bluuebunny/crossref_metadata_2025 huggingface dataset:
Diffusive mediator feedback explains the health-to-disease transition of skin inflammation
Authors: Sudo Maki , Fujimoto Koichi
Published: May 2023

The spatiotemporal dynamics of inflammation provide vital insights into the understanding of skin inflammation. Skin inflammation primarily depends on the regulatory feedback between pro- and anti-inflammatory mediators. Healthy skin exhibits faded erythema. In contrast, diseased skin exhibits expanding erythema with diverse patterns, clinically classified into five types: circular, annular, arcuate, gyrate, and polycyclic. Inflammatory diseases with expanding erythema are speculated to result from the overproduction of pro-inflammatory mediators. However, the mechanism by which feedback selectively drives the switch from a healthy fading erythema to each of the five types of diseased expanding erythema remains unclear. This study theoretically elucidates the imbalanced production between pro- and anti-inflammatory mediators and prospective treatment strategies for each expansion pattern. Our literature survey showed that eleven diseases exhibit some of the five expanding erythema, suggesting a common spatiotemporal regulation underlying different patterns and diseases. Accordingly, a reaction-diffusion model incorporating mediator feedback reproduced the five observed types of diseased expanding and healthy fading patterns. Importantly, the fading pattern transitioned to the arcuate, gyrate, and polycyclic patterns when the productions of anti-inflammatory and pro-inflammatory mediators were lower and higher, respectively, than in the healthy condition. Further depletion of anti-inflammatory mediators caused a circular pattern, whereas further overproduction of pro-inflammatory mediators caused an annular pattern. Mechanistically, the bistability due to stabilization of the diseased state exhibits circular and annular patterns, whereas the excitability exhibits the gyrate, polycyclic, arcuate, and fading patterns as the threshold of pro-inflammatory mediator concentration relative to the healthy state increases. These dynamic regulations of diffusive mediator feedback provide effective treatment strategies for mediator production wherein skins recover from each expanding pattern toward a fading pattern. Thus, these strategies can estimate disease severity and risk based on erythema patterns, paving the way for developing noninvasive and personalized treatments for inflammatory skin diseases.
The genomic and cellular basis of biosynthetic innovation in rove beetles
Authors: Kitchen Sheila A. , Naragon Thomas H. , Brückner Adrian , Ladinsky Mark S. , Quinodoz Sofia A. , Badroos Jean M. , Viliunas Joani W. , Wagner Julian M. , Miller David R. , Yousefelahiyeh Mina , Antoshechkin Igor A. , Eldredge K. Taro , Pirro Stacy , Guttman Mitchell , Davis Steven R. , Aardema Matthew L. , Parker Joseph
Published: May 2023

How evolution at the cellular level potentiates change at the macroevolutionary level is a major question in evolutionary biology. With >66,000 described species, rove beetles (Staphylinidae) comprise the largest metazoan family. Their exceptional radiation has been coupled to pervasive biosynthetic innovation whereby numerous lineages bear defensive glands with diverse chemistries. Here, we combine comparative genomic and single-cell transcriptomic data from across the largest rove beetle clade, Aleocharinae. We retrace the functional evolution of two novel secretory cell types that together comprise the tergal gland—a putative catalyst behind Aleocharinae’s megadiversity. We identify key genomic contingencies that were critical to the assembly of each cell type and their organ-level partnership in manufacturing the beetle’s defensive secretion. This process hinged on evolving a mechanism for regulated production of noxious benzoquinones that appears convergent with plant toxin release systems, and synthesis of an effective benzoquinone solvent that weaponized the total secretion. We show that this cooperative biosynthetic system arose at the Jurassic-Cretaceous boundary, and that following its establishment, both cell types underwent ∼150 million years of stasis, their chemistry and core molecular architecture maintained almost clade-wide as Aleocharinae radiated globally into tens of thousands of lineages. Despite this deep conservation, we show that the two cell types have acted as substrates for the emergence of adaptive, biochemical novelties—most dramatically in symbiotic lineages that have infiltrated social insect colonies and produce host behavior-manipulating secretions. Our findings uncover genomic and cell type evolutionary processes underlying the origin, functional conservation and evolvability of a chemical innovation in beetles.
Brain Dissection: fMRI-trained Networks Reveal Spatial Selectivity in the Processing of Natural Images
Authors: Sarch Gabriel H. , Tarr Michael J. , Fragkiadaki Katerina , Wehbe Leila
Published: May 2023

The alignment between deep neural network (DNN) features and cortical responses currently provides the most accurate quantitative explanation for higher visual areas [1, 2, 3, 4]. At the same time, these model features have been critiqued as uninterpretable explanations, trading one black box (the human brain) for another (a neural network). In this paper, we train networks to directly predict, from scratch, brain responses to images from a large-scale dataset of natural scenes [5]. We then use “network dissection” [6], an explainable AI technique used for enhancing neural network interpretability by identifying and localizing the most significant features in images for individual units of a trained network, and which has been used to study category selectivity in the human brain [7]. We adapt this approach to create a hypothesis-neutral model that is then used to explore the tuning properties of specific visual regions beyond category selectivity, which we call “brain dissection”. We use brain dissection to examine a range of ecologically important, intermediate properties, including depth, surface normals, curvature, and object relations across sub-regions of the parietal, lateral, and ventral visual streams, and scene-selective regions. Our findings reveal distinct preferences in brain regions for interpreting visual scenes, with ventro-lateral areas favoring closer and curvier features, medial and parietal areas opting for more varied and flatter 3D elements, and the parietal region uniquely preferring spatial relations. Scene-selective regions exhibit varied preferences, as the retrosplenial complex prefers distant and outdoor features, while the occipital and parahippocampal place areas favor proximity, verticality, and in the case of the OPA, indoor elements. Such findings show the potential of using explainable AI to uncover spatial feature selectivity across the visual cortex, contributing to a deeper, more fine-grained understanding of the functional characteristics of human visual cortex when viewing natural scenes.
Ten years and a million links: building a global taxonomic library connecting persistent identifiers for names, publications and people
Authors: Page Roderic D. M.
Published: May 2023

A major gap in the biodiversity knowledge graph is a connection between taxonomic names and the taxonomic literature. While both names and publications often have persistent identifiers (PIDs), such as Life Science Identifiers (LSIDs) or Digital Object Identifiers (DOIs), LSIDs for names are rarely linked to DOIs for publications. This article describes efforts to make those connections across three large taxonomic databases: Index Fungorum, International Plant Names Index (IPNI), and the Index of Organism Names (ION). Over a million names have been matched to DOIs or other persistent identifiers for taxonomic publications. This represents approximately 36% of names for which publication data is available. The mappings between LSIDs and publication PIDs are made available through ChecklistBank. Applications of this mapping are discussed, including a web app to locate the citation of a taxonomic name, and a knowledge graph that uses data on researcher’s ORCID ids to connect taxonomic names and publications to authors of those names.
ChromaX: a fast and scalable breeding program simulator
Authors: Younis Omar G. , Turchetta Matteo , Suarez Daniel Ariza , Yates Steven , Studer Bruno , Athanasiadis Ioannis N. , Krause Andreas , Buhmann Joachim M. , Corinzia Luca
Published: May 2023

ChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated breeding value calculations, and selection processes. By utilizing GPU processing, it can perform these simulations up to two orders of magnitude faster than existing tools with standard hardware. This offers breeders and scientists new opportunities to simulate genetic gain and optimize breeding schemes.

Availability and Implementation

The documentation is available athttps://chromax.readthedocs.io

The code is available athttps://github.com/kora-labs/chromax

Contact

omargallalaly.younis@inf.ethz.ch,luca.corinzia@inf.ethz.ch,matteo.turchetta@inf.ethz.ch
Caspase-2 is essential for proliferation and self-renewal of nucleophosmin-mutated acute myeloid leukemia
Authors: Sakthivel Dharaniya , Brown-Suedel Alexandra N. , Keane Francesca , Huang Shixia , Sherry Kenneth Mc , Charendoff Chloé I. , Dunne Kevin P. , Robichaux Dexter J. , Le BaoChau , Shin Crystal S. , Carisey Alexandre F. , Flanagan Jonathan M. , Bouchier-Hayes Lisa
Published: May 2023

Mutation in nucleophosmin (NPM1) causes relocalization of this normally nucleolar protein to the cytoplasm (NPM1c+). Despite NPM1 mutation being the most common driver mutation in cytogenetically normal adult acute myeloid leukemia (AML), the mechanisms of NPM1c+-induced leukemogenesis remain unclear. Caspase-2 is a pro-apoptotic protein activated by NPM1 in the nucleolus. Here, we show that caspase-2 is also activated by NPM1c+ in the cytoplasm, and DNA damage-induced apoptosis is caspase-2-dependent inNPM1c+AML but not inNPM1wtcells. Strikingly, inNPM1c+cells, loss of caspase-2 results in profound cell cycle arrest, differentiation, and down-regulation of stem cell pathways that regulate pluripotency including impairment in the AKT/mTORC1 and Wnt signaling pathways. In contrast, there were minimal differences in proliferation, differentiation, or the transcriptional profile ofNPM1wtcells with and without caspase-2. Together, these results show that caspase-2 is essential for proliferation and self-renewal of AML cells that have mutated NPM1. This study demonstrates that caspase-2 is a major effector of NPM1c+ function and may even be a druggable target to treatNPM1c+AML and prevent relapse.
METASPACE-ML: Context-specific metabolite annotation for imaging mass spectrometry using machine learning
Authors: Wadie Bishoy , Stuart Lachlan , Rath Christopher M. , Drotleff Bernhard , Mamedov Sergii , Alexandrov Theodore
Published: May 2023

Imaging mass spectrometry is a powerful technology enabling spatial metabolomics, yet metabolites can be assigned only to a fraction of the data generated. METASPACE-ML is a machine learning-based approach addressing this challenge which incorporates new scores and computationally-efficient False Discovery Rate estimation. For training and evaluation, we use a comprehensive set of 1,710 datasets from 159 researchers from 47 labs encompassing both animal and plant-based datasets representing multiple spatial metabolomics contexts derived from the METASPACE knowledge base. Here we show that, METASPACE-ML outperforms its rule-based predecessor, exhibiting higher precision, increased throughput, and enhanced capability in identifying low-intensity and biologically-relevant metabolites.
Body posture, gaze, and predator detection: how stalking behaviour may influence colour vision evolution
Authors: de Moraes Pedro Z. , Diniz Pedro , Pessoa Daniel M. A.
Published: May 2023

The success of a predatory attack is related to how much a predator manages to approach a prey without being detected. Some carnivore mammals use environmental objects as visual obstacles during stalking behaviour, allowing them to get closer to their prey while only showing parts of their coat or faces during movement or visual monitoring. Here, we investigate the influence of carnivores’ body postures and gaze on their detection by potential prey. To do so, we photographed taxidermized carnivore models (cougar, ocelot and lesser grison) in natural scenes and presented them to human dichromats (i.e., colourblind) and trichromats (i.e., normal colour vision). Our findings highlight the importance of predators’ complete body outline and gaze as search images during predator detection tasks. We also demonstrate how the coat and facial colour pattern of predators may camouflage their body outline and gaze, hampering predator detection. Furthermore, we observed that carnivore coat colour patterns may serve as an additional cue for trichromats, particularly in hidden carnivore detection tasks that proved to be more difficult for dichromats. We discuss our results within the context of a predator-prey arms race scenario, considering the evolutionary processes that may have generated the evidence presented in this study.
Synaptic architecture of leg and wing premotor control networks inDrosophila
Authors: Lesser Ellen , Azevedo Anthony W. , Phelps Jasper S. , Elabbady Leila , Cook Andrew , Syed Durafshan Sakeena , Mark Brandon , Kuroda Sumiya , Sustar Anne , Moussa Anthony , Dallmann Chris J. , Agrawal Sweta , Lee Su-Yee J. , Pratt Brandon , Skutt-Kakaria Kyobi , Gerhard Stephan , Lu Ran , Kemnitz Nico , Lee Kisuk , Halageri Akhilesh , Castro Manuel , Ih Dodam , Gager Jay , Tammam Marwan , Dorkenwald Sven , Collman Forrest , Schneider-Mizell Casey , Brittain Derrick , Jordan Chris S. , Macrina Thomas , Dickinson Michael , Lee Wei-Chung Allen , Tuthill John C.
Published: May 2023

Animal movement is controlled by motor neurons (MNs), which project out of the central nervous system to activate muscles. MN activity is coordinated by complex premotor networks that allow individual muscles to contribute to many different behaviors. Here, we use connectomics to analyze the wiring logic of premotor circuits controlling theDrosophilaleg and wing. We find that both premotor networks cluster into modules that link MNs innervating muscles with related functions. Within most leg motor modules, the synaptic weights of each premotor neuron are proportional to the size of their target MNs, establishing a circuit basis for hierarchical MN recruitment. In contrast, wing premotor networks lack proportional synaptic connectivity, which may allow wing steering muscles to be recruited with different relative timing. By comparing the architecture of distinct limb motor control systems within the same animal, we identify common principles of premotor network organization and specializations that reflect the unique biomechanical constraints and evolutionary origins of leg and wing motor control.
Spatial periodicity in grid cell firing is explained by a neural sequence code of 2-D trajectories
Authors: R.G. Rebecca , Ascoli Giorgio A , Sutton Nate M , Dannenberg Holger
Published: May 2023

Spatial periodicity in grid cell firing has been interpreted as a neural metric for space providing animals with a coordinate system in navigating physical and mental spaces. However, the specific computational problem being solved by grid cells has remained elusive. Here, we provide mathematical proof that spatial periodicity in grid cell firing is the only possible solution to a neural sequence code of 2-D trajectories and that the hexagonal firing pattern of grid cells is the most parsimonious solution to such a sequence code. We thereby provide a likely teleological cause for the existence of grid cells and reveal the underlying nature of the global geometric organization in grid maps as a direct consequence of a simple local sequence code. A sequence code by grid cells provides intuitive explanations for many previously puzzling experimental observations and may transform our thinking about grid cells.
Mechanisms of memory storage and retrieval in hippocampal area CA3
Authors: Li Yiding , Briguglio John J. , Romani Sandro , Magee Jeffrey C.
Published: May 2023

Hippocampal area CA3 is thought to play a central role in memory formation and retrieval. Although various network mechanisms have been hypothesized to mediate these computations, direct evidence is lacking. Using intracellular membrane potential recordings from CA3 neurons and optogenetic manipulations in behaving mice we found that place field activity is produced by a symmetric form of Behavioral Timescale Synaptic Plasticity (BTSP) at recurrent synaptic connections among CA3 principal neurons but not at synapses from the dentate gyrus (DG). Additional manipulations revealed that excitatory input from the entorhinal cortex (EC) but not DG was required to update place cell activity based on the animal’s movement. These data were captured by a computational model that used BTSP and an external updating input to produce attractor dynamics under online learning conditions. Additional theoretical results demonstrate the enhanced memory storage capacity of such networks, particularly in the face of correlated input patterns. The evidence sheds light on the cellular and circuit mechanisms of learning and memory formation in the hippocampus.

One Sentence Summary

Evidence from behaving mice points to cellular and circuit mechanisms that underlie observed attractor dynamics in area CA3.
AutoUnmix: an autoencoder-based spectral unmixing method for multi-color fluorescence microscopy imaging
Authors: Jiang Yuan , Sha Hao , Liu Shuai , Qin Peiwu , Zhang Yongbing
Published: May 2023

Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores.
Progressive excitability changes in the medial entorhinal cortex in the 3xTg mouse model of Alzheimer’s disease pathology
Authors: Chen Lingxuan , Christenson Wick Zoé , Vetere Lauren M. , Vaughan Nick , Jurkowski Albert , Galas Angelina , Diego Keziah S. , Philipsberg Paul , Cai Denise J. , Shuman Tristan
Published: May 2023

Alzheimer’s disease (AD) is a chronic neurodegenerative disorder that is characterized by memory loss and progressive cognitive impairments. In mouse models of AD pathology, studies have found neuronal and synaptic deficits in the hippocampus, but less is known about what happens in the medial entorhinal cortex (MEC), which is the primary spatial input to the hippocampus and an early site of AD pathology. Here, we measured the neuronal intrinsic excitability and synaptic activity in MEC layer II (MECII) stellate cells, MECII pyramidal cells, and MEC layer III (MECIII) excitatory neurons at early (3 months) and late (10 months) time points in the 3xTg mouse model of AD pathology. At 3 months of age, prior to the onset of memory impairments, we found early hyperexcitability in MECII stellate and pyramidal cells’ intrinsic properties, but this was balanced by a relative reduction in synaptic excitation (E) compared to inhibition (I), suggesting intact homeostatic mechanisms regulating activity in MECII. Conversely, MECIII neurons had reduced intrinsic excitability at this early time point with no change in the synaptic E/I ratio. By 10 months of age, after the onset of memory deficits, neuronal excitability of MECII pyramidal cells and MECIII excitatory neurons was largely normalized in 3xTg mice. However, MECII stellate cells remained hyperexcitable and this was further exacerbated by an increased synaptic E/I ratio. This observed combination of increased intrinsically and synaptically generated excitability suggests a breakdown in homeostatic mechanisms specifically in MECII stellate cells at this post-symptomatic time point. Together, these data suggest that the breakdown in homeostatic excitability mechanisms in MECII stellate cells may contribute to the emergence of memory deficits in AD.
Nest-building using place cells for spatial navigation in an artificial neural network
Authors: Portegys Thomas E.
Published: May 2023

Abstract

An animal behavior problem is presented in the form of a nest-building task that involves two cooperating birds, a male and female. The female builds a nest into which she lays an egg. The male’s job is to forage in a forest for food for both himself and the female. In addition, the male must fetch stones from a nearby desert for the female to use as nesting material. The task is completed when the nest is built and an egg is laid in it. A goal-seeking neural network and a recurrent neural network were trained and tested with little success. The goal-seeking network was then enhanced with “place cells”, allowing the birds to spatially navigate the world, building the nest while keeping themselves fed. Place cells are neurons in the hippocampus that map space.
Lipid bilayer strengthens the cooperative network of membrane proteins
Authors: Muhammednazaar Shaima , Yao Jiaqi , Necelis Matthew R. , Park Yein C. , Shen Zhongtian , Bridges Michael D. , Guo Ruiqiong , Swope Nicole , Rhee May S. , Kim Miyeon , Kim Kelly H. , Hubbell Wayne L. , Fleming Karen G. , Columbus Linda , Kang Seung-gu , Hong Heedeok
Published: May 2023

Although membrane proteins fold and function in a lipid bilayer constituting cell membranes, their structure and functionality can be recapitulated in diverse amphiphilic assemblies whose compositions deviate from native membranes. It remains unclear how various hydrophobic environments can stabilize membrane proteins and whether lipids play any role therein. Here, using the evolutionary unrelated α-helical and β-barrel membrane proteins ofEscherichia coli, we find that the hydrophobic thickness and the strength of amphiphile– amphiphile packing are critical environmental determinants of membrane protein stability. Lipid solvation enhances stability by facilitating residue burial in the protein interior and strengthens the cooperative network by promoting the propagation of local structural perturbations. This study demonstrates that lipids not only modulate membrane proteins’ stability but also their response to external stimuli.
Intra- and Inter-host Evolution of Human Norovirus in Healthy Adults
Authors: Ramani Sasirekha , Javornik Cregeen Sara J. , Surathu Anil , Neill Frederick H. , Muzny Donna M. , Doddapaneni Harsha , Menon Vipin K. , Hoffman Kristi L. , Ross Matthew C. , Metcalf Ginger , Opekun Antone R. , Graham David Y. , Gibbs Richard A. , Petrosino Joseph F. , Estes Mary K. , Atmar Robert L.
Published: May 2023

Background

Human noroviruses are a leading cause of acute and sporadic gastroenteritis worldwide. The evolution of human noroviruses in immunocompromised persons has been evaluated in many studies. Much less is known about the evolutionary dynamics of human norovirus in healthy adults.

Methods

We used sequential samples collected from a controlled human infection study with GI.1/Norwalk/US/68 virus to evaluate intra- and inter-host evolution of a human norovirus in healthy adults. Up to 12 samples from day 1 to day 56 post-challenge were sequenced using a norovirus-specific capture probe method.

Results

Complete genomes were assembled, even in samples that were below the limit of detection of standard RT-qPCR assays, up to 28 days post-challenge. Analysis of 123 complete genomes showed changes in the GI.1 genome in all persons, but there were no conserved changes across all persons. Single nucleotide variants resulting in non-synonymous amino acid changes were observed in all proteins, with the capsid VP1 and nonstructural protein NS3 having the largest numbers of changes.

Conclusions

These data highlight the potential of a new capture-based sequencing approach to assemble human norovirus genomes with high sensitivity and demonstrate limited conserved immune pressure-driven evolution of GI.1 virus in healthy adults.
Proximal Molecular Probe Transfer (PROMPT), a new approach for identifying sites of protein/nucleic acid interaction in cells by correlated light and electron microscopy
Authors: Castillon Guillaume A , Phan Sebastien , Hu Junru , Boassa Daniela , Adams Stephen R , Ellisman Mark H
Published: May 2023

The binding and interaction of proteins with nucleic acids such as DNA and RNA constitutes a fundamental biochemical and biophysical process in all living organisms. Identifying and visualizing such temporal interactions in cells is key to understanding their function. To image sites of these events in cells across scales, we developed a method, named PROMPT for PROximal Molecular Probe Transfer, which is applicable to both light and correlative electron microscopy. This method relies on the transfer of a bound photosensitizer from a protein known to associate with specific nucleic acid sequence, allowing the marking of the binding site on DNA or RNA in fixed cells. The method produces a fluorescent mark at the site of their interaction, that can be made electron dense and reimaged at high resolution in the electron microscope. As proof of principle, we labeledin situthe interaction sites between the histone H2B and nuclear DNA. As an example of application for specific RNA localizations we labeled different nuclear and nucleolar fractions of the protein Fibrillarin to mark and locate where it associates with RNAs, also using electron tomography. While the current PROMPT method is designed for microscopy, with minimal variations, it can be potentially expanded to analytical techniques.
A single polymorphic residue in humans underlies species-specific restriction of HSV-1 by the antiviral protein MxB
Authors: Bayer Avraham , Child Stephanie J. , Malik Harmit S. , Geballe Adam P.
Published: May 2023

Myxovirus resistance proteins (MxA and MxB) are interferon-induced proteins that exert antiviral activity against a diverse range of RNA and DNA viruses. In primates, MxA has been shown to inhibit myxoviruses, bunyaviruses, and hepatitis B virus, whereas MxB restricts retroviruses and herpesviruses. As a result of their conflicts with viruses, both genes have been undergoing diversifying selection during primate evolution. Here, we investigate how MxB evolution in primates has affected its restriction of herpesviruses. In contrast to human MxB, we find that most primate orthologs, including the closely related chimpanzee MxB, do not inhibit HSV-1 replication. However, all primate MxB orthologs tested restrict human cytomegalovirus. Through the generation of human and chimpanzee MxB chimeras we show that a single residue, M83, is the key determinant of restriction of HSV-1 replication. Humans are the only primate species known to encode a methionine at this position, whereas most other primate species encode a lysine. Residue 83 is also the most polymorphic residue in MxB in human populations, with M83 being the most common variant. However, ∼2.5% of human MxB alleles encode a threonine at this position, which does not restrict HSV-1. Thus, a single amino acid variant in MxB, which has recently risen to high frequency in humans, has endowed humans with HSV-1 antiviral activity.

Importance

Herpesviruses present a major global disease burden. Understanding the host cell mechanisms that block viral infections as well as how viruses can evolve to counteract these host defenses is critically important for understanding viral disease pathogenesis, and for developing therapeutic tools aimed at treating or preventing viral infections. Additionally, understanding how these host and viral mechanisms adapt to counter one another can aid in identifying the risks of, and barriers to, cross-species transmission events. As highlighted by the recent SARS-CoV-2 pandemic, episodic transmission events can have severe consequences for human health. This study reveals that the major human variant of the antiviral protein MxB inhibits the human pathogen HSV-1, whereas human minor variants and orthologous MxB genes from even closely related primates do not. Thus, in contrast to the many antagonistic virus-host interactions in which the virus is successful in thwarting the defense systems of their native hosts, in this case the human gene appears to be at least temporarily winning at this interface of the primate-herpesviral evolutionary arms race. Our findings further show that a polymorphism at amino acid 83 in a small fraction of the human population is sufficient to abrogate MxB’s ability to inhibit HSV-1, which could have important implications for human susceptibility to HSV-1 pathogenesis.
Essential role of the Conserved Oligomeric Golgi complex inToxoplasma gondii
Authors: Marsilia Clem , Batra Mrinalini , Pokrovskaya Irina D. , Wang Chengqi , Chaput Dale , Naumova Daria A. , Lupashin Vladimir V. , Suvorova Elena S.
Published: May 2023

Survival of the apicomplexan parasiteToxoplasma gondiidepends on the proper functioning of many glycosylated proteins. Glycosylation is performed in the major membranous organelles ER and Golgi apparatus that constitute a significant portion of the intracellular secretory system. The secretory pathway is bidirectional: cargo is delivered to target organelles in the anterograde direction, while the retrograde flow maintains the membrane balance and proper localization of glycosylation machinery. Despite the vital role of the Golgi in parasite infectivity, little is known about its biogenesis in apicomplexan parasites. In this study we examinedT. gondiiConserved Oligomeric Golgi (COG) complex and determined that, contrary to predictions,T. gondiiexpresses the entire eight-subunit complex and each complex subunit is essential for tachyzoite growth. Deprivation of the COG complex induces a pronounced effect on Golgi and ER membranes, which suggests theT. gondiiCOG complex has wider role in intracellular membrane trafficking. We demonstrated that besides its conservative role in protein glycosylation and retrograde intra-Golgi trafficking, the COG complex also interacted with anterograde and novel transport machinery. Furthermore, we identified coccidian-specific components of the Golgi transport system: TgUlp1 and TgGlp1. Protein structure and phylogenetic analyses revealed that TgUlp1 is an adaptation of the conservative Golgi tethering factor Uso1/p115, and together with Golgi-localized TgGlp1, TgUlp1 showed dominant interactions with the trafficking machinery that predicted to operate the endosome-to-Golgi recycling. Together, our study showed thatT. gondiihas expanded function of the conservative Golgi tethering COG complex and evolved additional regulators of the transport likely to serve parasite-specific secretory organelles.
Identification of PS1/gamma-secretase and glutamate transporter GLT-1 interaction sites
Authors: Perrin Florian , Sinha Priyanka , Mitchell Shane , Maesako Masato , Berezovska Oksana
Published: May 2023

The recently discovered interaction between Presenilin 1 (PS1), a catalytic subunit of γ-secretase responsible for generating amyloid-β (Aβ) peptides, and GLT-1, a major glutamate transporter in the brain (EAAT2) provides a mechanistic link between these two key factors involved in Alzheimer’s disease (AD) pathology. Modulating this interaction can be crucial to understand the consequence of such crosstalk in AD context and beyond. However, the interaction sites between these two proteins are unknown. Herein, we utilized an alanine scanning approach coupled with FRET-based fluorescence lifetime imaging microscopy (FLIM) to identify the interaction sites between PS1 and GLT-1 in their native environment within intact cells. We found that GLT-1 residues at position 276 to 279 (TM5) and PS1 residues at position 249 to 252 (TM6) are crucial for GLT-1/PS1 interaction. These results have been cross validated using AlphaFold Multimer prediction. To further investigate whether this interaction of endogenously expressed GLT-1 and PS1 can be prevented in primary neurons, we designed PS1/GLT-1 cell-permeable peptides (CPPs) targeting the PS1 or GLT-1 binding site. We used HIV TAT domain to allow for cell penetration which was assayed in neurons. First, we assessed the toxicity and penetration of CPPs by confocal microscopy. Next, to ensure the efficiency of CPPs, we monitored the modulation of GLT-1/PS1 interaction in intact neurons by FLIM. We saw significantly less interaction between PS1 and GLT-1 with both CPPs. Our study establishes a new tool to study the functional aspect of GLT-1/PS1 interaction and its relevance in normal physiology and AD models.
Neuropsychology of cognitive aging in rhesus monkeys
Authors: Baxter Mark G. , Roberts Mary T. , Roberts Jeffrey A. , Rapp Peter R.
Published: May 2023

Aged rhesus monkeys, like aged humans, show declines in cognitive function. We present cognitive test data from a large sample of male and female rhesus monkeys, 34 young (3.5-13.6 years) and 71 aged (19.9-32.5 years of age at the start of cognitive testing). Monkeys were tested on spatiotemporal working memory (delayed response), visual recognition memory (delayed nonmatching-to-sample), and stimulus-reward association learning (object discrimination), tasks with an extensive evidence base in nonhuman primate neuropsychology. On average, aged monkeys performed worse than young on all three tasks. Acquisition of delayed response and delayed nonmatching-to-sample was more variable in aged monkeys than in young.

Performance scores on delayed nonmatching-to-sample and object discrimination were associated with each other, but neither was associated with performance on delayed response. Sex and chronological age were not reliable predictors of individual differences in cognitive outcome among the aged monkeys. These data establish population norms for cognitive tests in young and aged rhesus monkeys in the largest sample reported to date. They also illustrate independence of cognitive aging in task domains dependent on the prefrontal cortex and medial temporal lobe.

(181 words)
mRNA condensation fluidizes the cytoplasm
Authors: Xie Ying , Liu Tiewei , Gresham David , Holt Liam J
Published: May 2023

The intracellular environment is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cell physiology. When exposed to stress, mRNAs released after translational arrest condense with RNA binding proteins, resulting in the formation of membraneless RNA protein (RNP) condensates known as processing bodies (P-bodies) and stress granules (SGs). However, the impact of the assembly of these condensates on the biophysical properties of the crowded cytoplasmic environment remains unclear. Here, we find that upon exposure to stress, polysome collapse and condensation of mRNAs increases mesoscale particle diffusivity in the cytoplasm. Increased mesoscale diffusivity is required for the efficient formation of Q-bodies, membraneless organelles that coordinate degradation of misfolded peptides that accumulate during stress. Additionally, we demonstrate that polysome collapse and stress granule formation has a similar effect in mammalian cells, fluidizing the cytoplasm at the mesoscale. We find that synthetic, light-induced RNA condensation is sufficient to fluidize the cytoplasm, demonstrating a causal effect of RNA condensation. Together, our work reveals a new functional role for stress-induced translation inhibition and formation of RNP condensates in modulating the physical properties of the cytoplasm to effectively respond to stressful conditions.
The Type VI Secretion System of the Emerging PathogenStenotrophomonas maltophiliahas Antibacterial Properties
Authors: Crisan Cristian V. , Van Tyne Daria , Goldberg Joanna B.
Published: May 2023

Antagonistic behaviors between bacterial cells can have profound effects on microbial populations and disease outcomes. Polymicrobial interactions may be mediated by contact-dependent proteins with antibacterial properties. The Type VI Secretion System (T6SS) is a macromolecular weapon used by Gram-negative bacteria to translocate proteins into adjacent cells. The T6SS is used by pathogens to escape immune cells, eliminate commensal bacteria, and facilitate infection.Stenotrophomonas maltophiliais a Gram-negative opportunistic pathogen that causes a wide range of infections in immunocompromised patients and infects the lungs of patients with cystic fibrosis. Infections with the bacterium can be deadly and are challenging to treat because many isolates are multidrug-resistant. We found that globally dispersedS. maltophiliaclinical and environmental strains possess T6SS genes. We demonstrate that the T6SS of anS. maltophiliapatient isolate is active and can eliminate other bacteria. Furthermore, we provide evidence that the T6SS contributes to the competitive fitness ofS. maltophiliaagainst a co-infectingPseudomonas aeruginosaisolate, and that the T6SS alters the cellular organization ofS. maltophiliaandP. aeruginosaco-cultures. This study expands our knowledge of the mechanisms employed byS. maltophiliato secrete antibacterial proteins and compete against other bacteria.

IMPORTANCE

Infections with the opportunistic pathogenStenotrophomonas maltophiliacan be fatal for immunocompromised patients. The mechanisms used by the bacterium to compete against other prokaryotes are not well understood. We found that the T6SS allowsS. maltophiliato eliminate other bacteria and contributes to the competitive fitness against a co-infecting isolate. The presence of T6SS genes in isolates across the globe highlights the importance of this apparatus as a weapon in the antibacterial arsenal ofS. maltophilia. The T6SS may confer survival advantages toS. maltophiliaisolates in polymicrobial communities in both environmental settings and during infections.
Host subversion of bacterial metallophore usage drives copper intoxication
Authors: Hossain Saika , Morey Jacqueline R. , Neville Stephanie L. , Ganio Katherine , Radin Jana N. , Norambuena Javiera , Boyd Jeffrey M. , McDevitt Christopher A. , Kehl-Fie Thomas E.
Published: May 2023

Microorganisms can acquire metal ions in metal-limited environments using small molecules called metallophores. While metals and their importers are essential, metals can also be toxic, and metallophores have limited ability to discriminate metals. The impact of the metallophore-mediated non-cognate metal uptake on bacterial metal homeostasis and pathogenesis remains to be defined. The globally significant pathogenStaphylococcus aureususes the Cnt system to secrete the metallophore staphylopine in zinc-limited host niches. Here, we show that staphylopine and the Cnt system facilitate bacterial copper uptake, potentiating the need for copper detoxification. Duringin vivoinfection, staphylopine usage increasedS. aureussusceptibility to host-mediated copper stress, indicating that the innate immune response can harness the antimicrobial potential of altered elemental abundances in host niches. Collectively, these observations show that while the broad-spectrum metal-chelating properties of metallophores can be advantageous, the host can exploit these properties to drive metal intoxication and mediate antibacterial control.

IMPORTANCE

During infection bacteria must overcome the dual threats of metal starvation and intoxication. This work reveals that the zinc-withholding response of the host sensitizesStaphylococcus aureusto copper intoxication. In response to zinc starvationS. aureusutilizes the metallophore staphylopine. The current work revealed that the host can leverage the promiscuity of staphylopine to intoxicateS. aureusduring infection. Significantly, staphylopine-like metallophores are produced by a wide range of pathogens, suggesting that this is a conserved weakness that the host can leverage to toxify invaders with copper. Moreover, it challenges the assumption that the broad-spectrum metal binding of metallophores is inherently beneficial to bacteria.
An open-source, high resolution, automated fluorescence microscope
Authors: Zehrer Ando C. , Martin-Villalba Ana , Diederich Benedict , Ewers Helge
Published: May 2023

Fluorescence microscopy is a fundamental tool in the life sciences, but the availability of sophisticated equipment required to yield high-quality, quantitative data is a major bottleneck in data production in many laboratories worldwide. This problem has long been recognized and the abundancy of low-cost electronics and the simplification of fabrication through 3D-printing have led to the emergence of open-source scientific hardware as a research field. Cost effective fluorescence microscopes can be assembled from cheaply mass-produced components, but lag behind commercial solutions in image quality. On the other hand, blueprints of sophisticated microscopes such as light-sheet or super-resolution systems, custom-assembled from high quality parts, are available, but require a high level of expertise from the user.

Here we combine the UC2 microscopy toolbox with high-quality components and integrated electronics and software to assemble an automated high-resolution fluorescence microscope. Using this microscope, we demonstrate high resolution fluorescence imaging for fixed and live samples. When operated inside an incubator, long-term live-cell imaging over several days was possible. Our microscope reaches single molecule sensitivity, and we performed single particle tracking and SMLM super-resolution microscopy experiments in cells. Our setup costs a fraction of its commercially available counterparts but still provides a maximum of capabilities and image quality. We thus provide a proof of concept that high quality scientific data can be generated by lay users with a low-budget system and open-source software. Our system can be used for routine imaging in laboratories that do not have the means to acquire commercial systems and through its affordability can serve as teaching material to students.
Quantitative Determination of Protein Concentrations in Living Cells
Authors: Brinkenfeldt Nikolaj K. , Dias André , Moreno-Pescador Guillermo , Bendix Poul Martin , Martinez Karen L.
Published: May 2023

Biological systems are regulated by molecular interactions which are tuned by the concentrations of each of the molecules involved. Cells exploit this feature by regulating protein expression, to adapt their responses to overstimulation. Correlating events in single cells to the concentrations of proteins involved can therefore provide important mechanistic insight into cell behavior. Unfortunately, quantification of molecular densities by fluorescence imaging becomes non-trivial due to the diffraction limited resolution of the imaged volume. We show here an alternative approach to overcome this limitation in optical quantification of protein concentrations which is based on calibrating protein volume and surface densities in a model membrane system. We exploit the ability of fluorescently labeled annexin V to bind membranes in presence of calcium. By encapsulating known concentrations of annexin V, we can directly infer the membrane density of annexin V after addition of Ca2+ and correlate the density with the measured fluorescence signal. Our method, named Calmet, enables quantitative determination of the concentration of cytosolic and membrane associated proteins. The applicability of Calmet is demonstrated by quantification of a transmembrane protein receptor (beta 1 adrenergic receptor) labeled by SNAP tagged fluorophores and expressed in HEK293 cells. Calmet is a generic method suitable for the determination of a broad range of concentrations and densities and can be used on regular fluorescence images captured by confocal laser scanning microscopy.
Formation of clathrin-pits and ATP-independent cholesterol-dependent tubules initiates mechano-regulation on de-adhesion
Authors: Mandal Tithi , Biswas Arikta , Ghosh Tanmoy , Manikandan Sreekanth , Kundu Avijit , Banerjee Ayan , Mitra Dhrubaditya , Sinha Bidisha
Published: May 2023

Adherent cells ensure membrane homeostasis during de-adhesion by various mechanisms including endocytosis. Although mechano-chemical feedbacks involved in this process have been studied, the step-by-step build-up and resolution of the mechanical changes by endocytosis is not well understood. To investigate this, we study the de-adhesion of HeLa cells using a combination of interference reflection microscopy, optical-trapping and fluorescence experiments. We found that de-adhesion enhanced membrane height fluctuations of the basal membrane in the presence of an intact cortex. A reduction in the tether-force was also noted at the apical side. However, membrane fluctuations reveal phases of an initial drop in effective tension followed by a saturation. The area fractions of early (Rab5-labelled) and recycling (Rab4-labelled) endosomes as well as transferrin-labelled pits close to the basal plasma membrane also transiently increased. On blocking dynamin-dependent scission of endocytic pits, the regulation of fluctuations was not blocked but proceeded uncontrolled. Interestingly, the regulation could not be suppressed by ATP or cholesterol depletion individually but was arrested on depleting both. The data strongly supports pit-formation to be central to the reduction in fluctuations whether in normal or ATP depleted condition. Furthermore, while in normal conditions the contribution of clathrin-mediated endocytosis is clear, under ATP-depleted conditions we propose that cholesterol-dependent pits spontaneously regulate tension.

We show that during de-adhesion, cell edges retract, creating membrane folds and increasing fluctuations. Cells increase the rate of endocytosis to regulate back their membrane fluctuations. This is achieved by forming invaginations. Dynamin-dependent pathways are majorly involved, while cholesterol-dependent ATP-independent mechanisms also contribute.