bluuebunny/crossref_metadata_2025 huggingface dataset:
Late Pleistocene shell midden microstratigraphy indicates a complex history of human–environment interactions in the uplands of northern Vietnam
Authors: McAdams Conor , Morley Mike W. , Fu Xiao , Kandyba Alexander V. , Derevianko Anatoly P. , Nguyen Dong Truong , Doi Nguyen Gia , Roberts Richard G.
Published: March 2022

Northern Vietnam is situated on a major route of Pleistocene hominin dispersal in East Asia, and the area's karstic caves preserve many prehistoric shell middens. Fossil and genomic evidence suggest a complex human history in this region and more widely across Southeast Asia and southern China, but related archaeological investigations are hampered by challenging site stratigraphies. Recent investigations of shell middens in other geographical settings have revealed the microstratigraphic complexity of these anthropogenic deposits. But caves promote distinctive site formation processes, while tropical climates may catalyse geomorphic and diagenetic changes. These environmental factors complicate the interpretation of northern Vietnam's shell middens and constraining their effects upon the formation, preservation and destruction of these sites is critical to understanding the archaeology of this region. We examine two archaeological cave sites, dated to the Late Pleistocene and located in the limestone uplands surrounding the Hanoi Basin. Each contains multiple shell midden layers associated with prehistoric occupation and burials. Using thin-section micromorphology (microstratigraphy), we reconstruct the depositional and post-depositional histories of these sites, presenting a geoarchaeological framework of interpretation that is applicable to shell middens in mainland Southeast Asia and tropical zones more widely. This work represents a further step towards improving our understanding of prehistoric human dispersals and adaptations in this region.

This article is part of the theme issue ‘Tropical forests in the deep human past’.
Ice Age megafauna rock art in the Colombian Amazon?
Authors: Iriarte José , Ziegler Michael J. , Outram Alan K. , Robinson Mark , Roberts Patrick , Aceituno Francisco J. , Morcote-Ríos Gaspar , Keesey T. Michael
Published: March 2022

Megafauna paintings have accompanied the earliest archaeological contexts across the continents, revealing a fundamental inter-relationship between early humans and megafauna during the global human expansion as unfamiliar landscapes were humanized and identities built into new territories. However, the identification of extinct megafauna from rock art is controversial. Here, we examine potential megafauna depictions in the rock art of Serranía de la Lindosa, Colombian Amazon, that includes a giant sloth, a gomphothere, a camelid, horses and three-toed ungulates with trunks. We argue that they are Ice Age rock art based on the (i) naturalistic appearance and diagnostic morphological features of the animal images, (ii) late Pleistocene archaeological dates from La Lindosa confirming the contemporaneity of humans and megafauna, (iii) recovery of ochre pigments in late Pleistocene archaeological strata, (iv) the presence of most megafauna identified in the region during the late Pleistocene as attested by archaeological and palaeontological records, and (v) widespread depiction of extinct megafauna in rock art across the Americas. Our findings contribute to the emerging picture of considerable geographical and stylistic variation of geometric and figurative rock art from early human occupations across South America. Lastly, we discuss the implications of our findings for understanding the early human history of tropical South America.

This article is part of the theme issue ‘Tropical forests in the deep human past’.
A palaeoecological perspective on the transformation of the tropical Andes by early human activity
Authors: Bush M. B. , Rozas-Davila A. , Raczka M. , Nascimento M. , Valencia B. , Sales R. K. , McMichael C. N. H. , Gosling W. D.
Published: March 2022

Palaeoecological records suggest that humans have been in the Andes since at least 14 000 years ago. Early human impacts on Andean ecosystems included an increase in fire activity and the extinction of the Pleistocene megafauna. These changes in Andean ecosystems coincided with rapid climate change as species were migrating upslope in response to deglacial warming. Microrefugia probably played a vital role in the speed and genetic composition of that migration. The period from
ca
14 500 to 12 500 years ago was when novel combinations of plant species appeared to form no-analogue assemblages in the Andes. By 12 000 years ago most areas in what are today the Andean grasslands were being burned and modified by human activity. As the vegetation of these highland settings has been modified by human activity for the entirety of the Holocene, they should be regarded as long-term manufactured landscapes. The sharp tree lines separating Andean forests from grasslands that we see today were probably also created by repeated burning and owe their position more to human-induced fire than climatic constraints. In areas that were readly penetrated by humans on the forested slopes of the Andes, substantial modification and settlement had occurred by the mid-Holocene. In hard-to-reach areas, however, the amount of human modification may always have been minimal, and these slopes can be considered as being close to natural in their vegetation.

This article is part of the theme issue ‘Tropical forests in the deep human past’.
Diverse functions for acyltransferase-3 proteins in the modification of bacterial cell surfaces
Authors: Pearson Caroline , Tindall Sarah , Potts Jennifer R. , Thomas Gavin H. , van der Woude Marjan W.
Published: March 2022

The acylation of sugars, most commonly via acetylation, is a widely used mechanism in bacteria that uses a simple chemical modification to confer useful traits. For structures like lipopolysaccharide, capsule and peptidoglycan, that function outside of the cytoplasm, their acylation during export or post-synthesis requires transport of an activated acyl group across the membrane. In bacteria this function is most commonly linked to a family of integral membrane proteins – acyltransferase-3 (AT3). Numerous studies examining production of diverse extracytoplasmic sugar-containing structures have identified roles for these proteins in O-acylation. Many of the phenotypes conferred by the action of AT3 proteins influence host colonisation and environmental survival, as well as controlling the properties of biotechnologically important polysaccharides and the modification of antibiotics and antitumour drugs by Actinobacteria. Herein we present the first systematic review, to our knowledge, of the functions of bacterial AT3 proteins, revealing an important protein family involved in a plethora of systems of importance to bacterial function that is still relatively poorly understood at the mechanistic level. By defining and comparing this set of functions we draw out common themes in the structure and mechanism of this fascinating family of membrane-bound enzymes, which, due to their role in host colonisation in many pathogens, could offer novel targets for the development of antimicrobials.
DENSS-Multiple: A Structure Reconstruction Method using Multiple Contrast Variation of Small-Angle Neutron Scattering Based on the DENSS Algorithm
Authors: Sumner Jacob , Qian Shuo
Published: March 2022

Small-angle neutron scattering (SANS) provides easily manipulable neutron contrast variation that has been widely exploited to study the structure and function of biological macromolecules and their complex in solution. Here, we developed a method called DENSS-Multiple based on the DENSS (DENsity from Solution Scattering) algorithm to provide ab initio structure reconstruction with SANS contrast variation data. This new tool can exploit additional information in different SANS contrasts for improved ab initio reconstruction results.
In vivoassessment of mechanical properties during axolotl development and regeneration using confocal Brillouin microscopy
Authors: Riquelme-Guzmán Camilo , Beck Timon , Edwards-Jorquera Sandra , Schlüßler Raimund , Müller Paul , Guck Jochen , Möllmert Stephanie , Sandoval-Guzmán Tatiana
Published: March 2022

In processes such as development and regeneration, where large cellular and tissue rearrangements occur, cell fate and behavior are strongly influenced by tissue mechanics. While most well-established tools probing mechanical properties require an invasive sample preparation, confocal Brillouin microscopy captures mechanical parameters optically with high resolution in a contact-free and label-free fashion. In this work, we took advantage of this tool and the transparency of the highly regenerative axolotl to probe its mechanical propertiesin vivofor the first time. We mapped the Brillouin frequency shift with high resolution in developing limbs and regenerating digits, the most studied structures in the axolotl. We detected a gradual increase in the cartilage Brillouin frequency shift, suggesting decreasing tissue compressibility during both development and regeneration. Moreover, we were able to correlate such increase with the regeneration stage, which was undetected with fluorescence microscopy imaging. The present work evidences the potential of Brillouin microscopy to unravel the mechanical changes occurringin vivoin axolotls, setting the basis to apply this technique in the growing field of epimorphic regeneration.
Automatic determination of the handedness of Single-Particle maps of macromolecules solved by CryoEM
Authors: Condado J. Garcia , Muñoz-Barrutia A. , Sorzano C.O.S.
Published: March 2022

Single-Particle Analysis by Cryo-Electron Microscopy is a well-established technique to elucidate the three-dimensional (3D) structure of biological macromolecules. The orientation of the acquired projection images must be initially estimated without any reference to the final structure. In this step, algorithms may find a mirrored version of all the orientations resulting in a mirrored 3D map. It is as compatible with the acquired images as its unmirrored version from the image processing point of view, only that it is not biologically plausible.

In this article, we introduce HaPi (Handedness Pipeline), the first method to automatically determine the hand of electron density maps of macromolecules solved by CryoEM. HaPi is built by training two 3D convolutional neural networks. The first determines α-helices in a map, and the second determines whether the α-helix is left-handed or right-handed. A consensus strategy defines the overall map hand. The pipeline is trained on simulated and experimental data. The handedness can be detected only for maps whose resolution is better than 5Å. HaPi can identify the hand in 89% of new simulated maps correctly. Moreover, we evaluated all the maps deposited at the Electron Microscopy Data Bank and 11 structures uploaded with the incorrect hand were identified.
A primary patient-derived model for investigating functional heterogeneity within the human Leukemic Stem Cell Compartment
Authors: Boutzen Héléna , Chan-Seng-Yue Michelle , Murison Alex , Mbong Nathan , Wagenblast Elvin , Arlidge Christopher , Tonekaboni Seyed Ali Madani , Orouji Elias , Arruda Andrea , Mitchell Amanda , Notta Faiyaz , Lupien Mathieu , Minden Mark D. , Kaufmann Kerstin B. , Dick John E.
Published: March 2022

The ability of leukemic stem cells (LSC) to evade therapy and fuel leukemic progression causing relapse impedes therapeutic success in acute myeloid leukemia (AML). The LSC pool within a patient sample is not homogenous but comprises distinct LSC subsets that vary in self-renewal and propagation properties. The stemness programs that underlie LSC types are poorly understood since human LSC studies require primary patient samples where LSC numbers are low and isolation methods impure. To overcome these challenges, we developed a patient-derived AML model system (OCI-AML22) displaying a functionally, transcriptionally and epigenetically defined cellular hierarchy driven by functional LSCs that can be immunophenotypically identified and isolated. Through single cell and functional approaches, the OCI-AML22 LSC fraction was found to contain distinct LSCs that vary in proliferative and differentiation properties. OCI-AML22 represents a valuable resource to decipher mechanisms driving stemness and the multiple layers of heterogeneity within LSCs.
Macro-Chemical Biology: Engineering Biomimetic Trogocytosis with Farnesylated Chemically Self-Assembled Nanorings
Authors: Wang Yiao , Rozumalski Lakmal , Lichtenfels Caitlin , Petersberg Jacob R. , Kilic Ozgun , Distefano Mark D. , Wagner Carston R.
Published: March 2022

With the recent success of cell-based therapies, there has been a rapidly emerging interest in the engineering of cell-cell interactions and communications. Inspired by the natural intercellular material transfer process of trans-endocytosis or trogocytosis, we proposed that targeted farnesylated chemically self-assembled nanorings (farnesyl-CSANs) could serve as a biomimetic trogocytosis vehicle for engineering directional cargo transfer between cells; thus, allowing cell-cell interactions to be monitored, as well as facilitating communication between the cells by delivery of bioactive species. The membranes of sender cells were stably modified by hydrophobic insertion with the targeted farnesyl-CSANs and to be efficiently transferred to receiver cells expressing the appropriate receptor by endocytosis. CSAN-assisted cell-cell cargo transfer (C4T) was demonstrated to be receptor-specific and dependent on direct cell-cell interactions, the rate of receptor internalization and the amount of receptor expression. In addition, C4T was shown to facilitate cell-to-cell delivery of an apoptosis inducing drug, as wells as antisense oligonucleotides (ASO). Taken together, the C4T approach is a potentially versatile biomimetic trogocytosis platform that can be used to monitor cell-cell interactions, as well as the engineering of cell-cell communications, such as cell-based drug delivery.
Cross-comparison of state of the art neuromorphological simulators on modern CPUs and GPUs using the Brain Scaffold Builder
Authors: De Schepper R. , Akar N. Abi , Hater T. , Huisman B. F. B. , D’Angelo E. , Morrison A. , Casellato C.
Published: March 2022

A variety of software simulators exist for neuronal networks, and a subset of these tools allow the scientist to model neurons in high morphological detail. The scalability of such simulation tools over a wide range in neuronal networks sizes and cell complexities is predominantly limited by effective allocation of components of such simulations over computational nodes, and the overhead in communication between them. In order to have more scalable simulation software, it is therefore important to develop a robust benchmarking strategy that allows insight into specific computational bottlenecks for models of realistic size and complexity. In this study, we demonstrate the use of the Brain Scaffold Builder (BSB; De Schepper et al., 2021) as a framework for performing such benchmarks. We perform a comparison between the well-known neuromorphological simulator NEURON (Carnevale and Hines, 2006), and Arbor (Abi Akar et al., 2019), a new simulation library developed within the framework of the Human Brain Project. The BSB can construct identical neuromorphological and network setups of highly spatially and biophysically detailed networks for each simulator. This ensures good coverage of feature support in each simulator, and realistic workloads. After validating the outputs of the BSB generated models, we execute the simulations on a variety of hardware configurations consisting of two types of nodes (GPU and CPU). We investigate performance of two different network models, one suited for a single machine, and one for distributed simulation. We investigate performance across different mechanisms, mechanism classes, mechanism combinations, and cell types. Our benchmarks show that, depending on the distribution scheme deployed by Arbor, a speed-up with respect to NEURON of between 60 and 400 can be achieved. Additionally Arbor can be up to two orders of magnitude more energy efficient.
Dopaminergic modulation of dynamic emotion perception
Authors: Schuster B.A. , Sowden S. , Rybicki A.J. , Fraser D.S. , Press C. , Holland P. , Cook J.L.
Published: March 2022

Emotion recognition abilities are fundamental to our everyday social interaction. A large number of clinical populations show impairments in this domain, with emotion recognition atypicalities being particularly prevalent among disorders exhibiting a dopamine system disruption (e.g., Parkinson’s disease). Although this suggests a role for dopamine in emotion recognition, studies employing dopamine manipulation in healthy volunteers have exhibited mixed neural findings and no behavioural modulation. Interestingly, whilst a dependence of dopaminergic drug effects on individual baseline dopamine function has been well established in other cognitive domains, the emotion recognition literature so far has failed to account for these possible interindividual differences. The present within-subjects study therefore tested the effects of the dopamine D2 antagonist haloperidol on emotion recognition from dynamic, whole-body stimuli while accounting for interindividual differences in baseline dopamine. 33 healthy male and female adults rated emotional point-light walkers (PLWs) once after ingestion of 2.5 mg haloperidol and once after placebo. To evaluate potential mechanistic pathways of the dopaminergic modulation of emotion recognition, participants also performed motoric and counting-based indices of temporal processing. Confirming our hypotheses, effects of haloperidol on emotion recognition depended on baseline dopamine function, where individuals with low baseline dopamine showed enhanced, and those with high baseline dopamine decreased emotion recognition. Drug effects on emotion recognition were related to drug effects on movement-based and explicit timing mechanisms, indicating possible mediating effects of temporal processing. Results highlight the need for future studies to account for baseline dopamine and suggest putative mechanisms underlying the dopaminergic modulation of emotion recognition.

Significance statement

A high prevalence of emotion recognition difficulties amongst clinical conditions where the dopamine system is affected suggests an involvement of dopamine in emotion recognition processes. However, previous psychopharmacological studies seeking to confirm this role in healthy volunteers thus far have failed to establish whether dopamine affects emotion recognition and lack mechanistic insights. The present study uncovered effects of dopamine on emotion recognition in healthy individuals by controlling for interindividual differences in baseline dopamine function and investigated potential mechanistic pathways via which dopamine may modulate emotion recognition. Our findings suggest that dopamine may influence emotion recognition via its effects on temporal processing, providing new directions for future research on typical and atypical emotion recognition.
Spatial Transcriptomics-based Identification of Molecular Markers for Nanomedicine Distribution in Tumor Tissue
Authors: Park Jeong-Bin , Choi Jin-Yeong , Choi Hongyoon , Im Hyung-Jun
Published: March 2022

The intratumoral accumulation of nanomedicine has been considered a passive process, referred to as the enhanced permeability and retention (EPR) effect. Recent studies have suggested that the tumor uptake of nanomedicines follows an energy-dependent pathway rather than being a passive process. Herein, to explore the factor candidates that are associated with nanomedicine tumor uptake, we developed a molecular marker identification platform by integrating microscopic fluorescence images of a nanomedicine distribution with spatial transcriptomics (ST) information. When this approach is applied to PEGylated liposomes, molecular markers related to hypoxia, glucose metabolism and apoptosis can be identified as being related to the intratumoral distribution of the nanomedicine. We expect that our method can be applied to explain the distribution of a wide range of nanomedicines and that the data obtained from this analysis can enhance the precise utilization of nanomedicines.
A gut-derived hormone switches dietary preference after mating in Drosophila
Authors: Malita Alina , Kubrak Olga , Koyama Takashi , Ahrentløv Nadja , Halberg Kenneth V. , Texada Michael J. , Nagy Stanislav , Rewitz Kim
Published: March 2022

Animals must adapt their dietary choices to meet their nutritional needs. How these needs are detected and translated into nutrient-specific appetites that drive food-choice behaviors is poorly defined. Here, we show that the enteroendocrine cells (EECs) of the adult female Drosophila midgut sense nutrients and in response release neuropeptide F (NPF), an ortholog of mammalian NPY-family gut-brain hormones. Gut-derived NPF acts via effects on glucagon-like adipokinetic hormone (AKH) signaling to induce sugar satiety and to drive hunger for protein-rich food, and on adipose tissue to promote storage of ingested nutrients. Suppression of gut NPF leads to overconsumption of dietary sugar while decreasing intake of protein-rich yeast. Furthermore, we show a female-specific function of gut-derived NPF in the suppression of AKH signaling after mating. This induces a dietary switch that promotes preference for protein-containing food to support reproduction. Together, our findings suggest that the gut NPF-AKH axis regulates appetite that drives specific food choices to ensure homeostatic consumption of nutrients, providing insight into the hormonal mechanisms that underlie nutrient-specific hungers.
Comprehensive analysis of cis- and trans-acting factors affecting Break-Induced Replication
Authors: Uribe-Calvillo Tannia , Maestroni Laetitia , Marsolier Marie-Claude , Khadaroo Basheer , Arbiol Christine , Schott Jonathan , Llorente Bertrand
Published: March 2022

Break-induced replication (BIR) is a highly mutagenic eukaryotic homologous DNA recombination pathway that repairs one-ended DNA double strand breaks such as broken DNA replication forks and eroded telomeres. While searching for cis-acting factors regulating BIR efficiency, we found that BIR efficiency is the highest close to chromosome ends. The variations of BIR efficiency as a function of the length of DNA to replicate can be described as a combination of two decreasing exponential functions, a property in line with repeated cycles of strand invasion, elongation and dissociation that characterize BIR. Interestingly, the apparent processivity of BIR depends on the length of DNA already synthesized. BIR is more susceptible to disruption during the synthesis of the first ∼35-40 kb of DNA than later, notably when the template chromatid is being transcribed or heterochromatic. Finally, we show that the Srs2 helicase promotes BIR from both telomere proximal and telomere distal regions in diploid cells but only from telomere proximal sites in haploid cells. Altogether, we bring new light on the factors impacting a last resort DNA repair pathway.
Deep networks may capture biological behaviour for shallow, but not deep, empirical characterizations
Authors: Neri Peter
Published: March 2022

We assess whether deep convolutional networks (DCN) can account for a most fundamental property of human vision: detection/discrimination of elementary image elements (bars) at different contrast levels. The human visual process can be characterized to varying degrees of ‘depth’, ranging from percentage of correct detections to detailed tuning and operating characteristics of the underlying perceptual mechanism. We challenge deep networks with the same stimuli/tasks used with human observers and apply equivalent characterization of the stimulus-response coupling. In general, we find that popular DCN architectures do not account for signature properties of the human process. For shallow depth of characterization, some variants of network-architecture/training-protocol produce human-like trends; however, richer empirical descriptors expose glaring discrepancies. These results urge caution in assessing whether neural networks do or do not capture human behaviour: ultimately, our ability to assess ‘success’ in this area can only be as good as afforded by the depth of behavioural characterization against which the network is evaluated. We propose a novel set of metrics/protocols that impose stringent constraints on the evaluation of DCN behaviour as adequate approximation of biological processes.
A comprehensive single-cell expression atlas of human AML leukemia-initiating cells unravels the contribution of HIF pathway and its therapeutic potential
Authors: Velasco-Hernandez Talia , Trincado Juan L. , Vinyoles Meritxell , Closa Adria , Gutiérrez-Agüera Francisco , Molina Oscar , Rodríguez-Cortez Virginia C , Petazzi Paolo , Beneyto-Calabuig Sergi , Velten Lars , Romecin Paola , Casquero Raquel , Abollo-Jiménez Fernando , Díaz de la Guardia Rafael , Lorden Patricia , Bataller Alex , Lapillonne Helene , Stam Ronald W , Vives Susana , Torrebadell Montserrat , Fuster Jose Luis , Bueno Clara , Eyras Eduardo , Heyn Holger , Menéndez Pablo
Published: March 2022

Relapse remains a major challenge in the clinical management of acute myeloid leukemia (AML), and is driven by rare therapy-resistant leukemia-initiating stem cells (LSCs) that reside in specific bone marrow niches. Hypoxia signaling keeps cells in a quiescent and metabolically relaxed state, desensitizing them to chemotherapy. This suggests the hypothesis that hypoxia contributes to AML-LSC function and chemoresistance and is a therapeutic target to sensitize AML-LSCs to chemotherapy. Here, we provide a comprehensive single-cell expression atlas (119,000 cells) of AML cells and AML-LSCs in paired diagnostic-relapse samples from risk-stratified patients with AML. The HIF/hypoxia pathway is attenuated in AML-LSCs compared with differentiated AML cells, but is enhanced when compared with healthy hematopoietic cells. Accordingly, chemical inhibition cooperates with standard-of-care chemotherapy to impair leukemogenesis, substantially eliminating AML-LSCs. These findings support the HIF pathway as a stem cell regulator in human AML, and reveal avenues for combinatorial targeted and chemotherapy-based approaches to specifically eliminate AML-LSCs.
Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies Against Delta and Omicron in Mice
Authors: van Vuren Petrus Jansen , McAuley Alexander J. , Kuiper Michael J. , Singanallur Nagendrakumar B. , Bruce Matthew P. , Riddell Shane , Goldie Sarah , Mangalaganesh Shruthi , Chahal Simran , Drew Trevor W. , Blasdell Kim R. , Tachedjian Mary , Caly Leon , Druce Julian D. , Ahmed Shahbaz , Khan Mohammad Suhail , Malladi Sameer Kumar , Singh Randhir , Pandey Suman , Varadarajan Raghavan , Vasan Seshadri S.
Published: March 2022

As existing vaccines fail to completely prevent COVID-19 infections or community transmission, there is an unmet need for vaccines that can better combat SARS-CoV-2 variants of concern (VOC). We have previously developed highly thermo-tolerant monomeric and trimeric receptor binding domain derivatives that can withstand 100°C for 90 minutes and 37°C for four weeks, and help eliminate cold chain requirements. We show that mice immunised with these vaccine formulations elicit high titres of antibodies that neutralise SARS-CoV-2 variants VIC31 (with Spike: D614G mutation), Delta and Omicron (BA.1.1) VOC. Compared to VIC31, there was an average 14.4-fold reduction in neutralisation against BA.1.1 for the three monomeric antigen-adjuvant combinations, and 16.5-fold reduction for the three trimeric antigen-adjuvant combinations; the corresponding values against Delta were 2.5 and 3.0. Our findings suggest that monomeric formulations are suitable for the upcoming Phase I human clinical trials, and that there is potential for increasing efficacy with vaccine matching to improve responses against emerging variants. These findings are consistent with in silico modelling and AlphaFold predictions which show that while oligomeric presentation can be generally beneficial, it can make important epitopes inaccessible, and also carries the risk of eliciting unwanted antibodies against the oligomerisation domain.
Follicle cell contact maintains main body axis polarity in theDrosophila melanogasteroocyte
Authors: Milas Ana , de-Carvalho Jorge , Telley Ivo A.
Published: March 2022

InDrosophila melanogasterthe anterior-posterior body axis is maternally established and governed by differential localization of partitioning defective (Par) proteins within the oocyte. At mid-oogenesis, Par-1 accumulates at the posterior end of the oocyte while Par-3/Bazooka is excluded there but maintains its localization along the remaining oocyte cortex. This mutual exclusion leads to a polarized microtubule network and accumulation of posterior determinantoskarlater in oogenesis. Reciprocal biochemical interactions between Par proteins can explain their cortical exclusion and domain formation – for example, Par-1 excludes Par-3 by phosphorylation. However, past studies have proposed the need for somatic cells at the posterior end to initiate oocyte polarization by providing a trigger signal. To date, despite modern screening approaches and genetic manipulation, neither the molecular identity nor the nature of the signal is known. Here, we provide the first evidence that mechanical contact of posterior follicle cells (PFCs) with the oocyte cortex causes the posterior exclusion of Bazooka and maintains oocyte polarity. We show that Bazooka prematurely accumulates exclusively where posterior follicle cells have been mechanically detached or ablated. This occurs before Par-1 is removed suggesting that phosphorylation of Bazooka by Par-1 is not sufficient to maintain Bazooka exclusion in the absence of PFC contact. Furthermore, we provide evidence that PFC contact maintains Par-1 andoskarlocalization and microtubule cytoskeleton polarity in the oocyte. Our observations suggest that cell-cell contact mechanics modulates Par protein binding sites at the oocyte cortex.
Mechanosensory Systems and Sensory Integration MediateC. elegansNegative Gravitaxis
Authors: Ackley Caroline , Washiashi Lindsey , Ziaei Kajbaf Neda , Krishnamurthy Ruchira , Sun Zhenxuan , Duong Vivian , Choe Kaylin , Lane Elijah , Wood Cricket , Smith Eleanor , Pellegrini Giulia , Sherwin Mark , Joshi Pradeep , Rothman Joel H.
Published: March 2022

The ability to sense Earth’s gravitational pull is essential for orientation, navigation, and proprioception in many organisms. We report here thatC. elegansexhibits pronounced negative gravitaxis, or movement away from the Earth’s center, independent of orientation of the geomagnetic field. This behavior is antagonized by light and electromagnetic fields, suggesting that it is integrated with other sensory inputs. We found that MEC-5/7/12, and TRPA-1, but not MEC-4/10 DEG/ENaC channels or other proteins involved in gentle touch transduction, are essential for negative gravitaxis, suggesting that the sensory system for detecting and responding to gravity is separable from touch sensation. We also found that the PVD neurons but not touch receptor neurons (TRNs) are required for this behavior. These findings implicate an interconnected mechanism for gravity sensation involving an ion channel that is also present in the mammalian vestibular system, suggesting possible homology in gravity sensing across animal phylogeny.
The Endoplasmic Reticulum Membrane Complex Promotes Proteostasis of GABAAReceptors
Authors: Whittsette Angela , Wang Ya-Juan , Mu Ting-Wei
Published: March 2022

The endoplasmic reticulum membrane complex (EMC) plays a critical role in the biogenesis of tail-anchored and a subset of multi-pass membrane proteins in the endoplasmic reticulum. However, due to the nearly exclusive expression of neurotransmitter-gated ion channels in the central nervous system, the role of the EMC in their biogenesis is not well understood. In this study, we demonstrated that the EMC positively regulates the surface trafficking and thus function of endogenous γ-aminobutyric acid (GABAA) receptors, the primary inhibitory ion channels in the mammalian brain. Further, among ten EMC subunits, EMC3 and EMC6 have the most prominent effects, indicating a subunit-specific contribution. EMC3 and EMC6 show endogenous interactions with major neuroreceptors, which depends on their transmembrane domains. Overexpression of EMC3 and EMC6 is sufficient to restore the function of epilepsy-associated GABAAreceptor variants, suggesting that operating EMC has the potential to ameliorate neurological diseases associated with protein conformational defects.

In brief

The multi-subunit EMC serves as an insertase for a subset of membrane proteins and enables their biogenesis in the endoplasmic reticulum. However, the subunit-specific effect of the EMC on multi-pass neuroreceptors is not well understood. Whittsette et al. demonstrate that EMC3 and EMC6 interact with GABAAreceptors and positively regulate their trafficking and function.

Highlights

EMC3 and EMC6 positively regulate the function of endogenous GABAAreceptors.

The EMC interacts with major endogenous neuroreceptors.

The interaction between EMC and GABAAreceptors depends on the EMC transmembrane domains.

Overexpressing the EMC is sufficient to restore the function of pathogenic GABAAreceptor variants.
Eukaryotic initiation factor 2α kinases regulate virulence functions, stage conversion, and the stress response in Entamoeba invadens
Authors: Walters Heather A. , Welter Brenda H. , Orobio-Hurtado Ronny , Moss Harrison C. , Villano Martha A. , Sullivan William J. , Temesvari Lesly A.
Published: March 2022

Entamoeba histolytica is a protozoan parasite that causes amoebic dysentery and liver abscess. This pathogen possesses a two-stage life cycle consisting of an environmentally stable cyst and a pathogenic amoeboid trophozoite. Since infection is acquired by ingestion of cysts from contaminated food and water, this parasite is prevalent in underdeveloped countries. A reptilian pathogen, Entamoeba invadens, which can encyst in culture, has long-served as a surrogate to study stage conversion. In the host, the Entamoebae must manage stress including nutrient deprivation and host immune pressure. In many systems, the stress response is characterized by down-regulation of translation, which is initiated by the phosphorylation of eukaryotic initiation factor-2 alpha (eIF2α). In mammalian cells, this phosphorylation is carried out by a family of eIF2α kinases. A canonical eIF2α translational control system exists in the Entamoebae; however, no eIF2α kinases have been characterized. In this study, we identified two eIF2α kinases in E. invadens, EiIF2K-A and EiIF2K-B. Their identity as eIF2α kinases was validated using a heterologous yeast system. We used an RNAi Trigger-mediated silencing system to reduce expression of EiIF2K-A, which also reduced expression of EiIF2K-B. Parasites with decreased kinase expression exhibited decreased phosphorylation of eIF2α and increased sensitivity to oxidative stress. Diminished kinase expression also correlates with an increased rate of encystation, a decreased the rate of excystation, and an increase in several virulence functions, erythrophagocytosis and adhesion to host cells. Taken together, these data suggest that EiIF2K-A and EiIF2K-B are authentic eIF2α kinases that may regulate the Entamoeba stress response.

Importance

Entamoeba histolytica is a human pathogen that causes dysentery and affects millions of people worldwide. This parasite possesses a two-stage life cycle: an environmentally stable cyst and the pathogenic trophozoite. Cysts are ingested from contaminated food and water; thus, this parasite in prevalent in underdeveloped countries. Current therapies commonly cause adverse side effects; therefore, new treatments are needed. In the host, Entamoeba experiences stress brought on, in part, by the host immune system. Understanding stage conversion and the stress response of this pathogen may lead to new drug therapies. Using the model organism, E. invadens, we identified two kinases, similar to those involved in stress and stage conversion in other systems. We determined that these kinases may regulate the oxidative stress response, stage conversion, and virulence. This work is significant as it will inform future studies on the life cycle and pathogenicity of the Entamoeba species.
Immunogenicity of an Ad26-based SARS-CoV-2 Omicron Vaccine in Naïve Mice and SARS-CoV-2 Spike Pre-immune Hamsters
Authors: Swart Maarten , de Wilde Adriaan , Schmit-Tillemans Sonja , Verspuij Johan , Daal Chenandly , Choi Ying , Perkasa Aditya , Kourkouta Eleni , Tahiri Issam , Mulders Michel , Gil Ana Izquierdo , Muchene Leacky , Juraszek Jarek , Vellinga Jort , Custers Jerome , Bos Rinke , Schuitemaker Hanneke , Wegmann Frank , Roozendaal Ramon , Kuipers Harmjan , Zahn Roland
Published: March 2022

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant sparked concern due to its fast spread and the unprecedented number of mutations in the spike protein that enables it to partially evade spike-based COVID-19 vaccine-induced humoral immunity. In anticipation of a potential need for an Omicron spike-based vaccine, we generated an Ad26 vector encoding an Omicron (BA.1) spike protein (Ad26.COV2.S.529). Ad26.COV2.S.529 encodes for a prefusion stabilized spike protein, similar to the current COVID-19 vaccine Ad26.COV2.S encoding the Wuhan-Hu-1 spike protein. We verified that spike expression by Ad26.COV2.S.529 was comparable to Ad26.COV2.S. Immunogenicity of Ad26.COV2.S.529 was then evaluated in naïve mice and SARS-CoV-2 Wuhan-Hu-1 spike pre-immunized hamsters. In naïve mice, Ad26.COV2.S.529 elicited robust neutralizing antibodies against SARS-CoV-2 Omicron (BA.1) but not to SARS-CoV-2 Delta (B.1.617.2), while the opposite was observed for Ad26.COV2.S. In pre-immune hamsters, Ad26.COV2.S.529 vaccination resulted in robust increases in neutralizing antibody titers against both SARS-CoV-2 Omicron (BA.1) and Delta (B.1.617.2), while Ad26.COV2.S vaccination only increased neutralizing antibody titers against the Delta variant. Our data imply that Ad26.COV2.S.529 can both expand and boost a Wuhan-Hu-1 spike-primed humoral immune response to protect against distant SARS-CoV-2 variants.
Acid-Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer
Authors: Zhou Yi , Chang Wennan , Lu Xiaoyu , Wang Jin , Zhang Chi , Xu Ying
Published: March 2022

Acid-base homeostasis is a fundamental property of living cells and its persistent disruption in human cells can lead to a wide range of diseases. We have conducted computational modeling and analysis of transcriptomic data of 4750 human tissue samples of nine cancer types in the TCGA database. Built on our previous study, we have quantitatively estimated the (average) production rate of OH− by cytosolic Fenton reactions, which continuously disrupt the intracellular pH homeostasis. Our predictions indicate that all or a subset of 43 reprogrammed metabolisms (RMs) are induced to produce net protons (H+) at comparable rates of Fenton reactions to keep the intracellular pH stable. We have then discovered that a number of well-known phenotypes of cancers, including increased growth rate, metastasis rate and local immune cell composition, can be naturally explained in terms of the Fenton reaction level and the induced RMs. This study strongly suggests the possibility to have a unified framework for studies of cancer-inducing stressors, adaptive metabolic reprogramming, and cancerous behaviors. In addition, strong evidence is provided to demonstrate that a popular view of that Na+/H+ exchangers, along with lactic acid exporters and carbonic anhydrases are responsible for the intracellular alkalization and extracellular acidification in cancer may not be justified.
Misinterpreting the horseshoe effect in neuroscience
Authors: Proix Timothée , Perich Matthew G. , Milekovic Tomislav
Published: March 2022

Dimensionality reduction methods are frequently used to analyze high-dimensional activity of cortical neuron populations during behavior. The resulting oscillatory trajectories that consistently emerge from this analysis have been interpreted as a signature of latent dynamical systems. Here, we show that these oscillatory trajectories necessarily result from applying dimensionality reduction methods on recordings that approximately exhibit continuous variation in time, regardless of whether or not the recorded system incorporates latent dynamics.
Disentanglement of Entropy and Coevolution using Spectral Regularization
Authors: Wang Haobo , Feng Shihao , Liu Sirui , Ovchinnikov Sergey
Published: March 2022

The rise in the number of protein sequences in the post-genomic era has led to a major breakthrough in fitting generative sequence models for contact prediction, protein design, alignment, and homology search. Despite this success, the interpretability of the modeled pairwise parameters continues to be limited due to the entanglement of coevolution, phylogeny, and entropy. For contact prediction, post-correction methods have been developed to remove the contribution of entropy from the predicted contact maps. However, all remaining applications that rely on the raw parameters, lack a direct method to correct for entropy. In this paper, we investigate the origins of the entropy signal and propose a new spectral regularizer to down weight it during model fitting. We find the added regularizer to GREMLIN, a Markov Random Field or Potts model, allows for the inference of a sparse contact map without loss in precision, meanwhile improving interpretability, and resolving overfitting issues important for sequence evaluation and design.
Seasonal changes in membrane structure and excitability in central neurons of goldfish (Carassius auratus) under constant environmental conditions
Authors: Country Michael W. , Haase Kristina , Blank Katrin , Canez Carlos R. , Roberts Joshua A. , Campbell Benjamin F.N. , Smith Jeffrey C. , Pelling Andrew E. , Jonz Michael G.
Published: March 2022

Seasonal modifications in the structure of cellular membranes occur as an adaptive measure to withstand exposure to prolonged environmental change. Little is known about whether such changes may occur independently of external cues, such as photoperiod or temperature, or how they may impact the central nervous system (CNS). We compared membrane properties of central neurons isolated from the retina of goldfish (Carassius auratus), an organism well-adapted to extreme environmental change, during the summer and winter months. Goldfish were maintained in a facility under constant environmental conditions throughout the year. Analysis of whole-retina phospholipid composition using mass spectrometry-based lipidomics revealed a two-fold increase in phosphatidylethanolamine species during the winter, suggesting an increase in cell membrane fluidity. Atomic force microscopy was used to produce localized, nanoscale-force deformation of neuronal membranes. Measurement of Young’s modulus indicated increased membrane stiffness (or decreased elasticity) in neurons isolated during the winter. Voltage-clamp electrophysiology was used to assess physiological changes in neurons between seasons. Winter neurons displayed a hyperpolarized reversal potential (Vrev) and a significantly lower input resistance (Rin) compared to summer neurons. This was indicative of a decrease in membrane excitability during the winter. Subsequent measurement of intracellular Ca2+ activity using Fura-2 microspectrofluorometry confirmed a reduction in action potential activity, including duration and action potential profile, in neurons isolated during the winter. These studies demonstrate chemical and biophysical changes that occur in central neurons of goldfish throughout the year without exposure to seasonal cues, and suggest a novel mechanism of seasonal regulation of CNS activity.

SUMMARY STATEMENT

Central neurons isolated from the retina of goldfish held under constant environmental conditions undergo seasonal changes in membrane structure and excitability.
Widespread hybridization between invasive bleak (Alburnus alburnus) and native Iberian chubs (Squalius spp.): a neglected threat
Authors: Morgado-Santos M , Curto M , Alexandre CM , Alves MJ , Gante HF , Gkenas C , Medeiros JP , Pinheiro PJ , Almeida PR , Magalhães MF , Ribeiro F
Published: March 2022

Hybridization between native and exotic species is a major conservation issue. In Iberian rivers, which are simultaneously among the most invaded and diverse ecosystems, harboring a high proportion of endemic fishes, this issue is becoming highly concerning. To date, hybridization has been reported to occur between the invasive bleak Alburnus alburnus and the endemic chubs Squalius alburnoides and S. pyrenaicus, in some scattered locations. However, the bleak is increasingly spreading in the region, potentially increasing the risks of hybridization with these and other Squalius species. To gather a more comprehensive picture on the current extension of hybridization, we compiled and mapped records on hybrids between bleak and chubs collected by multiple research teams in different ongoing projects in the Portuguese territory, and genetically assessed the hybrid identity of specimens in an area of sympatry between bleak and S. carolitertii, using nuclear and mitochondrial markers. We found that hybridization with bleak is widespread in several Portuguese river basins and involves at least three endemic chubs, S. alburnoides, S. pyrenaicus and S. carolitertii. This may have serious consequences, including not only waste of reproductive effort and damage of genetic integrity, but also putative shifts on the reproductive dynamics of the Squalius system, which includes endemic hybrids, reproducing sexually and nonsexually. Hybridization should be recognized as a significant impact of biological invasions, and we recommend that future studies should characterize the fitness of hybrids and their ecological and genetic interactions with parental Iberian fish, to elucidate effective conservation measures.
Concordance of MERFISH Spatial Transcriptomics with Bulk and Single-cell RNA Sequencing
Authors: Liu Jonathan , Tran Vanessa , Vemuri Venkata Naga Pranathi , Byrne Ashley , Borja Michael , Kim Yang Joon , Agarwal Snigdha , Wang Ruofan , Awayan Kyle , Murti Abhishek , Taychameekiatchai Aris , Wang Bruce , Emanuel George , He Jiang , Haliburton John , Pisco Angela Oliveira , Neff Norma
Published: March 2022

Spatial transcriptomics extends single cell RNA sequencing (scRNA-seq) by providing spatial context for cell type identification and analysis. Imaging-based spatial technologies such as Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH) can achieve single-cell resolution, directly mapping single cell identities to spatial positions. MERFISH produces an intrinsically different data type than scRNA-seq and a technical comparison between the two modalities is necessary to ascertain how to best integrate them. We performed MERFISH on mouse liver and kidney and compared the resulting bulk and single-cell RNA statistics with those from the Tabula Muris Senis cell atlas as well as from two Visium datasets. MERFISH quantitatively reproduced the bulk RNA-seq and scRNA-seq results with improvements in overall dropout rates and sensitivity. Finally, we found that MERFISH independently resolved distinct cell types and spatial structure in both liver and kidney. Computational integration with the Tabula Muris Senis atlas did not enhance these results. We conclude that compared to scRNA-seq, MERFISH provides a quantitatively comparable method for measuring single-cell gene expression and can robustly identify cell types without the need for computational integration with scRNA-seq reference atlases.