken together, these results provide evidence that BMAL1 plays a direct role in telomere homeostasis by regulating rhythms in TERRA and heterochromatin. Loss of these rhythms may contribute to telomere erosion during aging.

Age modulates liver responses to asparaginase-induced amino acid stress in mice.

Asparaginase is an amino acid-depleting agent used to treat blood cancers. Metabolic complications due to asparaginase affect liver function in humans. To examine how the liver response to asparaginase changes during maturity to adulthood, here we treated juvenile (2-week), young adult (8-week), and mature adult (16-week) mice with drug or excipient for 1 week and conducted RNA-Seq and functional analyses. Asparaginase reduced body growth and liver mass in juveniles but not in the adult animals. Unbiased exploration of the effect of asparaginase on the liver transcriptome revealed that the integrated stress response (ISR) was the only molecular signature shared across the ages, corroborating similar eukaryotic initiation factor 2 phosphorylation responses to asparaginase at all ages. Juvenile livers exhibited steatosis and iron accumulation following asparaginase exposure along with a hepatic gene signature indicating that asparaginase uniquely affects lipid, cholesterol, and iron metabolism in juvenile mice. In contrast, asparaginase-treated adult mice displayed greater variability in liver function, which correlated with an acute-phase inflammatory response gene signature. Asparaginase-exposed adults also had a serine/glycine/one-carbon metabolism gene signature in liver that corresponded with reduced circulating glycine and serine levels. These results establish the ISR as a conserved response to asparaginase-mediated amino acid deprivation and provide new insights into the relationship between the liver transcriptome and hepatic function upon asparaginase exposure.

Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci.

BACKGROUND: Histone H3 lysine 4 tri-methylation (H3K4me3) and histone H3 lysine 9 tri-methylation (H3K9me3) are widely perceived to be opposing and often mutually exclusive chromatin modifications. However, both are needed for certain light-activated genes in Neurospora crassa (Neurospora), including frequency (frq) and vivid (vvd). Except for these 2 loci, little is known about how H3K4me3 and H3K9me3 impact and contribute to light-regulated gene expression. RESULTS: In this report, we performed a multi-dimensional genomic analysis to understand the role of H3K4me3 and H3K9me3 using the Neurospora light response as the system. RNA-seq on strains lacking H3 lysine 4 methyltransferase (KMT2/SET-1) and histone H3 lysine 9 methyltransferase (KMT1/DIM-5) revealed some light-activated genes had altered expression, but the light response was largely intact. Comparing these 2 mutants to wild-type (WT), we found that roughly equal numbers of genes showed elevated and reduced expression in the dark and the light making the environmental stimulus somewhat ancillary to the genome-wide effects. ChIP-seq experiments revealed H3K4me3 and H3K9me3 had only minor changes in response to light in WT, but there were notable alterations in H3K4me3 in Δkmt1/Δdim-5 and H3K9me3 in Δkmt2/Δset-1 indicating crosstalk and redistribution between the modifications. Integrated analysis of the RNA-seq and ChIP-seq highlighted context-dependent roles for KMT2/SET1 and KMT1/DIM-5 as either co-activators or co-repressors with some overlap as co-regulators. At a small subset of loci, H3K4 methylation is required for H3K9me3-mediated facultative heterochromatin including, the central clock gene frequency (frq). Finally, we used sequential ChIP (re-ChIP) experiment to confirm Neurospora contains K4/K9 bivalent domains. CONCLUSIONS: Collectively, these data indicate there are obfuscated regulatory roles for H3K4 methylation and H3K9 methylation depending on genome location with some minor overlap and co-dependency.