Biology subjects

Lopez, C.

Publications and source records attributed to Lopez, C..

49 records · Page 3Linked to original sources

bioRxiv2021

The rapid developmental rise of somatic inhibition disengages hippocampal dynamics from self-motion

Early electrophysiological brain oscillations recorded in preterm babies and newborn rodents are initially mostly ignited by bottom-up sensorimotor activity and only later can detach from external inputs. This is a hallmark of most developing brain areas including the hippocampus, which in the adult brain, functions in integrating external inputs onto internal dynamics. Such developmental disengagement from external inputs is likely a fundamental step for the proper development of cognitive internal models. Despite its importance, the developmental timeline and circuit basis for this disengagement remain unknown. To address this issue, we have investigated the daily evolution of CA1 dynamics and underlying circuits during the first two postnatal weeks of mouse development using two-photon calcium imaging in non-anesthetized pups. We show that the first postnatal week ends with an abrupt shift in the representation of self-motion in CA1. Indeed, most CA1 pyramidal cells switch from activated to inhibited by self-generated movements at the end of the first postnatal week whereas the majority of GABAergic neurons remain positively modulated throughout this period. This rapid switch occurs within two days and follows the rapid anatomical and functional surge of local somatic GABAergic innervation. The observed change in dynamics is consistent with a two-population model undergoing a strengthening of inhibition. We propose that this abrupt developmental transition inaugurates the emergence of internal cognitive models.

neuroscience↗

bioRxiv2021

Specific protein-membrane interactions promote the export of metallo-β-lactamases via outer membrane vesicles

Outer membrane vesicles (OMVs) act as carriers of resistance determinants such as metallo-{beta}-lactamases. The metallo-{beta}-lactamase NDM-1 is present in OMVs produced by Gram-negative bacteria since it is a lipidated, membrane-anchored protein. The soluble domain of NDM-1 also forms electrostatic interactions with the membrane. Herein, we show that these interactions promote its export into OMVs produced by Escherichia coli. We report that favorable electrostatic protein-membrane interactions are also at work in the soluble enzyme IMP-1, while being absent in VIM-2. These interactions correlate with an enhanced secretion into OMVs of IMP-1 compared to VIM-2. Disruption of these interactions in NDM-1 and IMP-1 impairs export into vesicles, confirming their role in defining the protein cargo in OMVs. These results also indicate that export of metallo-{beta}-lactamases into vesicles in their active form is a common phenomenon that involves cargo selection based on molecular features.

molecular biology↗

bioRxiv2021

What makes our lungs look red?

What makes our lungs look red? This seems to be a naIve and trivial question. Indeed, all the textbooks tell us that what makes our body red is the presence of blood, or more precisely the red blood cells (RBC). Here we provide some experimental evidence as well arguments to prove that this belief is wrong, or only partially true. In fact, we identified an important population of red cells located outside of the blood vessels as highly compacted clusters, in the connection tissues of the lungs of several species of animals including rat and human being. These red cells possessed each a nucleus, expressing several biomarkers of different cell types such as PF4, vWF, SCF-1R, CD200R, TGF-b, etc... Interestingly, being morphologically heterogeneous, they react collectively to certain stimuli. For example, they aggregated on collagen fibers forming clusters of cells resembling that observed in vivo. The red cells may have some features of Hematopoietic Stem Cells, since they were capable of differentiating into other cell types such as alveolar macrophages. In nasal polyps, these cells formed vessel-like structures, confined within a CD31-positive tubes. Upon exposure to toxic chemicals, they formed dense networks, suggesting a possible role in coagulation. Furthermore, the number of these red cells was greatly increased in the lungs of diseased donors, especially in the lungs of CF patients. Instead of being secreted as what happens in normal red cells, vWF proteins were tethered on the cytoplasmic membrane of the red cells isolated from the lungs of CF donors, which may explain at least partially the fibrotic nature of the CF lungs. Taken together, we conclude that what makes the lungs look red is not the red blood cells, rather a distinct population of red cells, we call them Red Soma Cells (RSC). We believe that the discovery and characterization of this important population of cells will have profound theoretic as well as therapeutic implications.

cell biology↗

bioRxiv2021

CA1 pyramidal cell diversity is rooted in the time of neurogenesis.

Cellular diversity supports the computational capacity and flexibility of cortical circuits. Accordingly, principal neurons at the CA1 output node of the hippocampus are increasingly recognized as a heterogeneous population. Their genes, molecular content, intrinsic morpho-physiology, connectivity, and function seem to segregate along the main anatomical axes of the hippocampus. Since these axes reflect the temporal order of principal cell neurogenesis, we directly examined the relationship between birthdate and CA1 pyramidal neuron diversity, focusing on the ventral hippocampus. We used a genetic fate-mapping approach that allowed tagging three groups of agematched principal neurons: pioneer, early- and late-born. Using a combination of neuroanatomy, slice physiology, connectivity tracing and cFos staining, we show that birthdate is a strong predictor of CA1 principal cell diversity. We unravel a subpopulation of pioneer neurons recruited in familiar environments with remarkable positioning, morpho-physiological features, and connectivity. Therefore, despite the expected plasticity of hippocampal circuits, given their role in learning and memory, the diversity of their main components is significantly predetermined at the earliest steps of development.

neuroscience↗

bioRxiv2020

Species exclusion and coexistence in a noisy voter model with a competition-colonization tradeoff

We introduce an asymmetric noisy voter model to study the joint effect of immigration and a competition-dispersal tradeoff in the dynamics of two species competing for space on a one-dimensional lattice. Individuals of one species can invade a nearest-neighbor site in the lattice, while individuals of the other species are able to invade sites at any distance but are less competitive locally, i.e., they establish with a probability g[≤] 1. The model also accounts for immigration, modeled as an external noise that may spontaneously replace an individual at a lattice site by another individual of the other species. This combination of mechanisms gives rise to a rich variety of outcomes for species competition, including exclusion of either species, mono-stable coexistence of both species at different population proportions, and bi-stable coexistence with proportions of populations that depend on the initial condition. Remarkably, in the bi-stable phase, the system undergoes a discontinuous transition as the intensity of immigration overcomes a threshold, leading to an irreversible loop dynamics that may cause the loss of the species with shorter dispersal range.

ecology↗

bioRxiv2020

The H-NS regulator plays a role in the stress induced by carbapenemase expression in Acinetobacter baumannii

Disruption of the histone-like nucleoid structuring protein (H-NS) was shown to affect the ability for Gram-negative bacteria to regulate genes associated with virulence, persistence, stress response, quorum sensing, biosynthesis pathways and cell adhesion. Here, we used the expression of metallo-{beta}-lactamases (MBLs) known to elicit envelope stress by the accumulation of toxic species in the periplasm to interrogate the role of H-NS in Acinetobacter baumannii, together with other stressors. Using a multidrug-resistant A. baumannii, we observed that H-NS plays a role in alleviating the stress triggered by MBL toxic precursors and counteract the effect of DNA-damaging agents, supporting its role in stress response. ImportanceCarbapenem-resistant A. baumannii (CRAB) is recognized as one of the most threatening gram-negative bacilli. H-NS is known to play a role in controlling the transcription of a variety of different genes, including those associated with stress response, persistence and virulence. In the present work, we uncovered a link between the role of H-NS in the A. baumannii stress response and its relationship with the envelope stress response and resistance to DNA-damaging agents. Overall, we posit a new role of H-NS, showing that H-NS serves to endure envelope stress that could also be a mechanism that alleviates the stress induced by MBL expression in A. baumannii. This could be an evolutionary advantage to further resist the action of carbapenems.

microbiology↗

bioRxiv2019

Visualization of the HIV-1 Env Glycan Shield Across Scales

The dense array of N-linked glycans on the HIV-1 Envelope Glycoprotein (Env), known as the "glycan shield", is a key determinant of immunogenicity, yet intrinsic heterogeneity confounds typical structure-function analysis. Here we present an integrated approach of single-particle electron cryomicroscopy (cryo-EM), computational modeling, and site-specific mass-spectrometry (MS) to probe glycan shield structure and behavior at multiple levels. We found that dynamics lead to an extensive network of inter-glycan interactions that drive the formation of higher-order structure within the glycan shield. This structure defines diffuse boundaries between buried and exposed protein surface and creates a mapping of potentially immunogenic sites on Env. Analysis of Env expressed in different cell lines revealed how cryo-EM can detect subtle changes in glycan occupancy, composition, and dynamics that impact glycan shield structure and epitope accessibility. Importantly, this identified unforeseen changes in the glycan shield of Env obtained from expression in the same CHO cell line used for GMP production. Finally, by capturing the enzymatic deglycosylation of Env in a time-resolved manner we found that highly connected glycan clusters are resistant to digestion and help stabilize the pre-fusion trimer, suggesting the glycan shield may function beyond immune evasion. Significance StatementThe HIV-1 Env "glycan shield" masks the surface of the protein from immune recognition, yet intrinsic heterogeneity defies a typical structure-function description. Using a complementary approach of cryo-EM, computational modeling, and mass-spectrometry we show how heterogeneity and dynamics affect glycan shield structure across scales. Our combined approach facilitated the development of new cryo-EM data analysis methods and allowed for validation of models against experiment. Comparison of Env across a range of glycosylation states revealed how subtle differences in composition impact glycan shield structure and affect the accessibility of epitopes on the surface. Finally, time-resolved cryo-EM experiments uncovered how highly connected glycan clusters help stabilize the pre-fusion trimer, suggesting the glycan shield may function beyond immune evasion.

biophysics↗

bioRxiv2019

Universal Loop assembly (uLoop): open, efficient, and species-agnostic DNA fabrication

Standardised Type IIS DNA assembly methods are becoming essential for biological engineering and research. Although a common syntax has been proposed to enable higher interoperability between DNA libraries, Golden Gate (GG)-based assembly systems remain specific to target organisms. Furthermore, these GG assembly systems become laborious and unnecessarily complicated beyond the assembly of 4 transcriptional units. Here, we describe \"universal Loop\" (uLoop) assembly, a simple system based on Loop assembly that enables hierarchical fabrication of large DNA constructs (> 30 kb) for any organism of choice. uLoop comprises two sets of four plasmids that are iteratively used as odd and even levels to compile DNA elements in an exponential manner (4n-1). The elements required for transformation/maintenance in target organisms are also assembled as standardised parts, enabling customisation of host-specific plasmids. Thus, this species-agnostic method decouples efficiency of assembly from the stability of vectors in the target organism. As a proof-of-concept, we show the engineering of multi-gene expression vectors in diatoms, yeast, plants and bacteria. These resources will become available through the OpenMTA for unrestricted sharing and open-access.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC=\"FIGDIR/small/744854v2_ufig.gif\" ALT=\"Figure 1\">\nView larger version (31K):\norg.highwire.dtl.DTLVardef@c36f4forg.highwire.dtl.DTLVardef@c0b007org.highwire.dtl.DTLVardef@64c810org.highwire.dtl.DTLVardef@8a94b0_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2019

Drug target discovery via network modeling: a mathematical model of the E. coli folate network response to trimethoprim

The antibiotic trimethoprim targets the bacterial dihydrofolate reductase enzyme and subsequently affects the entire folate network. We present an expanded mathematical model of trimethoprims action on the Escherichia coli folate network that greatly improves upon Kwon et al. (2008). The improvement upon the Kwon Model lends greater insight into the effects of trimethoprim at higher resolution and accuracy. More importantly, the presented mathematical model enables drug target discovery in a way the earlier model could not. Using the improved mathematical model as a scaffold, we use parameter optimization to search for new drug targets that replicate the effect of trimethoprim. We present the model and model-scaffold strategy as an efficient route for drug target discovery.

systems biology↗

bioRxiv2019

Spatial eco-evolutionary feedbacks mediate coexistence inprey-predator systems

Eco-evolutionary frameworks can explain certain features of communities in which ecological and evolutionary processes occur over comparable timescales. In the particular case of prey-predator systems, a combination of empirical and theoretical studies have explored this possibility, showing that the evolution of prey traits, predator traits or the coevolution of both can contribute to the stability of the community, as well as to the emergence of various types of population cycles. However, these studies overlook that interactions are spatially constrained, a crucial ingredient known to foster species coexistence per se. Here, we investigate whether evolutionary dynamics interacts with the spatial structure of a prey-predator community in which both species show limited mobility and predators perceptual ranges are subject to natural selection. In these conditions, our results unveil an eco-evolutionary feedback between species spatial mixing and predators perceptual range: different levels of species mixing select for different perceptual ranges, which in turn reshape the spatial distribution of preys and their interaction with predators. This emergent pattern of interspecific interactions feeds back to the efficiency of the various perceptual ranges, thus selecting for new ones. Finally, since prey-predator mixing is the key factor that regulates the intensity of predation, we explore the community-level implications of such feedback and show that it controls both coexistence times and species extinction probabilities. Author summaryEvolutionary processes occurring on temporal scales that are comparable to those of ecological change can result in reciprocal interactions between ecology and evolution termed eco-evolutionary feedbacks. Such interplay is clear in prey-predator systems, in which predation alters the distribution of resources (preys). In turn, changes in the abundance and spatial distribution of preys may lead to the evolution of new predation strategies, which may change again the properties of the prey population. Here, we investigate the interplay between limited mobility, species mixing, and finite perception in a prey-predator system. We focus on the case in which predator perceptual ranges are subject to natural selection and examine, via coexistence times and species extinction probabilities, whether the resulting eco-evolutionary dynamics mediates the stability of the community. Our results confirm the existence of such eco-evolutionary feedback and reveal its potential impact on community-level processes.

ecology↗

bioRxiv2018

Signal sequences in the genome of Mononegavirales regulate the generation of copy-back defective viral genomes

Defective viral genomes of the copy-back type (cbDVGs) are the primary initiators of the antiviral immune response during infection with respiratory syncytial virus (RSV) both in vitro and in vivo. However, the mechanism governing cbDVG generation remains unknown, thereby limiting our ability to manipulate cbDVG content in order to modulate the host response to infection. Here we report a specific genomic signal that mediates the generation of RSV cbDVGs. Using a customized bioinformatics tool, we identified regions in the RSV genome frequently used to generate cbDVGs during infection. We then created a minigenome system to validate the function of one of these sequences and to determine if specific nucleotides were essential for cbDVG generation at that position. Further, we created a recombinant virus that selectively produced a specific cbDVG based on variations introduced in this sequence. The identified sequence was also found as a common site for cbDVG generation during natural RSV infections, and common cbDVGs generated at this sequence were found among samples from various infected patients. These data demonstrate that sequences encoded in the viral genome are critical determinants of the location of cbDVG generation and, therefore, this is not a stochastic process. Most importantly, these findings open the possibility of genetically manipulating cbDVG formation to modulate infection outcome. Author summaryCopy-back defective viral genomes (cbDVGs) regulate infection and pathogenesis of Mononegavirales. cbDVG are believed to arise from random errors that occur during virus replication and the predominant hypothesis is that the viral polymerase is the main driver of cbDVG generation. Here we describe a specific genomic sequence in the RSV genome that is necessary for the generation of a large proportion of the cbDVG population present during infection. We identified specific nucleotides that when modified altered cbDVG generation at this position, and we created a recombinant virus that selectively produced cbDVGs based on mutations in this sequence. These data demonstrate that the generation of RSV cbDVGs is regulated by specific viral sequences and that these sequences can be manipulated to alter the content and quality of cbDVG generated during infection.

microbiology↗

bioRxiv2017

ACEseq - allele specific copy number estimation from whole genome sequencing

ACEseq is a computational tool for allele-specific copy number estimation in tumor genomes based on whole genome sequencing. In contrast to other tools it features GC-bias correction, unique replication timing-bias correction and integration of structural variant (SV) breakpoints for improved genome segmentation. ACEseq clearly outperforms widely used state-of-the art methods, provides a fully automated estimation of tumor cell content and ploidy, and additionally computes homologous recombination deficiency scores.

bioinformatics↗

bioRxiv2017

Replication Defective Viral Genomes Exploit A Cellular Pro-Survival Mechanism To Establish Viral Persistence

Replication defective viral genomes (DVGs) generated during virus replication are the primary triggers of antiviral immunity in many RNA virus infections. However, DVGs can also facilitate viral persistence. Why and how these two opposing functions of DVGs are achieved remain unknown. Here we report that during Sendai and respiratory syncytial virus infections DVGs selectively protect a subpopulation of cells from death and promote the establishment of persistent infections. We find that during Sendai virus infection this phenotype results from DVGs stimulating a MAVS-mediated TNF response that drives apoptosis of highly infected cells while extending the survival of cells enriched in DVGs. The pro-survival effect of TNF depends on the activity of the TNFR2/TRAF1 pathway that is regulated by MAVS signaling. These results identify TNF as a pivotal factor in determining cell fate during a viral infection and delineate a MAVS/TNFR2-mediated mechanism that drives the persistence of otherwise acute viruses.

microbiology↗