Miracle-dz/UniFAR-FTUs huggingface dataset:
Creating an early diagnostic test for Alzheimer's Disease

The aim of the research in this thesis was to discover and validate blood biomarkers of early Alzheimer’s Disease (AD). Existing and novel datasets from cohort studies were used for discovery and to attempt validation of previously reported biomarkers. For example, this thesis presents the first study to investigate associations between brain amyloid and blood metabolites. Further, this thesis presents the first study to combine more than one modality of blood biomarker in AD research and the first study to use a Bayesian methodology in this field. This thesis begins by aiming to validate candidate protein markers of brain amyloid burden in a novel proteomics dataset. Secondly, pathway-based methods are used to investigate the use of gene expression measurements as a potential biomarker of AD diagnosis. In the fourth chapter I generated a novel metabolomics dataset to investigate associations between blood metabolites and brain amyloid burden. A panel is found that predicts dichotomized amyloid burden with reasonable accuracy. The accuracy is improved by the inclusion of a candidate protein in the model. The fifth chapter of this thesis is focused on the use of a Bayesian methodology to predict measurements of amyloid using a variety of omics data. The Bayesian methodology allows incorporation of historical information by placing informative priors on demographic variables. No improvement is seen over demographics alone. The final chapter of this thesis aims to predict amyloid and tau burden using a polygenic risk score and levels of tau in blood. I have also considered a combined amyloid and tau pathology endpoint. The blood markers considered here do not improve predictive ability over demographics alone. Much of the work in this thesis highlights the importance of demographic factors in the diagnosis of early AD. The metabolite discovery work shows an improvement
Predicting future drinking among young adults: using ensemble machine-learning to combine MRI with psychometrics and behaviour

Background While most research into predictors of problematic alcohol use has focused on adolescence, young adults are also at elevated risk, and differ from adolescents and adults in terms of exposure to alcohol and neurodevelopment. Here we examined predictors of alcohol use among young adults at a 1-year follow-up using a broad predictive modelling approach. Methods Data in four modalities were included from 128 men aged between 18 and 25 years; functional MRI regions-of-interest from 1) a beer-incentive delay task, and 2) a social alcohol cue-exposure task, 3) grey matter data, and 4) non-neuroimaging data (i.e. psychometric and behavioural). These modalities were combined into an ensemble model to predict follow-up Alcohol Use Disorder Identification (AUDIT) scores, and were tested separately for their contribution. To reveal specificity for the prediction of future AUDIT scores, the same analyses were carried out for current AUDIT score. Results The ensemble resulted in a more accurate estimation of follow-up AUDIT score than any single modality. Only removal of the social alcohol cue-exposure task and of the non-neuroimaging data significantly worsened predictions. Reporting to need a drink in the morning to start the day was the strongest unique predictor of future drinking along with anterior cingulate cortex and cerebellar activity. Conclusions Alcohol-related task fMRI activity is a valuable predictor for future drinking among young adults alongside non-neuroimaging variables. Multi-modal prediction models best predict future drinking among young adults and may play an important part in the move towards individualized treatment and prevention efforts.
Quantifying biases in test-negative studies of vaccine effectiveness

Test-negative designs have become commonplace in assessments of seasonal influenza vaccine effectiveness. Vaccine effectiveness is measured from the exposure odds ratio (OR) of vaccination among individuals seeking treatment for acute respiratory illness and receiving a laboratory test for influenza infection. This approach is widely believed to correct for differential healthcare-seeking behavior among vaccinated and unvaccinated persons. However, the relation of the measured OR to true vaccine effectiveness is poorly understood. We derive the OR under circumstances of real-world test-negative studies. The OR recovers the true vaccine direct effect when two conditions are met: (1) that individuals’ vaccination decisions are uncorrelated with exposure or susceptibility to infection, and (2) that vaccination confers “all-or-nothing” protection (whereby certain individuals have no protection while others are perfectly protected). Biased effect size estimates arise if either condition is unmet. Such bias may suggest misleading associations of the OR with time since vaccination or the force of infection of influenza. The test-negative design may also fail to correct for differential healthcare-seeking behavior among vaccinated and unvaccinated persons without stringent criteria for enrollment and testing. Our findings demonstrate a need to reassess how data from test-negative studies are interpreted for policy decisions conventionally based on causal inferences.
Phosphatidylinositol 3-phosphate and Hsp70 protect Plasmodium falciparum from heat-induced cell death

Phosphatidylinositol 3-phosphate (PI(3)P) levels in Plasmodium falciparum correlate with tolerance to cellular stresses caused by artemisinin, a first-line malaria treatment, and environmental factors. However, the functional role of PI(3)P in the Plasmodium stress response and a possible mechanism of protection were unknown. Here, we used multiple chemical probes including PI3K inhibitors and known antimalarial drugs to examine the importance of PI(3)P under thermal conditions that recapitulate malaria fever. Live cell microscopy using both chemical and genetic reporters revealed that PI(3)P stabilizes the acidic and proteolytic digestive vacuole (DV) under heat stress. We demonstrate that heat-induced DV destabilization in PI(3)P-deficient P. falciparum precedes cell death and is reversible after withdrawal of the stress condition and the PI3K inhibitor. These phenotypes are not observed with an inactive structural analog of the PI3K inhibitor. A chemoproteomic and biochemical approach identified PfHsp70-1 as a parasite PI(3)P-binding protein. Targeting PfHsp70-1 with a small molecule inhibitor phenocopied PI(3)P-deficient parasites under heat shock. Furthermore, tunable knockdown of PfHsp70-1 showed that PfHsp70-1 downregulation causes DV destabilization and hypersensitizes parasites to heat shock and PI3K inhibitors. Our findings underscore a mechanistic link between PI(3)P and PfHsp70-1, and present a novel PI(3)P function in stabilizing the DV compartment during heat stress.
Application of probiotic Bacillus spp. isolated from African nightcrawler (Eudrilus eugeniae) on Nile Tilapia (Oreochromis niloticus L.)

Due to the emergence of antibiotic-resistant pathogens, probiotics in aquaculture are used for the prevention of infectious microbial diseases and substitute for antibiotics and chemotherapeutics. In this study, we evaluated the effect of probiotic Bacillus spp. isolated from African nightcrawler (Eudrilus eugeniae) on the growth, feed utilization, and disease resistance of Nile tilapia (Oreochromis niloticus). Four probiotic strains of Bacillus spp. (ANSCI9, BFAR9, RM3, and RM10) were individually incorporated in the commercial diet (control) at 108 CFU g-1 of feed. The experimental fish were fed at 5% of their body weight for 30 days, and subjected to a 14-day Aeromonas hydrophila challenge test afterward. The results showed the probiotic-treated groups have higher (P<0.05) average body weight (ABW) (4.51 ± 0.34 g) than the control (3.89 ± 0.17 g). The BFAR9 (2.73 ± 0.26 g) and RM10 (3.15 ± 0.30 g) showed higher (P<0.05) absolute growth (AG) than the control (2.20 ± 0.16 g). Furthermore, RM10 had higher (P<0.05) specific growth rate (SGR) (1.60 ± 0.10 % day-1) and relative growth rate (RGR) (181.39 ± 18.16 %) than the control (SGR=1.29 ± 0.07 % day-1; RGR=129.84 ± 9.77 %). Consequently, RM10 had significantly lower (P<0.05) feed conversion ratio (FCR) (1.99 ± 0.13) than the control (2.60 ± 0.16). The challenge test revealed that the probiotic-treated groups have higher (P<0.05) survival (81.25 ± 9.57 %) than the control (55.00 ± 19.15 %). These results revealed that the probiotic Bacillus spp. isolated from E. eugeniae improved the growth, feed utilization, and the disease resistance of Nile tilapia.
Functional Identification of Specialized Basal Ganglia Circuits that Regulate Vocal Motor Sequences

Production of learned vocalizations requires precise selection and accurate sequencing of appropriate vocal-motor actions. The basal ganglia are essential for the selection and sequencing of motor actions, but the cellular specializations and circuit mechanisms governing accurate sequencing of vocalizations are unknown. Here, we use single-nucleus RNA sequencing and genetic manipulations to map basal ganglia cell types and circuits involved in the production of songbird vocal sequences. We identify cell-type specializations in direct-like and indirect-like basal ganglia pathways, including evolutionary expansion of striatal and arkypallidal cell-types that could facilitate vocal sequencing. Surprisingly, we find that FoxP2, a gene important for vocal development, can potently and reversibly control accurate sequencing of adult birdsong, and that phasic dopamine selectively regulates repetition of syllables independent of its role in reinforcement-based learning of how they are sung. These findings identify key evolutionary specializations and circuits essential for selection and sequencing of vocal-motor actions necessary for vocal communication.
KSHV lytic mRNA is efficiently translated in the absence of eIF4F

Herpesvirus genomes are decoded by host RNA polymerase II, generating messenger ribonucleic acids (mRNAs) that are post-transcriptionally modified and exported to the cytoplasm. These viral mRNAs have 5 ′ -m7GTP caps and poly(A) tails that should permit assembly of canonical eIF4F cap-binding complexes to initiate protein synthesis. However, we have shown that chemical disruption of eIF4F does not impede KSHV lytic replication, suggesting that alternative translation initiation mechanisms support viral protein synthesis. Here, using polysome profiling analysis, we confirmed that eIF4F disassembly did not affect the efficient translation of viral mRNAs during lytic replication, whereas a large fraction of host mRNAs remained eIF4F-dependent. Lytic replication altered multiple host translation initiation factors (TIFs), causing caspase-dependent cleavage of eIF2α and eIF4G1 and decreasing levels of eIF4G2 and eIF4G3. Non-eIF4F TIFs NCBP1, eIF4E2 and eIF4G2 associated with actively translating messenger ribonucleoprotein (mRNP) complexes during KSHV lytic replication, but their depletion by RNA silencing did not affect virion production, suggesting that the virus does not exclusively rely on one of these alternative TIFs for efficient viral protein synthesis. METTL3, an N6-methyladenosine (m6A) methyltransferase that modifies mRNAs and influences translational efficiency, was dispensable for early viral gene expression and genome replication but required for late gene expression and virion production. METTL3 was also subject to caspase-dependent degradation during lytic replication, suggesting that its positive effect on KSHV late gene expression may be indirect. Taken together, our findings reveal extensive remodelling of TIFs during lytic replication, which may help sustain efficient viral protein synthesis in the context of host shutoff.Viruses use host cell protein synthesis machinery to create viral proteins. Herpesviruses have evolved a variety of ways to gain control over this host machinery to ensure priority synthesis of viral proteins and diminished synthesis of host proteins with antiviral properties. We have shown that a herpesvirus called KSHV disrupts normal cellular control of protein synthesis. A host cell protein complex called eIF4F starts translation of most cellular mRNAs, but we observed it is dispensable for efficient synthesis of viral proteins. Several proteins involved in alternative modes of translation initiation were likewise dispensable. However, an enzyme called METTL3 that modifies mRNAs is required for efficient synthesis of certain late KSHV proteins and productive infection. We observed caspase-dependent degradation of several host cell translation initiation proteins during infection, suggesting that the virus alters pools of available factors to favour efficient viral protein synthesis at the expense of host protein synthesis.
Remyelination alters the pattern of myelin in the cerebral cortex

Destruction of oligodendrocytes and myelin sheaths in cortical gray matter profoundly alters neural activity and is associated with cognitive disability in multiple sclerosis (MS). Myelin can be restored by regenerating oligodendrocytes from resident progenitors; however, it is not known whether regeneration restores the complex myelination patterns in cortical circuits. Here we performed time lapse in vivo two photon imaging in somatosensory cortex of adult mice to define the kinetics and specificity of myelin regeneration after acute oligodendrocyte ablation. These longitudinal studies revealed that the pattern of myelination in cortex changed dramatically after regeneration, as new oligodendrocytes were formed in different locations and new sheaths were often established along axon segments previously lacking myelin. Despite the dramatic increase in axonal territory available, oligodendrogenesis was persistently impaired in deeper cortical layers that experienced higher gliosis. The repeated reorganization of myelin patterns in MS may alter circuit function and contribute to cognitive decline.
Tau accumulates in Crohn’s disease gut

A sizeable body of evidence has recently emerged to suggest that gastrointestinal inflammation might be involved in the development of Parkinson’s disease. There is now strong epidemiological and genetical evidence linking Parkinson’s disease to inflammatory bowel diseases and we recently demonstrated that the neuronal protein alpha-synuclein, which is critically involved in Parkinson’s disease pathophysiology, is upregulated in inflamed segments of Crohn’s colon. The microtubule associated protein tau is another neuronal protein critically involved in neurodegenerative disorders but, in contrast to alpha-synuclein, no data are available about its expression and phosphorylation patterns in inflammatory bowel diseases. Here, we examined the expression levels of tau isoforms, their phosphorylation profile and truncation in colon biopsy specimens from 16 Crohn’s disease and 6 ulcerative colitis patients and compared them to samples from 16 controls. Additional experiments were performed in full thickness segments of colon of 5 Crohn’s disease and 5 control subjects, in primary cultures of rat enteric neurons and in Nrf2 knockout mice. Our results show the upregulation of two main human tau isoforms in the enteric nervous system in Crohn’s disease but not in ulcerative colitis. This upregulation was not transcriptionally regulated but instead likely resulted from a decrease in protein clearance via an Nrf2 pathway. Our findings, which provide the first detailed characterization of tau in Crohn’s disease, suggest that the key proteins involved in neurodegenerative disorders such as alpha-synuclein and tau, might also play a role in Crohn’s disease.
Fooling the classifier: Ligand antagonism and adversarial examples

Machine learning algorithms are sensitive to so-called adversarial perturbations. This is reminiscent of cellular decision-making where antagonist ligands may prevent correct signaling, like during the early immune response. We draw a formal analogy between neural networks used in machine learning and the general class of adaptive proofreading networks. We then apply simple adversarial strategies from machine learning to models of ligand discrimination. We show how kinetic proofreading leads to “boundary tilting” and identify three types of perturbation (adversarial, non adversarial and ambiguous). We then use a gradient-descent approach to compare different adaptive proofreading models, and we reveal the existence of two qualitatively different regimes characterized by the presence or absence of a critical point. These regimes are reminiscent of the “feature-to-prototype” transition identified in machine learning, corresponding to two strategies in ligand antagonism (broad vs. specialized). Overall, our work connects evolved cellular decision-making to classification in machine learning, showing that behaviours close to the decision boundary can be understood through the same mechanisms.
Transcription establishes microenvironments that organize euchromatin

Summary The three-dimensional organization of the genome is essential for development and health. Although the organization of euchromatin (transcriptionally permissive chromatin) dynamically adjusts to changes in transcription, the underlying mechanisms remain elusive. Here, we studied how transcription organizes euchromatin, using experiments in zebrafish embryonic cells and theory. We show that transcription establishes an interspersed pattern of chromatin domains and RNA-enriched microenvironments. Specifically, accumulation of RNA in the vicinity of transcription sites creates microenvironments that locally remodel chromatin by displacing not transcribed chromatin. Ongoing transcriptional activity stabilizes the interspersed pattern of chromatin domains and RNA-enriched microenvironments by establishing contacts between chromatin and RNA. We explain our observations with an active microemulsion model based on two macromolecular mechanisms: RNA/RNA-binding protein complexes generally segregate from chromatin, while transcribed chromatin is retained among RNA/RNA-binding protein accumulations. We propose that microenvironments might be central to genome architecture and serve as gene regulatory hubs. Graphical abstract Highlights Transcription establishes microenvironments that remodel euchromatin Microenvironments form by RNA accumulation in the vicinity of transcription sites Microenvironments exclude not transcribed DNA and retain transcribed DNA Euchromatin is organized like an active microemulsion, stabilized by transcription
Anti-inflammatory role of GM1 and modulatory effects of gangliosides on microglia functions

Gangliosides are sialic acid-containing glycosphingolipids highly enriched in the brain. Located mainly at the plasma membrane, gangliosides play important roles in signaling and cell-to-cell communication. Lack of gangliosides causes severe early onset neurodegenerative disorders, while more subtle deficits have been reported in Parkinson’s disease and in Huntington’s disease, two misfolded protein diseases with a neuroinflammatory component. On the other hand, administration of ganglioside GM1 provides neuroprotection in both diseases and in several other models of neuronal insult. While most studies have focused on the role of endogenous gangliosides and the effects of exogenously administered GM1 in neurons, their contribution to microglia functions that are affected in neurodegenerative conditions is largely unexplored. Microglia are the immune cells of the brain and play important homeostatic functions in health and disease. In this study, we show that administration of exogenous GM1 exerts a potent anti-inflammatory effect on microglia activated with LPS, IL-1β or upon phagocytosis of latex beads. These effects are partially reproduced by L-t-PDMP, a compound that stimulates the activity of the ganglioside biosynthetic pathway, while inhibition of ganglioside synthesis with GENZ-123346 increases microglial transcriptional response to LPS. We further show that administration of GM1 increases the uptake of apoptotic bodies and latex beads by microglia, as well as microglia migration and chemotaxis in response to ATP. On the contrary, decreasing microglial ganglioside levels results in a partial impairment in both microglial activities. Finally, increasing cellular ganglioside levels results in decreased expression and secretion of microglial brain derived neurotrophic factor (BDNF). Altogether, our data suggest that gangliosides are important modulators of microglia functions that are crucial to healthy brain homeostasis, and reveal that administration of ganglioside GM1 exerts an important anti-inflammatory activity that could be exploited therapeutically.
ProGen: Language Modeling for Protein Generation

Generative modeling for protein engineering is key to solving fundamental problems in synthetic biology, medicine, and material science. We pose protein engineering as an unsupervised sequence generation problem in order to leverage the exponentially growing set of proteins that lack costly, structural annotations. We train a 1.2B-parameter language model, ProGen, on ∼280M protein sequences conditioned on taxonomic and keyword tags such as molecular function and cellular component. This provides ProGen with an unprecedented range of evolutionary sequence diversity and allows it to generate with fine-grained control as demonstrated by metrics based on primary sequence similarity, secondary structure accuracy, and conformational energy.
Intracranial recordings demonstrate medial temporal lobe engagement in visual search in humans

Visual search is a fundamental human behavior, which has been proposed to include two component processes: inefficient search (Search) and efficient search (Pop-out). According to extant research, these two processes map onto two separable neural systems located in the frontal and parietal association cortices. In the present study, we use intracranial recordings from 23 participants to delineate the neural correlates of Search and Pop-out with an unprecedented combination of spatiotemporal resolution and coverage across cortical and subcortical structures. First, we demonstrate a role for the medial temporal lobe in visual search, on par with engagement in frontal and parietal association cortex. Second, we show a gradient of increasing engagement over anatomical space from dorsal to ventral lateral frontal cortex. Third, we confirm previous work demonstrating nearly complete overlap in neural engagement across cortical regions in Search and Pop-out. We further demonstrate Pop-out selectivity manifesting as activity increase in Pop-out as compared to Search in a distributed set of sites including frontal cortex. This result is at odds with the view that Pop-out is implemented in low-level visual cortex or parietal cortex alone. Finally, we affirm a central role for the right lateral frontal cortex in Search.
SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a transient secretory cell type in subsegmental bronchial branches

The SARS-CoV-2 pandemic affecting the human respiratory system severely challenges public health and urgently demands for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and replication. SARS-CoV-2 was reported to enter cells via binding to ACE2, followed by its priming by TMPRSS2. Here, we investigate ACE2 and TMPRSS2 expression levels and their distribution across cell types in lung tissue (twelve donors, 39,778 cells) and in cells derived from subsegmental bronchial branches (four donors, 17,521 cells) by single nuclei and single cell RNA sequencing, respectively. While TMPRSS2 is expressed in both tissues, in the subsegmental bronchial branches ACE2 is predominantly expressed in a transient secretory cell type. Interestingly, these transiently differentiating cells show an enrichment for pathways related to RHO GTPase function and viral processes suggesting increased vulnerability for SARS-CoV-2 infection. Our data provide a rich resource for future investigations of COVID-19 infection and pathogenesis.