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Viruses target mitochondria to promote their replication, and infection-induced stress during the progression of infection leads to the regulation of antiviral defenses and mitochondrial metabolism which are opposed by counteracting viral factors. The precise structural and functional changes that underlie how mitochondria react to the infection remain largely unclear. Here we show extensive transcriptional remodeling of protein-encoding host genes involved in the respiratory chain, apoptosis, and structural organization of mitochondria as herpes simplex virus type 1 lytic infection proceeds from early to late stages of infection. High-resolution microscopy and interaction analyses unveiled infection-induced emergence of rough, thin, and elongated mitochondria relocalized to the perinuclear area, a significant increase in the number and clustering of endoplasmic reticulum-mitochondria contact sites, and thickening and shortening of mitochondrial cristae. Finally, metabolic analyses demonstrated that reactivation of ATP production is accompanied by increased mitochondrial Ca2+ content and proton leakage as the infection proceeds. Overall, the significant structural and functional changes in the mitochondria triggered by the viral invasion are tightly connected to the progression of the virus infection.

During lytic herpes simplex virus 1 (HSV-1) infection, the expansion of the viral replication compartments leads to an enrichment of the host chromatin in the peripheral nucleoplasm. We have shown previously that HSV-1 infection induces the formation of channels through the compacted peripheral chromatin. Here, we used three-dimensional confocal and expansion microscopy, soft X-ray tomography, electron microscopy, and random walk simulations to analyze the kinetics of host chromatin redistribution and capsid localization relative to their egress site at the nuclear envelope. Our data demonstrated a gradual increase in chromatin marginalization, and the kinetics of chromatin smoothening around the viral replication compartments correlated with their expansion. We also observed a gradual transfer of capsids to the nuclear envelope. Later in the infection, random walk modeling indicated a gradually faster transport of capsids to the nuclear envelope that correlated with an increase in the interchromatin channels in the nuclear periphery. Our study reveals a stepwise and time-dependent mechanism of herpesvirus nuclear egress, in which progeny viral capsids approach the egress sites at the nuclear envelope via interchromatin spaces.

Parvoviral genome translocation from the plasma membrane into the nucleus is a coordinated multistep process mediated by capsid proteins. We used fast confocal microscopy line scan imaging combined with image correlation methods including auto-, pair- and cross-correlation, and number and brightness analysis, to study the parvovirus entry pathway at the single-particle level in living cells. Our results show that the endosome-associated movement of virus particles fluctuates from fast to slow. Fast transit of single cytoplasmic capsids to the nuclear envelope is followed by slow movement of capsids and fast diffusion of capsid fragments in the nucleoplasm. The unique combination of image analyses allowed us to follow the fate of intracellular single virus particles and their interactions with importin β revealing previously unknown dynamics of the entry pathway.

Various types of DNA viruses are known to elicit the formation of a large nuclear viral replication compartment and marginalization of the cell chromatin. We used three-dimensional soft x-ray tomography, confocal and electron microscopy, combined with numerical modelling of capsid diffusion to analyse the molecular organization of chromatin in herpes simplex virus 1 infection and its effect on the transport of progeny viral capsids to the nuclear envelope. Our data showed that the formation of the viral replication compartment at late infection resulted in the enrichment of heterochromatin in the nuclear periphery accompanied by the compaction of chromatin. Random walk modelling of herpes simplex virus 1-sized particles in a three-dimensional soft x-ray tomography reconstruction of an infected cell nucleus demonstrated that the peripheral, compacted chromatin restricts viral capsid diffusion, but due to interchromatin channels capsids are able to reach the nuclear envelope, the site of their nuclear egress.

Mammalian receptor-mediated endocytosis (RME) often involves at least one of three isoforms of the large GTPase dynamin (Dyn). Dyn pinches-off vesicles at the plasma membrane and mediates uptake of many viruses, although some viruses directly penetrate the plasma membrane. RME is classically interrogated by genetic and pharmacological interference, but this has been hampered by undesired effects. Here we studied virus entry in conditional genetic knock-out (KO) mouse embryonic fibroblasts lacking expression of all three dynamin isoforms (Dyn-KO-MEFs). The small canine parvovirus known to use a single receptor, transferrin receptor, strictly depended on dynamin. Larger viruses or viruses known to use multiple receptors, including alphaviruses, influenza, vesicular stomatitis, bunya, adeno, vaccinia, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and rhinoviruses infected Dyn-KO-MEFs, albeit at higher dosage than wild-type MEFs. In absence of the transmembrane protease serine subtype 2 (TMPRSS2), which normally activates the SARS-CoV-2 spike protein for plasma membrane fusion, SARS-CoV-2 infected angiotensin-converting enzyme 2 (ACE2)-expressing MEFs predominantly through dynamin- and actin-dependent endocytosis. In presence of TMPRSS2 the ancestral Wuhan-strain bypassed both dynamin-dependent and -independent endocytosis, and was less sensitive to endosome maturation inhibitors than the Omicron B1 and XBB variants, supporting the notion that the Omicron variants do not efficiently use TMPRSS2. Collectively, our study suggests that dynamin function at endocytic pits can be essential for infection with single-receptor viruses, while it is not essential but increases uptake and infection efficiency of multi-receptor viruses that otherwise rely on a functional actin network for infection. Author summary: To initiate their infection cycle, most viruses first need to enter their target cells, a process called endocytosis. In mammalian cells, endocytosis often involves a class of proteins called dynamins. While numerous viruses, including SARS-CoV-2, efficiently infect cells by dynamin-mediated endocytosis we found that in the absence of these proteins an alternative cell entry mechanism exists, allowing multiple pathogenic human viruses to enter and infect cells. Unlike the dynamin-mediated infection, the efficient internalization of viral particles via dynamin-independent endocytosis seems to always require functional actin fibers, which are structural components of the cell contractile cytoskeleton. Thus, multiple viruses can infect their target cells using at last two entry mechanisms, inhibiting both may provide effective antiviral therapies. [ABSTRACT FROM AUTHOR]

Open science (OS) awareness and skills are increasingly becoming an essential part of everyday scientific work as e.g., many journals require authors to share data. However, following an OS workflow can seem challenging at first. Thus, instructions by journals and other guidelines are important. But how comprehensive are they in the field of ecology and evolutionary biology (Ecol Evol)? To find this out, we reviewed 20 published OS guideline articles aimed for ecologists or evolutionary biologists, together with the data policies of 17 Ecol Evol journals to chart the current landscape of OS guidelines in the field, find potential gaps, identify field‐specific barriers for OS and discuss solutions to overcome these challenges. We found that many of the guideline articles covered similar topics, despite being written for a narrow field or specific target audience. Likewise, many of the guideline articles mentioned similar obstacles that could hinder or postpone a transition to open data sharing. Thus, there could be a need for a more widely known, general OS guideline for Ecol Evol. Following the same guideline could also enhance the uniformity of the OS practices carried on in the field. However, some topics, like long‐term experiments and physical samples, were mentioned surprisingly seldom, although they are typical issues in Ecol Evol. Of the journals, 15 out of 17 expected or at least encouraged data sharing either for all articles or under specific conditions, e.g. for registered reports and 10 of those required data sharing at the submission phase. The coverage of journal data policies varied greatly between journals, from practically non‐existing to very extensive. As journals can contribute greatly by leading the way and making open data useful, we recommend that the publishers and journals would invest in clear and comprehensive data policies and instructions for authors. [ABSTRACT FROM AUTHOR]

Aim: Global‐scale studies are necessary to draw general conclusions on how trophic interactions vary with urbanization and to explore how the effects of urbanization change along latitudinal gradients. We predict that the intensity of trophic interactions decreases in response to urbanization (quantified by human population density). Since trophic interactions are more intense at lower latitudes, we also expect major impacts of urbanization at higher latitudes, where base levels are essentially lower. Location: Global (881 study sites). Time period: 2000–2021. Major taxa studied: Birds, arthropods and woody plants. Methods: We compiled global data on insect herbivory and bird predation from studies that employed similar methods and fitted generalized linear mixed models to test how these trophic interactions vary with human population density, latitude and their interactions. Results: The intensity of herbivory and predation decreased with an increase in human population density at lower latitudes. Surprisingly, it remained unaffected at intermediate latitudes and even increased at higher latitudes. Main conclusions: The observed patterns may be attributed to local climate changes in urban areas, such as the Urban Heat Island effect, which disrupts thermal stability in the tropics while increasing niche availability at polar latitudes. [ABSTRACT FROM AUTHOR]

Epithelial cells are in continuous dynamic biochemical and physical interaction with their extracellular environment. Ultimately, this interplay guides fundamental physiological processes. In these interactions, cells generate fast local and global transients of Ca2+ ions, which act as key intracellular messengers. However, the mechanical triggers initiating these responses have remained unclear. Light‐responsive materials offer intriguing possibilities to dynamically modify the physical niche of the cells. Here, a light‐sensitive azobenzene‐based glassy material that can be micropatterned with visible light to undergo spatiotemporally controlled deformations is used. Real‐time monitoring of consequential rapid intracellular Ca2+ signals reveals that the mechanosensitive cation channel Piezo1 has a major role in generating the Ca2+ transients after nanoscale mechanical deformation of the cell culture substrate. Furthermore, the studies indicate that Piezo1 preferably responds to shear deformation at the cell‐material interphase rather than to absolute topographical change of the substrate. Finally, the experimentally verified computational model suggests that Na+ entering alongside Ca2+ through the mechanosensitive cation channels modulates the duration of Ca2+ transients, influencing differently the directly stimulated cells and their neighbors. This highlights the complexity of mechanical signaling in multicellular systems. These results give mechanistic understanding on how cells respond to rapid nanoscale material dynamics and deformations. [ABSTRACT FROM AUTHOR]

In vivo, cells are surrounded by a constantly changing microenvironment, which regulates many cell functions such as differentiation, migration, and cell death. Stimuli‐responsive biomaterials aim to mimic this interaction between cells and extracellular matrix in vitro. However, reproducing dynamic signaling noninvasively without affecting the cell viability remains a challenge. Herein, a dynamic cell culturing platform consisting of a light‐responsive azobenzene molecular glass film and a protective polydimethylsiloxane (PDMS) coating is developed. By tuning the PDMS layer thickness, surface relief gratings (SRGs) can be efficiently photoinscribed on the platform surface. The SRGs can also be erased with light in the presence of PDMS, i.e., the topography can be reversibly photomodulated. The inscribed SRGs can guide epithelial cell orientation along the topography. The erasure parameters are targeted toward cell culturing environment, enabling experiments with live cells. Finally, the photoresponsive platform is patterned with proteins by microcontact printing, allowing its biofunctionalization and the combination of microtopography and protein patterns. This study paves the way for using reconfigurable cell culture platforms for the dynamic control of cell–material interactions. The PDMS coating has potential to protect underneath material, broadening the spectrum of possible materials for dynamic cell culture platforms. [ABSTRACT FROM AUTHOR]