Global histone H2B degradation regulates insulin/IGF signaling-mediated nutrient stress.

Eukaryotic organisms adapt to environmental fluctuations by altering their epigenomic landscapes and transcriptional programs. Nucleosomal histones carry vital epigenetic information and regulate gene expression, yet the mechanisms underlying chromatin-bound histone exchange remain elusive. Here, we found that histone H2Bs are globally degraded in Caenorhabditis elegans during starvation. Our genetic screens identified mutations in ubiquitin and ubiquitin-related enzymes that block H2B degradation in starved animals, identifying lysine 31 as the crucial residue for chromatin-bound H2B ubiquitination and elimination. Retention of aberrant nucleosomal H2B increased the association of the FOXO transcription factor DAF-16 with chromatin, generating an ectopic gene expression profile detrimental to animal viability when insulin/IGF signaling was reduced in well-fed animals. Furthermore, we show that the ubiquitin-proteasome system regulates chromosomal histone turnover in human cells. During larval development, C. elegans epidermal cells undergo H2B turnover after fusing with the epithelial syncytium. Thus, histone degradation may be a widespread mechanism governing dynamic changes of the epigenome.

Inhibition of histone H3-H4 chaperone pathways rescues C. elegans sterility by H2B loss.

Oncohistone mutations are crucial drivers for tumorigenesis, but how a living organism governs the loss-of-function oncohistone remains unclear. We generated a histone H2B triple knockout (3KO) strain in Caenorhabditis elegans, which decreased the embryonic H2B, disrupted cell divisions, and caused animal sterility. By performing genetic suppressor screens, we uncovered that mutations defective in the histone H3-H4 chaperone UNC-85 restored H2B 3KO fertility by decreasing chromatin H3-H4 levels. RNA interference of other H3-H4 chaperones or H3 or H4 histones also rescued H2B 3KO sterility. We showed that blocking H3-H4 chaperones recovered cell division in C. elegans carrying the oncohistone H2BE74K mutation that distorts the H2B-H4 interface and induces nucleosome instability. Our results indicate that reducing chromatin H3-H4 rescues the dysfunctional H2B in vivo and suggest that inhibiting H3-H4 chaperones may provide an effective therapeutic strategy for treating cancers resulting from loss-of-function H2B oncohistone.

DYF-5/MAK-dependent phosphorylation promotes ciliary tubulin unloading.

Cilia are microtubule-based organelles that power cell motility and regulate sensation and signaling, and abnormal ciliary structure and function cause various ciliopathies. Cilium formation and maintenance requires intraflagellar transport (IFT), during which the kinesin-2 family motor proteins ferry IFT particles carrying axonemal precursors such as tubulins into cilia. Tubulin dimers are loaded to IFT machinery through an interaction between tubulin and the IFT-74/81 module; however, little is known of how tubulins are unloaded when arriving at the ciliary tip. Here, we show that the ciliary kinase DYF-5/MAK phosphorylates multiple sites within the tubulin-binding module of IFT-74, reducing the tubulin-binding affinity of IFT-74/81 approximately sixfold. Ablation or constitutive activation of IFT-74 phosphorylation abnormally elongates or shortens sensory cilia in Caenorhabditis elegans neurons. We propose that DYF-5/MAK-dependent phosphorylation plays a fundamental role in ciliogenesis by regulating tubulin unloading.

In situ structure of intestinal apical surface reveals nanobristles on microvilli.

Microvilli are actin-bundle-supported membrane protrusions essential for absorption, secretion, and sensation. Microvilli defects cause gastrointestinal disorders; however, mechanisms controlling microvilli formation and organization remain unresolved. Here, we study microvilli by vitrifying the Caenorhabditis elegans larvae and mouse intestinal tissues with high-pressure freezing, thinning them with cryo-focused ion-beam milling, followed by cryo-electron tomography and subtomogram averaging. We find that many radial nanometer bristles referred to as nanobristles project from the lateral surface of nematode and mouse microvilli. The C. elegans nanobristles are 37.5 nm long and 4.5 nm wide. Nanobristle formation requires a protocadherin family protein, CDH-8, in C. elegans. The loss of nanobristles in cdh-8 mutants slows down animal growth and ectopically increases the number of Y-shaped microvilli, the putative intermediate structures if microvilli split from tips. Our results reveal a potential role of nanobristles in separating microvilli and suggest that microvilli division may help generate nascent microvilli with uniformity.

Actin filament debranching regulates cell polarity during cell migration and asymmetric cell division.

The formation of the branched actin networks is essential for cell polarity, but it remains unclear how the debranching activity of actin filaments contributes to this process. Here, we showed that an evolutionarily conserved coronin family protein, the Caenorhabditis elegans POD-1, debranched the Arp2/3-nucleated actin filaments in vitro. By fluorescence live imaging analysis of the endogenous POD-1 protein, we found that POD-1 colocalized with Arp2/3 at the leading edge of the migrating C. elegans neuroblasts. Conditional mutations of POD-1 in neuroblasts caused aberrant actin assembly, disrupted cell polarity, and impaired cell migration. In C. elegans one-cell-stage embryos, POD-1 and Arp2/3, moved together during cell polarity establishment, and inhibition of POD-1 blocked Arp2/3 motility and affected the polarized cortical flow, leading to symmetric segregation of cell fate determinants. Together, these results indicate that F-actin debranching organizes actin network and cell polarity in migrating neuroblasts and asymmetrically dividing embryos.

RAB6A functions as a critical modulator of the stem-like subsets in cholangiocarcinoma.

RAB6A is a member of RAB GTPase family and plays an important role in the targeted transport of neurotrophic receptors and inflammatory cytokines. RAB6A-mediated secretory pathway is involved in many physiological and pathological processes. Defects in RAB6A-mediated secretory pathway may lead to the development of many diseases, including cancer. However, its role in cholangiocarcinoma (CCA) has not yet been revealed. We explored the regulatory role of RAB6A in the stem-like subsets of CCA. We showed that RAB6A knockdown (KD) impedes cancer stem cells (CSCs) properties and epithelial-mesenchymal transition in vitro and that suppression of RAB6A inhibits tumor growth in vivo. We screened target cargos of RAB6A in CCA cells and identified a extracellular matrix component as the target cargo. RAB6A binds directly to OPN, and RAB6A KD suppressed OPN secretion and inhibited the interaction between OPN and αV integrin receptor. Moreover, RAB6A KD inhibited the AKT signaling pathway, which is a downstream effector of the integrin receptor signaling. In addition, shRNA targeting OPN blocked endogenous expression of OPN and consequently weakened CSCs properties in RAB6A-formed spheres. Similarly, inhibitor of AKT signaling, MK2206 also impedes oncogenic function of RAB6A in the stem-like subsets of CCA cells. In conclusion, our findings showed that RAB6A sustains CSCs phenotype maintenance by modulating the secretion of OPN and consequentially activating the downstream AKT signaling pathway. Targeting the RAB6A/OPN axis may be an effective strategy for CCA therapy.

Spatial confinement of receptor activity by tyrosine phosphatase during directional cell migration.

Directional cell migration involves signaling cascades that stimulate actin assembly at the leading edge, and additional pathways must inhibit actin polymerization at the rear. During neuroblast migration in Caenorhabditis elegans, the transmembrane protein MIG-13/Lrp12 acts through the Arp2/3 nucleation-promoting factors WAVE and WASP to guide the anterior migration. Here we show that a tyrosine kinase, SRC-1, directly phosphorylates MIG-13 and promotes its activity on actin assembly at the leading edge. In GFP knockin animals, SRC-1 and MIG-13 distribute along the entire plasma membrane of migrating cells. We reveal that a receptor-like tyrosine phosphatase, PTP-3, maintains the F-actin polarity during neuroblast migration. Recombinant PTP-3 dephosphorylates SRC-1-dependent MIG-13 phosphorylation in vitro. Importantly, the endogenous PTP-3 accumulates at the rear of the migrating neuroblast, and its extracellular domain is essential for directional cell migration. We provide evidence that the asymmetrically localized tyrosine phosphatase PTP-3 spatially restricts MIG-13/Lrp12 receptor activity in migrating cells.

Applying a Deep-Learning-Based Keypoint Detection in Analyzing Surface Nanostructures.

Scanning tunneling microscopy (STM) imaging has been routinely applied in studying surface nanostructures owing to its capability of acquiring high-resolution molecule-level images of surface nanostructures. However, the image analysis still heavily relies on manual analysis, which is often laborious and lacks uniform criteria. Recently, machine learning has emerged as a powerful tool in material science research for the automatic analysis and processing of image data. In this paper, we propose a method for analyzing molecular STM images using computer vision techniques. We develop a lightweight deep learning framework based on the YOLO algorithm by labeling molecules with its keypoints. Our framework achieves high efficiency while maintaining accuracy, enabling the recognitions of molecules and further statistical analysis. In addition, the usefulness of this model is exemplified by exploring the length of polyphenylene chains fabricated from on-surface synthesis. We foresee that computer vision methods will be frequently used in analyzing image data in the field of surface chemistry.

The spectrin-based membrane skeleton is asymmetric and remodels during neural development in C. elegans.

Perturbation of spectrin-based membrane mechanics causes hereditary elliptocytosis and spinocerebellar ataxia, but the underlying cellular basis of pathogenesis remains unclear. Here, we introduced conserved disease-associated spectrin mutations into the Caenorhabditis elegans genome and studied the contribution of spectrin to neuronal migration and dendrite formation in developing larvae. The loss of spectrin resulted in ectopic actin polymerization outside of the existing front and secondary membrane protrusions, leading to defective neuronal positioning and dendrite morphology in adult animals. Spectrin accumulated in the lateral region and rear of migrating neuroblasts and redistributes from the soma into the newly formed dendrites, indicating that the spectrin-based membrane skeleton is asymmetric and remodels to regulate actin assembly and cell shape during development. We affinity-purified spectrin from C. elegans and showed that its binding partner ankyrin functions with spectrin. Asymmetry and remodeling of the membrane skeleton might enable spatiotemporal modulation of membrane mechanics for distinct developmental events.

Metagenomic and Metatranscriptomic Responses of Chemical Dispersant Application during a Marine Dilbit Spill.

The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1,500 mL) microcosms without nutrient addition using a low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved in the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic-based metagenome-assembled genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed that dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating that the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. IMPORTANCE In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days), whereas exerting insignificant effects in the late stage (50 days), from both substance removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation and clarified their degradation and antioxidation mechanisms. These findings help us to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response.

FBXO31 sensitizes cancer stem cells-like cells to cisplatin by promoting ferroptosis and facilitating proteasomal degradation of GPX4 in cholangiocarcinoma.

BACKGROUND & AIMS: Cholangiocarcinoma (CCA) is a malignant tumour originating from the biliary epithelium that easily infiltrates, metastasizes and recurs. The deficiency of FBXO31 facilitates the initiation and progression of several types of cancer. However, the involvement of FBXO31 in CCA progression has remained unclear. METHODS: qRT-PCR was used to detect the expression of FBXO31 in CCA. The biological functions of FBXO31 were confirmed in vivo and in vitro. Sphere formation and flow cytometry were used to identify the stem cell properties of CCA. RESULTS: FBXO31 is downregulated in CCA and that deficiency of FBXO31 is associated with the TNM stage of CCA. Functional studies showed FBXO31 inhibits cell growth, migration, invasion, cancer stem cell (CSC) properties and epithelial-mesenchymal transition (EMT) in vitro and impedes tumour growth in vivo. In addition, overexpression of FBXO31 increases the cisplatin (CDDP) sensitivity of CCA cells. RNA-sequencing analysis revealed that FBXO31 is involved in redox biology and metal ion metabolism in CCA cells during CDDP treatment. Further studies revealed that FBXO31 enhances ferroptosis induced by CDDP in CCA and CSC-like cells. FBXO31 enhances ubiquitination of glutathione peroxidase 4 (GPX4), which leads to proteasomal degradation of GPX4. Moreover, overexpression of GPX4 compromises the promoting effects of FBXO31 on CDDP-induced ferroptosis in CCA and CSC-like cells. CONCLUSIONS: Our studies indicate that FBXO31 functions as a tumour suppressor in CCA and sensitizes CSC-like cells to CDDP by promoting ferroptosis and facilitating the proteasomal degradation of GPX4.

On-surface synthesis of ethers through dehydrative coupling of hydroxymethyl substituents.

On-surface synthesis has been a subject of intensive research during the last decade. Various chemical reactions have been developed on surfaces to prepare compounds and carbon nanostructures, most of which are centered on the carbon-carbon bond formation. Despite the vast progress so far, the diversity of functional groups in organic chemistry has been far less explored in on-surface synthesis. Herein, we study the surface-assisted synthesis of ethers through the homocoupling of hydroxymethyl substituents on Ag(111). By using two hydroxymethyl substituent functionalized molecular precursors with different symmetries, we have achieved the formation of ether chains and rings. High-resolution scanning tunneling microscopy complemented with density functional theory calculations are used to support our findings and offer mechanistic insights into the reaction. This work expands the toolbox of on-surface reactions for the bottom-up fabrication of more sophisticated functional nanostructures.

Dermal exposure to synthetic musks: Human health risk assessment, mechanism, and control strategy.

Synthetic musks (SMs) have been widely used as odor additives in personal care products (PCPs). Dermal exposure to SMs is the main pathway of the accumulation of these chemicals in human kerateins and poses potential health risks. In this study, in silico methods were established to reduce the human health risk of SMs from dermal exposure by investigating the risk mechanisms, designing lower bioaccumulation ability SMs and suggesting proper PCP ingredients using molecular docking, molecular dynamics simulation, and quantitative structure-activity relationship (QSAR) models. The binding energy, a parameter reflecting the binding ability of SMs and human keratin protein (4ZRY), was used as the indicator to assess the human health risk of SMs. According to the mechanism analysis, total energy was found as the most influential molecular structural feature influencing the bioaccumulation ability of a SM, and as one of the main factors influencing the function (i.e., odor sensitivity) of an SM. The 3D-QSAR models were constructed to control the human health risk of SMs by designing lower-risk SMs derivatives. The phantolide (PHAN)- 58 was determined to be the optimum SM derivative with lower bioaccumulation ability (reduced 17.25%) and improved odor sensitivity (increased 7.91%). A further reduction of bioaccumulation ability of PHAN-58 was found when adding proper body wash ingredients (i.e., alkyl ethoxylate sulfate (AES), dimethyloldimethyl (DMDM), EDTA-Na4, ethylene glycol distearate (EGDS), hydroxyethyl cellulose (HEC), lemon yellow and octyl glucose), leading to a significant reduction of the bioaccumulation ability (42.27%) compared with that of PHAN. Results demonstrated that the proposed theoretical mechanism and control strategies could effectively reduce the human health risk of SMs from dermal exposure.

A Deep-Learning Framework for the Automated Recognition of Molecules in Scanning-Probe-Microscopy Images.

Computer vision as a subcategory of deep learning tackles complex vision tasks by dealing with data of images. Molecular images with exceptionally high resolution have been achieved thanks to the development of techniques like scanning probe microscopy (SPM). However, extracting useful information from SPM image data requires careful analysis which heavily relies on human supervision. In this work, we develop a deep learning framework using an advanced computer vision algorithm, Mask R-CNN, to address the challenge of molecule detection, classification and instance segmentation in binary molecular nanostructures. We employ the framework to determine two triangular-shaped molecules of similar STM appearance. Our framework could accurately differentiate two molecules and label their positions. We foresee that the application of computer vision in SPM images will become an indispensable part in the field, accelerating data mining and the discovery of new materials.

Centriole translocation and degeneration during ciliogenesis in Caenorhabditis elegans neurons.

Neuronal cilia that are formed at the dendritic endings of sensory neurons are essential for sensory perception. However, it remains unclear how the centriole-derived basal body is positioned to form a template for cilium formation. Using fluorescence time-lapse microscopy, we show that the centriole translocates from the cell body to the dendrite tip in the Caenorhabditis elegans sensory neurons. The centriolar protein SAS-5 interacts with the dynein light-chain LC8 and conditional mutations of cytoplasmic dynein-1 block centriole translocation and ciliogenesis. The components of the central tube are essential for the biogenesis of centrioles, which later drive ciliogenesis in the dendrite; however, the centriole loses these components at the late stage of centriole translocation and subsequently recruits transition zone and intraflagellar transport proteins. Together, our results provide a comprehensive model of ciliogenesis in sensory neurons and reveal the importance of the dynein-dependent centriole translocation in this process.

Hippo kinases maintain polarity during directional cell migration in Caenorhabditis elegans.

Precise positioning of cells is crucial for metazoan development. Despite immense progress in the elucidation of the attractive cues of cell migration, the repulsive mechanisms that prevent the formation of secondary leading edges remain less investigated. Here, we demonstrate that Caenorhabditis elegans Hippo kinases promote cell migration along the anterior-posterior body axis via the inhibition of dorsal-ventral (DV) migration. Ectopic DV polarization was also demonstrated in gain-of-function mutant animals for C. elegans RhoG MIG-2. We identified serine 139 of MIG-2 as a novel conserved Hippo kinase phosphorylation site and demonstrated that purified Hippo kinases directly phosphorylate MIG-2S139 Live imaging analysis of genome-edited animals indicates that MIG-2S139 phosphorylation impedes actin assembly in migrating cells. Intriguingly, Hippo kinases are excluded from the leading edge in wild-type cells, while MIG-2 loss induces uniform distribution of Hippo kinases. We provide evidence that Hippo kinases inhibit RhoG activity locally and are in turn restricted to the cell body by RhoG-mediated polarization. Therefore, we propose that the Hippo-RhoG feedback regulation maintains cell polarity during directional cell motility.

Pillar[5]arene-Based 3D Hybrid Supramolecular Polymer for Green Catalysis in Water.

Pillar[n]arene-based supramolecular polymers have attracted great interest because of their tunable morphologies and external stimuli responsiveness. However, most of the investigations of supramolecular polymers previously reported were focused on their formation and transformation, and investigations on their applications are rare. Herein, we designed and prepared hybrid polymeric materials by incorporating Pd nanoparticles into a supramolecular polymer, constructed from a pillar[5]arene dimer and a three-arm guest. The obtained hybrid polymer was fully characterized by scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, scanning electron microscopy-energy-dispersive X-ray mapping, and X-ray diffraction technologies. Importantly, the hybrid supramolecular polymeric materials exhibited desirable catalytic activity for reductions of toxic nitroaromatics and C-C bond-forming Suzuki-Miyaura reaction in aqueous solution.

CED-10-WASP-Arp2/3 signaling axis regulates apoptotic cell corpse engulfment in C. elegans.

Efficient clearance of apoptotic cells is essential for tissue homeostasis in metazoans. Genetic studies in Caenorhabditis elegans have identified signaling cascades that activate CED-10/Rac1 GTPase and promote actin cytoskeletal rearrangement during apoptotic cell engulfment. However, the molecular connection between CED-10 activation and actin reorganization remains elusive. Here, we provide evidence that CED-10 binds to the Arp2/3 nucleation promoting factor WASP; CED-10 recruits WASP and Arp2/3 to apoptotic cell corpses in the phagocytes. The loss of WASP and Arp2/3 impaired cell corpse engulfment. Furthermore, we uncover that a WASP-activating factor SEM-5/GRB2 functions in the phagocytes to promote cell corpse clearance. Together, our results suggest CED-10 reorganizes the actin cytoskeleton by recruiting the WASP-Arp2/3 actin nucleation factors during apoptotic cell engulfment.

Occurrence, Impact, Analysis and Treatment of Metformin and Guanylurea in Coastal Aquatic Environments of Canada, USA and Europe.

This review discusses the occurrence, impact, analysis and treatment of metformin and guanylurea in coastal aquatic environments of Canada, USA and Europe. Metformin, a biguanide in chemical classification, is widely used as one of the most effective first-line oral drugs for type 2 diabetes. It is difficult to be metabolized by the human body and exists in both urine and faeces samples in these regions. Guanylurea is metformin's biotransformation product. Consequently, significant concentrations of metformin and guanylurea have been reported in wastewater treatment plants (WWTPs) and coastal aquatic environments. The maximum concentrations of metformin and guanylurea in surface water samples were as high as 59,000 and 4502ngL-1, respectively. Metformin can be absorbed in non-target organisms by plants and in Atlantic salmon (Salmo salar). Guanylurea has a confirmed mitotic activity in plant cells. Analysis methods of metformin are currently developed based on high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS). The removal of metformin from aquatic environments in the target regions is summarized. The review helps to fill a knowledge gap and provides insights for regulatory considerations. The potential options for managing these emerging pollutants are outlined too.

Synthetic Musks: A Class of Commercial Fragrance Additives in Personal Care Products (PCPs) Causing Concern as Emerging Contaminants.

Synthetic musks (SMs) are promising fragrance additives used in personal care products (PCPs). The widespread presence of SMs in environmental media remains a serious risk because of their harmful effects. Recently, the environmental hazards of SMs have been widely reported in various environmental samples including those from coastal and marine regions. This paper provides a systematic review of SMs, including their classification, synthetic routes, analysis and occurrence in environmental samples, fate and toxicity in the environment, as well as the associated risk assessment and pollution control. Research gaps and future opportunities were also identified with the hope of raising interest in this topic.