bluuebunny/crossref_metadata_2025 huggingface dataset:
Latent class regression improves the predictive acuity and clinical utility of survival prognostication amongst chronic heart failure patients
Authors: Mbotwa John L , de Kamps Marc , Baxter Paul D , Ellison George TH , Gilthorpe Mark S
Published: November 2020

The present study aimed to compare the predictive acuity of latent class regression (LCR) modelling with: standard generalised linear modelling (GLM); and GLMs that include the membership of subgroups/classes (identified through prior latent class analysis; LCA) as alternative or additional candidate predictors. Using real world demographic and clinical data from 1,802 heart failure patients enrolled in the UK-HEART2 cohort, the study found that univariable GLMs using LCA-generated subgroup/class membership as the sole candidate predictor of survival were inferior to standard multivariable GLMs using the same four covariates as those used in the LCA. The inclusion of the LCA subgroup/class membership together with these four covariates as candidate predictors in a multivariable GLM showed no improvement in predictive acuity. In contrast, LCR modelling resulted in a 10-14% improvement in predictive acuity and provided a range of alternative models from which it would be possible to balance predictive acuity against entropy to select models that were optimally suited to improve the efficient allocation of clinical resources to address the differential risk of the outcome (in this instance, survival). These findings provide proof-of-principle that LCR modelling can improve the predictive acuity of GLMs and enhance the clinical utility of their predictions. These improvements warrant further attention and exploration, including the use of alternative techniques (including machine learning algorithms) that are also capable of generating latent class structure while determining outcome predictions, particularly for use with large and routinely collected clinical datasets, and with binary, count and continuous variables.
Genome-wide association mapping identifies Yellow Rust resistance locus in Ethiopian Durum Wheat germplasm
Authors: Alemu Sisay Kidane , Huluka Ayele Badebo , Geletu Kassahun Tesfaye , Uauy Cristobal
Published: November 2020

Durum wheat is an important cereal grown in Ethiopia, a country which is also its center for genetic diversity. Yellow (stripe) rust caused by Puccinia striiformis fsp tritici is one of the most devastating diseases threatening Ethiopian wheat production. To identify sources of genetic resistance to combat this pathogen, we conducted a genome wide association study of yellow rust resistance on 300 durum wheat accessions comprising 261 landraces and 39 cultivars. The accessions were evaluated for their field resistance in an alpha lattice design (10 × 30) in two replications at Meraro, Kulumsa and Chefe-Donsa in the 2015 and 2016 main growing seasons. Disease Scoring was carried out using a modified Cobb scale and then converted to Coefficient of Infection (CI). Analysis of the 35K Axiom Array genotyping data resulted in a total of 8,797 polymorphic SNPs of which 7,093 were used in subsequent analyses. Population structure analysis suggested two groups in which the cultivars clearly stood out separately from the landraces. We identified twelve SNPs significantly associated with yellow rust resistance across four chromosomes (1A, 1B, 2B, and 7B). Six of the SNPs (AX-95171339, AX-94436448, AX-95238778, AX-95096041, AX-94730403 & AX-94427201), were consistently identified on chromosome 1B at the three field locations and combined across the six environments. The phenotypic variation (R2) explained by all six SNPs on chromosome 1B ranged from 63.7 – 65.4%. Locus-based analysis of phenotypic values between resistant and susceptible allele resulted in a significant difference at (p < 0.001). Further investigation across the genomic interval encompassing the identified loci indicated the presence of disease resistance protein (NBS-LRR class) family and RPM1 in the vicinity of the loci. This study provides SNPs for tracking the QTL associated with yellow rust resistance in durum wheat improvement programs.
PP2A-Cdc55 phosphatase coordinates actomyosin ring contraction and septum formation during cytokinesis
Authors: Moyano-Rodríguez Yolanda , Vaquero David , Vilalta-Castany Odena , Foltman Magdalena , Sanchez-Diaz Alberto , Queralt Ethel
Published: November 2020

Eukaryotic cells divide and separate all their components after chromosome segregation by a process called cytokinesis to complete cell division. Cytokinesis is highly regulated by recruitment of the components to the division site and through post-translational modifications such as phosphorylations. The budding yeast mitotic kinases Cdc28-Clb2, Cdc5, and Dbf2-Mob1 phosphorylate several cytokinetic proteins contributing to the regulation of cytokinesis. The PP2A-Cdc55 phosphatase regulates mitosis counteracting Cdk1- and Cdc5-dependent phosphorylation. This prompted us to propose that PP2A-Cdc55 could also be counteracting the mitotic kinases during cytokinesis. Here, we demonstrate that primary septum formation and actomyosin ring contraction are impaired in the absence of PP2A-Cdc55. In addition, by in vivo and in vitro assays, we show that PP2A-Cdc55 dephosphorylates the chitin synthase II (Chs2 in budding yeast) a component of the Ingression Progression Complexes (IPCs) involved in cytokinesis. Interestingly, the non-phosphorylable version of Chs2 rescues the asymmetric AMR contraction observed in cdc55Δ mutant cells. Therefore, timely dephosphorylation of the Chs2 by PP2A-Cdc55 is crucial for proper actomyosin ring contraction. These findings reveal a new mechanism of cytokinesis regulation by the PP2A-Cdc55 phosphatase and extend our knowledge in the involvement of multiple phosphatases during cytokinesis.
D1- and D2-like receptors differentially mediate the effects of dopaminergic transmission on cost/benefit evaluation and motivation in monkeys
Authors: Hori Yukiko , Nagai Yuji , Mimura Koki , Suhara Tetsuya , Higuchi Makoto , Bouret Sebastien , Minamimoto Takafumi
Published: November 2020

It has been widely accepted that dopamine (DA) plays a major role in motivation, yet the specific contribution of DA signaling at D1-like receptor (D1R) and D2-like receptor (D2R) to cost-benefit trade-off remains unclear. Here, by combining pharmacological manipulation of DA receptors (DARs) and positron emission tomography imaging, we assessed the relationship between the degree of D1R/D2R blockade and changes in benefit- and cost-based motivation for goal-directed behavior of macaque monkeys. We found that the degree of blockade of either D1R or D2R was associated with a reduction of the positive impact of reward amount and increasing delay-discounting. Workload-discounting was selectively increased by D2R antagonism. In addition, blocking both D1R and D2R had a synergistic effect on delay-discounting but an antagonist effect on workload-discounting. These results provide fundamental in-sight into the distinct mechanisms of DA action in the regulation of the cost and benefit-based motivation, which have important implications for motivational alterations in both neurological and psychiatric disorders.
Differential host response to a herpesvirus: Marek’s disease virus peptides on chicken MHC class II molecules are derived from only a few genes and illustrate a new mode of peptide binding
Authors: Halabi Samer , Ghosh Michael , Stevanović Stefan , Rammensee Hans-Georg , Bertzbach Luca D. , Kaufer Benedikt B. , Moncrieffe Martin C. , Kaspers Bernd , Härtle Sonja , Kaufman Jim
Published: November 2020

Viral diseases pose major threats to humans and other animals, including the billions of chickens that are an important food source as well as a public health concern due to zoonotic pathogens. Unlike humans and other typical mammals, the major histocompatibility complex (MHC) of chickens can confer decisive resistance or susceptibility to many viral diseases. An iconic example is Marek’s disease, caused by an oncogenic herpesvirus with over 100 genes. Classical MHC class I and class II molecules present antigenic peptides to T lymphocytes, and it has been hard to understand how such MHC molecules could be involved in susceptibility to Marek’s disease, given the potential number of peptides from over 100 genes. We used a new in vitro infection system and immunopeptidomics to determine peptide motifs for the two class II molecules expressed by the MHC haplotype B2, which is known to confer resistance to Marek’s disease. Surprisingly, we found that the vast majority of viral peptide epitopes presented by chicken class II molecules arise from only four viral genes, nearly all having the peptide motif for BL2, the dominantly-expressed class II molecule in chickens. We expressed BL2 linked to several MDV peptides, and determined one X-ray crystal structure, showing how a single small amino acid in the binding site causes a crinkle in the peptide, leading to core binding peptide of ten amino acids, compared to the nine amino acids in all other reported class II molecules. The limited number of potential T cell epitopes from such a complex virus can explain the differential MHC-determined resistance to MDV, but raises questions of mechanism and opportunities for vaccine targets in this important food species, as well as providing a basis for understanding class II molecules in other species including humans.
Valid statistical approaches for clustered data: A Monte Carlo simulation study
Authors: McLaurin Kristen A. , Fairchild Amanda J. , Shi Dexin , Booze Rosemarie M. , Mactutus Charles F.
Published: November 2020

The translation of preclinical studies to human applications is associated with a high failure rate, which may be exacerbated by limited training in experimental design and statistical analysis. Nested experimental designs, which occur when data have a multilevel structure (e.g., in vitro: cells within a culture dish; in vivo: rats within a litter), often violate the independent observation assumption underlying many traditional statistical techniques. Although previous studies have empirically evaluated the analytic challenges associated with multilevel data, existing work has not focused on key parameters and design components typically observed in preclinical research. To address this knowledge gap, a Monte Carlo simulation study was conducted to systematically assess the effects of inappropriately modeling multilevel data via a fixed effects ANOVA in studies with sparse observations, no between group comparison within a single cluster, and interactive effects. Simulation results revealed a dramatic increase in the probability of type 1 error and relative bias of the standard error as the number of level-1 (e.g., cells; rats) units per cell increased in the fixed effects ANOVA; these effects were largely attenuated when the nesting was appropriately accounted for via a random effects ANOVA. Thus, failure to account for a nested experimental design may lead to reproducibility challenges and inaccurate conclusions. Appropriately accounting for multilevel data, however, may enhance statistical reliability, thereby leading to improvements in translatability. Valid analytic strategies are provided for a variety of design scenarios.
DNA polymerase theta suppresses mitotic crossing over
Authors: Carvajal-Garcia Juan , Crown K. Nicole , Ramsden Dale A. , Sekelsky Jeff
Published: November 2020

Polymerase theta-mediated end joining (TMEJ) is a chromosome break repair pathway that is able to rescue the lethality associated with the loss of proteins involved in early steps in homologous recombination (e.g., BRCA1/2). This is due to the ability of polymerase theta (Pol θ) to use resected, 3’ single stranded DNA tails to repair chromosome breaks. These resected DNA tails are also the starting substrate for homologous recombination. However, it remains unknown if TMEJ can compensate for the loss of proteins involved in more downstream steps during homologous recombination. Here we expand the number of homologous recombination proteins synthetic lethal with Pol θ to the Holliday junction resolvases SLX4 and GEN1. SLX4 and GEN1 are required for viability in the absence of Pol θ inDrosophila melanogaster,and lack of all three proteins results in very high levels of apoptosis. We observe that flies deficient in Pol θ and SLX4 are extremely sensitive to DNA damaging agents, and mammalian cells require either Pol θ or SLX4 to survive. Our results suggest that TMEJ and Holliday junction formation/resolution share a common DNA substrate, likely a homologous recombination intermediate, that when left unrepaired leads to cell death. One major consequence of Holliday junction resolution by SLX4 and GEN1 is cancer-causing loss of heterozygosity due to mitotic crossing over. We measured mitotic crossovers in flies after a Cas9-induced chromosome break, and observed that this mutagenic form of repair is increased in the absence of Pol θ. This demonstrates that TMEJ can function upstream of the Holiday junction resolvases to protect cells from loss of heterozygosity. Our work argues that Pol θ can thus compensate for the loss of the Holliday junction resolvases by utilizing homologous recombination intermediates, suppressing mitotic crossing over and preserving the genomic stability of cells.

Author summary

Chromosome breaks are a common threat to the stability of DNA. Mutations in genes involved in the early steps of homologous recombination (BRCA1andBRCA2), a mostly error-free chromosome break repair pathway, lead to hereditary breast cancer. Cells lacking BRCA1 and BRCA2 rely on DNA polymerase theta, a key protein for a more error-prone pathway, for survival. Using fruit flies and mammalian cells, we have shown that mutations in genes involved in later steps of homologous recombination (SLX4andGEN1) also make cells reliant on polymerase theta. Moreover, we have shown that polymerase theta acts upstream of a type of homologous recombination that is error-prone and depends on SLX4 and GEN1. This form of homologous recombination, termed Holliday junction resolution, creates mitotic crossovers, which can lead to loss of heterozygosity and cancer. Our results expand the cellular contexts that make cells depend on polymerase theta for survival, and the substrates that this protein can use to repair chromosome breaks.
Elevated expression of complement C4 in the mouse prefrontal cortex causes schizophrenia-associated phenotypes
Authors: Druart Mélanie , Nosten-Bertrand Marika , Poll Stefanie , Crux Sophie , Nebeling Felix , Delhaye Célia , Dubois Yaëlle , Leboyer Marion , Tamouza Ryad , Fuhrmann Martin , Le Magueresse Corentin
Published: November 2020

Accumulating evidence supports immune involvement in the pathogenesis of schizophrenia, a severe psychiatric disorder. In particular, high expression variants of C4, a gene of the innate immune complement system, were shown to confer susceptibility to schizophrenia. However, how elevated C4 expression may impact brain circuits remains largely unknown. We used in utero electroporation to overexpress C4 in the mouse prefrontal cortex (PFC). We found reduced glutamatergic input to pyramidal cells of juvenile and adult, but not of newborn C4-overexpressing (C4-OE) mice, together with decreased spine density, which mirrors spine loss observed in the schizophrenic cortex. Using time-lapse two-photon imaging in vivo, we observed that these deficits were associated with decreased dendritic spine gain and elimination in juvenile C4-OE mice, which may reflect poor formation and/or stabilization of immature spines. In juvenile and adult C4-OE mice we found evidence for NMDA receptor hypofunction, another schizophrenia-associated phenotype, and synaptic accumulation of calcium-permeable AMPA receptors. Alterations in cortical GABAergic networks have been repeatedly associated with schizophrenia. We found that functional GABAergic transmission was reduced in C4-OE mice, in line with diminished GABA release probability from parvalbumin interneurons, lower GAD67 expression and decreased intrinsic excitability in parvalbumin interneurons. These cellular abnormalities were associated with working memory impairment. Our results substantiate the causal relationship between an immunogenetic risk factor and several distinct cortical endophenotypes of schizophrenia, and shed light on the underlying cellular mechanisms.
Human induced pluripotent stem cell-derived vessels as dynamic atherosclerosis model on a chip
Authors: Mallone A. , Gericke C. , Hosseini V. , Chahbi K. , Haenseler W. , Emmert M. Y. , von Eckardstein A. , Walther J. H. , Vogel V. , Weber B , Hoerstrup S. P.
Published: November 2020

Atherosclerosis is an arterial disease characterized by intravascular plaques. Disease hallmarks are vessel stenosis and hyperplasia, eventually escalating into plaque rupture and acute clinical presentations. Innate immune cells and local variations in hemodynamics are core players in the pathology, but their mutual relationship has never been investigated before due to the lack of modeling systems with adequate degree of complexity. Here, we combined computational fluid dynamics and tissue-engineering to achieve, for the first time in vitro, full atherosclerotic plaque development. Our model incorporates induced pluripotent stem cell-derived populations into small-caliber arteries that are cultured in atheroprone conditions. Using machine-learning-aided immunophenotyping, molecular and nanoprobe-based tensile analyses, we found that immune cells, extracellular matrix components and tensional state were comparable between in vitro and ex vivo human lesions. Our results provide further insights into the relation between hemodynamics and inflammation, introducing a versatile, scalable modeling tool to study atherosclerosis onset and progression.
Scavenger receptor A1 participates in the phagocytosis ofLeptospira interrogansand leads to subsequent high inflammatory responses and bacterial dissemination in leptospirosis
Authors: Wang Yanchun , Fan Xia , Du Lin , Liu Boyu , Xiao Haihan , Zhang Yan , Wu Yunqiang , Liu Fuli , Chang Yung-Fu , Guo Xiaokui , He Ping
Published: November 2020

Leptospirosis, caused by pathogenicLeptospiraspecies, has emerged as a widespread zoonotic disease worldwide. Macrophages mediate the elimination of pathogens through phagocytosis and cytokine production. Scavenger receptor A1 (SR-A1), one of the critical receptors mediating this process, plays a complicated role in innate immunity. However, the role of SR-A1 in the immune response against pathogenicLeptospirainvasion is unknown. In the present study, we found that SR-A1 is an important nonopsonic phagocytic receptor on murine macrophages forLeptospira. We also found that leptospiral LPS is the ligand of SR-A1. However, intraperitoneal injection of leptospires into WT mice presented with more severe jaundice, subcutaneous hemorrhaging, and higher bacteria burdens in blood and tissues than that of SR-A1-/-mice. Exacerbated cytokine and inflammatory mediator levels were also observed in WT mice and higher recruited macrophages in the liver than those of SR-A1-/-mice. Our findings collectively reveal that although beneficial in the uptake ofLeptospiraby macrophage, SR-A1 might be exploited byLeptospirato promote bacterial dissemination and modulate inflammatory activation, which causes a more severe infection in the host. These results provide our new insights into the innate immune response during early infection byL. interrogans.
Rat perichondrium transplanted to articular cartilage defects forms articular-like, hyaline cartilage
Authors: Dou Zelong , Muder Daniel , Baroncelli Marta , Bendre Ameya , Gkourogianni Alexandra , Ottosson Lars , Vedung Torbjörn , Nilsson Ola
Published: November 2020

Reconstruction of articular surfaces destroyed by infection or trauma is hampered by the lack of suitable graft tissues. Perichondrium autotransplants have been used for this purpose. However, the role of the transplanted perichondrium in the healing of resurfaced joints have not been investigated. Perichondrial and periosteal tissues were harvested from rats hemizygous for a ubiquitously expressed enhanced green fluorescent protein (EGFP) transgene and transplanted into full-thickness articular cartilage defects at the trochlear groove of distal femur in wild-type littermates. As an additional control, cartilage defects were left without a transplant (no transplant control). Distal femurs were collected 3, 14, 56, 112 days after surgery. Transplanted cells and their progenies were readily detected in the defects of perichondrium and periosteum transplanted animals but not in defects left without a transplant. Perichondrium transplants expressed SOX9 and with time differentiated into a hyaline cartilage that expanded and filled out the defects with Col2a1-positive chondrocytes and a matrix rich in proteoglycans. Interestingly, at later timepoints the cartilaginous perichondrium transplants were actively remodeled into bone at the transplant-bone interface and at post-surgery day 112 EGFP-positive perichondrium cells at the articular surface were positive for Prg4. In addition, both perichondrium and periosteum transplants contributed cells to the subchondral bone and bone marrow, suggesting differentiation into osteoblast/osteocytes as well as bone marrow cells. In summary, we found that perichondrium transplanted to articular cartilage defects develops into an articular-like, hyaline cartilage that integrates with the subchondral bone, and is maintained for an extended time. The findings indicate that perichondrium is a suitable tissue for repair and engineering of articular cartilage.
Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist
Authors: Isaikina Polina , Tsai Ching-Ju , Dietz Nikolaus , Pamula Filip , Grahl Anne , Goldie Kenneth N. , Guixà-González Ramon , Schertler Gebhard F.X. , Hartley Oliver , Stahlberg Henning , Maier Timm , Deupi Xavier , Grzesiek Stephan
Published: November 2020

The human CC chemokine receptor 5 (CCR5) is a G protein-coupled receptor (GPCR) that plays a major role in inflammation and is involved in the pathology of cancer, HIV, and COVID-19. Despite its significance as a drug target, the activation mechanism of CCR5, i.e. how chemokine agonists transduce the activation signal through the receptor, is yet unknown. Here, we report the cryo-EM structure of wild-type CCR5 in an active conformation bound to the chemokine super-agonist [6P4]CCL5 and the heterotrimeric Gi protein. The structure provides the rationale for the sequence-activity relation of agonist and antagonist chemokines. The N-terminus of agonist chemokines pushes onto an aromatic connector that transmits activation to the canonical GPCR microswitch network. This activation mechanism differs significantly from other CC chemokine receptors that bind shorter chemokines in a shallow binding mode and have unique sequence signatures and a specialized activation mechanism.

One-sentence summary

The structure of CCR5 in complex with the chemokine agonist [6P4]CCL5 and the heterotrimeric Gi protein reveals its activation mechanism
Ultrafast end-to-end protein structure prediction enables high-throughput exploration of uncharacterised proteins
Authors: Kandathil Shaun M , Greener Joe G , Lau Andy M , Jones David T
Published: November 2020

Deep learning-based prediction of protein structure usually begins by constructing a multiple sequence alignment (MSA) containing homologues of the target protein. The most successful approaches combine large feature sets derived from MSAs, and considerable computational effort is spent deriving these input features. We present a method that greatly reduces the amount of preprocessing required for a target MSA, while producing main chain coordinates as a direct output of a deep neural network. The network makes use of just three recurrent networks and a stack of residual convolutional layers, making the predictor very fast to run, and easy to install and use. Our approach constructs a directly learned representation of the sequences in an MSA, starting from a one-hot encoding of the sequences. When supplemented with an approximate precision matrix, the learned representation can be used to produce structural models of comparable or greater accuracy as compared to our original DMPfold method, while requiring less than a second to produce a typical model. This level of accuracy and speed allows very large-scale 3-D modelling of proteins on minimal hardware, and we demonstrate that by producing models for over 1.3 million uncharacterized regions of proteins extracted from the BFD sequence clusters. After constructing an initial set of approximate models, we select a confident subset of over 30,000 models for further refinement and analysis, revealing putative novel protein folds. We also provide updated models for over 5,000 Pfam families studied in the original DMPfold paper.

Significance Statement

We present a deep learning-based predictor of protein tertiary structure that uses only a multiple sequence alignment (MSA) as input. To date, most emphasis has been on the accuracy of such deep learning methods, but here we show that accurate structure prediction is also possible in very short timeframes (a few hundred milliseconds). In our method, the backbone coordinates of the target protein are output directly from the neural network, which makes the predictor extremely fast. As a demonstration, we generated over 1.3 million models of uncharacterised proteins in the BFD, a large sequence database including many metagenomic sequences. Our results showcase the utility of ultrafast and accurate tertiary structure prediction in rapidly exploring the “dark space” of proteins.
A set of common movements within GPCR-G-protein complexes from variability analysis of cryo-EM datasets
Authors: Marino Jacopo , Schertler Gebhard F.X.
Published: November 2020

G-protein coupled receptors (GPCRs) are among the most versatile signal transducers in the cell. Once activated, GPCRs sample a large conformational space and couple to G-proteins to initiate distinct signaling pathways. The dynamical behavior of GPCR-G-protein complexes is difficult characterize structurally. Here, we report on the use of variability analysis to characterize the inherent flexibility within the cryo-EM dataset of the rhodopsin-Gi-protein complex (Tsai et al., 2019), on which this article builds on. We compare the outcome of this analysis with recently published results obtained on the cannabinoid-Gi- and secretin-Gs-receptor complexes. Despite differences related to the biochemical compositions of the three samples, a set of consensus movements emerges. We anticipate that systematic variability analysis on GPCR-G-protein complexes may provide useful information not only at the biological level, but also for improving the preparation of more stable samples for cryo-EM single-particle analysis.
A mechanism for hippocampal memory recall based on excitatory-inhibitory fluctuations in neocortex
Authors: Koolschijn Renée S. , Shpektor Anna , Ip I. Betina , Clarke William T. , Dupret David , Emir Uzay E. , Barron Helen C.
Published: November 2020

The brain has a remarkable capacity to acquire and store memories that can later be selectively recalled. These processes are supported by the hippocampus which is thought to index memory recall by reinstating information stored across distributed neocortical circuits. However, the mechanism that supports this interaction remains unclear. Here, in humans, we show that recall of a visual cue from a paired associate is accompanied by a transient increase in the ratio between glutamate and GABA in visual cortex. Moreover, these excitatory-inhibitory fluctuations are predicted by activity in the hippocampus. These data suggest the hippocampus gates memory recall by indexing information stored across neocortical circuits using a disinhibitory mechanism.
LARP6C regulates selective mRNA translation to promote pollen tube guidance inArabidopsis thaliana
Authors: Billey Elodie , Hafidh Said , Cruz-Gallardo Isabel , Litholdo Celso G. , Jean Viviane , Carpentier Marie-Christine , Picart Claire , Kulichova Katarina , Honys David , Conte Maria R. , Deragon Jean-Marc , Bousquet-Antonelli Cécile
Published: November 2020

In angiosperms, non-motile sperm cells are delivered to the ovules for fertilization via a guided growth of the pollen tube. RNA binding proteins are key regulators that control mRNA fate post-transcriptionally and thus essential for normal cell function. But very little is known on the mechanistic bases of mRNA regulations andtrans-acting factors governing male-female signalling. Here we demonstrate that the evolutionarily conserved RNA binding protein LARP6C is necessary for pollen tube guidance and fertilization.larp6closs-of-function mutants exhibit male induced fertility defects as mutant pollen tubes frequently are unable to find ovules for fertilization. In mature pollen, LARP6C localises with a pollen specific poly(A) binding protein to cytoplasmic foci likely containing mRNPs. With RNA immunoprecipitation and sequencing, we demonstrate that LARP6C is associatedin vivowith mRNAs required for pollen tube guidance or polarized cell growth. We further demonstrate usingin vitroandin plantatransient assays that LARP6C binds 5’-UTR box motifs to orchestrate the balance between translation, decay and storage of its mRNA targets. We propose a model where LARP6C maintains its mRNA target in translationally silent state likely to promote localized translation and guided pollen tube growth upon paracrine signalling.
Bacterial respiration during stationary phase induces intracellular damage that leads to dormancy
Authors: Cesar Spencer , Willis Lisa , Huang Kerwyn Casey
Published: November 2020

Most bacteria frequently encounter nutrient-depleted conditions, necessitating regulatory mechanisms that alter cellular physiology and allow for survival of starvation. Here, we show that regrowth of Escherichia coli from prolonged stationary phase upon encountering fresh nutrients is heterogeneous, with one subpopulation suddenly regrowing after a delay (dormancy) and another of nongrowing cells that represented an increasing fraction as the culture aged. Moreover, a sizeable fraction of cells rejuvenated immediately, even when the inoculum was from very old cultures. The size of the dormant and nongrowing subpopulations depended on the time cells had endured stationary phase, as opposed to time-dependent changes to the medium. Regrowth of dormant cells was correlated with the dissolution of polar phase-bright foci that likely represent aggregates of damage, and a deep-learning algorithm was able to distinguish cellular fates based on a single stationary-phase image. Growth restarted in dormant cells after the upregulation of chaperones and DNA repair enzymes, and deletion of the chaperone DnaK resulted in compromised stationary-phase cell morphology and higher incidence of non-growing cells. A mathematical model of damage accumulation and division-mediated partitioning was in quantitative agreement with experimental data, including the small population of cells capable of immediate regrowth even in old cultures. Cells that endured stationary-phase without the ability to respire all immediately and homogeneously regrew in fresh nutrients, indicating that respiration in stationary phase is the driver of dormancy. These findings establish the importance of intracellular damage control when nutrients are sparse, and repair when nutrients are plentiful.
Seeded assembly in vitro does not replicate the structures of α-synuclein filaments from multiple system atrophy
Authors: Lövestam Sofia , Schweighauser Manuel , Murayama Shigeo , Saito Yuko , Tomita Taisuke , Ando Takashi , Hasegawa Kazuko , Yoshida Mari , Tarutani Airi , Hasegawa Masato , Goedert Michel , Scheres Sjors H.W.
Published: November 2020

The propagation of conformational strains by templated seeding is central to the prion concept. Seeded assembly of α-synuclein into filaments is believed to underlie the prion-like spreading of protein inclusions in a number of human neurodegenerative diseases, including Parkinson's disease, dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). We previously determined the atomic structures of α-synuclein filaments from the putamen of five individuals with MSA. Here, we used filament preparations from three of these brains for the in vitro seeded assembly of recombinant human α-synuclein. We find that the structures of the seeded assemblies differ from those of the seeds, suggesting that additional, as yet unknown, factors play a role in the propagation of pathology. Identification of these factors will be essential for understanding the prion-like spreading of α-synuclein proteinopathies.
Establishment ofCulex modestusin Belgium and a glance into the virome of Belgian mosquito species
Authors: Wang Lanjiao , Rosas Ana Lucia Rosales , De Coninck Lander , Shi Chenyan , Bouckaert Johanna , Matthijnssens Jelle , Delang Leen
Published: November 2020

Culex modestusmosquitoes are known transmission vectors of West Nile virus and Usutu virus. Their presence has been reported across several European countries, including only one larva confirmed in Belgium in 2018. Mosquitoes were collected in the city of Leuven and surroundings in the summer of 2019 and 2020. Species identification was performed based on morphological features and partial sequences of the mitochondrial cytochrome oxidase subunit 1 (COI) gene. The 107 mosquitoes collected in 2019 belonged to eight mosquito species:Cx. pipiens(24.3%),Cx. modestus(48.6%),Cx. torrentium(0.9%),Culiseta annulata(0.9%),Culiseta morsitans(0.9%),Ae. sticticus(14.0%),Ae. cinereus(9.3%) andAnopheles plumbeus(0.9%), suggesting the presence of an establishedCx. modestuspopulation in Belgium. Collection ofCx. modestusmosquitoes at the same locations in 2020, confirmed the establishment in the region.

Haplotype network analysis of the COI sequences forCx. modestusshowed that the Belgian population is rather diverse, suggesting that it may have been established in Belgium for some time. The BelgianCx. modestuspopulation was most closely related to populations from the UK and Germany. Characterization of the virome of the collected mosquitoes resulted in the identification of at least 33 eukaryotic viral species. Nine (near-) complete genomes belonging to 6 viral species were identified, all of which were closely related to known viruses.

In conclusion, we here report the presence ofCx. modestusin the surroundings of Leuven, Belgium. As this species is known to be a vector of several arboviruses, the implementation of vector surveillance programs monitoring this species is recommended.

Importance

Culex modestusis a mosquito species that plays a role as a ‘bridge’ vector, being able to transmit pathogens between birds, as well as from birds to mammals, including humans. In Belgium, this mosquito species was considered absent, until the finding of one larva in 2018 and subsequent evidence of a large population in 2019-2020 described here. We collected mosquitoes in the summer of 2019 and 2020 in the city of Leuven and surroundings. The mosquito species was identified by morphological and molecular methods, demonstrating the presence ofCx. modestusin this region. The ability of mosquitoes to transmit pathogens can depend on several factors, one of them being their natural virus composition. Therefore, we identified the mosquito-specific viruses harboured by Belgian mosquitoes. AsCx. modestusis able to transmit viruses such as West Nile virus and Usutu virus, the establishment of this mosquito species may increase the risk of virus transmission in the region. It is thus advisable to implement mosquito surveillance programs monitoring this species.
Dimorphism in Dental Tissues: Sex differences in Archaeological Individuals for Multiple Tooth Types
Authors: Fernée Christianne , Zakrzewski Sonia , Brown Katharine Robson
Published: November 2020

Objectives

Dimorphism in the dentition has been observed in human populations worldwide. However, research has largely focused on traditional linear crown measurements. As imaging systems, such as micro-computed tomography (micro-CT), become increasingly more accessible, new dental measurements such as dental tissue size and proportions can be obtained. This research investigates the variation of dental tissues and proportions by sex in archaeological samples.

Materials and Methods

Upper and lower first incisor to second premolar tooth rows were obtained from 30 individuals (n=300), from 3 archaeological samples. The teeth were micro-CT scanned and surface area and volumetric measurements were obtained from the surface meshes extracted. Dental wear was also recorded and differences between sexes determined.

Results

Enamel and crown measurements were found to be larger in females. Conversely, dentine and root measurements were larger in males.

Discussion

The findings support the potential use of dental tissues to estimate sex of individuals from archaeological samples, whilst also indicating that individuals aged using current dental ageing methods may be under- or over-aged due to sex differences in enamel thickness.
Identification of Gli1 as a progenitor cell marker for meniscus development and injury repair
Authors: Wei Yulong , Sun Hao , Gui Tao , Yao Lutian , Zhong Leilei , Yu Wei , Heo Su-Jin , Han Lin , Liu X. Sherry , Zhang Yejia , Koyama Eiki , Long Fanxin , Zgonis Miltiadis , Mauck Robert L , Ahn Jaimo , Qin Ling
Published: November 2020

Meniscal tears are associated with a high risk of osteoarthritis but currently have no disease-modifying therapies. Using Gli1-CreER tdTomato mice, we found that Gli1+ cells contribute to the development of meniscus horns from 2 weeks of age. In adult mice, Gli1+ cells resided at the superficial layer of meniscus and expressed known mesenchymal progenitor markers. In culture, meniscal Gli1+ cells possessed high progenitor activities under the control of Hh signal. Meniscus injury at the anterior horn induced a quick expansion of Gli1+ cells. Normally, the tissue healed slowly, leading to cartilage degeneration. Ablation of Gli1+ cells further hindered this repair process. Strikingly, intra-articular injection of Gli1+ meniscal cells or an Hh activator right after injury accelerated the bridging of the interrupted ends and attenuated signs of osteoarthritis. Taken together, our work identified a novel progenitor population in meniscus and proposes a new treatment for repairing injured meniscus and preventing osteoarthritis.
Visual motion processing recruits regions selective for auditory motion in early deaf individuals
Authors: Benetti Stefania , Zonca Joshua , Ferrari Ambra , Rezk Mohamed , Rabini Giuseppe , Collignon Olivier
Published: November 2020

In early deaf individuals, the auditory deprived temporal brain regions become engaged in visual processing. In our study we tested further the hypothesis that intrinsic functional specialization guides the expression of cross-modal responses in the deprived auditory cortex. We used functional MRI to characterize the brain response to horizontal, radial and stochastic visual motion in early deaf and hearing individuals matched for the use of oral or sign language. Visual motion showed enhanced response in the ‘deaf’ mid-lateral planum temporale, a region selective to auditory motion as demonstrated by a separate auditory motion localizer in hearing people. Moreover, multivariate pattern analysis revealed that this reorganized temporal region showed enhanced decoding of motion categories in the deaf group, while visual motion-selective region hMT+/V5 showed reduced decoding when compared to hearing people. Dynamic Causal Modelling revealed that the ‘deaf’ motion-selective temporal region shows a specific increase of its functional interactions with hMT+/V5 and is now part of a large-scale visual motion selective network. In addition, we observed preferential responses to radial, compared to horizontal, visual motion in the ‘deaf’ right superior temporal cortex region that also show preferential response to approaching/receding sounds in the hearing brain. Overall, our results suggest that the early experience of auditory deprivation interacts with intrinsic constraints and triggers a large-scale reallocation of computational load between auditory and visual brain regions that typically support the multisensory processing of motion information.

Highlights

Auditory motion-sensitive regions respond to visual motion in the deaf

Reorganized auditory cortex can discriminate between visual motion trajectories

Part of the deaf auditory cortex shows preference for in-depth visual motion

Deafness might lead to computational reallocation between auditory/visual regions.
Deep neural network and field experiments reveal how transparent wing windows reduce detectability in moths
Authors: Arias Mónica , Tedore Cynthia , Elias Marianne , Leroy Lucie , Madec Clément , Matos Louane , Renoult Julien P. , Gomez Doris
Published: November 2020

Lepidoptera – a group of insects in which wing transparency has arisen multiple times - exhibit much variation in the size and position of transparent wing zones. However, little is known as to how this variability affects detectability. Here, we test how the size and position of transparent elements affect predation of artificial moths by wild birds in the field. We also test whether deep neural networks (DNNs) might be a reasonable proxy for live predators, as this would enable one to rapidly test a larger range of hypotheses than is possible with live animals. We compare our field results with results from six different DNN architectures (AlexNet, VGG-16, VGG-19, ResNet-18, SqueezeNet, and GoogLeNet). Our field experiment demonstrated the effectiveness of transparent elements touching wing borders at reducing detectability, but showed no effect of transparent element size. DNN simulations only partly matched field results, as larger transparent elements were also harder for DNNs to detect. The lack of consistency between wild predators’ and DNNs’ responses raises questions about what both experiments were effectively testing, what is perceived by each predator type, and whether DNNs can be considered to be effective models for testing hypotheses about animal perception and cognition.
Cooperation with non-kin: Context-dependent acceptance of alien queens by polygynous ant workers
Authors: De Gasperin Ornela , Blacher Pierre , Chapuisat Michel
Published: November 2020

Relatedness underlies the evolution of reproductive altruism, yet eusocial insect colonies occasionally accept unrelated reproductive queens. To better understand this seemingly paradox, we investigated whether acceptance of unrelated queens by workers is an incidental phenomenon resulting from failure to recognize non-nestmate queens, or whether it is an adaptive behavior favored in specific contexts where cooperation is preferable to rejection. Our study system is the socially polymorphic Alpine silver ant,Formica selysi. Within populations some colonies have a single queen (monogynous), and others have multiple, sometimes unrelated, breeding queens (polygynous). Social organization is determined by a supergene with two haplotypes. In a first experiment we investigated whether workers from polygynous colonies were inherently more prone to accepting unrelated queens than workers from the alternate, monogynous social form. We found that workers rejected all alien queens, independently of their social origin and of the number of queens heading their colony. We then investigated whether queen acceptance was favored in specific conditions. We found that workers from polygynous colonies accepted alien queens when these queens were accompanied by workers. These results show that workers flexibly adjust their acceptance of alien queens according to the situation. We discuss how conditional acceptance of unrelated queens may be adaptive by providing benefits through increased colony size and/or genetic diversity, and by avoiding the rejection costs resulting from fighting.
Phytochrome contributes to blue-light-mediated stem elongation and associated shade-avoidance response in mature Arabidopsis plants
Authors: Kong Yun , Zheng Youbin
Published: November 2020

Our recent studies on ornamental plants and microgreens indicate that blue-light-mediated stem elongation is related to phytochrome activity, which was based on the calculated phytochrome photoequilibrium. To examine whether phytochromes really contribute to the blue light’s effect, plant phenotypic responses were investigated in wild type Arabidopsis (Col-0), and its quintuple phytochrome (phyA phyB phyC phyD phyE) mutant plants under the following light treatments: (1) R, a pure red light from 660-nm LED; (2) B, a pure blue light from 455-nm LED; (3) BR, a impure blue light from LED combination of 94% B and 6% R; and (4) BRF, another impure blue light from LED combination of BR and 6 µmol m−2 s−1 of FR (735 nm). For all the light treatments, a photosynthetic photon flux density of ≈100 μmol m−2 s−1 were provided by 24-h lighting daily inside a walk-in growth chamber, which had an air temperature of ≈ 23 °C. The calculated phytochrome photoequilibrium was 0.89, 0.50, 0.69, and 0.60 for R, B, BR, and BRF, respectively, indicating a higher phytochrome activity under R and BR than B and BRF. After 18 days of light treatment, B or BRF increased main stem length in wild-type plants compared with R, but BR had an inhibition effect similar to R. Also, B and BRF relative to R or BR induced earlier flowering and reduced leaf size in wild type plants, showing typical shade-avoidance responses. In phytochrome-deficient mutant plants, the above shade-avoidance responses were inhibited under B or BRF, and induced under BR. However, as an exception, hypocotyl length, a growth trait during the de-etiolation stage, was reduced under B, BR and BRF vs. R regardless of phytochrome absence. It suggests that for mature Arabidopsis plants, phytochrome plays an active role in blue-light-mediated stem elongation and associated shade-avoidance response.
A spontaneous genetically-induced epiallele at a retrotransposon shapes host genome function
Authors: Bertozzi Tessa M. , Hanin Geula , Takahashi Nozomi , Kazachenka Anastasiya , Ferguson-Smith Anne C.
Published: November 2020

Intracisternal A-particles (IAPs) are endogenous retroviruses (ERVs) responsible for most insertional mutations in the mouse. Full-length IAPs harbour genes flanked by long terminal repeats (LTRs). Here, we identify a solo LTR IAP variant (C57iap1solo) recently formed in the inbred C57BL/6J mouse strain. In contrast to the C57BL/6J full-length IAP at this locus (C57iap1full), C57iap1solo lacks DNA methylation and H3K9 trimethylation. The distinct DNA methylation levels between the two alleles are established during preimplantation development, likely due to loss of KRAB zinc finger protein binding at the C57iap1solo variant. C57iap1solo methylation increases and becomes more variable in a hybrid genetic background yet is unresponsive to maternal dietary methyl supplementation. Differential epigenetic modification of the two variants is associated with metabolic differences and tissue-specific changes in adjacent gene expression. Our characterisation of C57iap1 as a genetically-induced epiallele with functional consequences establishes a new model to study transposable element repression and host-element co-evolution.