Biology subjects

Martin, A.

Publications and source records attributed to Martin, A..

At least 145 records · Page 8Linked to original sources

bioRxiv2020

FAM72A antagonizes UNG2 to promote mutagenic uracil repair during antibody maturation

Activation-induced cytidine deaminase (AID) catalyzes the deamination of deoxycytidines within Immunoglobulin (Ig) genes to induce somatic hypermutation (SHM) and class switch recombination (CSR) 1,2. AID-induced deoxyuracils within Ig loci are recognized and processed by subverted base excision and mismatch repair pathways that ensure a mutagenic outcome in B lymphocytes 3-8. However, it is unclear why DNA repair pathways that remove deoxyuracil from DNA are not efficient at faithfully repairing AID-induced lesions. Here, we identified through a genome-wide CRISPR screen that FAM72A, a protein with no ascribed function, is a major determinant for the error-prone processing of deoxyuracil. Fam72a-deficient CH12F3-2 B cells and primary B cells from Fam72a-/- mice have reduced CSR and SHM frequencies. The SHM spectrum in B cells from Fam72a-/- mice is opposite to that observed in Ung2-/- mice 9, suggesting that UNG2 is hyperactive in FAM72A-deficient cells. Indeed, FAM72A binds to UNG2 resulting in reduced UNG2 activity, and significantly reduced protein levels in the G1 phase, coinciding with peak AID activity. This effect leads to increased genome-wide deoxyuracils in B cells. By antagonizing UNG2, FAM72A therefore increases U*G mispairs that engage mutagenic mismatch repair promoting error-prone processing of AID-induced deoxyuracils. This work shows that FAM72A bridges base-excision repair and mismatch repair to modulate antibody maturation.

immunology↗

bioRxiv2020

Resting-state functional connectivity and psychopathology in Klinefelter syndrome (47, XXY)

Klinefelter syndrome (47, XXY; Henceforth: XXY syndrome) is a high impact but poorly understood genetic risk factor for neuropsychiatric impairment. Here, we provide the first neuroimaging study to map resting-state functional connectivity (rsFC) changes in XXY syndrome and ask how these might relate to brain anatomy and psychopathology. We collected resting state functional magnetic resonance imaging data from 75 individuals with XXY and 84 healthy XY males. We implemented a brain-wide screen to identify regions with altered global rsFC in XXY vs. XY males, and then used seed-based analysis to decompose these alterations. We further compared rsFC changes with regional changes in brain volume from voxel-based morphometry and tested for correlations between rsFC and symptom variation within XXY syndrome. We found that XXY syndrome was characterized by increased global rsFC in the left dorsolateral prefrontal cortex (DLPFC), associated with overconnectivity with diverse rsFC networks. Regional rsFC changes were partly coupled to regional volumetric changes in XXY syndrome. Within the precuneus, variation in DLPFC rsFC within XXY syndrome was correlated with the severity of psychopathology in XXY individuals. Our findings provide the first view of altered functional brain connectivity in XXY syndrome and delineate links between these alterations and those relating to both brain anatomy and psychopathology. Taken together, these insights advance biological understanding of XXY syndrome as a disorder in its own right, and as a model of genetic risk for psychopathology more broadly.

neuroscience↗

bioRxiv2020

Extracellular vesicles as predictors of individual response to exercise training in youth living with obesity

Exercise is associated with various health benefits, including the prevention and management of obesity and cardiometabolic risk factors. However, a strong heterogeneity in the adaptive response to exercise training exists. The objective of this study was to evaluate if changes in extracellular vesicles (EVs) after acute aerobic exercise (AE) were associated with the responder phenotype following 6-weeks of resistance exercise training. This is a secondary analysis of plasma samples from the EXIT trial (clinical trial #02204670). Eleven sedentary youth with obesity (15.7{+/-}0.5 years, BMI [≥] 95th percentile) underwent an acute bout of AE (60% heart rate reserve, 45 min). Blood was collected before exercise [at time (AT) 0 min], during [AT15, 30, 45 min], and 75 min after exercise [AT120]. Afterward, youth participated in 6-week resistance training program, and were categorized into responders (RE) or non-responders (NRE) based on changes in insulin sensitivity as measured by the Matsuda Index. EVs were isolated using size exclusion chromatography (Izon(R)). The primary outcome variable was EV biophysical profile, which includes size, zeta potential, protein yield and expression of markers associated with EV subtypes. The variables were analyzed in a single-blind fashion. Overall, there was a general increase in EV production in both groups. Average EV size was larger in RE (~147 nm) vs. NRE (~124 nm; p<0.05). Average EV size at AT0 was associated with absolute change in Matsuda index following 6-weeks of resistance training (r=0.44, p=0.08). EV size distribution revealed RE preferentially expressed EVs between 150 - 250 nm in size, whereas NRE expressed EVs between 50 - 100 nm (p<0.05). At baseline, RE-EVs contained ~25% lower Tsg101 protein, ~85% higher MMP2 content, while CD63 levels remained unchanged between the groups. Total protein yield in RE-EVs was higher than NRE at AT15 (p<0.05). Our data suggest that youth with obesity that respond to exercise training produce larger EVs, with lower exosome- and higher microvesicle-specific protein expression. RE-EVs also had higher EV protein yield during AE. The relationship between larger EV subtypes and/or cargo, and the individual response to exercise has yet to be fully elucidated.

physiology↗

bioRxiv2020

The human hippocampus plays a time-limited role in retrieving autobiographical memories

The necessity of the human hippocampus for remote autobiographical recall remains fiercely debated. The standard model of consolidation predicts a time-limited role for the hippocampus, but the competing multiple trace/trace transformation theories posit indefinite involvement. Lesion evidence remains inconclusive, and the inferences one can draw from fMRI have been limited by reliance on covert (silent) recall, which obscures dynamic, moment-to-moment content of retrieved memories. Here, we capitalized on advances in fMRI denoising to employ overtly spoken recall. Forty participants retrieved recent and remote memories, describing each for approximately two minutes. Details associated with each memory were identified and modeled in the fMRI timeseries data using a variant of the Autobiographical Interview procedure, and activity associated with the recall of recent and remote memories was then compared. Posterior hippocampal regions exhibited temporally-graded activity patterns (recent events > remote events), as did several regions of frontal and parietal cortex. Consistent with predictions of the standard model, recall-related hippocampal activity differed from a non-autobiographical control task only for recent, and not remote, events. Task-based connectivity between posterior hippocampal regions and others associated with mental scene construction also exhibited a temporal gradient, with greater connectivity accompanying the recall of recent events. These findings support predictions of the standard model of consolidation and demonstrate the potential benefits of overt recall in neuroimaging experiments.

neuroscience↗

bioRxiv2020

Tasting Pictures: Viewing Images of Foods Evokes Taste-Quality-Specific Activity in Gustatory Insular Cortex

Previous studies have shown that the conceptual representation of food involves brain regions associated with taste perception. The specificity of this response, however, is unknown. Does viewing pictures of food produce a general, non-specific response in taste-sensitive regions of the brain? Or, is the response specific for how a particular food tastes? Building on recent findings that specific tastes can be decoded from taste-sensitive regions of insular cortex, we asked whether viewing pictures of foods associated with a specific taste (e.g., sweet, salty, sour) can also be decoded from these same regions and if so, are the patterns of neural activity elicited by the pictures and their associated tastes similar? Using ultra-high resolution functional magnetic resonance imaging at high magnetic field strength (7-Tesla), we were able to decode specific tastes delivered during scanning, as well as the specific taste category associated with food pictures within the dorsal mid-insula, a primary taste responsive region of brain. Thus, merely viewing food pictures triggers an automatic retrieval of specific taste quality information associated with the depicted foods, within gustatory cortex. However, the patterns of activity elicited by pictures and their associated tastes were unrelated, thus suggesting a clear neural distinction between inferred and directly experienced sensory events. These data show how higher-order inferences derived from stimuli in one modality (i.e. vision) can be represented in brain regions typically thought to represent only low-level information about a different modality (i.e. taste). Significance StatementDoes a picture of an apple taste sweet? Previous studies have shown that viewing food pictures activates brain regions involved in taste perception. However, its unclear if this response is actually specific to the taste of depicted foods. Using ultra-high resolution functional magnetic resonance imaging and multi-voxel pattern analysis, we decoded specific tastes delivered during scanning, as well as the dominant tastes associated with food pictures within primary taste cortex. Thus, merely viewing pictures of food evokes an automatic retrieval of information about the taste of those foods. These results show how higher-order information from one sensory modality (i.e. vision) can be represented in brain regions thought to represent only low-level information from a different modality (i.e. taste).

neuroscience↗

bioRxiv2020

Mechanism of cell polarisation and first lineage segregation in the human embryo

The formation of differential cell lineages in the mammalian blastocyst from the totipotent zygote is crucial for implantation and the success of the whole pregnancy. The first lineage segregation generates the polarised trophectoderm (TE) tissue, which forms the placenta, and the apolar inner cell mass (ICM), which mainly gives rise to all foetal tissues and also the yolk sac1-3. The mechanism underlying this cell fate segregation has been extensively studied in the mouse embryo4,5. However, when and how it takes place in the human embryo remains unclear. Here, using time-lapse imaging and 325 surplus human embryos, we provide a detailed characterisation of morphological events and transcription factor expression and localisation to understand how they lead to the first lineage segregation in human embryogenesis. We show that the first lineage segregation of the human embryo is triggered by cell polarisation that occurs at the 8-cell stage in two sequential steps. In the first step, F-actin becomes apically polarised concomitantly with embryo compaction. In the second step, the Par complex becomes polarised to form the apical cellular domain. Mechanistically, we show that activation of Phospholipase C (PLC) triggers actin polarisation and is therefore essential for apical domain formation, as is the case in mouse embryos6. Finally, we show that, in contrast to the mouse embryo, the key extra-embryonic determinant GATA37,8 is expressed not only in extra-embryonic lineage precursors upon blastocyst formation. However, the cell polarity machinery enhances the expression and nuclear accumulation of GATA3. In summary, our results demonstrate for the first time that cell polarisation reinforces the first lineage segregation in the human embryo.

developmental biology↗

bioRxiv2020

Insufficient Eye Tracking Data Leads to Errors in Evaluating Typical and Atypical Fixation Preferences

Eye tracking provides insights into social processing and its deficits in disorders such as autism spectrum disorder (ASD), especially in conjunction with dynamic, naturalistic stimuli. However, reliance on manual stimuli segmentation severely limits scalability. We assessed how the amount of available data impacts individual reliability of fixation preference for different facial features, and the effect of this reliability on between-group differences. We trained an artificial neural network to segment 22 Hollywood movie clips (7410 frames). We then analyzed fixation preferences in typically developing participants and participants with ASD as we incrementally introduced movie data for analysis. Although fixations were initially variable, results stabilized as more data was added. Additionally, while those with ASD displayed significantly fewer face-centered fixations (p<.001), they did not differ in eye or mouth fixations. Our results highlight the validity of treating fixation preferences as a stable individual trait, and the risk of misinterpretation with insufficient data.

neuroscience↗

bioRxiv2020

Intranasal Immunization with a Lentiviral Vector Coding for SARS-CoV-2 Spike Protein Confers Vigorous Protection in Pre-Clinical Animal Models

To develop a vaccine candidate against COVID-19, we generated a Lentiviral Vector (LV), eliciting neutralizing antibodies against the Spike glycoprotein of SARS-CoV-2. Systemic vaccination by this vector in mice, in which the expression of the SARS-CoV-2 receptor hACE2 has been induced by transduction of respiratory tract cells by an adenoviral vector, conferred only partial protection, despite an intense serum neutralizing activity. However, targeting the immune response to the respiratory tract through an intranasal boost with this LV resulted in > 3 log10 decrease in the lung viral loads and avoided local inflammation. Moreover, both integrative and non-integrative LV platforms displayed a strong vaccine efficacy and inhibited lung deleterious injury in golden hamsters, which are naturally permissive to SARS-CoV-2 replication and restitute the human COVID-19 physiopathology. Our results provide evidence of marked prophylactic effects of the LV-based vaccination against SARS-CoV-2 and designate the intranasal immunization as a powerful approach against COVID-19. HighlightsA lentiviral vector encoding for Spike predicts a promising COVID-19 vaccine Targeting the immune response to the upper respiratory tract is key to protection Intranasal vaccination induces protective mucosal immunity against SARS-CoV-2 Lung anti-Spike IgA responses correlate with protection and reduced inflammation

immunology↗

bioRxiv2020

A pentameric protein ring with novel architecture is required for herpesviral packaging

Genome packaging in large double-stranded DNA viruses requires a powerful molecular motor to force the viral genome into nascent capsids. This process appears mechanistically similar in two evolutionarily distant viruses, the herpesviruses and the tailed bacteriophages, which infect different kingdoms of life. While the motor and mechanism as a whole are thought to be conserved, accessory factors that influence packaging are divergent and poorly understood, despite their essential roles. An accessory factor required for herpesviral packaging is encoded by ORF68 in the oncogenic virus Kaposis sarcoma-associated herpesvirus (KSHV), whose homolog in Epstein Barr Virus (EBV) is BFLF1. Here, we present structures of both KSHV ORF68 and EBV BFLF1, revealing that these proteins form a highly similar homopentameric ring. The central channel of this ring is positively charged, and we demonstrate that this region of KSHV ORF68 binds double-stranded DNA. Mutation of individual positively charged residues within but not outside the channel ablates DNA binding, and in the context of KSHV infection these mutants fail to package the viral genome or produce progeny virions. Thus, we propose a model in which ORF68 facilitates the transfer of newly replicated viral genomes to the packaging motor.

microbiology↗

bioRxiv2020

Dynamics of altruistic fluid transport in egg development

From insects to mice, oocytes develop within cysts alongside nurse-like sister germ cells. Prior to fertilization, the nurse cells cytoplasmic contents are transported into the oocyte, which grows as its sister cells regress and die. Although critical for fertility, the biological and physical mechanisms underlying this transport process are poorly understood. Here, we combined live imaging of germline cysts, genetic perturbations, and mathematical modeling to investigate the dynamics and mechanisms that enable directional and complete cytoplasmic transport in Drosophila melanogaster egg chambers. We discovered that during nurse cell (NC) dumping, most cytoplasm is transported into the oocyte independently of changes in myosin-II contractility, with dynamics instead explained by an effective Young-Laplaces law, suggesting hydraulic transport induced by baseline cell surface tension. A minimal flow network model inspired by the famous two-balloon experiment and genetic analysis of a myosin mutant correctly predicts the directionality of transport time scale, as well as its intercellular pattern. Long thought to trigger transport through squeezing, changes in actomyosin contractility are required only once cell volume is reduced by [~]75%, in the form of surface contractile waves that drive NC dumping to completion. Our work thus demonstrates how biological and physical mechanisms cooperate to enable a critical developmental process that, until now, was thought to be a mainly biochemically regulated phenomenon.

developmental biology↗

bioRxiv2020

The gene cortex controls scale colour identity in Heliconius

In Heliconius butterflies, wing pattern diversity is controlled by a few genes of large effect that regulate colour pattern switches between morphs and species across a large mimetic radiation. One of these genes, cortex, has been repeatedly associated with colour pattern evolution in butterflies. Here we carried out CRISPR knock-outs in multiple Heliconius species and show that cortex is a major determinant of scale cell identity. Chromatin accessibility profiling and introgression scans identified cis-regulatory regions associated with discrete phenotypic switches. CRISPR perturbation of these regions in black hindwing genotypes recreated a yellow bar, revealing their spatially limited activity. In the H. melpomene/timareta lineage, the candidate CRE from yellow-barred phenotype morphs is interrupted by a transposable element, suggesting that cis-regulatory structural variation underlies these mimetic adaptations. Our work shows that cortex functionally controls scale colour fate and that its cis-regulatory regions control a phenotypic switch in a modular and pattern-specific fashion.

evolutionary biology↗

bioRxiv2020

Enhanced inter-regional coupling of neural responses underlies long-term behavioral priming

Stimulus identification commonly improves with repetition over long delays ("repetition priming"), whereas neural activity commonly decreases ("repetition suppression"). Multiple models have been proposed to explain this brain-behavior relationship, predicting alterations in functional and/or effective connectivity (Synchrony and Predictive Coding models), in the latency of neural responses (Facilitation model), and in the relative similarity of neural representations (Sharpening model). Here, we test these predictions with fMRI during overt and covert naming of repeated and novel objects. While we find partial support for predictions of the Facilitation and Sharpening models in the left fusiform gyrus and left frontal cortex, the strongest support was observed for the Synchrony model, with increased coupling between right temporoparietal and anterior cingulate cortex for repeated objects that correlated with priming magnitude across participants. Despite overlap with regions showing repetition suppression, increased coupling and repetition suppression varied independently, establishing that they follow from distinct mechanisms. HighlightsO_LITested four prominent neural models of repetition suppression and long-term priming C_LIO_LIConnectivity analyses supported Synchrony model but not Predictive Coding model C_LIO_LITiming, spatial similarity of responses partially support Facilitation, Sharpening C_LIO_LIRepetition suppression was independent of coupling, implying distinct mechanisms C_LI eTOCGotts et al. test four prominent neural models of repetition suppression and behavioral priming. They show that the model with the most support is the Synchrony model: a whole-brain connectivity analysis revealed that temporoparietal cortex has increased coupling with anterior cingulate cortex following repetition, particularly for strongly primed objects.

neuroscience↗

bioRxiv2020

Acoustic regularities in infant-directed vocalizations across cultures

The forms of many species vocal signals are shaped by their functions1-15. In humans, a salient context of vocal signaling is infant care, as human infants are altricial16, 17. Humans often alter their vocalizations to produce "parentese", speech and song produced for infants that differ acoustically from ordinary speech and song18-35 in fashions that have been proposed to support parent-infant communication and infant language learning36-39; modulate infant affect33, 40-45; and/or coordinate communicative interactions with infants46-48. These theories predict a form-function link in infant-directed vocalizations, with consistent acoustic differences between infant-directed and adult-directed vocalizations across cultures. Some evidence supports this prediction23, 27, 28, 32, 49-52, but the limited generalizability of individual ethnographic reports and laboratory experiments53 and small stimulus sets54, along with intriguing reports of counterexamples55-62, leave the question open. Here, we show that people alter the acoustic forms of their vocalizations in a consistent fashion across cultures when speaking or singing to infants. We collected 1,615 recordings of infant- and adult-directed singing and speech produced by 410 people living in 21 urban, rural, and small-scale societies, and analyzed their acoustic forms. We found cross-culturally robust regularities in the acoustics of infant-directed vocalizations, such that infant-directed speech and song were reliably classified from acoustic features found across the 21 societies studied. The acoustic profiles of infant-directedness differed across language and music, but in a consistent fashion worldwide. In a secondary analysis, we studied whether listeners are sensitive to these acoustic features, playing the recordings to 51,065 people recruited online, from many countries, who guessed whether each vocalization was infant-directed. Their intuitions were largely accurate, predictable in part by acoustic features of the recordings, and robust to the effects of linguistic relatedness between vocalizer and listener. By uniting rich cross-cultural data with computational methods, we show links between the production of vocalizations and cross-species principles of bioacoustics, informing hypotheses of the psychological functions and evolution of human communication.

animal behavior and cognition↗

bioRxiv2020

An artificial intelligence based first-line defence against COVID-19: digitally screeningcitizens for risks via a chatbot

To combat the pandemic of the coronavirus disease (COVID-19), numerous governments have established phone hotlines to prescreen potential cases. These hotlines have struggled with the volume of callers, leading to wait times of hours or, even, an inability to contact health authorities. Symptoma is a symptom-to-disease digital health assistant that can differentiate more than 20,000 diseases with an accuracy of more than 90%. We tested the accuracy of Symptoma to identify COVID-19 using a set of diverse clinical cases combined with case reports of COVID-19. We showed that Symptoma can accurately distinguish COVID-19 in 96.32% of clinical cases. When considering only COVID-19 symptoms and risk factors, Symptoma identified 100% of those infected when presented with only three signs. Lastly, we showed that Symptomas accuracy far exceeds that of simple "yes-no" questionnaires widely available online. In summary, Symptoma provides unparalleled accuracy in systematically identifying cases of COVID-19 while also considering over 20,000 other diseases. Furthermore, Symptoma allows free text input, furthered with disease-specific follow up questions, in 36 languages. Combined, these results and accessibility give Symptoma the potential to be a key tool in the global fight against COVID-19. The Symptoma predictor is freely available online at https://www.symptoma.com.

bioinformatics↗

bioRxiv2020

RhoBAST - A Rhodamine-Binding Aptamer for Super-Resolution RNA Imaging

RhoBAST is a novel fluorescence light-up RNA aptamer (FLAP) that transiently binds a fluorogenic rhodamine dye. Fast dye association and dissociation result in intermittent fluorescence emission, facilitating single-molecule localization microscopy (SMLM) with an image resolution not limited by photobleaching. We demonstrate RhoBAST's excellent properties as a RNA marker by resolving subcellular and subnuclear structures of RNA in live and fixed cells by SMLM and structured illumination microscopy (SIM).

cell biology↗

bioRxiv2020

CCR5 deficiency impairs CD4+ T cell memory responses and antigenic sensitivity through increased ceramide synthesis

In CD4+ T cells, CCR5 is not only a coreceptor for HIV-1 infection, but also contributes to their functional fitness. Here we show that by limiting GATA-1-induced transcription of specific ceramide synthases, CCR5 signaling reduces ceramide levels and thereby increases T cell antigen receptor (TCR) nanoclustering in antigen-experienced mouse and human CD4+ T cells. This activity is CCR5-specific and independent of CCR5 costimulatory activity. CCR5-deficient mice showed reduced production of high affinity class-switched antibodies, but only after antigen rechallenge, which implies an impaired memory CD4+ T cell response. This study identifies a CCR5 function in the generation of CD4+ T cell memory responses, and establishes an antigen-independent mechanism that regulates TCR nanoclustering by altering specific lipid species.

immunology↗

bioRxiv2020

ILC1-derived IFN-gamma mediates cDC1-dependent host resistance against Toxoplasma gondii

Host resistance against intracellular pathogens requires a rapid IFN-{gamma} mediated immune response. We reveal that T-bet-dependent production of IFN-{gamma} is essential for the maintenance of inflammatory DCs at the site of infection with a common protozoan parasite, Toxoplasma gondii. A detailed analysis of the cellular sources for T-bet-dependent IFN-{gamma} identified that ILC1s, but not NK or TH1 cells, were involved in the regulation of inflammatory DCs via IFN-{gamma}. Mechanistically, we established that T-bet dependent ILC1-derived IFN-{gamma} is critical for the induction of IRF8, an essential transcription factor for cDC1s. Failure to upregulate IRF8 in DCs resulted in acute susceptibility to T. gondii infection. Our data identifies that ILC1-derived IFN-{gamma} is indispensable for host resistance against intracellular infection via maintaining IRF8+ inflammatory DCs at the site of infection. Author SummaryMounting a robust type I innate immune response is essential for resistance against numerous intracellular pathogens. The type I immune response is characterized by the production of IFN-{gamma}, a central cytokine required for multiple non-redundant effector functions against bacterial, viral, and parasitic pathogens. Previous work has shown that group 1 innate lymphocyte cells (ILC1s) together with NK and CD4+ T cells play an indispensable IFN-{gamma} mediated protective role against Toxoplasma gondii infection; yet, the pathway of how IFN-{gamma} produced by ILC1s defend against T. gondii remains unknown. In this work we identified that early production of IFN-{gamma} by ILC1 is essential for maintaining dendritic cells (DCs) during infection. Mechanistically, we reveal that ILC1-derived IFN-{gamma} is indispensable for inducing the transcription factor IRF8 that is critical for sustaining inflammatory DCs. Finally, we demonstrate that IRF8+ DCs are critical for parasite elimination.

immunology↗

bioRxiv2019

A genetic map of the response to DNA damage in human cells

The response to DNA damage is critical for cellular homeostasis, tumor suppression, immunity and gametogenesis. In order to provide an unbiased and global view of the DNA damage response in human cells, we undertook 28 CRISPR/Cas9 screens against 25 genotoxic agents in the retinal pigment epithelium-1 (RPE1) cell line. These screens identified 840 genes whose loss causes either sensitivity or resistance to DNA damaging agents. Mining this dataset, we uncovered that ERCC6L2, which is mutated in a bone-marrow failure syndrome, codes for a canonical non-homologous end-joining pathway factor; that the RNA polymerase II component ELOF1 modulates the response to transcription-blocking agents and that the cytotoxicity of the G-quadruplex ligand pyridostatin involves trapping topoisomerase II on DNA. This map of the DNA damage response provides a rich resource to study this fundamental cellular system and has implications for the development and use of genotoxic agents in cancer therapy.

cancer biology↗