bluuebunny/crossref_metadata_2025 huggingface dataset:
Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies
Authors: Jette Claudia A. , Cohen Alexander A. , Gnanapragasam Priyanthi N.P. , Muecksch Frauke , Lee Yu E. , Huey-Tubman Kathryn E. , Schmidt Fabian , Hatziioannou Theodora , Bieniasz Paul D. , Nussenzweig Michel C. , West Anthony P. , Keeffe Jennifer R. , Bjorkman Pamela J. , Barnes Christopher O.
Published: April 2021

Many anti-SARS-CoV-2 neutralizing antibodies target the ACE2-binding site on viral spike receptor-binding domains (RBDs). The most potent antibodies recognize exposed variable epitopes, often rendering them ineffective against other sarbecoviruses and SARS-CoV-2 variants. Class 4 anti-RBD antibodies against a less-exposed, but more-conserved, cryptic epitope could recognize newly-emergent zoonotic sarbecoviruses and variants, but usually show only weak neutralization potencies. We characterized two class 4 anti-RBD antibodies derived from COVID-19 donors that exhibited broad recognition and potent neutralization of zoonotic coronavirus and SARS-CoV-2 variants. C118-RBD and C022-RBD structures revealed CDRH3 mainchain H-bond interactions that extended an RBD β-sheet, thus reducing sensitivity to RBD sidechain changes, and epitopes that extended from the cryptic epitope to occlude ACE2 binding. A C118-spike trimer structure revealed rotated RBDs to allow cryptic epitope access and the potential for intra-spike crosslinking to increase avidity. These studies facilitate vaccine design and illustrate potential advantages of class 4 RBD-binding antibody therapeutics.
Geospatial characterizing of Under-Five Mortality in Alexandria, Egypt
Authors: Hassan Mahmoud Adel , Ramadan Ahmed , Tahoun Mohamed Mostafa , Omran Abdel Rahman , Ebrahim Ali Shaimaa Gad EL Karim , Khedr Esmail Ola Fahmy , Adel Elrewany Ehab Mohamed , Ahmed El-Meligy Passent Ehab El-din , Elzayat Amira Mahmoud , el Malawany Dina Hussein , Mahboob Amira Saad , Eldewiki Mohamed Kamal , Abdellatif Hammouda Esraa Abdellatif Mohamed , Ghazy Ramy Mohamed
Published: April 2021

This study aimed to identify geo-spatial pattern of under-five mortality (U5M) in Alexandria and its key determinants. We analyzed the geospatial distribution of 3064 deaths registered at 24 health offices reported from January 2018 to June 2019. The localities of Alexandria city were clustered into high and low incidence areas. Neonates represented 58.7% of U5M, while post-neonates and children were 31.1%, 10.2% respectively. Male deaths were significantly higher (P=0.036). The main leading causes of U5M were prematurity (28.32%), pneumonia (11.01%), cardiac arrest (10.57%), congenital malformation (9.95%), and childhood cardiovascular diseases (9.20%). Spatial distribution of U5M (including the most common three causes) tend to be clustered in western parts of Alexandria (El Hawaria, Bahig, Hamlis and Ketaa Maryiut). Another 9 clusters are at risk of being hotspots. Illiteracy, divorce, and poor locality characteristics (household size, population density, and access to water supply and sanitation), were statistically significant predictors of U5M.
Bedside formulation of a personalized multi-neoantigen vaccine against mammary carcinoma
Authors: Mohsen Mona O. , Speiser Daniel E. , Michaux Justine , Pak HuiSong , Stevenson Brian J. , Vogel Monique , Inchakalody Varghese P. , de Brot Simone , Coukos George , Dermime Said , Bassani-Sternberg Michal , Bachmann Martin F.
Published: April 2021

Abstract Figure

Graphical abstract

Individualized neoantigen vaccination against mammary carcinoma

Background

Harnessing the immune system to purposely recognize and destroy tumours represents a significant breakthrough in clinical oncology. Nonsynonymous mutations (neoantigenic peptides) were identified as powerful cancer targets. This knowledge can be exploited for further improvements of active immunotherapies, including cancer vaccines as T cells specific for neoantigens are not attenuated by immune tolerance mechanism and do not harm healthy tissues. The current study aimed at developing an optimized multi-target vaccine using short or long neoantigenic peptides utilizing virus-like particles (VLPs) as an efficient vaccine platform.

Methods

Here we identified mutations of murine mammary carcinoma cells by integrating mass spectrometry-based immunopeptidomics and whole exome sequencing. Neoantigenic peptides were synthesized and covalently linked to virus-like nanoparticles using a Cu-free click-chemistry method for easy preparation of vaccines against mouse mammary carcinoma.

Results

As compared to short peptides, vaccination with long peptides was superior in the generation of neoantigen-specific CD4+and CD8+T cells which readily produced IFN-γ and TNF-α. The resulting anti-tumour effect was associated with favourable immune re-polarization in the tumour microenvironment through reduction of myeloid-derived suppressor cells. Vaccination with long neoantigenic peptides also decreased post-surgical tumour recurrence and metastases, and prolonged mouse survival, despite the tumour’s low mutational burden.

Conclusion

Integrating mass spectrometry-based immunopeptidomics and whole exome-sequencing is an efficient technique for identifying neoantigenic peptides. A multi-target VLP-based vaccine shows a promising anti-tumour results in an aggressive murine mammary carcinoma cell line. Future clinical application using this strategy is readily feasible and practical, as click-chemistry coupling of personalized synthetic peptides to the nanoparticles can be done at the bedside directly before injection.
Effects of Escitalopram and Relearning on Cortical and Subcortical Grey Matter in Healthy Humans
Authors: Vanicek T , Reed MB , Seiger R , Godbersen M , Klöbl M , Unterholzner J , Spurny B , Gryglewski G , Handschuh P , Kraus C , Stimpfl T , Rupprecht R , Kasper S , Lanzenberger R
Published: April 2021

The antidepressant effect of selective serotonin reuptake inhibitors (SSRI) is related to increased neuroplasticity during relearning. Stress-induced dendritic atrophy in key brain areas for learning and memory such as the hippocampus and prefrontal cortex is reversed by SSRI treatment. This finding is accompanied by behavioral stabilization. The aim of this study was to investigated serotonergic modulation effects on structural neuroplasticity (cortical thickness, subcortical volumes) during relearning in healthy subjects. Participants performed daily associative learning tasks over 3 weeks followed by a 3-week relearning phase combined with intake of the SSRI escitalopram or placebo. Evidence suggests that SSRIs promote the brains susceptibility to change on the basis of environment factors. We found no effect of SSRI on grey matter measures during relearning. Here, non-findings might be a consequence of the implemented intensity and duration of study interventions. With sparse literature on healthy participants in this field, future studies will have to further elucidate SSRIs properties on relearning and structural neuroplasticity.
Antagonism of GluK1-containing Kainate Receptors Reduces Ethanol Consumption by Modulating Ethanol Reward and Withdrawal
Authors: Cardé Natalia A. Quijano , Perez Erika E. , Feinn Richard , Kranzler Henry R. , Biasi Mariella De
Published: April 2021

Alcohol use disorder (AUD) is a neuropsychiatric condition affecting millions of people worldwide. Topiramate (TPM) is an antiepileptic drug that has been shown to reduce ethanol drinking in humans. However, TPM is associated with a variety of adverse effects due to its interaction with many receptor systems and intracellular pathways. Thus, a better understanding of the role of TPM’s main molecular targets in AUD could yield better therapeutic tools. GluK1-containing kainate receptors (GluK1*KARs) are non-selectively inhibited by TPM, and genetic association studies suggest that this receptor system could be targeted to reduce drinking in AUD patients. We examined the efficacy of LY466195, a selective inhibitor of GluK1*KAR, in reducing ethanol consumption in the intermittent two-bottle choice paradigm in mice. The effect of LY466195 on various ethanol-related phenotypes was investigated by quantification of alcohol intake, physical signs of withdrawal, conditioned place preference (CPP) andin vivomicrodialysis in the nucleus accumbens. Selective GluK1*KAR inhibition reduced ethanol intake and preference in a dose-dependent manner. LY466195 treatment attenuated the physical manifestations of ethanol withdrawal and influenced the rewarding properties of ethanol. Interestingly, LY466195 injection also normalized changes in dopamine levels in response to acute ethanol in ethanol-dependent mice, but had no effect in ethanol-naïve mice, suggesting ethanol state-dependent effects. The data point to GluK1*KARs as an attractive pharmacological target for the treatment of AUD.
Connectivity networks and delineation of distinct coastal provinces along the Indian coastline using large-scale Lagrangian transport simulations
Authors: Bharti D. K. , Guizien Katell , Aswathi-Das M. T. , Vinayachandran P. N. , Shanker Kartik
Published: April 2021

Ocean circulation defines the scale of population connectivity in marine ecosystems, and is essential for conservation planning. We performed Lagrangian transport simulations and built connectivity networks to understand the patterns of oceanographic connectivity along the Indian coastline. In these networks, nodes are coastal polygons and the edges connecting them represent the magnitude of larval transfer between them. We assessed the variation in connectivity networks within and between two monsoonal seasons, across El Niño–Southern Oscillation (ENSO) years and for pelagic larval durations (PLD) up to 50 days. We detected well-connected communities, mapped frequent connectivity breaks and ranked coastal areas by their functional role using network centrality measures. Network characteristics did not differ based on the ENSO year, but varied based on season and PLD. Large scale connectance (entire Indian coastline) was small, ranging from 0.5% to 3.4%, and the number of cohesive coastal communities decreased from 60 (PLD <4 days) to 30 (PLD >20 days) with increasing PLD. Despite intra-seasonal variation in connectivity breaks, four disconnected provinces were consistently identified across the entire PLD range, which partially overlapped with observed genetic and biogeographic breaks along the Indian coastline. Our results support the adoption of an adaptive regional management framework guided by fine-scale analysis of connectivity within the four provinces delineated in the present study. A few sites within each province displayed notably higher centrality values than other nodes of the network, but showed variation with season and PLD, and could be targeted for national and transnational conservation and management plans.
Hippocampal gamma-band oscillopathy in a mouse model of Fragile X Syndrome
Authors: Pollali Evangelia , Hollnagel Jan-Oliver , Çalışkan Gürsel
Published: April 2021

Fragile X syndrome (FXS) is the most common inherited form of intellectual disability arising from the loss of fragile X mental retardation protein (FMRP), a protein that plays a central role in neuronal function and plasticity. FXS patients show sensory hypersensitivity, hyperarousal and hippocampus-dependent learning deficits that can be recapitulated in the FMR1 KO mice. Enhanced metabotropic glutamate receptor (mGluR) signaling and muscarinic acetylcholine receptor (mAChR) signaling in the FMR1 KO mouse are implicated as the primary causes of the disease pathogenesis. Furthermore, glutamatergic kainate receptor (KAR) function is reduced in the cortex of the FMR1 KO mice. Of note, activation of these signaling pathways leads to slow gamma-range oscillations in the hippocampusin vitroand abnormal gamma oscillations have been reported in FMR1 KO mice and patients with FXS. Thus, we hypothesized that aberrant activation of these receptors leads to the observed gamma oscillopathy. We recorded gamma oscillations induced by either cholinergic agonist carbachol (CCh), mGluR1/5 agonist Dihydroxyphenylglycine (DHPG) or ionotropic glutamatergic agonist KA from the hippocampal CA3 in WT and FMR1 KO micein vitro. We show a specific increase in the power of DHPG and CCh-induced gamma oscillations and reduction in the synchronicity of gamma oscillations induced by KA. We further elucidate an aberrant spiking activity during CCh-induced and kainate-induced gamma oscillations which may underlie the altered gamma oscillation synchronization in the FMR1 KO mice. Last, we also noted a reduced incidence of spontaneously-occurring hippocampal sharp wave-ripple events. Our study provides further evidence for aberrant hippocampal rhythms in the FMR1 KO mice and identifies potential signaling pathways underlying gamma band oscillopathy in FXS.
The P1 and P2 helices of the Guanidinium-II riboswitch interact in a ligand-dependent manner
Authors: Fuks Christin , Falkner Sebastian , Schwierz Nadine , Hengesbach Martin
Published: April 2021

Riboswitch RNAs regulate gene expression by conformational changes induced by environmental conditions and specific ligand binding. The guanidine-II riboswitch is proposed to bind the small molecule guanidinium and to subsequently form a kissing loop interaction between the P1 and P2 hairpins. While an interaction was shown for isolated hairpins in crystallization and EPR experiments, an intrastrand kissing loop formation has not been demonstrated. Here, we report the first evidence of this interactionin cisin a ligand and Mg2+dependent manner. Using single-molecule FRET spectroscopy and detailed structural information from coarse-grained simulations, we observe and characterize three interconvertible states representing an open and kissing loop conformation as well as a novel Mg2+dependent state for the guanidine-II riboswitch fromE. coli. The results further substantiate the proposed switching mechanism and provide detailed insight into the regulation mechanism for the guanidine-II riboswitch class. Combining single molecule experiments and coarse-grained simulations therefore provides a promising perspective in resolving the conformational changes induced by environmental conditions and to yield molecular insights into RNA regulation.
How adaptation, training, and customization contribute to benefits from exoskeleton assistance
Authors: Poggensee Katherine L. , Collins Steven H.
Published: April 2021

Exoskeletons can enhance human mobility, but we still know little about why they are effective. For example, we do not know the relative importance of training, how much is required, or what type is most effective; how people adapt with the device; or the relative benefits of customizing assistance. We conducted experiments in which naïve users learned to walk with ankle exoskeletons under one of three training regimens characterized by different levels of variation in device behavior. Assistance was also customized for one group. Following moderate-variation training, the benefits of customized assistance were large; metabolic rate was reduced by 39% compared to walking with the exoskeleton turned off. Training contributed about half of this benefit and customization about one quarter; a generic controller reduced energy cost by 10% before training and 31% afterwards. Training required much more exposure than typical of exoskeleton studies, about 109 minutes of assisted walking. Type of training also had a strong effect; the low-variation group required twice as long as the moderate-variation group to become expert, while the high-variation group never acquired this level of expertise. Curiously, all users adapted in a way that resulted in less mechanical power from the exoskeleton as they gained expertise. Customizing assistance required less time than training for all parameters except peak torque magnitude, which grew slowly over the study, suggesting a longer time-scale adaptation in the person. These results underscore the importance of training to the benefits of exoskeleton assistance and suggest the topic deserves more attention.
Dual reference method for high precision infrared measurement of leaf surface temperature under field conditions
Authors: Muller Jonathan D. , Rotenberg Eyal , Tatarinov Fyodor , Vishnevetsky Irina , Dingjan Tamir , Kribus Abraham , Yakir Dan
Published: April 2021

Temperature is a key control over biological activities from the cellular to the ecosystem scales. However, direct, high precision measurements of surface temperature of small objects such as leaves under field conditions with large variations in ambient conditions remain rare. Contact methods such as thermocouples are prone to large errors. The use of non-contact remote sensing methods such as thermal infrared measurements provides an ideal solution, but their accuracy has been low (in the order of ~2 °C) due to necessity for corrections for material emissivity and fluctuations in background radiation (Lbg).

A novel ‘dual-reference’ method was developed to increase the accuracy of infrared needle-leaf surface temperature measurements in the field. It accounts for variations inLbgand corrects for the systematic camera offset using two reference plates.

We accurately captured surface temperature and leaf-to-air temperature differences of needle-leaves in a forest ecosystem with large diurnal and seasonal temperature fluctuations with an uncertainty of ±0.23 and ±0.25 °C, respectively.

Routine high precision leaf temperature measurements even under harsh field conditions, such as demonstrated here, opens the way for investigating a wide range of leaf-scale processes and its dynamics.
Acute stress affects peripersonal space representation
Authors: Ellena Giulia , Bertoni Tommaso , Durand-Ruel Manon , Thoresen John , Sandi Carmen , Serino Andrea
Published: April 2021

Peripersonal space (PPS) is the region of space surrounding the body. It has a dedicated multisensory-motor representation, whose purpose is to predict and plan interactions with the environment, and which can vary depending on environmental circumstances. Here, we investigated the effect on the PPS representation of an experimentally induced stress response. We assessed PPS representation in healthy humans, before and after a stressful manipulation, by quantifying visuotactile interactions as a function of the distance from the body, while monitoring salivary cortisol concentration. Participants, who showed a cortisol stress response, presented enhanced visuotactile integration for stimuli close to the body and reduced for far stimuli. Conversely, individuals, with a less pronounced cortisol response, showed a reduced difference in visuotactile integration between the near and the far space. In our interpretation, physiological stress resulted in a freezing-like response, where multisensory-motor resources are allocated only to the area immediately surrounding the body.
Pressure drives rapid burst-like collective migration from 3D cancer aggregates
Authors: Raghuraman Swetha , Schubert Ann-Sophie , Bröker Stephan , Jurado Alejandro , Müller Annika , Brandt Matthias , Vos Bart E. , Hofemeier Arne D. , Abbasi Fatemeh , Stehling Martin , Wittkowski Raphael , Betz Timo
Published: April 2021

Collective migration of cells is a key behaviour observed during morphogenesis, wound healing and cancer cell invasion. Hence, understanding the different aspects of collective migration is at the core of further progress in describing and treating cancer and other pathological defects. The standard dogma in cell migration is that cells exert forces on the environment to move and cell-cell adhesion-based forces provide the coordination for collective migration. Here, we report a new collective migration mechanism that is independent of pulling forces on the extra-cellular matrix (ECM), as it is driven by the pressure difference generated inside model tumours. We observe a striking collective migration phenotype, where a rapid burst-like stream of HeLa cervical cancer cells emerges from the 3D aggregate embedded in matrices with low collagen concentration (0.5 mg ml−1). This invasion-like behaviour is recorded within 8 hours post embedding (hpe), and is characterised by high cell velocity and super-diffusive collective motion. We show that cellular swelling, triggered by the soft matrix, leads to a rise in intrinsic pressure, which eventually drives an invasion-like phenotype of HeLa cancer aggregates. These dynamic observations provide new evidence that pressure-driven effects need to be considered for a complete description of the mechanical forces involved in collective migration and invasion.
iPLA2-VIA is required for healthy aging in neurons, muscle, and female germline inDrosophila melanogaster
Authors: Banerjee Surya , Schonbrun Adina , Eizadshenass Sogol , Benji Shimshon , Cantor Yaakov Tzvi , Eliach Liam , Lubin Matthew , Narrowe Zev , Purow Jeremy , Shulman Benjamin , Wiener Leib , Steinhauer Josefa
Published: April 2021

Neurodegenerative disease (ND) is a growing health burden worldwide, but its causes and treatments remain elusive. Although most cases of ND are sporadic, rare familial cases have been attributed to single genes, which can be investigated in animal models. We have generated a new mutation in the calcium-independent phospholipase A2(iPLA2) VIA geneCG6718, theDrosophila melanogasterortholog of humanPLA2G6/PARK14, mutations in which cause a suite of NDs collectively calledPLA2G6-associated neurodegeneration (PLAN). Our mutants display age-related loss of climbing ability, a symptom of neurodegeneration in flies. Although phospholipase activity commonly is presumed to underlie iPLA2-VIA function, locomotor decline in our mutants is rescued by a transgene carrying a serine-to-alanine mutation in the catalytic residue, suggesting that important functional aspects are independent of phospholipase activity. Additionally, we find that iPLA2-VIA knockdown in either muscle or neurons phenocopies locomotor decline with age, demonstrating its necessity in both neuronal and non-neuronal tissues. Furthermore, RNA in situ hybridization shows high endogenousiPLA2-VIAmRNA expression in adult germ cells, and transgenic HA-tagged iPLA2-VIA colocalizes with mitochondria there. Mutant males are fertile with normal spermatogenesis, while fertility is reduced in mutant females. Mutant female germ cells display age-related mitochondrial aggregation, loss of mitochondrial potential, and elevated cell death. These results suggest that iPLA2-VIA is important for germline mitochondrial integrity inDrosophila,which may be relevant for understanding how PLAN develops.
Synthetic cell-based materials extract positional information from morphogen gradients
Authors: Dupin Aurore , Aufinger Lukas , Styazhkin Igor , Rothfischer Florian , Kaufmann Benedikt , Schwarz Sascha , Galensowske Nikolas , Clausen-Schaumann Hauke , Simmel Friedrich C.
Published: April 2021

Dynamic biomaterials composed of synthetic cellular structures have the potential to adapt and functionally differentiate guided by physical and chemical cues from their environment. Inspired by developing biological systems, which efficiently extract positional information from chemical morphogen gradients in the presence of environmental uncertainties, we here investigate the analogous question: how well can a synthetic cell determine its position within a synthetic multicellular structure? In order to calculate positional information in such systems, we created and analyzed a large number of replicas of synthetic cellular assemblies, which were composed of emulsion droplets connected via lipid bilayer membranes. The droplets contained cell-free two-node feedback gene circuits that responded to gradients of a genetic inducer acting as a morphogen. We found that in our system, simple anterior-posterior differentiation is possible, but positional information is limited by gene expression noise, and is also critically affected by the temporal evolution of the morphogen gradient and the life-time of the cell-free expression system contained in the synthetic cells. Using a 3D printing approach, we demonstrate morphogen-based differentiation also in larger tissue-like assemblies.
Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF
Authors: Gorbovytska Vladyslava , Kim Seung-Kyoon , Kuybu Filiz , Götze Michael , Um Dahun , Kang Keunsoo , Pittroff Andreas , Schneider Lisa-Marie , Leitner Alexander , Kim Tae-Kyung , Kuhn Claus-D.
Published: April 2021

Enhancer RNAs (eRNAs) are long non-coding RNAs that originate from enhancers. Although eRNA transcription is a canonical feature of activated enhancers, the molecular features required for eRNA function and the mechanism of how eRNAs impinge on target gene transcription have not been established. Thus, using eRNA-dependent RNA polymerase II (Pol II) pause release as a model, we examined the requirement of sequence, structure and length of eRNAs for their ability to stimulate Pol II pause release by detaching NELF from paused Pol II. We found eRNA not to exert their function through common structural or sequence motifs. Instead, efficient NELF release requires a single eRNA molecule that must contain unpaired guanosines to make multiple, allosteric contacts with several NELF subunits. By revealing the molecular determinants for eRNA function, our study mechanistically links eRNAs to Pol II pause release and provides new insight into the regulation of metazoan transcription.
Molecular mechanisms controlling the biogenesis of the TGF-β signal Vg1
Authors: Dingal P. C. Dave P. , Carte Adam N. , Montague Tessa G. , Lim Suan Medel B. , Schier Alexander F.
Published: April 2021

The TGF-beta signals Vg1 (Dvr1/Gdf3) and Nodal form heterodimers to induce vertebrate mesendoderm. The Vg1 proprotein is a monomer retained in the endoplasmic reticulum (ER) and is processed and secreted upon heterodimerization with Nodal, but the mechanisms underlying Vg1 biogenesis are largely elusive. Here we clarify the mechanisms underlying Vg1 retention, processing, secretion and signaling, and introduce a Synthetic Processing (SynPro) system that enables the programmed cleavage of ER-resident and extracellular proteins. First, we find that Vg1 can be processed by intra- or extracellular proteases. Second, Vg1 can be processed without Nodal but requires Nodal for secretion and signaling. Third, Vg1-Nodal signaling activity requires Vg1 processing, whereas Nodal can remain unprocessed. Fourth, Vg1 employs exposed cysteines, glycosylated asparagines, and BiP chaperone-binding motifs for monomer retention in the ER. These observations suggest two mechanisms for rapid mesendoderm induction: chaperone-binding motifs help store Vg1 as an inactive but ready-to-heterodimerize monomer in the ER, and the flexibility of Vg1 processing location allows efficient generation of active heterodimers both intra- and extracellularly. These results establish SynPro as a new in vivo processing system and define molecular mechanisms and motifs that facilitate the generation of active TGF-beta heterodimers.

Significance

The TGF-beta family members Nodal and Vg1 are the major inducers of mesendoderm formation during vertebrate embryogenesis. We previously established that the Vg1 proprotein is retained in the endoplasmic reticulum (ER), and that Nodal and Vg1 form heterodimers to pattern the early embryo. However, the mechanisms underlying the retention, processing, secretion, and signaling of Vg1 have been unclear. We found two mechanisms that embryos use to efficiently generate active Nodal-Vg1 heterodimers: (1) Vg1 employs its chaperone-binding motifs to ensure its retention as a ready-to-heterodimerize monomer in the ER; (2) Using a newly devised Synthetic Processing (SynPro) System, we found that Vg1 must be processed for signaling to occur, but its processing location is flexible.
Light Attention Predicts Protein Location from the Language of Life
Authors: Stärk Hannes , Dallago Christian , Heinzinger Michael , Rost Burkhard
Published: April 2021

Although knowing where a protein functions in a cell is important to characterize biological processes, this information remains unavailable for most known proteins. Machine learning narrows the gap through predictions from expert-designed input features leveraging information from multiple sequence alignments (MSAs) that is resource expensive to generate. Here, we showcased using embeddings from protein language models (pLMs) for competitive localization prediction without MSAs. Our lightweight deep neural network architecture used a softmax weighted aggregation mechanism with linear complexity in sequence length referred to as light attention (LA). The method significantly outperformed the state-of-the-art (SOTA) for ten localization classes by about eight percentage points (Q10). So far, this might be the highest improvement ofjust embeddingsover MSAs. Our new test set highlighted the limits of standard static data sets: while inviting new models, they might not suffice to claim improvements over the SOTA.

Availability

Online predictions are available athttp://embed.protein.properties. Predictions for the human proteome are available athttps://zenodo.org/record/5047020. Code is provided athttps://github.com/HannesStark/protein-localization.
Abscisic acid modulates auxin-responsive hypocotyl elongation
Authors: Emenecker Ryan J. , Cammarata Joseph , Yuan Irene , Strader Lucia C.
Published: April 2021

Auxin regulates many aspects of plant growth and development in concert with other plant hormones. Auxin interactions with these other phytohormones to regulate distinct processes is not fully understood. Using a forward genetics screen designed to identify seedlings resistant to the suppressive effects of auxin on dark-grown hypocotyl elongation, we identified a mutant defective inABA ALDEHYDE OXIDASE3(AAO3), which encodes for the enzyme that carries out the final step in the biosynthesis of the plant hormone abscisic acid (ABA). We found that all examined ABA deficient mutants display resistance to the inhibitory effects of auxin on dark-grown hypocotyl elongation, suggesting that aspects of ABA signaling are downstream of auxin in regulating dark-grown hypocotyl elongation. Conversely, these mutants display wild type responsiveness to auxin in root elongation assays, suggesting that ABA does not act downstream of auxin in regulating elongation of the root. Our RNA-seq analysis suggests that many auxin-repressed genes in the hypocotyl require an intact ABA pathway for full repression. Our results suggest a model in which auxin partially requires intact ABA biosynthesis in order to regulate hypocotyl elongation, but not to regulate primary root elongation, suggesting that the genetic interactions between these two pathways are tissue-dependent.
Withaferin A inhibits LFA-1-stimulated ZAP70 activity and T-cell motility
Authors: Fazil Mobashar Hussain Urf Turabe , Chirumamilla Chandra Sekhar , Perez-Novo Claudina , Kumar Sunil , Sze Siu Kwan , Berghe Wim Vanden , Verma Navin Kumar
Published: April 2021

Here we report that a steroidal lactone withaferin A (WFA) can inhibit T-cell motility, which is crucial for adaptive immune responses as well as autoimmune reactions. Tandem mass spectrometry identified WFA-interactome in human T-cells that were stimulated to migrateviacross-linking of the lymphocyte function-associated antigen-1 (LFA-1) integrin with the ligand intercellular adhesion receptor 1 (ICAM-1). Data revealed significant enrichment of the zeta-chain-associated protein kinase 70 (ZAP70) and cytoskeletal actin protein interaction networks. Phospho-peptide mapping and kinome analysis substantiated kinase signaling downstream of ZAP70 and cytoskeletal kinase pathways as key WFA targets, which was further confirmed byin silicoanalysis and molecular assays. The WFA-ZAP70 complex was disrupted by a redox agent dithiothreitol, suggesting a covalent binding interface. Moreover, WFA ablated the phosphorylation of the myosin light chain, further constraining T-cell motility. These studies identify a mechanism whereby WFA can impact T-cell motility. WFA can therefore be exploited to pharmacologically controlling host immune responses and preventing autoimmune-mediated pathologies.
A new paradoxosomatid millipede,Manikidesmus suriensis(Polydesmida: Paradoxosomatidae) from West Bengal, India
Authors: Bhakat Somnath
Published: April 2021

A new genus and species of the family Paradoxosomatidae from southern part of West Bengal, India is described. The new genusManikidesmusgen. n. is diagnosed by combination of following characters: reduced paranota, distinct pleural keel, unpaired sternal lamella on 5thsternite, prefemur with setal brush, setal brush on tibia and tarsus in male, lamina medialis long straight with a curved hook, expanded post femoral lamina with a spine and tibiotarsus with a spine on the distofemoral process.

The genus is distinguished from its Indian congeners by one or more diagnosed characters. InManikidesmus suriensis, sp. n. tibia and tarsus bear setal brush in male (vs. absent inOxidusandChondromorpha), gonopod femur short, flat and without post femoral demarcation (vs. long, thin cylindrical with post femoral demarcation inPolydrepanumandOrthomorpha), tibiotarsus of gonopod long and a spine on the distofemoral process (vs. short and without spine inAnoplodesmus). InKronopolites, coxa of gonopod densely bristled, collum with two rows of long bristles, femur long, slender and with a spine. All these characters are absent in the present genus. InStreptogonopus, gonopod femorite is distinctly demarcated from post femorite region and solenomere is twisted with solenophore but in the present species, femorite is not be separated from post femorite region and solenomere is free from solenophore.
A large lipoprotein mediates target specificity for T6SS-dependent killing
Authors: Speare Lauren , Woo Madison , Dunn Anne K. , Septer Alecia N.
Published: April 2021

Interbacterial competition is prevalent in host-associated microbiota, where it can shape community structure and function, impacting host health in both positive and negative ways. However, the factors that permit bacteria to discriminate among their various neighbors for targeted elimination of competitors remain elusive. We identified a specificity factor inVibriospecies that is used to target specific competitors for elimination. Here, we describe this specificity factor, which is associated with the broadly-distributed type VI secretion system (T6SS), by studying symbioticVibrio fischeri, which use the T6SS to compete for colonization sites in their squid host. We demonstrate that a large lipoprotein (TasL) allowsV. fischericells to restrict T6SS-dependent killing to certain genotypes by selectively integrating competitor cells into aggregates while excluding other cell types. TasL is also required for T6SS-dependent competition within juvenile squid, indicating the adhesion factor is active in the host. Because TasL homologs are found in other host-associated bacterial species, this newly-described specificity factor has the potential to impact microbiome structure within diverse hosts.
A chromosome-level genome assembly and annotation of a maize elite breeding line Dan340
Authors: Zhao Yikun , Wang Yuancong , Ma De , Feng Guang , Huo Yongxue , Liu Zhihao , Zhou Ling , Zhang Yunlong , Xu Liwen , Wang Liang , Zhao Han , Zhao Jiuran , Wang Fengge
Published: April 2021

Background

Maize is not only one of the most important crops grown worldwide for food, forage, and biofuel, but also an important model organism for fundamental research in genetics and genomics. Owing to its importance in crop science, genetics and genomics, several reference genomes of common maize inbred line (genetic material) have been released, but some genomes of important genetic germplasm resources in maize breeding research are still lacking. The maize cultivar Dan340 is an excellent backbone inbred line of the Luda Red Cob Group with several desirable characteristics, such as disease resistance, lodging resistance, high combining ability, and wide adaptability.

Findings

In this study, we constructed a high-quality chromosome-level reference genome for Dan340 by combining PacBio long HiFi sequencing reads, Illumina short reads and chromosomal conformational capture (Hi-C) sequencing reads. The final assembly of the Dan340 genome was 2,348.72 Mb, including 2,738 contigs and 2,315 scaffolds with N50 of 41.49 Mb and 215.35 Mb, respectively. Repeat sequences accounted for 73.40% of the genome size and 39,733 protein-coding genes were annotated. Analysis of genes in the Dan340 genome, together with those from B73, Mo17 and SK, were clustered into 27,654 gene families. There were 1,806 genes from 359 gene families that were specific to Dan340, of which many had functional gene ontology annotations relating to “porphyrin-containing compound metabolic process”, “tetrapyrrole biosynthetic process”, and “tetrapyrrole metabolic process”.

Conclusions

The completeness and continuity of the genome were comparable to those of other important maize inbred lines. The assembly and annotation of this genome not only facilitates our understanding about of intraspecific genome diversity in maize, but also provides a novel resource for maize breeding improvement.

Research Areas

Genetics and Genomics; Agriculture, Plant Genetics

Data Description
Intrinsic Lipid Curvatures of Mammalian Plasma Membrane Outer Leaflet Lipids and Ceramides
Authors: Kaltenegger Michael , Kremser Johannes , Frewein Moritz P. , Ziherl Primož , Bonthuis Douwe J. , Pabst Georg
Published: April 2021

We developed a global X-ray data analysis method to determine the intrinsic curvatures of lipids hosted in inverted hexagonal phases. In particular, we combined compositional modelling with molecular shape-based arguments to account for non-linear mixing effects of guest-in-host lipids on intrinsic curvature. The technique was verified by all-atom molecular dynamics simulations and applied to sphingomyelin and a series of phosphatidylcholines and ceramides with differing composition of the hydrocarbon chains. We report positive lipid curvatures for sphingomyelin and all phosphatidylcholines with disaturated and monounsaturated hydrocarbons. Substitution of the second saturated hydrocarbon with an unsaturated acyl chain in turn shifted the intrinsic lipid curvatures to negative values. All ceramides, with chain lengths varying between C2:0 and C24:0, displayed significant negative lipid curvature values. Moreover, we re-port non-additive mixing for C2:0 ceramide and sphingomyelin. Our findings manifest the high and manifold potential of lipids to modulate physiological membrane function.

Highlights

Molecular shape based theory for non-linear lipid curvature mixing

Global analysis of SAXS patterns inverted hexagonal phases using compositional modelling and Bayesian probability theory

MD simulations of inverted hexagonal phases

Non-additive mixing of palmitoyl sphingomyelin and C2:0 ceramide
Dorsal striatum and the temporal expectancy of an aversive event in Pavlovian odor fear learning
Authors: Boulanger-Bertolus Julie , Parrot Sandrine , Doyère Valérie , Mouly Anne-Marie
Published: April 2021

Interval timing, the ability to encode and retrieve the memory of intervals from seconds to minutes, guides fundamental animal behaviors across the phylogenetic tree. In Pavlovian fear conditioning, an initially neutral stimulus (conditioned stimulus, CS) predicts the arrival of an aversive unconditioned stimulus (US, generally a mild foot-shock) at a fixed time interval. Although some studies showed that temporal relations between CS and US events are learned from the outset of conditioning, the question of the memory of time and its underlying neural network in fear conditioning is still poorly understood. The aim of the present study was to investigate the role of the dorsal striatum in timing intervals in odor fear conditioning in male rats. To assess the animal’s interval timing ability in this paradigm, we used the respiratory frequency. This enabled us to detect the emergence of temporal patterns related to the odor-shock time interval from the early stage of learning, confirming that rats are able to encode the odor-shock time interval after few training trials. We carried out reversible inactivation of the dorsal striatum before the acquisition session and before a shift in the learned time interval, and measured the effects of this treatment on the temporal pattern of the respiratory rate. In addition, using intracerebral microdialysis, we monitored extracellular dopamine level in the dorsal striatum throughout odor-shock conditioning and in response to a shift of the odor-shock time interval. Contrary to our initial predictions based on the existing literature on interval timing, we found evidence suggesting that transient inactivation of the dorsal striatum may favor a more precocious buildup of the respiratory frequency’s temporal pattern during the odor-shock interval in a manner that reflected the duration of the interval. Our data further suggest that the conditioning and the learning of a novel time interval were associated with a decrease in dopamine level in the dorsal striatum, but not in the nucleus accumbens. These findings prompt a reassessment of the role of the striatum and striatal dopamine in interval timing, at least when considering Pavlovian aversive conditioning.
Notes of a protein crystallographer: the legacy of J.-B. J. Fourier – crystallography, time and beyond
Authors: Abad-Zapatero Celerino
Published: April 2021

The importance of the Fourier transform as a fundamental tool for crystallography is well known in the field. However, the complete legacy of Jean-Baptiste Joseph Fourier (1768–1830) as a pioneer Egyptologist and premier mathematician and physicist of his time, and the implications of his work in other scientific fields, is less well known. Significantly, his theoretical and experimental work on phenomena related to the transmission of heat founded the mathematical study of irreversible phenomena and introduced the flow of time in physico-chemical processes and geology, with its implications for biological evolution. Fourier's insights are discussed in contrast to the prevalent notion of reversible dynamic time in the early 20th century, which was dominated by Albert Einstein's (1875–1953) theory of general relativity versus the philosophical notion ofduréeproposed by the French philosopher Henri-Louis Bergson (1859–1941). The current status of the mathematical description of irreversible processes by Ilya Romanovich Prigogine (1917–2003) is briefly discussed as part of the enduring legacy of the pioneering work of J.-B. J. Fourier, first established nearly two centuries ago, in numerous scientific endeavors.
Structural studies of hemoglobin from two flightless birds, ostrich and turkey: insights into their differing oxygen-binding properties
Authors: Ramesh Pandian , Sundaresan Selvarajan Sigamani , Shobana Nagaraj , Vinuchakkaravarthy Thangaraj , Sivakumar Kandasamy , Yasien Sayed , Ponnuswamy Mondikalipudur Nanjappa Gounder
Published: April 2021

Crystal structures of hemoglobin (Hb) from two flightless birds, ostrich (Struthio camelus) and turkey (Meleagris gallopova), were determined. The ostrich Hb structure was solved to a resolution of 2.22 Å, whereas two forms of turkey Hb were solved to resolutions of 1.66 Å (turkey monoclinic structure; TMS) and 1.39 Å (turkey orthorhombic structure; TOS). Comparison of the amino-acid sequences of ostrich and turkey Hb with those from other avian species revealed no difference in the number of charged residues, but variations were observed in the numbers of hydrophobic and polar residues. Amino-acid-composition-based computation of various physical parameters, in particular their lower inverse transition temperatures and higher average hydrophobicities, indicated that the structures of ostrich and turkey Hb are likely to be highly ordered when compared with other avian Hbs. From the crystal structure analysis, the liganded state of ostrich Hb was confirmed by the presence of an oxygen molecule between the Fe atom and the proximal histidine residue in all four heme regions. In turkey Hb (both TMS and TOS), a water molecule was bound instead of an oxygen molecule in all four heme regions, thus confirming that they assumed the aqua-met form. Analysis of tertiary- and quaternary-structural features led to the conclusion that ostrich oxy Hb and turkey aqua-met Hb adopt the R-/RH-state conformation.
RETRACTED: Pentoxifylline prevents epileptic seizure via modulating HMGB1/RAGE/TLR4 signalling pathway and improves memory in pentylenetetrazol kindling rats
Authors: Badawi Ghada A. , Shokr Mustafa M. , Zaki Hala F. , Mohamed Ahmed F.
Published: April 2021

Epilepsy is a chronic widely prevalent neurologic disorder, affecting brain functions with a broad spectrum of deleterious consequences. High mobility group box1 (HMGB1) is a nuclear non‐histone protein that targets vital cell receptor of toll‐like receptor 4 (TLR4) and advanced glycation end products (RAGE). HMGB1 mediated TLR4/RAGE cascade has been scored as a key culprit in neuroinflammatory signalling that critically evokes development of impaired cognition and epilepsy. The current study aimed to investigate the neuroprotective effect of pentoxifylline (PTX) on pentylenetetrazol (PTZ)‐kindling rats by its anti‐inflammatory/antioxidant capacity and its impact on memory and cognition were investigated, too. PTZ was intraperitoneally injected 35 mg/kg, every 48 h, for 14 doses, to evoke kindling model. Phenytoin (30 mg/kg, i.p.) and PTX (60 mg/kg, i.p.) or their combination were given once daily for 27 days. PTX treatment showed a statistically significant effect on behavioural, histopathological and neurochemical analysis. PTX protected the PTZ kindling rats from epileptic seizures and improved memory and cognitive impairment through the Morris water maze (MWM) test. Furthermore, PTX reversed PTZ hippocampal neuronal loss by decreasing protein expression of amyloid‐β peptide (Aβ), Tau and β site‐amyloid precursor protein cleavage enzyme 1 (BACE1), associated with a marked reduction in expression of inflammatory mediators such as HMGB1, TL4, and RAGE proteins. Furthermore, PTX inhibited hippocampal apoptotic caspase 1 protein, total reactive oxygen species (TROS) along with upregulated erythroid 2‐related factor 2 (Nrf2) content. In conclusion, PTX or its combination with phenytoin represent a promising drug to inhibit the epilepsy progression via targeting the HMGB1/TLR4/RAGE signalling pathway.
Assessment of the safety and anti‐inflammatory effects of three Bacillus strains in the respiratory tract
Authors: Kim Hye‐Shin , Arellano Karina , Park Haryung , Todorov Svetoslav D. , Kim Bobae , Kang Hyeji , Park Yu Jin , Suh Dong Ho , Jung Eun Sung , Ji Yosep , Holzapfel Wilhelm H.
Published: April 2021

Chronic respiratory diseases are part of accumulating health problems partly due to worldwide increase in air pollution. By their antimicrobial and immunomodulatory properties, some probiotics constitute promising alternatives for the prevention and treatment of chronic respiratory diseases. We have isolated Bacillus strains from Korean fermented foods and selected three potentially probiotic strains (two Bacillus subtilis and one Bacillus amyloliquefaciens) based on safety, antimicrobial efficacy, activity against airborne pathogens and their immunomodulatory properties in vivo. Safety evaluation included in silico analysis for confirming absence of virulence genes. Safety for the respiratory tract was confirmed by an in vivo pathogenicity test using a murine model. Antimicrobial activity was displayed against several airborne pathogens. Potential antimicrobial metabolites such as 2,3‐butanediol and propylene glycol were identified as possible antagonistic agents. Immunomodulatory properties in vitro were confirmed by upregulation of IL‐10 expression in a macrophage cell line. Intranasal instillation and inhalation in an ovalbumin (OVA)‐induced lung inflammation murine model reduced T helper type 2 (Th2) cytokines at transcriptional and protein levels in the lungs. The safety and potentially beneficial role of these Bacillus strains could be demonstrated for the respiratory tract of a murine model.