Biology subjects

He, H.

Publications and source records attributed to He, H..

At least 109 records · Page 6Linked to original sources

bioRxiv2023

Design, construction and optimization of formaldehyde growth biosensors with broad application in Biotechnology

Formaldehyde is a key metabolite in natural and synthetic one-carbon metabolism as well as an important environmental toxin with high toxicity at low concentrations. To engineer efficient formaldehyde producing enzymes and to detect formaldehyde in industrial or environmental samples, it is important to establish highly sensitive, easy to use and affordable formaldehyde detection methods. Here, we transformed the workhorse bacterium Escherichia coli into biosensors that can detect a broad range of formaldehyde concentrations. Based on natural and promiscuous formaldehyde assimilation enzymes, we designed and engineered three different E. coli strains that depend on formaldehyde assimilation for cellular growth. After in depth characterization of these biosensors, we show that the formaldehyde sensitivity can be improved through adaptive laboratory evolution or modification of metabolic branch points. The metabolic engineering strategy presented in this work allowed the creation of E. coli biosensors that can detect formaldehyde in a concentration range from [~]30 M to [~]13 mM. Using the most sensitive strain, we benchmarked the in vivo activities of different, widely used NAD-dependent methanol dehydrogenases, the rate-limiting enzyme in synthetic methylotrophy. We also show that the strains can grow upon external addition of formaldehyde indicating their potential use for applications beyond enzyme engineering. The formaldehyde biosensors developed in this study are fully genomic and can be used as plug and play devices for screening large enzyme libraries. Thus, they have the potential to greatly advance enzyme engineering and might even be used for environmental monitoring or analysis of industrial probes. Highlights- Conversion of E. coli into three different formaldehyde growth biosensors - Biosensors are fully genomic and grow robustly when formaldehyde is present - Biosensors can detect formaldehyde concentrations ranging from [~]30 M to [~]13 mM - Benchmarking of biotechnological relevant methanol dehydrogenases reveals potential of biosensors for enzyme engineering - Biosensors grow upon direct addition of formaldehyde indicating potential use in environmental or industrial settings

bioengineering↗

bioRxiv2023

Sexual dimorphism in the social behaviour of Cntnap2 KO mice correlates with disrupted synaptic connectivity and increased microglial activity in the anterior cingulate cortex of males

A biological understanding of the apparent sex bias in autism is lacking. We have identified Cntnap2 KO mice as a model system to help better understand this dimorphism. Using this model, we observed social deficits in juvenile male KO mice only. These male-specific social deficits correlated with reduced spine densities of Layer 2/3 and Layer 5 pyramidal neurons in the Anterior Cingulate Cortex, a forebrain region prominently associated with the control of social behaviour. Furthermore, in male KO mice, microglia showed an increased activated morphology and phagocytosis of synaptic structures compared to WT mice, whereas no differences were seen in female KO and WT mice. Our data suggest that sexually dimorphic microglial activity may be involved in the aetiology of ASD, disrupting the development of neural circuits that control social behaviour by overpruning synapses at a developmentally critical period.

neuroscience↗

bioRxiv2023

Interleukin-16/STAT6 recruits CBP/p300 to upregulate TIMP-3 and promote atherosclerotic plaque stability

BackgroundAtherosclerotic plaque rupture increases the risk of ischemic heart disease and stroke and commonly causes sudden death. High levels of circulating or intraplaque interleukin 16 (IL-16) are clinically associated with a reduced incidence of cardiovascular events. Here, we investigated the effects of IL-16 on plaque phenotypic modification and identified the molecules involved in smooth muscle cells (SMCs). MethodsWe deleted IL-16 in ApoE-/- mice to generate IL16-/-ApoE-/- mice, and the double mutant was used for plaque phenotype analysis after a 24-week high-fat diet. RNA sequencing was performed to identify the changes in cellular processes and molecule expression in response to IL-16 defects. Affinity purification-mass spectrometry was used to identify the STAT6 binding protein. Bone marrow transplantation was used to investigate the effects of hematopoietic IL-16 deficiency or reconstitution on plaque stability. ResultsIL-16 deficiency reduced collagen deposition and increased the necrotic core area in the plaques of the brachiocephalic artery and aortic root lesions. Intraplaque TIMP-3 levels were found to be decreased in association with an increase in the proteolytic activity of MMPsinIL16-/-ApoE-/- mice. Next, we demonstrated that IL-16 activates the CD4/JAK2/STAT6 pathway and that STAT6 directly binds the TIMP-3 promoter in SMCs. Furthermore, IL-16 treatment increased the interaction of cAMP-response element binding protein (CBP)/p300 with STAT6, which promoted STAT6 acetylation and increased histone H3 acetylation in the TIMP-3 promoter. Inhibition of CBP/p300 resulted in decreased acetylation of STAT6 and TIMP-3 promoter histone H3 and TIMP-3 expression, suggesting a requirement for CBP/p300 as a coactivator. Finally, we found that hematopoietic-derived IL-16 from ApoE-/- mice or overexpression of TIMP-3 successfully attenuated plaque instability in IL16-/-ApoE-/- mice. ConclusionsIL-6 upregulates TIMP-3 expression and remodels the intraplaque extracellular matrix toward a stable phenotype, suggesting IL-16 as a potential target for intervening in atherosclerosis at later stages.

pathology↗

bioRxiv2023

CCR9 overexpression promotes T-ALL progression by enhancing cholesterol biosynthesis

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy of the lymphoid progenitor cells contributing to [~] 20% of the total ALL cases with higher prevalence in adults than the children. Despite the important role of human T-ALL cell lines in understanding the biology and treatment options, a detailed comparison of the tumorigenic potential of two commonly used T-ALL cell lines, MOLT4 and JURKAT cells is still lacking. In the present study, we compared the leukemogenic potentials of the two T-ALL cell lines (MOLT4 and JURKAT) in NOD-PrkdcscidIL2rgdull (NTG) mice and found that MOLT4 cells possessed a relatively higher aggressive phenotype characterized by their enhanced tissue infiltration as compared to the JURKAT cells. Gene expression profiling of the two cell lines revealed numerous differentially expressed genes (DEGs) including CC chemokine receptor 9 (CCR9), which augmented the invasion and metastasis of MOLT4 and JURKAT cells in vitro. The upregulation of CCR9 also promoted the tissue infiltration of JURKAT cells in the NTG mice. CCR9 overexpression increased cholesterol production by upregulating the expression of the core regulatory genes of the cholesterol biosynthesis pathway including MSMO1, MVD, and HMGCS1. Moreover, the upregulated expression of EGR1 was also found with CCR9 overexpression that modulated the expression of MSMO1, MVD, and HMGCS1. Notably, the treatment of the cells with simvastatin and siRNA-EGR1 decreased the aggressiveness of the CCR9 overexpressing JURKAT cells in vitro, suggesting the CCR9-EGR1 axis in T-ALL progression. This study highlights the distinct tumorigenic potentials of two T-ALL cell lines and reveals CCR9-regulated enhanced cholesterol biosynthesis in T-ALL. Simple summaryT-ALL is an aggressive cancer of the blood and bone marrow. In order to understand the biological mechanism of T-ALL, in vitro T-ALL cell lines are commonly employed. However, a comprehensive comparison of two common T-ALL cell lines, MOLT4 and JURKAT cells for T-ALL development is not yet available. We compared MOLT4 and JURKAT cells for T-ALL inducing potential and found that MOLT4 cells exhibited a relatively increased aggressiveness in mice as compared to JURKAT cells. We examined the molecular characteristics of two cell lines that could lead to differences in cancer development. Transcriptional profiling of MOLT4 and JURKAT cells revealed significant changes in the expression of several genes including CCR9. This aberrant expression of CCR9 impacted the migration and invasion of the T-ALL cell lines in vitro. In addition, higher expression levels of CCR9 also promoted T-ALL progression in vivo. Transcriptome analysis and gene ontology analysis of the DEGs of CCR9 over-expressing JURKAT cells indicated the enrichment of the genes in the cholesterol biosynthesis pathway, suggesting this metabolic rewiring mechanism as a strategy to cope with the increased energy demand of the malignant T-ALL cells.

cancer biology↗

bioRxiv2023

Carotenoid assembly regulates quinone diffusion and the Roseiflexus castenholzii reaction center-light harvesting complex architecture

Carotenoid (Car) pigments perform central roles in photosynthesis-related light harvesting (LH), photoprotection, and assembly of functional pigment-protein complexes. However, the relationships between Car depletion in the LH, assembly of the prokaryotic reaction center (RC)-LH complex, and quinone exchange are not fully understood. Here, we analyzed native RC-LH (nRC-LH) and Car-depleted RC-LH (dRC-LH) complexes in Roseiflexus castenholzii, a chlorosome-less filamentous anoxygenic phototroph that forms the deepest branch of photosynthetic bacteria. Newly identified exterior Cars functioned with the bacteriochlorophyll B800 to block the proposed quinone channel between LH{beta} subunits in the nRC-LH, forming a sealed LH ring that was disrupted by transmembrane helices from cytochrome c and subunit X to allow quinone shuttling. dRC-LH lacked subunit X, leading to an exposed LH ring with a larger opening, which together accelerated the quinone exchange rate. We also assigned amino acid sequences of subunit X and two hypothetical proteins Y and Z that functioned in forming the quinone channel and stabilizing the RC-LH interactions. This study reveals the structural basis by which Cars assembly regulates the architecture and quinone exchange of bacterial RC-LH complexes. These findings mark an important step forward in understanding the evolution and diversity of prokaryotic photosynthetic apparatus.

biochemistry↗

bioRxiv2023

Gene expression genetics of the striatum of Diversity Outbred mice

Brain transcriptional variation is a heritable trait that mediates complex behaviors, including addiction. Expression quantitative trait locus (eQTL) mapping reveals genomic regions harboring genetic variants that influence transcript abundance. In this study, we profiled transcript abundance in the striatum of 386 Diversity Outbred (J:DO) mice of both sexes using RNA-Seq. All mice were characterized using a behavioral battery of widely-used exploratory and risk-taking assays prior to transcriptional profiling. We performed eQTL mapping, incorporated the results into a browser-based eQTL viewer, and deposited co-expression network members in GeneWeaver. The eQTL viewer allows researchers to query specific genes to obtain allelic effect plots, analyze SNP associations, assess gene expression correlations, and apply mediation analysis to evaluate whether the regulatory variant is acting through the expression of another gene. GeneWeaver allows multi-species comparison of gene sets using statistical and combinatorial tools. This data resource allows users to find genetic variants that regulate differentially expressed transcripts and place them in the context of other studies of striatal gene expression and function in addiction-related behavior.

genetics↗

bioRxiv2023

Video-rate Mid-infrared Photothermal Imaging by Single Pulse Photothermal Detection per Pixel

By optically sensing the mid-infrared absorption induced photothermal effect, midinfrared photothermal (MIP) microscope enables super-resolution IR imaging and scrutinizing of biological systems in an aqueous environment. However, the speed of current lock-in based sample-scanning MIP system is limited to 1.0 millisecond or longer per pixel, which is insufficient for capturing dynamics inside living systems. Here, we report a single pulse laserscanning MIP microscope that dramatically increases the imaging speed by three orders of magnitude. We harness a lock-in free demodulation scheme which uses high-speed digitization to resolve single IR pulse induced contrast at nanosecond time scale. To realize single pulse photothermal detection at each pixel, we employ two sets of galvo mirrors for synchronized scanning of mid-infrared and probe beams to achieve an imaging line rate over 2 kHz. With video-rate imaging capability, we observed two types of distinct dynamics of lipids in living cells. Furthermore, by hyperspectral imaging, we chemically dissected a single cell wall at nanometer scale. Finally, with a uniform field of view over 200 by 200 m2 and 2 Hz frame rate, we mapped fat storage in free-moving C. elegans and live embryos.

bioengineering↗

bioRxiv2023

Proliferating cell nuclear antigen involves in temperature stress tolerance of Ulva prolifera

Ulva prolifera is the dominant species of "green tide", and has higher tolerance to environmental stresses such as temperature. However, the molecular mechanisms are still unclear. Here, transcriptome analysis, Western blot and RT-qPCR analysis of U. prolifera suggested that, under temperature stresses (4{degrees}C, 36{degrees}C), the expression of PCNA and CyclinA was promoted, and the MAPK signaling was activated. Besides, the results showed that PCNA interacted with CyclinA. Interestingly, the expression of miR-2916, which was predicted to bind PCNA at -552[~]-772, was negatively correlated with the expression of PCNA under temperature stresses (4{degrees}C, 36{degrees}C). In addition, the results showed that low temperature (4{degrees}C) had no obvious effect on the survival, the formation of cell walls, and the division of protoplasts. However, high temperature (36{degrees}C) had obvious effect on them. PCNA inhibitors increased the sensitivity of the protoplasts under temperature stresses. Together, our results suggested PCNA regulating the proliferation in response to the temperature stress of U. prolifera was associated with miR-2916/PCNA/CyclinA/MAPK pathway. In conclusion, the study preliminarily illuminates the molecular mechanism in response to temperature stress of U. prolifera, and may provide a new insight for prevention of green tide.

cell biology↗

bioRxiv2022

A Borrelia burgdorferi LptD Homolog Facilitates Flipping of Surface Lipoproteins Through the Spirochetal Outer Membrane

Borrelia spirochetes are unique among diderm bacteria in their lack of lipopolysaccharide (LPS) in the outer membrane (OM) and their abundance of surface-exposed lipoproteins with major roles in transmission, virulence, and pathogenesis. Despite their importance, little is known about how surface lipoproteins are translocated through the periplasm and the OM. In this study, we characterized Borrelia burgdorferi BB0838, a distant homolog of the OM LPS assembly protein LptD. Using a CRISPR interference approach, we showed that BB0838 is essential for cell growth. Upon BB0838 knockdown, sentinel surface lipoprotein OspA was retained in the inner leaflet of the OM, as determined by its inaccessibility to in situ proteolysis but its presence in OM vesicles. The secretion, insertion and topology of the B. burgdorferi OM porin P66 remained unaffected. MudPIT quantitative mass spectrometry analysis of the B. burgdorferi membrane-associated proteome further confirmed the selective periplasmic retention of surface lipoproteins under BB0838 knockdown conditions. Alphafold Multimer modeling predicted a B. burgdorferi LptB2FGCAD complex spanning the periplasm. Together, this indicates that BB0838 facilitates the essential terminal step in a distinctive spirochetal lipoprotein secretion pathway that evolved in parallel to the LPS secretion pathway in gram-negative bacteria. Hence, BB0838/LptDBb represents an attractive target for novel antimicrobials.

microbiology↗

bioRxiv2022

Inducible CRISPRi-based operon silencing and selective in trans gene complementation in Borrelia burgdorferi

To accelerate genetic studies on the Lyme disease pathogen Borrelia burgdorferi, we developed an enhanced CRISPR interference (CRISPRi) approach for IPTG-inducible repression of specific B. burgdorferi genes. The entire system is encoded on a compact 11-kb shuttle vector plasmid that allows for inducible expression of both the sgRNA module and a non-toxic codon-optimized dCas9 protein. We validated this CRISPRi system by targeting the genes encoding for OspA and OspB, abundant surface lipoproteins co-expressed by a single operon, and FlaB, the major subunit forming the periplasmic flagella. As in other systems, sgRNAs complementary to the non-template strand were consistently effective in gene repression, with 4- to 994-fold reductions in targeted transcript levels and concomitant reductions of in proteins levels. Furthermore, we showed that ospAB knockdowns could be selectively complemented in trans for OspA expression via the insertion of synonymous or non-synonymous CRISPRi-resistant PAM mutant (PAM*) ospA alleles into a unique site within the plasmid. Together, this establishes CRISPRi PAM* as a robust new genetic tool to simplify the study of B. burgdorferi genes, bypassing the need for gene disruptions by allelic exchange and avoiding rare-codon toxicity from heterologous expression of dCas9. SIGNIFICANCEBorrelia burgdorferi, the causative agent of Lyme disease, is a tick-borne pathogen of global importance. Here, we expand the genetic toolbox for studying B. burgdorferi physiology and pathogenesis by establishing a single-plasmid-based CRISPRi system with optional in trans complementation for the functional study of essential and non-essential proteins.

microbiology↗

bioRxiv2022

The Cation/H+ exchanger OsCAX2 is involved in cadmium tolerance and accumulation through vacuolar sequestration in rice

Excessive cadmium (Cd) in rice grains is a serious food safety problem. The development of Cd-safe varieties requires the identification of germplasms and genes with major effect on Cd accumulation but without negative effects on other important traits. Here, we reported that OsCAX2, a member of the rice Cation/H+ exchanger (CAX) family, is an important Cd transporter. OsCAX2 encodes a tonoplast-localized protein and is strongly upregulated by Cd, mainly expresses in root exodermis, parenchyma in cortex, endodermis and stele cells. Depletion of OsCAX2 resulted in enhanced Cd sensitivity and root-to-shoot translocation in rice, while overexpression of OsCAX2 significantly increased Cd tolerance and reduced Cd transport by promoting root Cd influx and vacuolar storage, which ultimately reduced Cd transport via xylem. OsCAX2 also had significant effects on tissues/organs distribution of Cd but had no effects on grain yield and agronomic traits. Importantly, the OsCAX2 overexpressing lines had more than 70% lower grain Cd accumulation, increased iron (Fe), zinc (Zn) and manganese (Mn) and reduced copper (Cu) accumulation. Therefore, OsCAX2 is an ideal gene for developing Cd-safe rice varieties via transgenic approach.

plant biology↗

bioRxiv2022

Engineering CAR-NK cells targeting CD33 with concomitant extracellular secretion of anti CD16 antibody revealed superior antitumor effects toward myeloid leukemia

Acute myeloid leukemia (AML) is a common form of acute leukemia and current drugs are overall unsatisfactory. In the present study, we report an immune cell therapy strategy by employing genetically-modified bifunctional CAR-NK cells that combines efficient targeting of AML cells via the CD33 molecule with the concomitant stimulation of NK cell cytotoxicity through the expression and extracellular secretion of anti-CD16 antibody (B16) that binds back to the FC receptor of NK cells. Comparing to CAR-NK cells that target CD33 only, the bifunctional CD33/B16 CAR-NK cells showed superior killing efficiency toward AML cells in vitro, which increased about 4 times based on the number of cells needed to achieve 80% killing activity. In vivo study with xenograft model also revealed effective clearance of leukemic cells and much longer survival - no relapse or death for at least 60 days. In addition, the safety of CAR-NK is not changed with additional expression of B16 as determined by the release of cytokines. These data revealed a promising CAR-NK approach to treat AML patients, which may improve CAR-NK based treatment in general and have potential applications to deal with other tumors as well.

immunology↗

bioRxiv2022

Integrated Network Pharmacology and Experimental Analysis Unveil Modulation of EGFR/MAPK Signaling Cascades in Acute Cerebral Ischemia-Reperfusion Injury by Qing-Tong-Hua-Yu Decoction

ObjectiveBased on network pharmacology, the response of Qing-tong-hua-yu Decoction (QTHY) to the regulation of EGFR/MAPK signaling cascade in cerebral ischemia-reperfusion injury was discussed and the possible mechanism of the protective effect of QTHY on the cerebral ischemia-reperfusion injury was studied. MethodsA compound-target disease-function-pathway network was established and analyzed based on the network pharmacology approach used in Chinese medicine. The correlation, which is between effect of the components of QTHY Decoction against CI/RI with EGFR/MAPK signalling cascade response, was observed. And then the degree of neurological deficits in each group was assessed after cerebral ischemia for 2 hours and reperfusion for 3 hours, 24 hours, 3 days and 7 days. Expression levels of EGFR and p44/42MAPK in ischemic brain tissue at different time points in various groups of rats were tested by Western bolt (WB), real-time quantitative PCR (RT-qPCR) and immunohistochemistry (IHC). ResultsNetwork pharmacology analysis revealed that QTHY-mediated treatment involved 439 key targets, in which the effect of QTHY groups against CI/RI was associated with EGFR/MAPK signaling cascade. QTHY treatment reduced neurological deficit scores and improved ischemic changes in rats. In addition, QTHY promoted EGFR and p44/42MAPK expression in the SVZ through the EGFR/MAPK signaling cascade, with varying degrees of improvement at different time points. ConclusionQTHY can better improve cerebral ischemia injury in CI / RI rats and exert the neuroprotective effect of cerebral ischemia-reperfusion injury. This may be related to the potential of QTHY to activate the EGFR / MAPK signaling cascade, which is consistent with the results of network pharmacology analysis.

neuroscience↗

bioRxiv2022

Flaver: mining transcription factors in genome-wide transcriptome profiling data using weighted rank correlation statistics

BackgroundMining key transcription factors (TFs) in genome-wide transcriptome profiling data has been an active research area for many years and it has been partially solved by mathematically modelling the ranking orders of genes in the target gene-set for the TF of interest in the gene-list ranked by expression values, called gene-set enrichment analysis (GSEA). However, in some application scenarios the gene-set itself also has a rank attribute, such as the putative target gene-set predicted by the Grit software and other alternatives like FIMO and Pscan. New algorithms must be developed to analyze these data properly. Methodology/Principal FindingsBy implementing the weighted Kendalls tau statistic, we proposed a method for genome-wide transcriptome profiling data mining that can identify the key TFs orchestrating a profile. Theoretical properties of the proposed method were established, and its advantages over the GSEA approach were demonstrated when analyzing the RNA-Atlas datasets. The results showed that the top-rated TFs by our method always have experimentally supported evidences in the literatures. Benchmarking using gene ontology (GO) annotations in the AmiGO database indicated that the geometry performance (SQR_P) of our method is higher than GSEA in more than 14% of the cases. SignificanceThe developed method is suitable for analyzing the significance of overrepresentation of ranked gene-sets in a ranked gene-list. A software implementing the method, called "Flaver", was developed and is publicly available at http://www.thua45.cn/flaver under an academic free license. Author SummaryIdentification of the regulation roles of TFs in the transcriptome is fundamental in understanding various biological processes. Improve the performance of the prediction tools is important because accurate TF-mining in transcriptome data can finely improve the efficiency of wet-lab experiments. Also, genome wide TF-mining can provide new target genes for transcriptome regulation analysis in system biology perspective. This study developed a new TF-mining tool based on weighted rank correlation statistical method. The tool has better performance in analyzing ranked gene-set and ranked gene-list than its competitor, the GSEA tool. It can help the researchers in identification of the most important TFs in transcriptional data.

bioinformatics↗

bioRxiv2022

Synthetic carbon fixation via the autocatalytic serine threonine cycle

Atmospheric CO2 poses a major threat to life on Earth by causing global warming and climate change. On the other hand, it is the only carbon source that is scalable enough to establish a circular carbon economy. Accordingly, technologies to capture and convert CO2 to reduced one-carbon (C1) molecules (e.g. formate) using renewable energy are improving fast. Driven by the idea of creating sustainable bioproduction platforms, natural and synthetic C1-utilization pathways are engineered into industrially relevant microbes. The realization of synthetic C1-assimilation cycles in living organisms is a promising but challenging endeavour. Here, we engineer the autocatalytic serine threonine cycle, a synthetic C1-assimilation route in Escherichia coli. Our stepwise engineering approach in tailored selection strains combined with adaptive laboratory evolution experiments enabled the organism to grow on formate. The synthetic strain uses formate as the sole carbon and energy source and is capable of growing at ambient CO2 concentrations, demonstrating the feasibility of establishing synthetic C1-assimilation cycles over laboratory timescales.

synthetic biology↗

bioRxiv2022

Mesenchymal stem cell suppresses the efficacy of CAR-T toward killing lymphoma cells by modulating the microenvironment through stanniocalcin-1

Stem cells play critical roles both in the development of cancer and therapy resistance. Although mesenchymal stem cells (MSCs) can actively migrate to tumor sites, their impact on CAR-T immunotherapy has been little addressed. Using an in vitro cell co-culture model including lymphoma cells and macrophages, here we report that the CAR-T cell mediated cytotoxicity was significantly inhibited in the presence of MSCs. MSC caused an increase of CD4+ T cells and Treg cells but decrease of CD8+ T cells. In addition, MSCs stimulated the expression of indoleamine 2,3-dioxygenase (IDO) and programmed cell death-ligand 1 (PD-L1) that contribute to the immune-suppressive function of tumor. Moreover, MSCs suppressed key components of NLRP3 inflammasome by modulating mitochondrial ROS release. Interestingly, all these suppressive events hindering CAR-T efficacy could be abrogated if the STC1 gene, which encodes the glycoprotein hormone staniocalcin-1, was knockdown in MSC. Using xenograft mice, we confirmed that CAR-T function could also be inhibited by MSC in vivo and STC1 played a critical role. These data revealed a novel function of MSC and staniocalcin-1 in suppressing CAR-T efficacy, which should be considered in cancer therapy and may also have potential applications in controlling the toxicity arising from excessive immune response.

cancer biology↗

bioRxiv2022

An R-R-type MYB transcription factor promotes nonclimacteric pepper fruit ripening pigmentation

Carotenoids act as phytohormones and volatile compound precursors that influence plant development and confer characteristic colours, affecting both the aesthetic and nutritional value of fruits. Carotenoid pigmentation in ripening fruits is highly dependent on developmental trajectories. Transcription factors incorporate developmental and phytohormone signalling to regulate the biosynthesis process. In contrast to the well-established pathways regulating ripening-related carotenoid biosynthesis in climacteric fruit, carotenoid regulation in nonclimacteric fruit is poorly understood. Capsanthin is the primary carotenoid of nonclimacteric pepper (Capsicum) fruit; its biosynthesis is tightly associated with fruit ripening, and it confers red pigment to the ripening fruit. In this study, using a weighted gene coexpression network and expression analysis, we identified an R-R-type MYB transcription factor, DIVARICATA1, and demonstrated that it is tightly associated with the levels of carotenoid biosynthetic genes (CBGs) and capsanthin accumulation. DIVARICATA1 encodes a nucleus-localized protein that functions primarily as a transcriptional activator. Functional analyses demonstrated that DIVARICATA1 positively regulates CBG transcript levels and capsanthin contents by directly binding to and activating the CBG promoter transcription. Furthermore, the association analysis revealed a significant positive association between DIVARICATA1 transcription level and capsanthin content. Abscisic acid (ABA) promotes capsanthin biosynthesis in a DIVARICATA1-dependent manner. Comparative transcriptomic analysis of DIVARICATA1 in pepper and its orthologue in a climacteric fruit, tomato, suggests that its function might be subject to divergent evolution among the two species. This study illustrates the transcriptional regulation of capsanthin biosynthesis and offers a novel target for breeding peppers with high red colour intensity.

plant biology↗

bioRxiv2022

Pupil-linked phasic arousal relates to the reduction of response inhibition: inferences from a simultaneous pupillometry and EEG-fMRI study

Attention reorienting is a critical cognitive function which drives how we respond to novel and unexpected stimuli. In recent years, arousal has been linked to attention reorienting. The timing and spatial organization of the interactions between the arousal and reorienting systems, however, remain only partially revealed. Here, we investigate the dynamics between the two systems through simultaneous recordings of pupillometry, EEG, and fMRI of healthy human subjects while they performed an auditory target detection task. We used pupil diameter and activity in the noradrenergic locus coeruleus to infer arousal, and found these measures linked to distinct cortical activity at various temporal stages of the reorienting response. Specifically, our results provide the first demonstration in humans of how phasic pupil-linked arousal relates to the reduction of response inhibition, an inference which otherwise would remain hidden without the help of simultaneous multi-modal acquisitions.

neuroscience↗