bluuebunny/crossref_metadata_2025 huggingface dataset:
Harlequin Frogs (Lysapsus) prefer mild places to park
Authors: Ganci Carolina Cunha , Ortega Zaida , Provete Diogo B.
Published: June 2020

Temperature affects most aspects of ectotherms’ life history, including physiology and behavior. Studying thermal sensitivity of jumping performance in frogs can help understanding the influence of temperature on different aspects of frog life. Still, studies on the effects of temperature on amphibians are commonly carried out on terrestrial and tree species, creating a gap for aquatic species. We experimentally tested the thermal sensitivity of jumping performance of the Uruguay Harlequin Frog,Lysapsus limellum, assessing three measures: response time, distance of first jump, and total distance travelled. We hypothesized that individuals submitted to extreme temperatures would increase response time, decrease first jump distance, and increase total jump distance. We used an arena with a gradient of air temperature (Ta) ranging from 20 to 40 °C. We placed frogs at different Taand stimulated them to jump. Then, we analysed the influence of Taon the three estimates of jumping performance, using generalized additive models. We found that temperature affected all three measurements of jumping performance, but some relationships were stronger than others. Extreme temperatures increased response time, reduced first jump distance, and increased total distance. The effect was weaker for response time and first jump distance, but substantially stronger for total distance jumped. Although individuals under extreme temperatures experience a reduced jumping performance, they travelled longer distances to find areas with milder temperatures. Thus, we showed thatL. limellumthermoregulates by means of behavior, moving through places at different thermal conditions. Additionally, benefits of displacing to thermally suitable places -in terms of enhanced jumping performance-are bigger than the costs of jumping at reduced locomotor performance, at least under experimental conditions. Our results can help understand how climate change affects the locomotor performance of Neotropical amphibians.
The commitment of barley microspores into embryogenesis involves miRNA-directed regulation of members of the SPL, GRF and HD-ZIPIII transcription factor families
Authors: Bélanger Sébastien , Baldrich Patricia , Lemay Marc-André , Marchand Suzanne , Esteves Patricio , Meyers Blake C. , Belzile François
Published: June 2020

Microspore embryogenesis is a model for developmental plasticity and cell fate decisions. To investigate the role of miRNAs in this development, we sequenced sRNAs and the degradome of barley microspores collected prior to (day 0) and after (days 2 and 5) the application of a stress treatment known to induce embryogenesis. Microspores isolated at these timepoints were uniform in both appearance and in their complements of sRNAs. We detected 68 miRNAs in microspores. The abundance of 51 of these miRNAs differed significantly during microspore development. One group of miRNAs was induced when the stress treatment was applied, prior to being repressed when microspores transitioned to embryogenesis. Another group of miRNAs were up-regulated in day-2 microspores and their abundance remained stable or increased in day-5 microspores, a timepoint at which the first clear indications of the transition towards embryogenesis were visible. Collectively, these miRNAs might play a role in the modulation of the stress response, the repression of gametic development, and/or the gain of embryogenic potential. A degradome analysis allowed us to validate the role of miRNAs in regulating 41 specific transcripts. We showed that the transition of microspores toward the embryogenesis pathway involves miRNA-directed regulation of members of theARF, SPL, GRFandHD-ZIPIIItranscription factor families. We noted that 41.5% of these targets were shared between day-2 and day-5 microspores while 26.8% were unique to day-5 microspores. The former set may act to disrupt transcripts involved in pollen development while the latter set may drive the commitment to embryogenesis.
SCIM: Universal Single-Cell Matching with Unpaired Feature Sets
Authors: Stark Stefan G. , Ficek Joanna , Locatello Francesco , Bonilla Ximena , Chevrier Stéphane , Singer Franziska ,   Tumor Profiler Consortium, Rätsch Gunnar , Lehmann Kjong-Van
Published: June 2020

Abstract

Motivation

Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.

Results

We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an auto-encoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 93% and 84% cell-matching accuracy for each one of the samples respectively.

Availability

https://github.com/ratschlab/scim
Neural signatures of pathological hyperdirect pathway activity in Parkinson’s disease
Authors: Oswal Ashwini , Yeh Chien-Hung , Neumann Wolf-Julian , Gratwicke James , Akram Harith , Horn Andreas , Zrinzo Ludvic , Foltynie Tom , Limousin Patricia , Bogacz Rafal , Husain Masud , Brown Peter , Litvak Vladimir
Published: June 2020

Parkinson’s disease (PD) is characterised by the emergence of pathological patterns of oscillatory synchronisation across the cortico-basal-ganglia circuit. The relationship between anatomical connectivity and oscillatory synchronisation within this system remains poorly understood. We address this by integrating evidence from invasive electrophysiology, magnetoencephalography, tractography and computational modelling in patients. Coupling between supplementary motor area (SMA) and subthalamic nucleus (STN) within the high beta frequency (21-30 Hz) range correlated with fibre tract densities between these two structures. Additionally within the STN, non-linear waveform features suggestive of cortical synchronisation correlated with cortico-STN fibre densities. Finally, computational modelling revealed that exaggerated hyperdirect cortical inputs to the STN in the upper beta frequency range can provoke the generation of widespread pathological synchrony at lower beta (13-20 Hz) frequencies. These observations reveal a spectral signature of the hyperdirect pathway at high beta frequencies and provide evidence for its pathophysiological role in oscillatory network dysfunction in PD.

One sentence summary

Signatures of the hyperdirect pathway and its likely role in pathological network disruption in Parkinson’s disease are identified.
Identifying likely transmission pairs with pathogen sequence data using Kolmogorov Forward Equations; an application toM.bovisin cattle and badgers
Authors: Rossi Gianluigi , Crispell Joseph , Balaz Daniel , Lycett Samantha J. , Delahay Richard J. , Kao Rowland R.
Published: June 2020

Established methods for whole-genome-sequencing (WGS) technology allow for the detection of single-nucleotide polymorphisms (SNPs) in the pathogen genomes sourced from host samples. The information obtained can be used to track the pathogen’s evolution in time and potentially identify ‘who-infected-whom’ with unprecedented accuracy. Successful methods include ‘phylodynamic approaches’ that integrate evolutionary and epidemiological data. However, they are typically computationally intensive, require extensive data, and are best applied when there is a strong molecular clock signal and substantial pathogen diversity.

To determine how much transmission information can be inferred when pathogen genetic diversity is low and metadata limited, we propose an analytical approach that combines pathogen WGS data and sampling times from infected hosts. It accounts for ‘between-scale’ processes, in particular within-host pathogen evolution and between-host transmission. We applied this to a well-characterised population with an endemicMycobacterium bovis(the causative agent of bovine/zoonotic tuberculosis, bTB) infection.

Our results show that, even with such limited data and low diversity, the computation of the transmission probability between host pairs can help discriminate between likely and unlikely infection pathways and therefore help to identify potential transmission networks, but can be sensitive to assumptions about within-host evolution.
How understudied populations have contributed to our understanding of Alzheimer’s disease genetics
Authors: Dehghani Nadia , Bras Jose , Guerreiro Rita
Published: June 2020

The majority of genome-wide association studies have been conducted using samples with a European genetic background. As a field, we acknowledge this limitation and the need to increase the diversity of populations studied. A major challenge when designing and conducting such studies is to assimilate large samples sizes so that we attain enough statistical power to detect variants associated with disease, particularly when trying to identify variants with low and rare minor allele frequencies. In this study, we aimed to illustrate the benefits, to genetic characterization of Alzheimer’s disease (AD), in researching currently understudied populations. This is important for both fair representation of world populations and the translatability of findings. To that end, we have conducted a literature search to understand the contributions of studies, on different populations, to AD genetics. We systematically quantified the number of studies identifying mutations in known disease-causing genes, in a world-wide manner, and discussed the contributions of research in understudied populations to the identification of novel genetic factors in this disease. Additionally, we compared the effects of genome-wide significant SNPs across populations by focusing on loci that show different association profiles between populations (a key example being APOE). This work functions to both highlight how understudied populations have furthered our understanding of AD genetics, and to help us gage our progress in understanding the genetic architecture of this disease in all populations.
Transdiagnostic dimensions of psychopathology explain individuals’ unique deviations from normative neurodevelopment in brain structure
Authors: Parkes Linden , Moore Tyler M. , Calkins Monica E. , Cook Philip A. , Cieslak Matthew , Roalf David R. , Wolf Daniel H. , Gur Ruben C. , Gur Raquel E. , Satterthwaite Theodore D. , Bassett Danielle S.
Published: June 2020

Psychopathology is rooted in neurodevelopment. However, clinical and biological heterogeneity, together with a focus on case-control approaches, have made it difficult to link dimensions of psychopathology to abnormalities of neurodevelopment. Here, using the Philadelphia Neurodevelopmental Cohort, we built normative models of cortical volume and tested whether deviations from these models better predicted psychiatric symptoms compared to raw cortical volume. Specifically, drawing on thep-factorhypothesis, we distilled 117 clinical symptom measures into six orthogonal psychopathology dimensions: overall psychopathology, anxious-misery, externalizing disorders, fear, positive psychotic symptoms, and negative psychotic symptoms. We found that multivariate patterns of deviations yielded improved out-of-sample prediction of psychopathology dimensions compared to multivariate patterns of raw cortical volume. We also found that correlations between overall psychopathology and deviations in ventromedial prefrontal, inferior temporal, dorsal anterior cingulate, and insular cortices were stronger than those observed for specific dimensions of psychopathology (e.g., anxious-misery). Notably, these same regions are consistently implicated in a range of putatively distinct disorders. Finally, we performed conventional case-control comparisons of deviations in a group of individuals with depression and a group with attention-deficit hyperactivity disorder (ADHD). We observed spatially overlapping effects between these groups that diminished when controlling for overall psychopathology. Together, our results suggest that modeling cortical brain features as deviations from normative neurodevelopment improves prediction of psychiatric symptoms in out-of-sample testing, and thatp-factormodels of psychopathology may assist in separating biomarkers that are disorder-general from those that are disorder-specific.
Lef1 expression in fibroblasts maintains developmental potential in adult skin to regenerate wounds
Authors: Phan Quan M. , Fine Gracelyn , Salz Lucia , Herrera Gerardo G. , Wildman Ben , Driskell Iwona M. , Driskell Ryan R.
Published: June 2020

Scars are a serious health concern that impacts the clinical outcome and long-term well-being of burn victims and individuals with genetic skin conditions associated with wound healing. In this study using mouse as the model, we identify regenerative factors in neonatal skin that will transform adult skin to regenerate instead of repairing wounds with a scar, without perturbing normal development and homeostasis. We utilized single-cell RNA-sequencing (scRNA-seq) to probe unsorted cells from Regenerating, Scarring, Homeostatic, and Developing skin. Our results revealed a transient regenerative cell type in Developing skin, called papillary fibroblasts, which are defined by the expression of a canonical Wnt transcription factor Lef1. Tissue specific ablation of Lef1 inhibited skin regeneration. Importantly, ectopic expression of Lef1 in dermal fibroblasts did not disrupt development and aging, but primed adult skin to undergo enhanced regeneration. Here, we reveal the possibility of transferring the regenerative abilities of neonatal skin to adult tissue by expressing Lef1 in dermal fibroblasts. Finally, we have generated an expandable web resource with a search function to display gene expression in the context of our scRNA-seq data (https://skinregeneration.org/).
Prelimbic-amygdala overexcitability mediates trait vulnerability in a novel mouse model of acute social defeat stress
Authors: Grossman Yael S. , Fillinger Clementine , Manganaro Alessia , Voren George , Waldman Rachel , Zou Tiffany , Janssen William , Kenny Paul , Dumitriu Dani
Published: June 2020

BACKGROUND

Depression is a debilitating neuropsychiatric disorder with 20% lifetime prevalence in the developed world but only approximately half of afflicted individuals respond to currently available therapies. While there is growing understanding of the neurobiological underpinnings of the depressed brain, much less is known about the preexisting circuitry leading to selective vulnerability versus resilience. Elucidating these networks could lead to novel preventative approaches.

METHODS

We developed a model of acute social defeat stress (ASDS) that allows classification of male mice into “susceptible” (socially avoidant) versus “resilient” (expressing control-level social approach) one hour after exposure to six minutes of social stress. Using circuit tracing and high-resolution confocal imaging, we explored differences in activation and dendritic spine density and morphology in the prelimbic to basolateral amygdala (PL→BLA) circuit in resilient versus susceptible mice. To test the functional relevance of identified structure/function differences to divergent behavioral responses, we used an intersectional chemogenetic approach to inhibit the PL→BLA circuit during or prior to ASDS.

RESULTS

Susceptible mice had greater PL→BLA recruitment during ASDS and activated PL→BLA neurons from susceptible mice had more and larger mushroom spines compared to resilient mice. Inhibition of the PL→BLA circuit led to a population shift towards resilience.

CONCLUSION

Preexisting PL→BLA structure/function differences mediate divergent behavioral responses to ASDS in male mice. These results support the PL→BLA circuit as a biomarker of trait vulnerability and potential target for prevention of stress-induced psychopathology.
Fourier-transform-based attribution priors improve the interpretability and stability of deep learning models for genomics
Authors: Tseng Alex M. , Shrikumar Avanti , Kundaje Anshul
Published: June 2020

Deep learning models can accurately map genomic DNA sequences to associated functional molecular readouts such as protein–DNA binding data. Base-resolution importance (i.e. “attribution”) scores inferred from these models can highlight predictive sequence motifs and syntax. Unfortunately, these models are prone to overfitting and are sensitive to random initializations, often resulting in noisy and irreproducible attributions that obfuscate underlying motifs. To address these shortcomings, we propose a novel attribution prior, where the Fourier transform of input-level attribution scores are computed at training-time, and high-frequency components of the Fourier spectrum are penalized. We evaluate different model architectures with and without attribution priors trained on genome-wide binary or continuous molecular profiles. We show that our attribution prior dramatically improves models’ stability, interpretability, and performance on held-out data, especially when training data is severely limited. Our attribution prior also allows models to identify biologically meaningful sequence motifs more sensitively and precisely within individual regulatory elements. The prior is agnostic to the model architecture or predicted experimental assay, yet provides similar gains across all experiments. This work represents an important advancement in improving the reliability of deep learning models for deciphering the regulatory code of the genome.
Highly sensitive and specific multiplex antibody assays to quantify immunoglobulins M, A and G against SARS-CoV-2 antigens
Authors: Dobaño Carlota , Vidal Marta , Santano Rebeca , Jiménez Alfons , Chi Jordi , Barrios Diana , Ruiz-Olalla Gemma , Melero Natalia Rodrigo , Carolis Carlo , Parras Daniel , Serra Pau , de Aguirre Paula Martínez , Carmona-Torre Francisco , Reina Gabriel , Santamaria Pere , Mayor Alfredo , García-Basteiro Alberto , Izquierdo Luis , Aguilar Ruth , Moncunill Gemma
Published: June 2020

Reliable serological tests are required to determine the prevalence of antibodies against SARS-CoV-2 antigens and to characterise immunity to the disease in order to address key knowledge gaps in the context of the COVID-19 pandemic. Quantitative suspension array technology (qSAT) assays based on the xMAP Luminex platform overcome the limitations of rapid diagnostic tests and ELISA with their higher precision, dynamic range, throughput, miniaturization, cost-efficacy and multiplexing capacity. We developed three qSAT assays to detect IgM, IgA and IgG to a panel of eight SARS-CoV-2 antigens including spike (S), nucleoprotein (N) and membrane (M) protein constructs. The assays were optimized to minimize processing time and maximize signal to noise ratio. We evaluated the performance of the assays using 128 plasmas obtained before the COVID-19 pandemic (negative controls) and 115 plasmas from individuals with SARS-CoV-2 diagnosis (positive controls), of whom 8 were asymptomatic, 58 had mild symptoms and 49 were hospitalized. Pre-existing IgG antibodies recognizing N, M and S2 proteins were detected in negative controls suggestive of cross-reactive to common cold coronaviruses. The best performing antibody isotype/antigen signatures had specificities of 100% and sensitivities of 94.94% at ≥14 days since the onset of symptoms and 96.08% at ≥21 days since the onset of symptoms, with AUC of 0.992 and 0.999, respectively. Combining multiple antibody markers as assessed by qSAT assays has the highest efficiency, breadth and versatility to accurately detect low-level antibody responses for obtaining reliable data on prevalence of exposure to novel pathogens in a population. Our assays will allow gaining insights into antibody correlates of immunity required for vaccine development to combat pandemics like the COVID-19.
Amyotrophic lateral sclerosis associated mislocalisation of TDP-43 to the cytoplasm causes cortical hyperexcitability and reduced excitatory neurotransmission in the motor cortex
Authors: Dyer MS , Lewis KE , Walker AK , Dickson TC , Woodhouse A , Blizzard CA
Published: June 2020

Amyotrophic lateral sclerosis (ALS) is a chronic neurodegenerative disease pathologically characterised by mislocalisation of the RNA binding protein TAR-DNA binding protein 43 (TDP-43) from the nucleus to the cytoplasm. Changes to neuronal excitability and synapse dysfunction in the motor cortex are early pathological changes occurring in people with ALS and mouse models of disease. To investigate the effect of mislocalized TDP-43 on the function of motor cortex neurons we utilised mouse models that express either human wild-type (TDP-43WT) or nuclear localization sequence-deficient TDP-43 (TDP-43ΔNLS) on an inducible promoter that is restricted to the forebrain. Pathophysiology was investigated through immunohistochemistry and whole-cell patch-clamp electrophysiology. Thirty days expression TDP-43ΔNLSin adult mice (60 days of age) does not cause any changes in the number of NeuN positive nor CTIP2 positive neurons in the motor cortex. However at this time-point the expression of TDP-43ΔNLSdrives intrinsic hyperexcitability in layer V excitatory neurons of the motor cortex. This hyperexcitability occurs concomitantly with a decrease in excitatory synaptic input to these cells. This pathophysiology is not present when TDP-43WTexpression is driven, demonstrating that the localisation of TDP-43 to the cytoplasm is crucial for the altered excitability phenotype. This study has important implications for the mechanisms of toxicity of one of the most notorious proteins linked to ALS, TDP-43. We provide the first evidence that TDP-43 mislocalization causes aberrant synaptic function and a hyperexcitability phenotype in the motor cortex, linking some of the earliest dysfunctions to arise in people with ALS to mislocalisation of TDP-43.
Computational Investigation Of Blood Flow And Flow-mediated Transport In Arterial Thrombus Neighborhood
Authors: Teeraratkul Chayut , Irwin Zachariah , Shadden Shawn C. , Mukherjee Debanjan
Published: June 2020

A pathologically formed blood clot or thrombus is central to major cardiovascular diseases like heart attack and stroke. Detailed quantitative evaluation of flow and flow-mediated transport processes in the thrombus neighborhood within large artery hemodynamics is crucial for understanding disease progression and assessing treatment efficacy. This, however, remains a challenging task owing to the complexity of pulsatile viscous flow interactions with arbitrary shape and heterogeneous microstructure of realistic thrombi. Here, we address this challenge by conducting a systematic parametric simulation based study on characterizing unsteady hemodynamics and flow-mediated transport in the neighborhood of an arterial thrombus. We use a hybrid particle-continuum based finite element approach to handle arbitrary thrombus shape and microstructural variations. Results from a cohort of 50 different unsteady flow scenarios are presented, including unsteady vortical structures, pressure-gradient across the thrombus boundary, finite time Lyapunov exponents, and dynamic coherent structures that organize advective transport. We clearly illustrate the combined influence of three key parameters - thrombus shape, microstructure, and extent of wall disease - in terms of: (a) determining hemodynamic features in the thrombus neighborhood; and (b) governing the balance between advection, permeation, and diffusion to regulate transport processes in the thrombus neighborhood.
Hot droughts compromise interannual survival across all group sizes in a cooperatively breeding bird
Authors: Bourne Amanda R. , Cunningham Susan J. , Spottiswoode Claire N. , Ridley Amanda R.
Published: June 2020

Increasingly harsh and unpredictable climate regimes are affecting animal populations around the world as climate change advances. One relatively unexplored aspect of species vulnerability to climate change is whether and to what extent responses to environmental stressors might be mitigated by variation in group size in social species. We used a 15-year dataset for a cooperatively-breeding bird, the southern pied babblerTurdoides bicolor, to determine the impact of temperature, rainfall, and group size on body mass change and interannual survival in both juveniles and adults. Hot and dry conditions were associated with reduced juvenile growth, mass loss in adults, and compromised survival between years in both juveniles (−86%) and adults (−60%). Individuals across all group sizes experienced similar effects of climatic conditions. Larger group sizes may not buffer individual group members against the impacts of hot and dry conditions, which are expected to increase in frequency and severity in future.
Sensitivity of commercial Anti-SARS-CoV-2 serological assays in a high-prevalence setting
Authors: Müller Lisa , Ostermann Philipp N. , Walker Andreas , Wienemann Tobias , Mertens Alexander , Adams Ortwin , Andree Marcel , Hauka Sandra , Lübke Nadine , Keitel Verena , Drexler Ingo , Di Cristanziano Veronica , Hermsen Derik Franz , Kaiser Rolf , Boege Friedrich , Klein Florian , Schaal Heiner , Timm Jörg , Senff Tina
Published: June 2020

We analysed SARS-CoV-2 specific antibody responses in 42 social and working contacts of a super-spreader from the Heinsberg area in Germany. Consistent with a high-prevalence setting 26 individuals had SARS-CoV-2 antibodies determined by in-house neutralisation testing. These results were compared with four commercial assays, suggesting limited sensitivity of the assays in such a high-prevalence setting. Although SARS-CoV-2 nucleocapsid-restricted tests showed a better sensitivity, spike-based assays had a stronger correlation with neutralisation capacity.
The actin networks of chytrid fungi reveal evolutionary loss of cytoskeletal complexity in the fungal kingdom
Authors: Prostak Sarah M. , Robinson Kristyn A. , Titus Margaret A. , Fritz-Laylin Lillian K.
Published: June 2020

Cells from across the eukaryotic tree use actin polymers and a number of conserved regulators for a wide variety of functions including endocytosis, cytokinesis, and cell migration. Despite this conservation, the actin cytoskeleton has undergone significant evolution and diversification, highlighted by the differences in the actin cytoskeletal networks of mammalian cells and yeast. Chytrid fungi diverged before the emergence of the Dikarya (multicellular fungi and yeast), and therefore provide a unique opportunity to study the evolution of the actin cytoskeleton. Chytrids have two life stages: zoospore cells that can swim with a flagellum, and sessile sporangial cells that, like multicellular fungi, are encased in a chitinous cell wall. Here we show that zoospores of the amphibian-killing chytrid Batrachochytrium dendrobatidis (Bd) build dynamic actin structures that resemble those of animal cells, including pseudopods, an actin cortex, and filopodia-like actin spikes. In contrast, Bd sporangia assemble actin patches similar to those of yeast, as well as perinuclear actin shells. Our identification of actin cytoskeletal elements in the genomes of five species of chytrid fungi indicate that these actin structures are controlled by both fungal-specific components as well as actin regulators and myosin motors found in animals but not other fungal lineages. The use of specific small molecule inhibitors indicate that nearly all of Bd’s actin structures are dynamic and use distinct nucleators: while pseudopods and actin patches are Arp2/3-dependent, the actin cortex appears formin-dependent, and actin spikes require both nucleators. The presence of animal- and yeast-like actin cytoskeletal components in the genome combined with the intermediate actin phenotypes in Bd suggests that the simplicity of the yeast cytoskeleton may be due to evolutionary loss.
The genetic organization of subcortical volumetric change is stable throughout the lifespan
Authors: Fjell Anders M , Grydeland Håkon , Wang Yunpeng , Amlien Inge , Bartrés-Faz David , Brandmaier Andreas M. , Düzel Sandra , Elman Jeremy , Franz Carol , Håberg Asta K. , Kietzmann Tim C. , Kievit Rogier A. , Kremen William S , Krogsrud Stine K , Kühn Simone , Lindenberger Ulman , Macià Didac , Mowinckel Athanasia M. , Nyberg Lars , Panizzon Matthew S. , Solé-Padullés Cristina , Sørensen Øystein , Westerhausen René , Walhovd Kristine B
Published: June 2020

While development and aging of the cerebral cortex show a similar topographic organization and are mainly governed by the same genes, it is unclear whether the same is true for subcortical structures, which follow fundamentally different ontogenetic and phylogenetic principles than the cerebral cortex. To test the hypothesis that genetically governed neurodevelopmental processes can be traced in subcortical structures throughout life, we analyzed a longitudinal magnetic resonance imaging dataset (n = 974, age 4-89 years), identifying five clusters of longitudinal change in development. With some exceptions, these clusters followed placement along the cranial axis in embryonic brain development, suggesting continuity in the pattern of change from prenatal stages. Developmental change patterns were conserved through the lifespan and predicted general cognitive function in an age-invariant manner. The results were replicated in longitudinal data from the Lifebrain consortium (n = 756, age 19-83 years). Genetic contributions to longitudinal brain changes were calculated from the Vietnam Era Twin Study of Aging (n = 331 male twins, age 51-60 years), revealing that distinct sets of genes tended to govern change for each developmental cluster. This finding was confirmed with single nucleotide polymorphisms and cross-sectional MRI data from the UK Biobank (n = 20,588, age 40-69), demonstrating significantly higher co-heritability among structures belonging to the same developmental clusters. Together, these results suggest that coordination of subcortical change adheres to fundamental principles of lifespan continuity, genetic organization and age-invariant relationships to cognitive function.

Significance statement

Here we show that subcortical change during childhood development is organized in clusters. These clusters tend to follow the main gradient of embryonic brain development, and are stable across life. This means that subcortical regions changing together in childhood also change together throughout the rest of life, in accordance with a lifespan perspective on brain development and aging. Twin and single nucleotide polymorphism-based heritability analyses in middle-aged and older adults showed that volume and volume change of regions within each developmental cluster tended to be governed by the same sets of genes. Thus, volumetric changes across subcortical regions are tightly organized, and the coordinated change can be described in a lifespan perspective according to ontogenetic and genetic influences.
Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle
Authors: Mermet Jérôme , Yeung Jake , Naef Félix
Published: June 2020

The circadian clock drives extensive temporal gene expression programs controlling daily changes in behavior and physiology. In mouse liver, transcription factors dynamics, chromatin modifications, and RNA Polymerase II (PolII) activity oscillate throughout the 24-hour (24h) day, regulating the rhythmic synthesis of thousands of transcripts. Also, 24h rhythms in gene promoter-enhancer chromatin looping accompany rhythmic mRNA synthesis. However, how chromatin organization impinges on temporal transcription and liver physiology remains unclear. Here, we applied time-resolved chromosome conformation capture (4C-seq) in livers of WT and arrhythmicBmal1knockout mice. In WT, we observed 24h oscillations in promoter-enhancer contact at multiple loci including the core-clock genesPeriod1, Period2andBmal1. In addition, we detected rhythmic PolII activity, chromatin modifications and transcription involving stable chromatin loops at gene promoters representing key liver function such as glucose and lipid metabolism and detoxification. Intriguingly, these contacts persisted in clock-impaired mice in which both PolII activity and chromatin marks no longer oscillated. Finally, we observed chromatin interaction hubs connecting neighbouring genes showing coherent transcription regulation across genotypes. Thus, both clock-controlled and clock-independent chromatin topology underlie rhythmic regulation of liver physiology.
Exosite inhibition of A Disintegrin And Metalloproteinase with Thrombospondin motif (ADAMTS)-5 by a glycoconjugated arylsulfonamide
Authors: Salvatore Santamaria , Cuffaro Doretta , Nuti Elisa , Ciccone Lidia , Tuccinardi Tiziano , Liva Francesca , D’Andrea Felicia , de Groot Rens , Rossello Armando , Ahnström Josefin
Published: June 2020

ADAMTS-5 is a major protease involved in the turnover of proteoglycans such as aggrecan and versican. Its aggrecanase activity has been directly linked to the etiology of osteoarthritis (OA), identifying ADAMTS-5 as a pharmaceutical target for OA treatment. However, most existing ADAMTS-5 inhibitors target its active site and therefore suffer from poor selectivity. Here, using a novel approach, we have designed a new class of sugar-based arylsulfonamide inhibitors, which are selective for ADAMTS-5 through binding to a previously unknown substrate-binding site (exosite). Docking calculations combined with molecular dynamics simulations demonstrated that our lead compound is a cross-domain inhibitor that targets the interface of the metalloproteinase and disintegrin-like domains. Targeted mutagenesis identified disintegrin-like domain residues K532 and K533 as an exosite which is critical for substrate recognition. Furthermore, we show that this exosite acts as major determinant for inhibitor binding and, therefore, can be targeted for development of selective ADAMTS-5 inhibitors.
Late ESCRT Machinery Mediates The Recycling And Rescue of Invariant Surface Glycoprotein 65 inTrypanosoma brucei
Authors: Umaer Khan , Bangs James D.
Published: June 2020

TheEndosomalSortingComplexRequired forTransport machinery consists of four protein complexes (ESCRT 0-IV) and the post ESCRT ATPase Vps4. ESCRT mediates cargo delivery for lysosomal degradation via formation of multivesicular bodies.Trypanosoma bruceicontains orthologues of ESCRT I-III and Vps4. Trypanosomes also have a ubiquitinylated invariant surface glycoprotein (ISG65) that is delivered to the lysosome by ESCRT, however, we previously implicated TbVps4 in rescue and recycling of ISG65. Here we use conditional silencing to investigate the role of TbVps24, a phosphoinositide-binding ESCRT III component, on protein trafficking. TbVps24 localizes to the TbRab7+late endosome, and binds PI(3,5)P2, the product of the TbFab1 kinase, both of which also localize to late endosomes. TbVps24 silencing is lethal, and negatively affects biosynthetic trafficking of the lysosomal markers p67 and TbCathepsin L. However, the major phenotype of silencing is accelerated degradation and depletion of the surface pool of ISG65. Thus, TbVps24 silencing phenocopies that of TbVps4 in regard to ISG65 trafficking. This presents a paradox since we have previously found that depletion of TbFab1 completely blocks ISG65 turnover. We propose a model in which late ESCRT components operate at two sites, one PI(3,5)P2-dependent (degradation) and one PI(3,5)P2-independent (recycling), to regulate ISG65 homeostasis.
Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution
Authors: Lawson Catherine L. , Kryshtafovych Andriy , Adams Paul D. , Afonine Pavel V. , Baker Matthew L. , Barad Benjamin A. , Bond Paul , Burnley Tom , Cao Renzhi , Cheng Jianlin , Chojnowski Grzegorz , Cowtan Kevin , Dill Ken A. , DiMaio Frank , Farrell Daniel P. , Fraser James S. , Herzik Mark A. , Hoh Soon Wen , Hou Jie , Hung Li-Wei , Igaev Maxim , Joseph Agnel P. , Kihara Daisuke , Kumar Dilip , Mittal Sumit , Monastyrskyy Bohdan , Olek Mateusz , Palmer Colin M. , Patwardhan Ardan , Perez Alberto , Pfab Jonas , Pintilie Grigore D. , Richardson Jane S. , Rosenthal Peter B. , Sarkar Daipayan , Schäfer Luisa U. , Schmid Michael F. , Schröder Gunnar F. , Shekhar Mrinal , Si Dong , Singharoy Abishek , Terashi Genki , Terwilliger Thomas C. , Vaiana Andrea , Wang Liguo , Wang Zhe , Wankowicz Stephanie A. , Williams Christopher J. , Winn Martyn , Wu Tianqi , Yu Xiaodi , Zhang Kaiming , Berman Helen M. , Chiu Wah
Published: June 2020

This paper describes outcomes of the 2019 Cryo-EM Map-based Model Metrics Challenge sponsored by EMDataResource (www.emdataresource.org). The goals of this challenge were (1) to assess the quality of models that can be produced using current modeling software, (2) to check the reproducibility of modeling results from different software developers and users, and (3) compare the performance of current metrics used for evaluation of models. The focus was on near-atomic resolution maps with an innovative twist: three of four target maps formed a resolution series (1.8 to 3.1 Å) from the same specimen and imaging experiment. Tools developed in previous challenges were expanded for managing, visualizing and analyzing the 63 submitted coordinate models, and several novel metrics were introduced. The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual laboratory experiments and holdings of structure data archives such as the Protein Data Bank. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived from these benchmark maps by 13 participating teams, representing both widely used and novel modeling approaches. We also evaluate the pros and cons of the commonly used metrics to assess model quality and recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed density in the cryo-EM map.
Cortical dynamics underlying social behavior in dominance hierarchy and spatial navigation
Authors: Lara-Vasquez Ariel , Espinosa Nelson , Morales Cristian , Moran Constanza , Billeke Pablo , Gallagher Joseph , Strohl Joshua J. , Huerta Patricio T. , Fuentealba Pablo
Published: June 2020

Rodents establish dominance hierarchy as a social ranking system in which one subject acts as dominant over all the other subordinate individuals. Dominance hierarchy regulates food access and mating opportunities, but little is known of its significance in collective behavior, for instance during navigation for foraging or migration. Here, we implemented a simplified goal-directed spatial navigation task in mice and found that the social context exerts significant influence on individual decision-making, even when efficient navigation rules leading to reward had been previously learned. Thus, decision-making and consequent task performance were strongly dependent on contingent social interactions arising during collective navigation, yet their influence on individual behavior was outlined by dominance hierarchy. Dominant animals did not behave as leaders during navigation; conversely, they were most sensitive to social context. Social ranking in turn was reflected in the neural activity and connectivity patterns of the prefrontal cortex and hippocampus, both in anesthetized and behaving mice. These results suggest that the interplay between contingent social interactions and dominance hierarchy can regulate behavioral performance, supported by the intrinsic matrix of coordinated activity in the hippocampal-prefrontal circuit.

Significance Statement

Decision-making is shaped by intrinsic features, such as memory-stored information, and external influences, such as social interactions, yet their interplay is not well understood. We studied decision-making during collective behavior and found that instead of prioritizing memory-based pertinent information, mice shifted their individual decisions according to contingent social interactions arising in the social context. Conversely, constitutive social interactions, such as dominance hierarchy, were relevant to outline the effect of the social environment on individual behavior. Our results suggest that intrinsic hippocampal-cortical activity and connectivity patterns define social interactions. Hence, intrinsic cortical dynamics underlie behavioral performance during social decision-making.
3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy
Authors: Fäßler Florian , Zens Bettina , Hauschild Robert , Schur Florian K.M.
Published: June 2020

Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.
ComPotts: Optimal alignment of coevolutionary models for protein sequences
Authors: Talibart Hugo , Coste François
Published: June 2020

To assign structural and functional annotations to the ever increasing amount of sequenced proteins, the main approach relies on sequence-based homology search methods, e.g. BLAST or the current state-of-the-art methods based on profile Hidden Markov Models (pHMMs), which rely on significant alignments of query sequences to annotated proteins or protein families. While powerful, these approaches do not take coevolution between residues into account. Taking advantage of recent advances in the field of contact prediction, we propose here to represent proteins by Potts models, which model direct couplings between positions in addition to positional composition. Due to the presence of non-local dependencies, aligning two Potts models is computationally hard. To tackle this task, we introduce an Integer Linear Programming formulation of the problem and present ComPotts, an implementation able to compute the optimal alignment of two Potts models representing proteins in tractable time. A first experimentation on 59 low sequence identity pairwise alignments, extracted from 3 reference alignments from sisyphus and BaliBase3 databases, shows that ComPotts finds better alignments than the other tested methods in the majority of these cases.
High rates of genome rearrangements and pathogenicity ofShigellaspp
Authors: Seferbekova Zaira , Zabelkin Alexey , Yakovleva Yulia , Afasizhev Robert , Dranenko Natalia O. , Alexeev Nikita , Gelfand Mikhail S. , Bochkareva Olga O.
Published: June 2020

Shigellaare pathogens originating within theEscherichialineage but frequently classified as a separate genus.Shigellagenomes contain numerous insertion sequences (ISs) that lead to pseudogenization of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes ofE. coliandShigellastrains to assess the contribution of genomic rearrangements toShigellaevolution. We found thatShigellaexperienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenicE. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in differentShigellalineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by allShigellastrains that also showed a high level of sequence conservation in the promoter and further in the 5’ intergenic region. In the only available enteroinvasiveE. coli(EIEC) strain, which is a pathogenicE. coliwith a phenotype intermediate betweenShigellaand non-pathogenicE. coli, we found a rate of genome rearrangements comparable to those in otherE. coliand no functional copies of the twoShigella-specific E3 ubiquitin ligases. These data indicate that accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands.

Importance

PathogenicEscherichia colistrains frequently cause infections in humans. ManyE. coliexist in nature and their ability to cause disease is fueled by their ability to incorporate novel genetic information by extensive horizontal gene transfer of plasmids and pathogenicity islands. The emergence of antibiotic-resistantShigellaspp., which are pathogenic forms ofE. coli, coupled with the absence of an effective vaccine against them, highlights the importance of the continuing study of these pathogenic bacteria. Our study contributes to the understanding of genomic properties associated with molecular mechanisms underpinning the pathogenic nature ofShigella. We characterize the contribution of insertion sequences to the genome evolution of these intracellular pathogens and suggest a role of upstream regions of chromosomalipaHgenes in theShigellapathogenesis. The methods of rearrangement analysis developed here are broadly applicable to the analysis of genotype-phenotype correlation in historically recently emerging bacterial pathogens.