A delicate decision between repair and degradation of damaged lysosomes.

The destination of a damaged lysosome is either being repaired if the damage is small or degraded through a lysosome-specific macroautophagy/autophagy pathway named lysophagy when the damage is too extensive to repair. Even though previous studies report lumenal glycan exposure during lysosome damage as a signal to trigger lysophagy, it is possibly beneficial for cells to initiate lysophagy earlier than membrane rupture. In a recently published article, Gahlot et al. determined that SPART/SPG20 senses lipid-packing defects and recruits and activates the ubiquitin ligase ITCH, which labels damaged lysosomes with ubiquitin chains to initiate lysophagy.

Functional analysis of CYP71AV1 reveals the evolutionary landscape of artemisinin biosynthesis.

Artemisinin biosynthesis, unique to Artemisia annua, is suggested to have evolved from the ancestral costunolide biosynthetic pathway commonly found in the Asteraceae family. However, the evolutionary landscape of this process is not fully understood. The first oxidase in artemisinin biosynthesis, CYP71AV1, also known as amorpha-4,11-diene oxidase (AMO), has specialized from ancestral germacrene A oxidases (GAOs). Unlike GAO, which exhibits catalytic promiscuity toward amorpha-4,11-diene, the natural substrate of AMO, AMO has lost its ancestral activity on germacrene A. Previous studies have suggested that the loss of the GAO copy in A. annua is responsible for the abolishment of the costunolide pathway. In the genome of A. annua, there are two copies of AMO, each of which has been reported to be responsible for the different product profiles of high- and low-artemisinin production chemotypes. Through analysis of their tissue-specific expression and comparison of their sequences with those of other GAOs, it was discovered that one copy of AMO (AMOHAP) exhibits a different transcript compared to the reported artemisinin biosynthetic genes and shows more sequence similarity to other GAOs in the catalytic regions. Furthermore, in a subsequent in vitro enzymatic assay, the recombinant protein of AMOHAP unequivocally demonstrated GAO activity. This result clearly indicates that AMOHAP is a GAO rather than an AMO and that its promiscuous activity on amorpha-4,11-diene has led to its misidentification as an AMO in previous studies. In addition, the divergent expression pattern of AMOHAP compared to that of the upstream germacrene A synthase may have contributed to the abolishment of costunolide biosynthesis in A. annua. Our findings reveal a complex evolutionary landscape in which the emergence of a new metabolic pathway replaces an ancestral one.

Tunable anisotropic van der Waals films of 2M-WS2 for plasmon canalization.

In-plane anisotropic van der Waals materials have emerged as a natural platform for anisotropic polaritons. Extreme anisotropic polaritons with in-situ broadband tunability are of great significance for on-chip photonics, yet their application remains challenging. In this work, we experimentally characterize through Fourier transform infrared spectroscopy measurements a van der Waals plasmonic material, 2M-WS2, capable of supporting intrinsic room-temperature in-plane anisotropic plasmons in the far and mid-infrared regimes. In contrast to the recently revealed natural hyperbolic plasmons in other anisotropic materials, 2M-WS2 supports canalized plasmons with flat isofrequency contours in the frequency range of ~ 3000-5000 cm-1. Furthermore, the anisotropic plasmons and the corresponding isofrequency contours can be reversibly tuned via in-situ ion-intercalation. The tunable anisotropic and canalization plasmons may open up further application perspectives in the field of uniaxial plasmonics, such as serving as active components in directional sensing, radiation manipulation, and polarization-dependent optical modulators.

Stability Strategies and Applications of Iodide Perovskites.

Iodide perovskites have demonstrated their unprecedented high efficiency and commercialization potential, and their superior optoelectronic properties, such as high absorption coefficient, high carrier mobility, and narrow direct bandgap, have attracted much attention, especially in solar cells, photodetectors, and light-emitting diodes (LEDs). However, whether it is organic iodide perovskite, organic-inorganic hybrid iodide perovskite or all-inorganic iodide perovskite the stability of these iodide perovskites is still poor and the contamination is high. In recent years, scholars have studied more iodide perovskites to improve their stability as well as optoelectronic properties from various angles. This paper systematically reviews the strategies (component engineering, additive engineering, dimensionality reduction engineering, and phase mixing engineering) used to improve the stability of iodide perovskites and their applications in recent years.

Influence of Input Features and EMG Type on Ankle Joint Torque Prediction With Support Vector Regression.

Reliable and accurate EMG-driven prediction of joint torques are instrumental in the control of wearable robotic systems. This study investigates how different EMG input features affect the machine learning algorithm-based prediction of ankle joint torque in isometric and dynamic conditions. High-density electromyography (HD-EMG) of five lower leg muscles were recorded during isometric contractions and dynamic tasks. Four datasets (HD-EMG, HD-EMG with reduced dimensionality, features extracted from HD-EMG with Convolutional Neural Network, and bipolar EMG) were created and used alone or in combination with joint kinematic information for the prediction of ankle joint torque using Support Vector Regression. The performance was evaluated under intra-session, inter-subject, and inter-session cases. All HD-EMG-derived datasets led to significantly more accurate isometric ankle torque prediction than the bipolar EMG datasets. The highest torque prediction accuracy for the dynamic tasks was achieved using bipolar EMG or HD-EMG with reduced dimensionality in combination with kinematic features. The findings of this study contribute to the knowledge allowing an informed selection of appropriate features for EMG-driven torque prediction.

Layer-dependent exciton polarizability and the brightening of dark excitons in few-layer black phosphorus.

The evolution of excitons from 2D to 3D is of great importance in photo-physics, yet the layer-dependent exciton polarizability hasn't been investigated in 2D semiconductors. Here, we determine the exciton polarizabilities for 3- to 11-layer black phosphorus-a direct bandgap semiconductor regardless of the thickness-through frequency-resolved photocurrent measurements on dual-gate devices and unveil the carrier screening effect in relatively thicker samples. By taking advantage of the broadband photocurrent spectra, we are also able to reveal the exciton response for higher-index subbands under the gate electrical field. Surprisingly, dark excitons are brightened with intensity even stronger than the allowed transitions above certain electrical field. Our study not only sheds light on the exciton evolution with sample thickness, but also paves a way for optoelectronic applications of few-layer BP in modulators, tunable photodetectors, emitters and lasers.

Tunable optical topological transitions of plasmon polaritons in WTe2 van der Waals films.

Naturally existing in-plane hyperbolic polaritons and the associated optical topological transitions, which avoid the nano-structuring to achieve hyperbolicity, can outperform their counterparts in artificial metasurfaces. Such plasmon polaritons are rare, but experimentally revealed recently in WTe2 van der Waals thin films. Different from phonon polaritons, hyperbolic plasmon polaritons originate from the interplay of free carrier Drude response and interband transitions, which promise good intrinsic tunability. However, tunable in-plane hyperbolic plasmon polariton and its optical topological transition of the isofrequency contours to the elliptic topology in a natural material have not been realized. Here we demonstrate the tuning of the optical topological transition through Mo doping and temperature. The optical topological transition energy is tuned over a wide range, with frequencies ranging from 429 cm-1 (23.3 microns) for pure WTe2 to 270 cm-1 (37.0 microns) at the 50% Mo-doping level at 10 K. Moreover, the temperature-induced blueshift of the optical topological transition energy is also revealed, enabling active and reversible tuning. Surprisingly, the localized surface plasmon resonance in skew ribbons shows unusual polarization dependence, accurately manifesting its topology, which renders a reliable means to track the topology with far-field techniques. Our results open an avenue for reconfigurable photonic devices capable of plasmon polariton steering, such as canaling, focusing, and routing, and pave the way for low-symmetry plasmonic nanophotonics based on anisotropic natural materials.

Twist-Angle and Thickness-Ratio Tuning of Plasmon Polaritons in Twisted Bilayer van der Waals Films.

Stacking bilayer structures is an efficient way to tune the topology of polaritons in in-plane anisotropic films, e.g., by leveraging the twist angle (TA). However, the effect of another geometric parameter, the film thickness ratio (TR), on manipulating the plasmon topology in bilayers is elusive. Here, we fabricate bilayer structures of WTe2 films, which naturally host in-plane hyperbolic plasmons in the terahertz range. Plasmon topology is successfully modified by changing the TR and TA synergistically, manifested by the extinction spectra of unpatterned films and the polarization dependence of the plasmon intensity measured in skew ribbon arrays. Such TR- and TA-tunable topological transitions can be well explained based on the effective sheet optical conductivity by adding up those of the two films. Our study demonstrates TR as another degree of freedom for the manipulation of plasmonic topology in nanophotonics, exhibiting promising applications in biosensing, heat transfer, and the enhancement of spontaneous emission.

Regulation of autophagy gene expression and its implications in cancer.

Autophagy is a catabolic cellular process that targets and eliminates superfluous cytoplasmic components via lysosomal degradation. This evolutionarily conserved process is tightly regulated at multiple levels as it is critical for the maintenance of homeostasis. Research in the past decade has established that dysregulation of autophagy plays a major role in various diseases, such as cancer and neurodegeneration. However, modulation of autophagy as a therapeutic strategy requires identification of key players that can fine tune the induction of autophagy without complete abrogation. In this Review, we summarize the recent discoveries on the mechanism of regulation of ATG (autophagy related) gene expression at the level of transcription, post transcription and translation. Furthermore, we briefly discuss the role of aberrant expression of ATG genes in the context of cancer.

Transcriptional regulation of autophagy and its implications in human disease.

Macroautophagy/autophagy is a conserved catabolic pathway that is vital for maintaining cell homeostasis and promoting cell survival under stressful conditions. Dysregulation of autophagy is associated with a variety of human diseases, such as cancer, neurodegenerative diseases, and metabolic disorders. Therefore, this pathway must be precisely regulated at multiple levels, involving epigenetic, transcriptional, post-transcriptional, translational, and post-translational mechanisms, to prevent inappropriate autophagy activity. In this review, we focus on autophagy regulation at the transcriptional level, summarizing the transcription factors that control autophagy gene expression in both yeast and mammalian cells. Because the expression and/or subcellular localization of some autophagy transcription factors are altered in certain diseases, we also discuss how changes in transcriptional regulation of autophagy are associated with human pathophysiologies.

Bidirectional roles of the Ccr4-Not complex in regulating autophagy before and after nitrogen starvation.

Macroautophagy/autophagy is a highly conserved catabolic process by which cytoplasmic constituents are delivered to the vacuole/lysosome for degradation and recycling. To maintain cellular homeostasis and prevent pathologies, the induction and amplitude of autophagy activity are finely controlled through regulation of ATG gene expression. Here we report that the Ccr4-Not complex in Saccharomyces cerevisiae has bidirectional roles in regulating autophagy before and after nutrient deprivation. Under nutrient-rich conditions, Ccr4-Not directly targets the mRNAs of several ATG genes in the core autophagy machinery to promote their degradation through deadenylation, thus contributing to maintaining autophagy at the basal level. Upon starvation, Ccr4-Not releases its repression of these ATG genes and switches its role to promote the expression of a different subset of ATG genes, which is required for sufficient autophagy induction and activity. These results reveal that the Ccr4-Not complex is indispensable to maintain autophagy at the appropriate amplitude in both basal and stress conditions.Abbreviations: AID, auxin-inducible degron; Ape1, aminopeptidase I; Atg, autophagy related; Cvt, cytoplasm-to-vacuole targeting; DMSO, dimethyl sulfoxide; IAA, indole-3-acetic acid; PA, protein A; RIP, RNA immunoprecipitation.

MCOLN3/TRPML3 bridges the regulation of autophagosome biogenesis by PtdIns3P and the calcium channel.

In recent years, an increasing number of studies have started to investigate the roles of ions and ion channels in macroautophagy/autophagy. One finding is that calcium regulates multiple stages of autophagy with lysosomal calcium release being important for autophagosome and lysosome fusion. MCOLN3/TRPML3, as a calcium-permeable channel that is located on both lysosomes and autophagosomes, has been suggested as an autophagy regulator and a candidate to provide the calcium for autophagic fusion, but how this channel is activated remains unclear. In a recent article, Kim et al. demonstrate that MCOLN3 is a PtdIns3P downstream effector, and the activation of its channel function is critical for autophagosome biogenesis.

The coordination of V-ATPase and ATG16L1 is part of a common mechanism of non-canonical autophagy.

The conjugation of Atg8-family proteins with phospholipids on the double-membrane phagophore is one of the hallmarks of macroautopahgy/autophagy. However, in the past decades, Atg8-family proteins have also been identified on single-membrane structures, including the phagosome, endosome and lysosome. While the physiological importance of the non-canonical Atg8-family protein conjugation has been demonstrated, the mechanism of this process and the underlying regulation are still not very clear. In a recent paper, Hooper et al. found that during LC3-associated phagocytosis, reactive oxygen species are required for V-ATPase assembly, which is essential for the subsequent LC3 conjugation to the phagosome. Enhanced V-ATPase assembly and the direct engagement of ATG16L1 are also observed in a wide range of non-canonical Atg8-family protein conjugation processes, defining the V-ATPase and ATG16L1 as taking part in a common mechanism.

Effects of κ-Carrageenan and Guar Gum on the Rheological Properties and Microstructure of Phycocyanin Gel.

The effects of two polysaccharides on the performance and microstructure of phycocyanin gels were studied by choosing anionic polysaccharides (κ-carrageenan) and neutral polysaccharides (guar gum). The linear and nonlinear rheological properties and microstructure of the phycocyanin-polysaccharide composite gel were evaluated. The results show that both κ-carrageenan and guar gum can enhance the network structure of phycocyanin gel and weaken the frequency dependence. The sample with 0.4% κ-carrageenan has the highest gel strength. All samples exhibited Type I behavior (inter-cycling strain-thinning) and mainly elastic behavior. As the concentration of κ-carrageenan increases, hydrophobic interactions and disulfide bonds play an essential role in maintaining the three-dimensional structure of the gel. Too high a concentration of guar gum hinders the formation of protein disulfide bonds. This research can provide a theoretical basis for designing and developing new food products based on phycocyanin and different polysaccharides with ideal texture in the food industry.

How Cells Deal with the Fluctuating Environment: Autophagy Regulation under Stress in Yeast and Mammalian Systems.

Eukaryotic cells frequently experience fluctuations of the external and internal environments, such as changes in nutrient, energy and oxygen sources, and protein folding status, which, after reaching a particular threshold, become a type of stress. Cells develop several ways to deal with these various types of stress to maintain homeostasis and survival. Among the cellular survival mechanisms, autophagy is one of the most critical ways to mediate metabolic adaptation and clearance of damaged organelles. Autophagy is maintained at a basal level under normal growing conditions and gets stimulated by stress through different but connected mechanisms. In this review, we summarize the advances in understanding the autophagy regulation mechanisms under multiple types of stress including nutrient, energy, oxidative, and ER stress in both yeast and mammalian systems.

Vps13 is required for efficient autophagy in Saccharomyces cerevisiae.

Vps13 is a large, conserved protein that transports lipids between membranes. Its localization at multiple organelle membranes and membrane contact sites suggests its important physiological roles. In addition, the high correlation of mutant VPS13 with certain diseases, especially those involving neurodegeneration, makes this protein of considerable biomedical interest. Taking advantage of the fact that yeasts only have one Vps13 protein, the roles of yeast Vps13 have been well studied. However, whether and how Vps13 functions in macroautophagy/autophagy, a process of degradation of cytoplasmic cargoes, have been elusive questions. In this paper, we investigated the role of Vps13 in both non-selective and selective autophagy and found that this protein participates in non-selective autophagy, reticulophagy and pexophagy, but not mitophagy, and that Vps13 plays a role in the late stage of autophagy.

New regulators of PRKN-independent mitophagy.

Mitophagy, a type of selective autophagy targeting damaged or superfluous mitochondria, is critical to maintain cell homeostasis. Besides the well-characterized PRKN-dependent mitophagy, PRKN-independent mitophagy also plays significant physiological roles. In a recent study, researchers from Anne Simonsen's lab discovered two lipid binding kinases, GAK and PRKCD, as positive regulators of PRKN-independent mitophagy. The researchers further investigated how these two proteins regulate mitophagy and demonstrated their roles in vivo. Focusing on the less known PRKN-independent mitophagy regulators, these findings shed light on understanding the mechanism of mitophagy and its relation to diseases.

The Emerging Roles of Autophagy in Human Diseases.

Autophagy, a process of cellular self-digestion, delivers intracellular components including superfluous and dysfunctional proteins and organelles to the lysosome for degradation and recycling and is important to maintain cellular homeostasis. In recent decades, autophagy has been found to help fight against a variety of human diseases, but, at the same time, autophagy can also promote the procession of certain pathologies, which makes the connection between autophagy and diseases complex but interesting. In this review, we summarize the advances in understanding the roles of autophagy in human diseases and the therapeutic methods targeting autophagy and discuss some of the remaining questions in this field, focusing on cancer, neurodegenerative diseases, infectious diseases and metabolic disorders.

Layer-Dependent Pressure Effect on the Electronic Structure of 2D Black Phosphorus.

Through infrared spectroscopy, we systematically study the pressure effect on electronic structures of few-layer black phosphorus (BP) with layer number ranging from 2 to 13. We reveal that the pressure-induced shift of optical transitions exhibits strong layer dependence. In sharp contrast to the bulk counterpart which undergoes a semiconductor to semimetal transition under ∼1.8 GPa, the band gap of 2 L increases with increasing pressure until beyond 2 GPa. Meanwhile, for a sample with a given layer number, the pressure-induced shift also differs for transitions with different indices. Through the tight-binding model in conjunction with a Morse potential for the interlayer coupling, this layer- and transition-index-dependent pressure effect can be fully accounted. Our study paves a way for versatile van der Waals engineering of two-dimensional BP.

A perspective on the role of autophagy in cancer.

Autophagy refers to a ubiquitous set of catabolic pathways required to achieve proper cellular homeostasis. Aberrant autophagy has been implicated in a multitude of diseases including cancer. In this review, we highlight pioneering and groundbreaking research that centers on delineating the role of autophagy in cancer initiation, proliferation and metastasis. First, we discuss the autophagy-related (ATG) proteins and their respective roles in the de novo formation of autophagosomes and the subsequent delivery of cargo to the lysosome for recycling. Next, we touch upon the history of cancer research that centers upon ATG proteins and regulatory mechanisms that control an appropriate autophagic response and how these are altered in the diseased state. Then, we discuss the various discoveries that led to the idea of autophagy as a double-edged sword when it comes to cancer therapy. This review also briefly narrates how different types of autophagy-selective macroautophagy and chaperone-mediated autophagy, have been linked to different cancers. Overall, these studies build upon a steadfast trajectory that aims to solve the monumentally daunting challenge of finding a cure for many types of cancer by modulating autophagy either through inhibition or induction.