Biology subjects

Monti, M.

Publications and source records attributed to Monti, M..

34 records · Page 2Linked to original sources

bioRxiv2023

Early alterations of thalamo- and hippocampo-cortical functional connectivity are biomarkers of epileptogenesis after traumatic brain injury

The Epilepsy Bioinformatics Study for Antiepileptogenic Therapy (EpiBioS4Rx) study is a prospective multicenter clinical observational study to identify early biomarkers of epileptogenesis after moderate-to-severe traumatic brain injury (TBI). In this preliminary analysis of 37 patients, using a seed-based approach applied to acute (i.e., [≤] 14 days) functional magnetic resonance (MRI) imaging data, we directly test the hypothesis that the epileptogenic process following brain trauma is associated with functional changes within hippocampal and thalamo-cortical networks. Additionally, we hypothesize that the network connectivity involving thalamic and hippocampal circuits underlying early and late-onset epileptogenesis would differ. The three groups did not differ by sex distribution ({chi}2(2) = 1.8, p = .407), age (H(2) = 4.227, p = .121), admission Glasgow Coma Scale (H(2) = 3.850, p = .146) or postinjury day of the MRI session (H(2) = .695, p = .706). The primary finding is that patients with early seizures, a sign of early epileptogenesis, exhibited pattern 1, namely, an increased positive connectivity in thalamic and hippocampal networks, as compared to patients who had no epileptogenesis, or late epileptogenesis (p < .05, FWE-corrected at the cluster level). In contrast, this finding was absent in those patients who exhibited late seizures, with the latter group displayed pattern 2, namely, a lower positive and higher negative connectivity in the hippocampal network, as compared to patients who had no signs of epileptogenesis (p < .05, FWE-corrected at the cluster level). Patients with either pattern 1 or pattern 2 connectivity profiles in thalamic and hippocampal networks were significantly predictive of late (i.e., between 7 days and 2 years) epileptogenesis following brain trauma. A Receiver Operating Characteristic (ROC) Curve analysis model that included thalamic and hippocampal functional connectivity values presented an Area Under the Curve (AUC) 87.7, specificity 86.7, and sensitivity 84.6. Our results indicate that dysfunction in hippocampal and thalamo-cortical networks are potential biomarkers for early and late epileptogenesis following a TBI.

neuroscience↗

bioRxiv2023

Criticality supports cross-frequency cortical-thalamic information transfer during conscious states

Consciousness is thought to be regulated by bidirectional information transfer between the cortex and thalamus, but the nature of this bidirectional communication - and its possible disruption in unconsciousness - remains poorly understood. Here, we present two main findings elucidating mechanisms of corticothalamic information transfer during conscious states. First, we identify a highly preserved spectral channel of cortical-thalamic communication which is present during conscious states but which is diminished during the loss of consciousness and enhanced during psychedelic states. Specifically, we show that in humans, mice, and rats, information sent from either the cortex or thalamus via{delta} /{theta}/ waves (~1.5-13 Hz) is consistently encoded by the other brain region by high{gamma} waves (~50-100 Hz); moroever, unconsciousness induced by propofol anesthesia or generalized spike-and-wave seizures diminishes this cross-frequency communication, whereas the psychedelic 5-methoxy-N,N/-dimethyltryptamine (5-MeO-DMT) enhances this interregional communication. Second, we leverage numerical simulations and neural electrophysiology recordings from the thalamus and cortex of human patients, rats, and mice to show that these changes in cross-frequency cortical-thalamic information transfer are mediated by excursions of low-frequency thalamocortical electrodynamics toward/away from edge-of-chaos criticality, or the phase transition from stability to chaos. Overall, our findings link thalamic-cortical communication to consciousness, and further offer a novel, mathematically well-defined framework to explain the disruption to thalamic-cortical information transfer during unconscious states.

neuroscience↗

bioRxiv2022

The PRALINE database: Protein and Rna humAn singLe nucleotIde variaNts in condEnsates

SummaryBiological condensates are membraneless organelles with different material properties. Proteins and RNAs are the main components, but most of their interactions are still unknown. Here we introduce PRALINE, a database for the interrogation of proteins and RNAs contained in stress-granules, processing bodies, and other assemblies including droplets and amyloids. PRALINE provides information about the predicted and experimentally validated protein-protein, protein-RNA and RNA-RNA interactions. For proteins, it reports the liquid-liquid phase separation and liquid-solid phase separation propensities. For RNAs, it provides information on predicted secondary structure content. PRALINE shows detailed information on human single-nucleotide variants, their clinical significance and presence in protein and RNA binding sites, and how they can affect condensates physical properties. AvailabilityPRALINE is freely accessible on the web at http://alvinlee.bio.uniroma1.it/praline. Supplementary informationGeneral information is at http://alvinlee.bio.uniroma1.it/praline/about, where we provide a detailed description of the datasets and the tools employed in the database. Data provided in PRALINE are available at http://alvinlee.bio.uniroma1.it/praline/downloads. The tutorial is at http://alvinlee.bio.uniroma1.it/praline/tutorial.

bioinformatics↗

bioRxiv2022

Reconstruct a eukaryotic chromosome arm by de novo design and synthesis

The genome of an organism is inherited from its ancestor and keeps evolving over time, however, how much the current version could be altered remains unknown. Here, we use the left arm of chromosome XII (chrXIIL) as an example to probe the genome plasticity in Saccharomyces cerevisiae. A neochromosome was designed to harbor originally dispersed genes. The essentiality of sequences in chrXIIL was dissected by targeted DNA removal, chromosome truncation and random deletion. Notably, 12 genes were sufficient for survival, while 25 genes are required to retain robust fitness. Next, we demonstrated these genes could be reconstructed using synthetic regulatory sequences and recoded open-reading frames with "one-amino-acid-one-codon" strategy. Finally, we built a neochromsome, which could substitute for chrXIIL for cell viability, with these reconstructed genes. Our work not only highlights the high plasticity of yeast genome, but also illustrates the possibility of making functional chromosomes with completely artificial sequences. HIGHLIGHTSO_LIA neochromosome was designed to facilitate the assembly of exogenous DNA for stable expression in yeast C_LIO_LIThe left arm of chrXII could be minimized to just 12 genes to maintain viability, but additional genes were required to retain robust fitness C_LIO_LIComprehensive recoding and transcriptional refactoring using artificial regulatory sequences produced a functional chromosome arm C_LIO_LIA completely reconstructed neochromosome could replace the chrXIIL to maintain comparable fitness C_LI

synthetic biology↗

bioRxiv2022

A Theoretical Model reveals RNA sequestration in Alpha Synuclein Aggregates

Nucleic acids can act as potent modulators of protein aggregation, and RNA is able to either hinder or facilitate protein assembly depending on the molecular context. Here we used a computational approach to characterize the physico-chemical properties of regions involved in amyloid aggregation. In different experimental datasets we observed that, while the core is hydrophobic and highly ordered, external regions, more disordered, display a distinct tendency to interact with nucleic acids. To validate our predictions, we performed aggregation assays with -synuclein (aS140), a non-nucleic acid binding amyloidogenic protein, and a mutant truncated at the acidic C-terminus (aS103) that is predicted to sequester RNA. For both aS140 and aS103 we observed acceleration of the aggregation upon RNA addition with a significantly stronger effect for aS103. Due to the favorable electrostatics, we observed enhanced nucleic-acid sequestration ability for aS103 that entrapped a larger amount of RNA. Overall, our research suggests that RNA sequestration is a rather common phenomenon linked to protein aggregation and constitutes a gain-of-function mechanism to be further investigated. STATEMENT OF SIGNIFICANCEOur study indicates that aggregation confers RNA-binding ability to non-RNA-binding proteins such as alpha synuclein. The sequestration of RNA upon protein aggregation might alter RNA homeostasis and impact multiple biochemical cascades.

biochemistry↗

bioRxiv2022

A system-wide quantitative map of RNA and protein subcellular localisation dynamics

Existing methods to analyse RNA localisation are constrained to specific RNAs or subcellular niches, precluding the cell-wide mapping of RNA. We present Localisation of RNA (LoRNA), which maps, at once, RNAs to membranous (nucleus, ER and mitochondria) and membraneless compartments (cytosol, nucleolus and phase-separated granules). Simultaneous interrogation of all RNA locations allows the system-wide quantification of RNA proportional distribution and the comprehensive analysis of RNA subcellular dynamics. Moreover, we have re-engineered the LOPIT (Localisation Of Proteins by Isotope Tagging) method, enabling integration with LoRNA, to jointly map RNA and protein subcellular localisation. Applying this framework, we obtain a global re-localisation map for 31839 transcripts and 5314 proteins during the unfolded protein response, uncovering that ER-localised transcripts are more efficiently recruited to stress granules than cytosolic RNAs, and revealing eIF3d is key to sustain cytoskeletal function. Overall, we provide the most exhaustive map to date of RNA and protein subcellular dynamics.

cell biology↗

bioRxiv2021

Aggregation is a context-dependent constraint on protein evolution

Solubility is a requirement for many cellular processes. Loss of solubility and aggregation can lead to the partial or complete abrogation of protein function. Thus, understanding the relationship between protein evolution and aggregation is an important goal. Here, we analysed two deep mutational scanning experiments to investigate the role of protein aggregation in molecular evolution. In one data set, mutants of a protein involved in RNA biogenesis and processing, human TAR DNA binding protein 43 (TDP-43), were expressed in S. cerevisiae. In the other data set, mutants of a bacterial enzyme that controls resistance to penicillins and cephalosporins, TEM-1 beta-lactamase, were expressed in E. coli under the selective pressure of an antibiotic treatment. We found that aggregation differentiates the effects of mutations in the two different cellular contexts. Specifically, aggregation was found to be associated with increased cell fitness in the case of TDP-43 mutations, as it protects the host from aberrant interactions. By contrast, in the case of TEM-1 beta-lactamase mutations, aggregation is linked to a decreased cell fitness due to inactivation of protein function. Our study shows that aggregation is an important context-dependent constraint of molecular evolution and opens up new avenues to investigate the role of aggregation in different cellular contexts.

bioinformatics↗

bioRxiv2020

SHMT1-RNA interaction dynamically regulates serine and glycine concentration in cells

Human serine hydroxymethyltransferase (SHMT) regulates the serine-glycine one carbon metabolism and plays a role in cancer metabolic reprogramming. Two SHMT isozymes are acting in the cell: SHMT1 encoding the cytoplasmic isozyme, and SHMT2 encoding the mitochondrial one. Here we present a molecular model built on experimental data reporting the interaction between SHMT1 protein and SHMT2 mRNA, recently discovered in lung cancer cells. Using a stochastic dynamic model, we show that RNA moieties dynamically regulate serine and glycine concentration, shaping the system behaviour. For the first time we observe an active functional role of the RNA in the regulation of the serine-glycine metabolism and availability, which unravels a complex layer of regulation that cancer cells exploit to fine tune amino acids availability according to their metabolic needs. The quantitative model, complemented by an experimental validation in the lung adeno-carcinoma cell line H1299, exploits RNA molecules as metabolic switches of the SHMT1 activity. Our results pave the way for the development of RNA-based molecules able to unbalance serine metabolism in cancer cells.

biochemistry↗

bioRxiv2020

Structural analysis of SARS-CoV-2 andprediction of the human interactome

Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2000 coronaviruses and computed >100000 human protein interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genomic regions display different degrees of conservation. SARS-CoV-2 domain encompassing nucleotides 22500 - 23000 is conserved both at the sequence and structural level. The regions upstream and downstream, however, vary significantly. This part codes for the Spike S protein that interacts with the human receptor angiotensin-converting enzyme 2 (ACE2). Thus, variability of Spike S may be connected to different levels of viral entry in human cells within the population. Our predictions indicate that the 5 end of SARS-CoV-2 is highly structured and interacts with several human proteins. The binding proteins are involved in viral RNA processing such as double-stranded RNA specific editases and ATP-dependent RNA-helicases and have strong propensity to form stress granules and phase-separated complexes. We propose that these proteins, also implicated in viral infections such as HIV, are selectively recruited by SARS-CoV-2 genome to alter transcriptional and post-transcriptional regulation of host cells and to promote viral replication.

bioinformatics↗

bioRxiv2020

In-Silico evidence for two receptors based strategy of SARS-CoV-2

We propose a novel numerical method able to determine efficiently and effectively the relationship of complementarity between portions of protein surfaces. This innovative and general procedure, based on the representation of the molecular iso-electron density surface in terms of 2D Zernike polynomials, allows the rapid and quantitative assessment of the geometrical shape complementarity between interacting proteins, that was unfeasible with previous methods. We first tested the method with a large dataset of known protein complexes obtaining an overall area under the ROC curve of 0.76 in the blind recognition of binding sites and then applied it to investigate the features of the interaction between the Spike protein of SARS-CoV-2 and human cellular receptors. Our results indicate that SARS-CoV-2 uses a dual strategy: its spike protein could also interact with sialic acid receptors of the cells in the upper airways, in addition to the known interaction with Angiotensin-converting enzyme 2.

biophysics↗

bioRxiv2019

Thalamic and extra-thalamic connections of the Globus Pallidus in the human brain: The ultradirect pathway

A dominant framework for understanding loss and recovery of consciousness, particularly in the context of severe brain injury, focuses on cortico-subcortical recurrent interactions, with a strong emphasis on excitatory thalamofugal projections. Recent work in healthy volunteers and patients, however, suggests a previously unappreciated role for the globus pallidus pars externa in maintaining a state of consciousness - a finding that is consistent with non-human animal work demonstrating the existence of direct (i.e., extrathalamic) pallido-cortical projections as well as their involvement in modulating electrocortical arousal and sleep. Leveraging on the high-quality Human Connectome Project dataset, we report for the first time in humans, in vivo evidence of (direct) pallido-cortical and pallido-thalamic projections, distinguishing between internal and external pallidal regions. Our data confirm, in humans, the existence of an \"ultradirect\" extra-thalamic pallido-cortical pathway, with the pars externa connecting preferentially, and extensively, to prefrontal cortex and the pars interna primarily connecting to sensorimotor cortical areas. Furthermore, we also report, for the first time in humans, the likely existence of a direct pathway uniting the globus pallidus pars externa and the medio-dorsal areas of thalamus often implicated in maintenance and recovery of consciousness. Consistent with the pallido-cortical connectivity results, the pars interna appeared to predominantly connect with the sensorimotor areas of thalamus. Collectively, these findings demonstrate the existence in humans of an extra-thalamic \"ultradirect\" pallido-cortical pathway and suggest a central role of the external segment of the globus pallidum in supporting consciousness.

neuroscience↗

bioRxiv2019

Neural and computational mechanisms of analogical reasoning

The ability to generate and process semantic relations is central to many aspects of human cognition. Theorists have long debated whether such relations are coded as atomistic links in a semantic network, or as distributed patterns over some core set of abstract relations. The form and content of the conceptual and neural representations of semantic relations remains to be empirically established. The present study combined computational modeling and neuroimaging to investigate the representation and comparison of abstract semantic relations in the brain. By using sequential presentation of verbal analogies, we decoupled the neural activity associated with encoding the representation of the first-order semantic relation between words in a pair from that associated with the second-order comparison of two relations. We tested alternative computational models of relational similarity in order to distinguish between rival accounts of how semantic relations are coded and compared in the brain. Analyses of neural similarity patterns supported the hypothesis that semantic relations are coded, in the parietal cortex, as distributed representations over a pool of abstract relations specified in a theory-based taxonomy. These representations, in turn, provide the immediate inputs to the process of analogical comparison, which draws on a broad frontoparietal network. This study sheds light not only on the form of relation representations but also on their specific content.\n\nSignificanceRelations provide basic building blocks for language and thought. For the past half century, cognitive scientists exploring human semantic memory have sought to identify the code for relations. In a neuroimaging paradigm, we tested alternative computational models of relation processing that predict patterns of neural similarity during distinct phases of analogical reasoning. The findings allowed us to draw inferences not only about the form of relation representations, but also about their specific content. The core of these distributed representations is based on a relatively small number of abstract relation types specified in a theory-based taxonomy. This study helps to resolve a longstanding debate concerning the nature of the conceptual and neural code for semantic relations in the mind and brain.

neuroscience↗

bioRxiv2019

The TRAPP complex mediates secretion arrest induced by stress granule assembly

The TRAnsport-Protein-Particle (TRAPP) complex controls multiple membrane trafficking steps and is thus strategically positioned to mediate cell adaptation to diverse environmental conditions, including acute stress. We have identified TRAPP as a key component of a branch of the integrated stress response that impinges on the early secretory pathway. TRAPP associates with and drives the recruitment of the COPII coat to stress granules (SGs) leading to vesiculation of the Golgi complex and an arrest of ER export. Interestingly, the relocation of TRAPP and COPII to SGs only occurs in actively proliferating cells and is CDK1/2-dependent. We show that CDK1/2 activity controls the COPII cycle at ER exit sites (ERES) and that its inhibition prevents TRAPP/COPII relocation to SGs by stabilizing them at the ERES. Importantly, TRAPP is not just a passive constituent of SGs but controls their maturation since SGs that assemble in TRAPP-depleted cells are smaller and are no longer able to recruit RACK1 and Raptor, rendering the cells more prone to undergo apoptosis upon stress exposure.

cell biology↗

bioRxiv2018

Dissociating Language and Thought in Human Reasoning

What is the relationship between language and complex thought? In the context of deductive reasoning there are two main views. Under the first, which we label here the language-centric view, language is central to the syntax-like combinatorial operations of complex reasoning. Under the second, which we label here the language-independent view, these operations are dissociable from the mechanisms of natural language. We applied continuous theta burst stimulation (cTBS), a form of noninvasive neuromodulation, to healthy adult participants to transiently inhibit a subregion of Brocas area (BA44) associated in prior work with parsing the syntactic relations of natural language. We similarly inhibited a subregion of dorsomedial frontal cortex (BA8) which has been associated with core features of logical reasoning. There was a significant interaction between task and stimulation site. Post hoc tests revealed that performance on a linguistic reasoning task, but not deductive reasoning task, was significantly impaired after inhibition of BA44, and performance on a deductive reasoning task, but not linguistic reasoning task, was decreased after inhibition of BA8 (however not significantly). Subsequent linear contrasts supported this pattern. These novel results suggest that deductive reasoning may be dissociable from linguistic processes in the adult human brain, consistent with the language-independent view.

neuroscience↗

bioRxiv2018

Unbiased dynamic characterization of RNA-protein interactions by OOPS

Current methods for the identification of RNA-protein interactions require a quantity and quality of sample that hinders their application, especially for dynamic biological systems or when sample material is limiting. Here, we present a new approach to enrich RNA-Binding Proteins (RBPs): Orthogonal Organic Phase Separation (OOPS), which is compatible with downstream proteomics and RNA sequencing. OOPS enables recovery of RBPs and free protein, or protein-bound RNA and free RNA, from a single sample in an unbiased manner. By applying OOPS to human cell lines, we extract the majority of known RBPs, and importantly identify additional novel RBPs, including those from previously under-represented cellular compartments. The high yield and unbiased nature of OOPS facilitates its application in both dynamic and inaccessible systems. Thus, we have identified changes in RNA-protein interactions in mammalian cells following nocodazole cell-cycle arrest, and defined the first bacterial RNA-interactome. Overall, OOPS provides an easy-to-use and flexible technique that opens new opportunities to characterize RNA-protein interactions and explore their dynamic behaviour.

cell biology↗

bioRxiv2018

Theory of Circadian Metabolism

Many organisms repartition their proteome in a circadian fashion in response to the daily nutrient changes in their environment. A striking example is provided by cyanobacteria, which perform photosynthesis during the day to fix carbon. These organisms not only face the challenge of rewiring their proteome every 12 hours, but also the necessity of storing the fixed carbon in the form of glycogen to fuel processes during the night. In this manuscript, we extend the framework developed by Hwa and coworkers (Scott et al., Science 330, 1099 (2010)) for quantifying the relatinship between growth and proteome composition to circadian metabolism. We then apply this framework to investigate the circadian metabolism of the cyanobacterium Cyanothece, which not only fixes carbon during the day, but also nitrogen during the night, storing it in the polymer cyanophycin. Our analysis reveals that the need to store carbon and nitrogen tends to generate an extreme growth strategy, in which the cells predominantly grow during the day, as observed experimentally. This strategy maximizes the growth rate over 24 hours, and can be quantitatively understood by the bacterial growth laws. Our analysis also shows that the slow relaxation of the proteome, arising from the slow growth rate, puts a severe constraint on implementing this optimal strategy. Yet, the capacity to estimate the time of the day, enabled by the circadian clock, makes it possible to anticipate the daily changes in the environment and mount a response ahead of time. This significantly enhances the growth rate by counteracting the detrimental effects of the slow proteome relaxation.

systems biology↗