Receptor-mediated cargo hitchhiking on bulk autophagy.

While the molecular mechanism of autophagy is well studied, the cargoes delivered by autophagy remain incompletely characterized. To examine the selectivity of autophagy cargo, we conducted proteomics on isolated yeast autophagic bodies, which are intermediate structures in the autophagy process. We identify a protein, Hab1, that is highly preferentially delivered to vacuoles. The N-terminal 42 amino acid region of Hab1 contains an amphipathic helix and an Atg8-family interacting motif, both of which are necessary and sufficient for the preferential delivery of Hab1 by autophagy. We find that fusion of this region with a cytosolic protein results in preferential delivery of this protein to the vacuole. Furthermore, attachment of this region to an organelle allows for autophagic delivery in a manner independent of canonical autophagy receptor or scaffold proteins. We propose a novel mode of selective autophagy in which a receptor, in this case Hab1, binds directly to forming isolation membranes during bulk autophagy.

Wetting regulates autophagy of phase-separated compartments and the cytosol.

Compartmentalization of cellular material in droplet-like structures is a hallmark of liquid-liquid phase separation1,2, but the mechanisms of droplet removal are poorly understood. Evidence suggests that droplets can be degraded by autophagy3,4, a highly conserved degradation system in which membrane sheets bend to isolate portions of the cytoplasm within double-membrane autophagosomes5-7. Here we examine how autophagosomes sequester droplets that contain the protein p62 (also known as SQSTM1) in living cells, and demonstrate that double-membrane, autophagosome-like vesicles form at the surface of protein-free droplets in vitro through partial wetting. A minimal physical model shows that droplet surface tension supports the formation of membrane sheets. The model also predicts that bending sheets either divide droplets for piecemeal sequestration or sequester entire droplets. We find that autophagosomal sequestration is robust to variations in the droplet-sheet adhesion strength. However, the two sides of partially wetted sheets are exposed to different environments, which can determine the bending direction of autophagosomal sheets. Our discovery of this interplay between the material properties of droplets and membrane sheets enables us to elucidate the mechanisms that underpin droplet autophagy, or 'fluidophagy'. Furthermore, we uncover a switching mechanism that allows droplets to act as liquid assembly platforms for cytosol-degrading autophagosomes8 or as specific autophagy substrates9-11. We propose that droplet-mediated autophagy represents a previously undescribed class of processes that are driven by elastocapillarity, highlighting the importance of wetting in cytosolic organization.

Phase separation organizes the site of autophagosome formation.

Many biomolecules undergo liquid-liquid phase separation to form liquid-like condensates that mediate diverse cellular functions1,2. Autophagy is able to degrade such condensates using autophagosomes-double-membrane structures that are synthesized de novo at the pre-autophagosomal structure (PAS) in yeast3-5. Whereas Atg proteins that associate with the PAS have been characterized, the physicochemical and functional properties of the PAS remain unclear owing to its small size and fragility. Here we show that the PAS is in fact a liquid-like condensate of Atg proteins. The autophagy-initiating Atg1 complex undergoes phase separation to form liquid droplets in vitro, and point mutations or phosphorylation that inhibit phase separation impair PAS formation in vivo. In vitro experiments show that Atg1-complex droplets can be tethered to membranes via specific protein-protein interactions, explaining the vacuolar membrane localization of the PAS in vivo. We propose that phase separation has a critical, active role in autophagy, whereby it organizes the autophagy machinery at the PAS.

Wetting of phase-separated droplets on plant vacuole membranes leads to a competition between tonoplast budding and nanotube formation.

Seeds of dicotyledonous plants store proteins in dedicated membrane-bounded organelles called protein storage vacuoles (PSVs). Formed during seed development through morphological and functional reconfiguration of lytic vacuoles in embryos [M. Feeney et al., Plant Physiol. 177, 241-254 (2018)], PSVs undergo division during the later stages of seed maturation. Here, we study the biophysical mechanism of PSV morphogenesis in vivo, discovering that micrometer-sized liquid droplets containing storage proteins form within the vacuolar lumen through phase separation and wet the tonoplast (vacuolar membrane). We identify distinct tonoplast shapes that arise in response to membrane wetting by droplets and derive a simple theoretical model that conceptualizes these geometries. Conditions of low membrane spontaneous curvature and moderate contact angle (i.e., wettability) favor droplet-induced membrane budding, thereby likely serving to generate multiple, physically separated PSVs in seeds. In contrast, high membrane spontaneous curvature and strong wettability promote an intricate and previously unreported membrane nanotube network that forms at the droplet interface, allowing molecule exchange between droplets and the vacuolar interior. Furthermore, our model predicts that with decreasing wettability, this nanotube structure transitions to a regime with bud and nanotube coexistence, which we confirmed in vitro. As such, we identify intracellular wetting [J. Agudo-Canalejo et al., Nature 591, 142-146 (2021)] as the mechanism underlying PSV morphogenesis and provide evidence suggesting that interconvertible membrane wetting morphologies play a role in the organization of liquid phases in cells.

A 4H-SiC CMOS Oscillator-Based Temperature Sensor Operating from 298 K up to 573 K.

In this paper, we propose a temperature sensor based on a 4H-SiC CMOS oscillator circuit and that is able to operate in the temperature range between 298 K and 573 K. The circuit is developed on Fraunhofer IISB's 2 µm 4H-SiC CMOS technology and is designed for a bias voltage of 20 V and an oscillation frequency of 90 kHz at room temperature. The possibility to relate the absolute temperature with the oscillation frequency is due to the temperature dependency of the threshold voltage and of the channel mobility of the transistors. An analytical model of the frequency-temperature dependency has been developed and is used as a starting point for the design of the circuit. Once the circuit has been designed, numerical simulations are performed with the Verilog-A BSIM4SiC model, which has been opportunely tuned on Fraunhofer IISB's 2 µm 4H-SiC CMOS technology, and their results showed almost linear frequency-temperature characteristics with a coefficient of determination that was higher than 0.9681 for all of the bias conditions, whose maximum is 0.9992 at a VDD = 12.5 V. Moreover, we considered the effects of the fabrication process through a Monte Carlo analysis, where we varied the threshold voltage and the channel mobility with different values of the Gaussian distribution variance. For example, at VDD = 20 V, a deviation of 17.4% from the nominal characteristic is obtained for a Gaussian distribution variance of 20%. Finally, we applied the one-point calibration procedure, and temperature errors of +8.8 K and -5.8 K were observed at VDD = 15 V.

Phase separation in evaporating all-aqueous sessile drops.

The phase transition and phase distribution in an all-aqueous sessile drop containing polyethylene glycol (PEG) and dextran is studied. Evaporation of water triggers the formation of dextran-rich droplets close to the contact line of the drop that subsequently migrate towards the drop center. The likely reason for the droplet migration is Marangoni convection due to stresses at the interface between the dextran-rich droplets and the surrounding liquid.

Comparative incidence of early and late bloodstream and respiratory tract co-infection in patients admitted to ICU with COVID-19 pneumonia versus Influenza A or B pneumonia versus no viral pneumonia: wales multicentre ICU cohort study.

OBJECTIVE: The aim is to characterise early and late respiratory and bloodstream co-infection in patients admitted to intensive care units (ICUs) with SARS-CoV-2-related acute hypoxemic respiratory failure (AHRF) needing respiratory support in seven ICUs within Wales, during the first wave of the COVID-19 pandemic. We compare the rate of positivity of different secondary pathogens and their antimicrobial sensitivity in three different patient groups: patients admitted to ICU with COVID-19 pneumonia, Influenza A or B pneumonia, and patients without viral pneumonia. DESIGN: Multicentre, retrospective, observational cohort study with rapid microbiology data from Public Health Wales, sharing of clinical and demographic data from seven participating ICUs. SETTING: Seven Welsh ICUs participated between 10 March and 31 July 2020. Clinical and demographic data for COVID-19 disease were shared by each participating centres, and microbiology data were extracted from a data repository within Public Health Wales. Comparative data were taken from a cohort of patients without viral pneumonia admitted to ICU during the same period as the COVID-19 cohort (referred to as no viral pneumonia or 'no viral' group), and to a retrospective non-matched cohort of consecutive patients with Influenza A or B admitted to ICUs from 20 November 2017. The comparative data for Influenza pneumonia and no viral pneumonia were taken from one of the seven participating ICUs. PARTICIPANTS: A total of 299 consecutive patients admitted to ICUs with COVID-19 pneumonia were compared with 173 and 48 patients admitted with no viral pneumonia or Influenza A or B pneumonia, respectively. MAIN OUTCOME MEASURES: Primary outcome was to calculate comparative incidence of early and late co-infection in patients admitted to ICU with COVID-19, Influenza A or B pneumonia and no viral pneumonia. Secondary outcome was to calculate the individual group of early and late co-infection rate on a per-patient and per-sample basis, with their antimicrobial susceptibility and thirdly to ascertain any statistical correlation between clinical and demographic variables with rate of acquiring co-infection following ICU admission. RESULTS: A total of 299 adults (median age 57, M/F 2:1) were included in the COVID-19 ICU cohort. The incidence of respiratory and bloodstream co-infection was 40.5% and 15.1%, respectively. Staphylococcus aureus was the predominant bacterial pathogen within the first 48 h. Gram-negative organisms from Enterobacterales group were predominantly seen after 48 h in COVID-19 cohort. Comparative no viral pneumonia cohort had lower rates of respiratory tract infection and bloodstream infection. The influenza cohort had similar rates respiratory tract infection and bloodstream infection. Mortality in all three groups was similar, and no clinical or demographic variables were found to increase the rate of co-infection and ICU mortality. CONCLUSIONS: Higher incidence of bacterial co-infection was found in COVID-19 cohort as compared to the no viral pneumonia cohort admitted to ICUs for respiratory support.

Gtr/Ego-independent TORC1 activation is achieved through a glutamine-sensitive interaction with Pib2 on the vacuolar membrane.

TORC1 is a central regulator of cell growth in response to amino acids. The role of the evolutionarily conserved Gtr/Rag pathway in the regulation of TORC1 is well-established. Recent genetic studies suggest that an additional regulatory pathway, depending on the activity of Pib2, plays a role in TORC1 activation independently of the Gtr/Rag pathway. However, the interplay between the Pib2 pathway and the Gtr/Rag pathway remains unclear. In this study, we show that Pib2 and Gtr/Ego form distinct complexes with TORC1 in a mutually exclusive manner, implying dedicated functional relationships between TORC1 and Pib2 or Gtr/Rag in response to specific amino acids. Furthermore, simultaneous depletion of Pib2 and the Gtr/Ego system abolishes TORC1 activity and completely compromises the vacuolar localization of TORC1. Thus, the amino acid-dependent activation of TORC1 is achieved through the Pib2 and Gtr/Ego pathways alone. Finally, we show that glutamine induces a dose-dependent increase in Pib2-TORC1 complex formation, and that glutamine binds directly to the Pib2 complex. These data provide strong preliminary evidence for Pib2 functioning as a putative glutamine sensor in the regulation of TORC1.

Inverse scattering designs of dispersion-engineered planar waveguides.

We have introduced a semi-analytical IS technique suitable for multipole, rational function reflection coefficients, and used it for the design of dispersion-engineered planar waveguides. The technique is used to derive extensive dispersion maps, including higher dispersion coefficients, corresponding to three-, five- and seven-pole reflection coefficients. It is shown that common features of dispersion-engineered waveguides such as refractive-index trenches, rings and oscillations come naturally from this approach when the magnitude of leaky poles in increased. Increasing the number of poles is shown to offer a small but measureable change in higher order dispersion with designs dominated by a three pole design with a leaky pole pair of the smallest modulus.

Surface topography and wetting modifications of PEEK for implant applications.

Polyetheretherketone (PEEK) is considered as a substitute for metallic implant materials due to its extremely low elastic modulus (3-4 GPa). Despite its good mechanical properties, PEEK exhibits a slow integration with the bone tissue due to its relatively inert surface and low biocompatibility. We introduced a dual modification method, which combines the laser and plasma surface treatments to achieve hierarchically patterned PEEK surfaces. While the plasma treatment leads to nanotopography, the laser treatment induces microstructures over the PEEK surface. On the other hand, plasma and laser treatments induce inhomogeneity in the surface chemistry in addition to the tailored surface topography. Therefore, we coated the structured PEEK surfaces with a thin alumina layer by pulsed laser deposition (PLD) to get identical surface chemistry on each substrate. Such alumina-coated PEEK surfaces are used as a model to investigate the effect of the surface topography on the wetting independent from the surface chemistry. Prepared surfaces bring advantages of enhanced wetting, multiscaled topography, proven biocompatibility (alumina layer), and low elastic modulus (PEEK as substrate), which together may trigger the use of PEEK in bone and other implant applications.

The mechanism of Atg15-mediated membrane disruption in autophagy.

Autophagy is a lysosomal/vacuolar delivery system that degrades cytoplasmic material. During autophagy, autophagosomes deliver cellular components to the vacuole, resulting in the release of a cargo-containing autophagic body (AB) into the vacuole. AB membranes must be disrupted for degradation of cargo to occur. The lipase Atg15 and vacuolar proteases Pep4 and Prb1 are known to be necessary for this disruption and cargo degradation, but the mechanistic underpinnings remain unclear. In this study, we establish a system to detect lipase activity in the vacuole and show that Atg15 is the sole vacuolar phospholipase. Pep4 and Prb1 are required for the activation of Atg15 lipase function, which occurs following delivery of Atg15 to the vacuole by the MVB pathway. In vitro experiments reveal that Atg15 is a phospholipase B of broad substrate specificity that is likely implicated in the disruption of a range of membranes. Further, we use isolated ABs to demonstrate that Atg15 alone is able to disrupt AB membranes.

Academic investigator-initiated trials and the challenge of sponsor responsibility: the Cologne Sponsor Model.

BACKGROUND: With the amendment to the German Drug Law in 2004, the conduct of clinical trials changed by at least two main aspects: (1) The principles of Good Clinical Practice (GCP) were implemented in the national legislation, and (2) for the first time, the function of the sponsor of a clinical trial and the clinical trial itself have become legally binding definitions. By that, legal differences between industrial and academic clinical trials no longer exist. Clinical trials initiated by investigators have to fulfil the same requirements while the entire sponsor responsibility has to be carried out by the Coordinating Investigator or his institution including implementation of a quality management system according to the GCP. PURPOSE: The Cologne Sponsor Model is an effective approach with settings, structures, basic features, action, and reporting lines, as well as funding for clinical trials initiated in an academic environment. RESULTS: The University of Cologne assumes the sponsor responsibility for clinical trials organised by the university researchers according to law. Sponsor's duties are delegated to a central operational unit of the sponsor - the Clinical Trials Center Cologne - which further delegates duties to the Coordinating Investigator. Clinical Trials Center Cologne was established in 2002 to support the performance of clinical trials at the university by offering comprehensive advisory and practical services covering all aspects of study planning and conduct. Furthermore, a specialised division of its quality management department acts as an independent sponsor's Quality Assurance Unit. The Clinical Trials Center Cologne has established a quality management system consisting of different components (1) to enable a reasoned decision to subsequent delegation, (2) for risk-based surveillance of trial conduct (audits, monitoring-checks, and reports), and (3) support and training of the Coordinating Investigator. LIMITATIONS: Double functions of persons and departments in the university environment sometimes make it difficult to define roles in such a model. Therefore, it is necessary to establish clear reporting lines and moreover to monitor regularly and carefully the roles and responsibilities. CONCLUSIONS: With the combination of central management and support, control and independence of the researchers, our model represents a 'risk-based' system that offers a sensible option that fulfils the requirements of legal regulations and GCP for trials organised within the university environment.

Integrated 64 pixel UV image sensor and readout in a silicon carbide CMOS technology.

This work demonstrates the first on-chip UV optoelectronic integration in 4H-SiC CMOS, which includes an image sensor with 64 active pixels and a total of 1263 transistors on a 100 mm2 chip. The reported image sensor offers serial digital, analog, and 2-bit ADC outputs and operates at 0.39 Hz with a maximum power consumption of 60 µW, which are significant improvements over previous reports. UV optoelectronics have applications in flame detection, satellites, astronomy, UV photography, and healthcare. The complexity of this optoelectronic system paves the way for new applications such harsh environment microcontrollers.

Intracellular wetting mediates contacts between liquid compartments and membrane-bound organelles.

Protein-rich droplets, such as stress granules, P-bodies, and the nucleolus, perform diverse and specialized cellular functions. Recent evidence has shown the droplets, which are also known as biomolecular condensates or membrane-less compartments, form by phase separation. Many droplets also contact membrane-bound organelles, thereby functioning in development, intracellular degradation, and organization. These underappreciated interactions have major implications for our fundamental understanding of cells. Starting with a brief introduction to wetting phenomena, we summarize recent progress in the emerging field of droplet-membrane contact. We describe the physical mechanism of droplet-membrane interactions, discuss how these interactions remodel droplets and membranes, and introduce "membrane scaffolding" by liquids as a novel reshaping mechanism, thereby demonstrating that droplet-membrane interactions are elastic wetting phenomena. "Membrane-less" and "membrane-bound" condensates likely represent distinct wetting states that together link phase separation with mechanosensitivity and explain key structures observed during embryogenesis, during autophagy, and at synapses. We therefore contend that droplet wetting on membranes provides a robust and intricate means of intracellular organization.

Should I bend or should I grow: the mechanisms of droplet-mediated autophagosome formation.

Phase-separated droplets with liquid-like properties can be degraded by macroautophagy/autophagy, but the mechanism underlying this degradation is poorly understood. We have recently derived a physical model to investigate the interaction between autophagic membranes and such droplets, uncovering that intrinsic wetting interactions underlie droplet-membrane contacts. We found that the competition between droplet surface tension and the increasing tendency of growing membrane sheets to bend determines whether a droplet is completely engulfed or isolated in a piecemeal fashion, a process we term fluidophagy. Intriguingly, we found that another critical parameter of droplet-membrane interactions, the spontaneous curvature of the membrane, determines whether the droplet is degraded by autophagy or - counterintuitively - serves as a platform from which autophagic membranes expand into the cytosol. We also discovered that the interaction of membrane-associated LC3 with the LC3-interacting region (LIR) found in the autophagic cargo receptor protein SQSTM1/p62 and many other autophagy-related proteins influences the preferred bending directionality of forming autophagosomes in living cells. Our study provides a physical account of how droplet-membrane wetting underpins the structure and fate of forming autophagosomes.

Autophagy facilitates adaptation of budding yeast to respiratory growth by recycling serine for one-carbon metabolism.

The mechanism and function of autophagy as a highly-conserved bulk degradation pathway are well studied, but the physiological role of autophagy remains poorly understood. We show that autophagy is involved in the adaptation of Saccharomyces cerevisiae to respiratory growth through its recycling of serine. On respiratory media, growth onset, mitochondrial initiator tRNA modification and mitochondrial protein expression are delayed in autophagy defective cells, suggesting that mitochondrial one-carbon metabolism is perturbed in these cells. The supplementation of serine, which is a key one-carbon metabolite, is able to restore mitochondrial protein expression and alleviate delayed respiratory growth. These results indicate that autophagy-derived serine feeds into mitochondrial one-carbon metabolism, supporting the initiation of mitochondrial protein synthesis and allowing rapid adaptation to respiratory growth.

Agent-based modelling reveals strategies to reduce the fitness and metastatic potential of circulating tumour cell clusters.

Metastasis-the ability of cancer cells to disperse throughout the body and establish new tumours at distant locations-is responsible for most cancer-related deaths. Although both single and clusters of circulating tumour cells (CTCs) have been isolated from cancer patients, CTC clusters are generally associated with higher metastatic potential and worse prognosis. From an evolutionary perspective, being part of a cluster can provide cells with several benefits both in terms of survival (e.g. protection) and reproduction (group dispersal). Thus, strategies aimed at inducing cluster dissociation could decrease the metastatic potential of CTCs. However, finding agents or conditions that induce the dissociation of CTC clusters is hampered by the fact that their detection, isolation and propagation remain challenging. Here, we used a mechanistic agent-based model to (a) investigate the response of CTC clusters of various sizes and densities to different challenges-in terms of cell survival and cluster stability, and (b) make predictions as to the combination of factors and parameter values that could decrease the fitness and metastatic potential of CTC clusters. Our model shows that the resilience and stability of CTC clusters are dependent on both their size and density. Also, CTC clusters of distinct sizes and densities respond differently to changes in resource availability, with high-density clusters being least affected. In terms of responses to microenvironmental threats (such as drugs), increasing their intensity is, generally, least effective on high-density clusters. Lastly, we found that combining various levels of resource availability and threat intensity can be more effective at decreasing the survival of CTC clusters than each factor alone. We suggest that the complex effects that cluster density and size showed on both the resilience and stability of the CTC clusters are likely to have significant consequences for their metastatic potential and responses to therapies.

Kombucha: a novel model system for cooperation and conflict in a complex multi-species microbial ecosystem.

Kombucha, a fermented tea beverage with an acidic and effervescent taste, is composed of a multispecies microbial ecosystem with complex interactions that are characterized by both cooperation and conflict. In kombucha, a complex community of bacteria and yeast initiates the fermentation of a starter tea (usually black or green tea with sugar), producing a biofilm that covers the liquid over several weeks. This happens through several fermentative phases that are characterized by cooperation and competition among the microbes within the kombucha solution. Yeast produce invertase as a public good that enables both yeast and bacteria to metabolize sugars. Bacteria produce a surface biofilm which may act as a public good providing protection from invaders, storage for resources, and greater access to oxygen for microbes embedded within it. The ethanol and acid produced during the fermentative process (by yeast and bacteria, respectively) may also help to protect the system from invasion by microbial competitors from the environment. Thus, kombucha can serve as a model system for addressing important questions about the evolution of cooperation and conflict in diverse multispecies systems. Further, it has the potential to be artificially selected to specialize it for particular human uses, including the development of antimicrobial ecosystems and novel materials. Finally, kombucha is easily-propagated, non-toxic, and inexpensive, making it an excellent system for scientific inquiry and citizen science.

Identification of expression and function of the glucagon-like peptide-1 receptor in colonic smooth muscle.

The insulinotropic effects of the incretin hormone, glucagon-like peptide-1 (GLP-1) are mediated via GLP-1 receptors (GLP-1R) present on pancreatic ß cells. GLP-1 causes a decrease in the motility of stomach and intestine which involves both central and peripheral nervous systems. The expression and function of GLP-1R in gastrointestinal smooth muscle, however, are not clear. Muscle strips and isolated muscle cells were prepared from mouse colon and the effect of GLP-1(7-36) amide on acetylcholine (ACh)-induced contraction was measured. Muscle cells in culture were used to identify the expression of GLP-1R and the signaling pathways activated by GLP-1(7-36) amide. GLP-1R was expressed in the mucosal and non-mucosal tissue preparations derived from colon, and in smooth muscle cell cultures devoid of other cells such as enteric neurons. In colonic muscle strips, the addition of GLP-1(7-36) amide caused dose-dependent inhibition of acetylcholine-induced contractions. The effect of GLP-1(7-36) amide was partly inhibited by the neuronal blocker tetrodotoxin and nitric oxide (NO) synthase inhibitor l-NNA suggesting both NO-dependent neural and NO-independent direct effects on smooth muscle. In isolated colonic smooth muscle cells, GLP-1(7-36) amide caused an increase in Gαs activity, cAMP levels, and PKA activity, and inhibited ACh-induced contraction. The effect of GLP-1(7-36) amide on Gαs activity and cAMP levels was blocked by NF449, an inhibitor of Gαs, and the effect of GLP-1(7-36) amide on contraction was blocked by NF449 and myristoylated PKI, an inhibitor of PKA. We conclude that colonic smooth muscle cells express GLP-1R, and GLP-1(7-36) amide inhibits acetylcholine-induced contraction via GLP-1R coupled to the Gαs/cAMP/PKA pathway.

In Vitro Model-Systems to Understand the Biology and Clinical Significance of Circulating Tumor Cell Clusters.

The isolation of clusters of circulating tumor cells (CTCs) from cancer patients has recently challenged the accepted view that the initiation of secondary tumors during metastasis involves the dissemination of individual cancer cells. As such clusters appear to be more aggressive than single tumor cells, CTC clusters are now considered a main player in the metastatic process, and many studies are exploring their diagnostic, prognostic, and clinical significance. However, several technical challenges limit advances in this area. Here, we suggest the use of established cancer cell lines that grow as cell clusters in suspension as a complementary approach that can help in understanding the biology of CTC clusters and their clinical significance. We argue that the many similarities between these "surrogate" clusters and the CTC clusters isolated from patients (e.g., in terms of size, morphology, heterogeneous expression of epithelial and mesenchymal markers, and type of cell-cell junctions) make these cell lines ideal systems for the development of strategies aimed at preventing or slowing down the metastatic process by targeting CTC clusters.