bluuebunny/crossref_metadata_2025_split huggingface dataset:
The neuroecology of the water-to-land transition and the evolution of the vertebrate brain
Authors: MacIver Malcolm A. , Finlay Barbara L. 
Published: December 2021

The water-to-land transition in vertebrate evolution offers an unusual opportunity to consider computational affordances of a new ecology for the brain. All sensory modalities are changed, particularly a greatly enlarged visual sensorium owing to air versus water as a medium, and expanded by mobile eyes and neck. The multiplication of limbs, as evolved to exploit aspects of life on land, is a comparable computational challenge. As the total mass of living organisms on land is a hundredfold larger than the mass underwater, computational improvements promise great rewards. In water, the midbrain tectum coordinates approach/avoid decisions, contextualized by water flow and by the animal’s body state and learning. On land, the relative motions of sensory surfaces and effectors must be resolved, adding on computational architectures from the dorsal pallium, such as the parietal cortex. For the large-brained and long-living denizens of land, making the right decision when the wrong one means death may be the basis of planning, which allows animals to learn from hypothetical experience before enactment. Integration of value-weighted, memorized panoramas in basal ganglia/frontal cortex circuitry, with allocentric cognitive maps of the hippocampus and its associated cortices becomes a cognitive habit-to-plan transition as substantial as the change in ecology.This article is part of the theme issue ‘Systems neuroscience through the lens of evolutionary theory’.
Refocusing neuroscience: moving away from mental categories and towards complex behaviours
Authors: Pessoa Luiz , Medina Loreta , Desfilis Ester 
Published: December 2021

Mental terms—such as perception, cognition, action, emotion, as well as attention, memory, decision-making—are epistemically sterile. We support our thesis based on extensive comparative neuroanatomy knowledge of the organization of the vertebrate brain. Evolutionary pressures have moulded the central nervous system to promote survival. Careful characterization of the vertebrate brain shows that its architecture supports an enormous amount of communication and integration of signals, especially in birds and mammals. The general architecture supports a degree of ‘computational flexibility’ that enables animals to cope successfully with complex and ever-changing environments. Here, we suggest that the vertebrate neuroarchitecture does not respect the boundaries of standard mental terms, and propose that neuroscience should aim to unravel the dynamic coupling between large-scale brain circuits and complex, naturalistic behaviours.This article is part of the theme issue ‘Systems neuroscience through the lens of evolutionary theory’.
Escaping the nocturnal bottleneck, and the evolution of the dorsal and ventral streams of visual processing in primates
Authors: Kaas Jon H. , Qi Hui-Xin , Stepniewska Iwona 
Published: December 2021

Early mammals were small and nocturnal. Their visual systems had regressed and they had poor vision. After the extinction of the dinosaurs 66 mya, some but not all escaped the ‘nocturnal bottleneck’ by recovering high-acuity vision. By contrast, early primates escaped the bottleneck within the age of dinosaurs by having large forward-facing eyes and acute vision while remaining nocturnal. We propose that these primates differed from other mammals by changing the balance between two sources of visual information to cortex. Thus, cortical processing became less dependent on a relay of information from the superior colliculus (SC) to temporal cortex and more dependent on information distributed from primary visual cortex (V1). In addition, the two major classes of visual information from the retina became highly segregated into magnocellular (M cell) projections from V1 to the primate-specific temporal visual area (MT), and parvocellular-dominated projections to the dorsolateral visual area (DL or V4). The greatly expanded P cell inputs from V1 informed the ventral stream of cortical processing involving temporal and frontal cortex. The M cell pathways from V1 and the SC informed the dorsal stream of cortical processing involving MT, surrounding temporal cortex, and parietal–frontal sensorimotor domains.
This article is part of the theme issue ‘Systems neuroscience through the lens of evolutionary theory’.
Developmental resilience of synaptome architecture
Authors: Tomas-Roca Laura , Qiu Zhen , Fransén Erik , Gokhale Ragini , Bulovaite Edita , Price David J. , Komiyama Noboru H. , Grant Seth G.N. 
Published: December 2021

AbstractNeurodevelopmental disorders of genetic origin delay the acquisition of normal abilities and cause disabling phenotypes. Spontaneous attenuation and even complete amelioration of symptoms in early childhood and adolescence occur in many disorders1–10, suggesting that brain circuits possess an intrinsic capacity to repair themselves. We examined the molecular composition of almost a trillion excitatory synapses on a brain-wide scale between birth and adulthood in mice carrying a mutation in the homeobox transcription factor Pax6, a neurodevelopmental disorder model11. Pax6 haploinsufficiency had no impact on total synapse number at any age. By contrast, the postnatal expansion of synapse diversity and acquisition of normal synaptome architecture were delayed in all brain regions, interfering with network and cognitive functions. Specific excitatory synapse types and subtypes were affected in two key developmental age-windows. These phenotypes were reversed within 2-3 weeks of onset, restoring synaptome architecture to its normal developmental trajectory. Synapse subtypes with high rates of protein turnover mediated these events. These results show synaptome remodelling confers resilience to neurodevelopmental disorders.
Rapid selection of P323L in the SARS-CoV-2 polymerase (NSP12) in humans and non-human primate models and confers a large plaque phenotype
Authors: Dong Xiaofeng , Goldswain Hannah , Penrice-Randal Rebekah , Shawli Ghada T. , Prince Tessa , Williamson Maia Kavanagh , Randle Nadine , Jones Benjamin , Salguero Francisco J , Tree Julia A. , Hall Yper , Hartley Catherine , Erdmann Maximilian , Bazire James , Jearanaiwitayakul Tuksin ,   ISARIC4C investigators, Semple Malcolm G. , Openshaw Peter J. M. , Baille J. Kenneth , Emmett Stevan R. , Digard Paul , Matthews David A. , Turtle Lance , Darby Alistair , Davidson Andrew D. , Carroll Miles W. , Hiscox Julian A. 
Published: December 2021

AbstractThe mutational landscape of SARS-CoV-2 varies at both the dominant viral genome sequence and minor genomic variant population. An early change associated with transmissibility was the D614G substitution in the spike protein. This appeared to be accompanied by a P323L substitution in the viral polymerase (NSP12), but this latter change was not under strong selective pressure. Investigation of P323L/D614G changes in the human population showed rapid emergence during the containment phase and early surge phase of wave 1 in the UK. This rapid substitution was from minor genomic variants to become part of the dominant viral genome sequence. A rapid emergence of 323L but not 614G was observed in a non-human primate model of COVID-19 using a starting virus with P323 and D614 in the dominant genome sequence and 323L and 614G in the minor variant population. In cell culture, a recombinant virus with 323L in NSP12 had a larger plaque size than the same recombinant virus with P323. These data suggest that it may be possible to predict the emergence of a new variant based on tracking the distribution and frequency of minor variant genomes at a population level, rather than just focusing on providing information on the dominant viral genome sequence e.g., consensus level reporting. The ability to predict an emerging variant of SARS-CoV-2 in the global landscape may aid in the evaluation of medical countermeasures and non-pharmaceutical interventions.
Elevated ozone concentration and nitrogen addition increase poplar rust severity by shifting the phyllosphere microbial community
Authors: Tao Siqi , Zhang Yunxia , Tian Chengming , Duplessis Sébastien , Zhang Naili 
Published: December 2021

AbstractThe tropospheric ozone and nitrogen deposition are two major environmental pollutants. Numerous studies have focused on the negative impacts of elevated O3and the complementary effect of soil N addition to tree physiological characteristics. However, it was notoriously ignored of how elevated O3with N addition affect tree immunity in face of pathogen infection, as well as of the important roles of phyllosphere microbiome community in host-pathogen-environment interplay. Here, we examined the effects of elevated O3and soil N addition on poplar leaf rust (Melampsora larici-populina) severity of two susceptible hybrid poplars (clone ‘107’:Populus euramericanacv. ‘74/76’; clone ‘546’:P. deltoides⊆P. cathayana) in Free-Air-Controlled-Environment plots, besides, the link betweenMlp-susceptibility and changes in microbial community was determined using Miseq amplicon sequencing. Rust severity of clone ‘107’ significantly increased under elevated O3or N addition only, however, the negative impact of elevated O3could be significantly alleviated when simultaneously conducting N addition, likewise, this trade-off was also found in its phyllosphere microbialα-diversity responding to elevated O3and N addition. However, the rust severity of clone ‘546’ did not significantly differ in the cases of elevated O3and N addition.Mlpinfection altered microbial community composition and increased its sensitivity to elevated O3assessed by significantly different abundance of taxa. Elevated O3and N addition reduced the complexity of microbial community, which may explain the increased severity of poplar rust. These findings demonstrated that poplars need shifting phyllosphere microbial associations to optimize plant immunity in response to environmental changes.ImportanceExploitation of the interaction mechanisms between host plants and pathogens is the essential basis in disease control. However, while much was known about the molecular determinants in pathogenesis process in the past decades, less is known about the role of nonpathogenic microbial community in plant-pathogen interaction, especially when some host plants are currently encountering severe environmental stresses, such as elevated ozone concentration and superfluous nitrogen addition. Thus, we targeted at the widespread and detriment rust disease (poplar-poplar rust) to dissect the influences of elevated ozone and nitrogen addition on rust disease severity and how phyllosphere microbial groups interacting with both poplars and rust pathogen under these biotic stresses. Our findings could be used to prescribe ecological information about poplar plantation in areas with high levels of ozone pollution and better understand the important roles of microbiome in plant heath.
Zooplankton as a transitional host forEscherichia coliin freshwater
Authors: di Cesare Andrea , Riva Francesco , Colinas Noemi , Borgomaneiro Giulia , Borin Sara , Cabello-Yeves Pedro J. , Canale Claudia , Cedraro Nicholas , Citterio Barbara , Crotti Elena , Mangiaterra Gianmarco , Mapelli Francesca , Mondino Vincenzo , Vignaroli Carla , Quaranta Walter , Corno Gianluca , Fontaneto Diego , Eckert Ester M 
Published: December 2021

AbstractThis study shows thatEscherichia colican be temporarily enriched in zooplankton in natural conditions and that these bacteria can belong to different phylogroups and sequence types including environmental as well as clinical and animal isolates. We isolated 10E. colistrains and sequenced the genomes of two of them. Phylogenetically the two isolates were closer to strains isolated from poultry meat than with freshwaterE. coli, albeit their genomes were smaller than those from poultry. After isolation and fluorescent protein tagging of strains ED1 and ED157 we show thatDaphniasp. can take up these strains and release them alive again, thus forming a temporary host forE. coli. In a chemostat experiment we show that the association does not prolong the bacterial long-term survival, but that at low abundances it does also not significantly reduce the bacterial numbers. We demonstrate thatE. colidoes not belong to the core microbiota ofDaphnia, suffers from competition by the natural microbiota ofDaphnia, but can profit from its carapax to survive in water. All in all, this study suggests that the association ofE. colitoDaphniais only temporary but that the cells are viable therein and this might allow encounters with other bacteria for genetic exchange and potential genomic adaptations to the freshwater environment.ImportanceThe contamination of freshwaters with faecal derived bacteria is of major concern regarding drinking water acquisition and recreational activities. Ecological interactions promoting their persistence are still very scarcely studied. This study, which analyses the survival ofE. coliin the presence of zooplankton, is thus of ecological as well as water safety relevance.
Convalescence from prototype SARS-CoV-2 protects Syrian hamsters from disease caused by the Omicron variant
Authors: Ryan Kathryn A. , Watson Robert J. , Bewley Kevin R. , Burton Christopher , Carnell Oliver , Cavell Breeze E. , Challis Amy , Coombes Naomi S. , Emery Kirsty , Fell Rachel , Fotheringham Susan A. , Gooch Karen E. , Gowan Kathryn , Handley Alastair , Harris Debbie J. , Humphreys Richard , Johnson Rachel , Knott Daniel , Lister Sian , Morley Daniel , Ngabo Didier , Osman Karen L. , Paterson Jemma , Penn Elizabeth J. , Pullan Steven T. , Richards Kevin S. , Shaik Imam , Summers Sian , Thomas Stephen R. , Weldon Thomas , Wiblin Nathan R. , Vipond Richard , Hallis Bassam , Funnell Simon G. P. , Hall Yper 
Published: December 2021

AbstractThe mutation profile of the SARS-CoV-2 Omicron variant poses a concern for naturally acquired and vaccine-induced immunity. We investigated the ability of prior infection with an early SARS-CoV-2, 99.99% identical to Wuhan-Hu-1, to protect against disease caused by the Omicron variant. We established that infection with Omicron in naïve Syrian hamsters resulted in a less severe disease than a comparable dose of prototype SARS-CoV-2 (Australia/VIC01/2020), with fewer clinical signs and less weight loss. We present data to show that these clinical observations were almost absent in convalescent hamsters challenged with the same dose of Omicron 50 days after an initial infection with Australia/VIC01/2020. The data provide evidence for immunity raised against prototype SARS-CoV-2 being protective against Omicron in the Syrian hamster model. Further investigation is required to conclusively determine whether Omicron is less pathogenic in Syrian hamsters and whether this is predictive of pathogenicity in humans.
The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters
Authors: Abdelnabi Rana , Foo Caroline S. , Zhang Xin , Lemmens Viktor , Maes Piet , Slechten Bram , Raymenants Joren , André Emmanuel , Weynand Birgit , Dallemier Kai , Neyts Johan 
Published: December 2021

AbstractThe emergence of SARS-CoV-2 variants of concern (VoCs) has exacerbated the COVID-19 pandemic. End of November 2021, a new SARS-CoV-2 variant namely the omicron (B.1.1.529) emerged. Since this omicron variant is heavily mutated in the spike protein, WHO classified this variant as the 5th variant of concern (VoC). We previously demonstrated that the other SARS-CoV-2 VoCs replicate efficiently in Syrian hamsters, alike also the ancestral strains. We here wanted to explore the infectivity of the omicron variant in comparison to the ancestral D614G strain. Strikingly, in hamsters that had been infected with the omicron variant, a 3 log10 lower viral RNA load was detected in the lungs as compared to animals infected with D614G and no infectious virus was detectable in this organ. Moreover, histopathological examination of the lungs from omicron-infecetd hamsters revealed no signs of peri-bronchial inflammation or bronchopneumonia. Further experiments are needed to determine whether the omicron VoC replicates possibly more efficiently in the upper respiratory tract of hamsters than in their lungs.
Survival and detection of bivalve transmissible neoplasia from the soft-shell clam Mya arenaria (MarBTN) in seawater
Authors: Giersch Rachael M. , Hart Samuel F.M. , Reddy Satyatejas G. , Yonemitsu Marisa A. , Orellana Rosales María J. , Korn Madelyn , Geleta Brook M. , Countway Peter D. , Fernández Robledo José A. , Metzger Michael J. 
Published: December 2021

ABSTRACTMany pathogens can cause cancer, but cancer itself does not normally act as an infectious agent. However, transmissible cancers have been found in a few cases in nature: in Tasmanian devils, dogs, and several bivalve species. The transmissible cancers in dogs and devils are known to spread through direct physical contact, but the exact route of transmission of bivalve transmissible neoplasia (BTN) has not yet been confirmed. It has been hypothesized that cancer cells could be released by diseased animals and spread through the water column to infect/engraft into other animals. To test the feasibility of this proposed mechanism of transmission, we tested the ability of BTN cells from the soft-shell clam (Mya arenaria BTN, or MarBTN) to survive in artificial seawater. We found that BTN cells are highly sensitive to salinity, with acute toxicity at salinity levels lower than those found in their environment. BTN cells also survive longer at lower temperatures, with >48% of cells surviving a week in seawater at temperatures from 4°C to 16°C, and 49% surviving for more than two weeks at 4°C. With one clam donor, living cells were observed for more than eight weeks at 4°C. We also used qPCR of environmental DNA (eDNA) to detect the presence of BTN-specific DNA in the environment. We observed release of BTN-specific DNA into the water of aquaria from tanks with highly BTN-positive clams, and we detected BTN-specific DNA in seawater samples collected from BTN-endemic areas, although the level detected was much lower. Overall, these data show that BTN cells can survive well in seawater, and they are released into the water by diseased animals, supporting the hypothesis that BTN is spread from animal-to-animal by cells through seawater.
Distinct cDC subsets co-operate in CD40 agonist response while suppressive microenvironments and lack of antigens subvert efficacy
Authors: Murgaski Aleksandar , Kiss Máté , Van Damme Helena , Kancheva Daliya , Vanmeerbeek Isaure , Keirsse Jiri , Hadadi Eva , Brughmans Jan , Arnouk Sana M. , Hamouda Ahmed E. I. , Debraekeleer Ayla , Bosteels Victor , Elkrim Yvon , Boon Louis , Hoves Sabine , Vandamme Niels , Deschoemaeker Sofie , Janssens Sophie , Garg Abhishek D. , Schmittnägel Martina , Ries Carola H. , Laoui Damya 
Published: December 2021

ABSTRACTAgonistic αCD40 therapy has shown to inhibit cancer progression, but only in a fraction of patients. Hence, understanding the cancer cell-intrinsic and microenvironmental determinants of αCD40 therapy response is crucial to identify responsive patient populations and design efficient combination treatments. Here, we showed that the therapeutic efficacy of αCD40 in responder melanoma tumours, relied on pre-existing cDC1-primed CD8+ T cells, however cDC1s were dispensable after αCD40 administration. Surprisingly, in response to αCD40 the abundance of activated cDCs, potentially derived from cDC2s increased, thereby further activating antitumour CD8+ T cells. Hence, distinct cDC subsets are required to induce αCD40 responses. By contrast, lung tumours, characterised by a high abundance of macrophages, were resistant to αCD40 therapy. Combining αCD40 therapy with macrophage depletion led to tumour growth inhibition only in the presence of strong neoantigens. Accordingly, treatment with immunogenic cell-death inducing chemotherapy sensitised non-immunogenic tumours to αCD40 therapy.
Transgenic resources for functional studies on the hsrω gene in Drosophila
Authors: Sahu Ranjan Kumar , Trivedi Deepti , Lakhotia Subhash Chandra 
Published: December 2021

AbstractThe hsrω gene of Drosophila melanogaster, an early discovered non-coding developmentally active and stress-inducible gene, has pleiotropic actions through its multiple nuclear and cytoplasmic non-coding transcripts. With a view to understand this diverse functions and mechanisms of actions of this gene, we generated a series of transgenic lines for over-expression or RNAi of different transcripts and CRISPR-Cas9 mediated deletion alleles. These are described here.
EMX2 transcriptionally regulates Nfib expression in neural progenitor cells during early cortical development
Authors: Lim Jonathan W. C. , Bunt Jens , Bridges Caitlin R. , Moey Ching , Jacobs Matisse T. , Chen Kok-Siong , Richards Linda J. 
Published: December 2021

AbstractThe nuclear factor one (NFI) transcription factors play key roles in regulating the onset of both neuronal and glial differentiation during cortical development. Reduced NFI expression results in delayed differentiation, which is associated with neurodevelopmental disorders in humans that include intellectual disability, agenesis of the corpus callosum and macrocephaly. Despite their importance, our understanding of how individual NFI family members are regulated during cortical development remains limited. Here, we demonstrate that in mice, the homeobox transcription factor EMX2 regulates Nfib expression in radial glial cells during cortical development. Using a combination of bioinformatics, molecular and histological approaches, we demonstrate that EMX2 is able to bind to the Nfib promoter to up-regulate Nfib expression. Unexpectedly, in vivo over-expression of EMX2 in wildtype animals does not further up-regulate NFIB but instead leads to its down-regulation. Therefore, our findings suggest that EMX2 is capable of both activating and repressing Nfib, in a context-dependent manner. This bi-directional control over Nfib expression enables fine-tuning of the total level of NFI proteins expressed and could be important for cell-type specific NFI functions.