Biology subjects

Perez, S.

Publications and source records attributed to Perez, S..

32 records · Page 2Linked to original sources

bioRxiv2023

Performance of amplicon and capture based next-generation sequencing approaches for the epidemiological surveillance of Omicron SARS-CoV-2 and other variants of concern.

To control the SARS-CoV-2 pandemic, healthcare systems have focused on ramping up their capacity for epidemiological surveillance through viral whole genome sequencing. In this paper, we tested the performance of two protocols of SARS-CoV-2 nucleic acid enrichment, an amplicon enrichment using different versions of the ARTIC primer panel and a hybrid-capture method using KAPA RNA Hypercap. We focused on the challenge of the Omicron variant sequencing, the advantages of automated library preparation and the influence of the bioinformatic analysis in the final consensus sequence. All 94 samples were sequenced using Illumina iSeq 100 and analysed with two bioinformatic pipelines: a custom-made pipeline and an Illumina-owned pipeline. We were unsuccessful in sequencing six samples using the capture enrichment due to low reads. On the other hand, amplicon dropout and mispriming caused the loss of mutation G21987A and the erroneous addition of mutation T15521A respectively using amplicon enrichment. Overall, we found high sequence agreement regardless of method of enrichment, bioinformatic pipeline or the use of automation for library preparation in eight different SARS-CoV-2 variants. Automation and the use of a simple app for bioinformatic analysis can simplify the genotyping process, making it available for more diagnostic facilities and increasing global vigilance.

microbiology↗

bioRxiv2023

Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota

Despite significant advances in reconstructing genome-scale metabolic networks, the understanding of cellular metabolism remains incomplete for many organisms. A promising approach for elucidating cellular metabolism is analysing the full scope of enzyme promiscuity, which exploits the capacity of enzymes to bind to non-annotated substrates and generate novel reactions. To guide time-consuming costly experimentation, different computational methods have been proposed for exploring enzyme promiscuity. One relevant algorithm is PROXIMAL, which strongly relies on KEGG to define generic reaction rules and link specific molecular substructures with associated chemical transformations. Here, we present a completely new pipeline, PROXIMAL2, which overcomes the dependency on KEGG data. In addition, PROXIMAL2 introduces two relevant improvements with respect to the former version: i) correct treatment of multi-step reactions and ii) tracking of electric charges in the transformations. We compare PROXIMAL and PROXIMAL2 in recovering annotated products from substrates in KEGG reactions, finding a highly significant improvement in the level of accuracy. We then applied PROXIMAL2 to predict degradation reactions of phenolic compounds in the human gut microbiota. The results were compared to RetroPath RL, a different and relevant enzyme promiscuity method. We found a significant overlap between these two methods but also complementary results, which open new research directions into this relevant question in nutrition.

biochemistry↗

bioRxiv2023

FBP1 is a nonenzymatic safety valve that curtails AKT activation to prevent insulin hyperresponsiveness

Insulin inhibits gluconeogenesis and stimulates glucose conversion to glycogen and lipids. How these activities are coordinated to prevent hypoglycemia and hepatosteatosis is not clear. Fructose-1,6 bisphosphatase (FBP1) is rate controlling for gluconeogenesis. However, inborn human FBP1 deficiency does not cause hypoglycemia unless accompanied by fasting or starvation, which also trigger paradoxical hepatomegaly, hepatosteatosis, and hyperlipidemia in affected individuals. Hepatocyte FBP1-ablated mice exhibit identical fasting-conditional pathologies along with AKT hyperactivation, whose inhibition reversed hepatomegaly, hepatosteatosis and hyperlipidemia but not hypoglycemia. Surprisingly, fasting-mediated AKT hyperactivation is insulin-dependent. FBP1 prevents insulin hyperresponsiveness, independently of its catalytic activity, by interacting with AKT, PP2A-C and Aldolase-B (ALDOB) to specifically accelerate AKT dephosphorylation. Enhanced by fasting and weakened by elevated insulin, FBP1:AKT:PP2A-C:ALDOB complex formation, which is disrupted by human FBP1 deficiency mutations or a C-terminal FBP1 truncation, prevents insulin-triggered liver pathologies and maintains lipid and glucose homeostasis. Conversely, a complex disrupting peptide reverses diet-induced insulin resistance.

molecular biology↗

bioRxiv2022

Lactate supply overtakes glucose when neural computational and cognitive loads scale up

The neural computational power is determined by neuroenergetics, but how and which energy substrates are allocated to various forms of memory engram is unclear. To solve this question, we asked whether neuronal fueling by glucose or lactate scales differently upon increasing neural computation and cognitive loads. Here, using electrophysiology, two-photon imaging, cognitive tasks and mathematical modeling, we show that both glucose and lactate are involved in engram formation, with lactate supporting long-term synaptic plasticity evoked by high stimulation load activity patterns and high attentional load in cognitive tasks, and glucose being sufficient for less demanding neural computation and learning tasks. Overall, these results demonstrate that glucose and lactate metabolisms are differentially engaged in neuronal fueling depending on the complexity of the activity-dependent plasticity and behavior. One sentence summaryNeuronal fueling by lactate versus glucose scales differently according to engram level and memory load.

neuroscience↗

bioRxiv2022

MECP2 expression coincides with age-dependent tactile sensory deficits in a female mouse model for Rett syndrome

Rett syndrome is characterized by an early period of typical development and then, regression of learned motor and speech skills in girls. Loss of MECP2 protein is thought to cause Rett syndrome phenotypes. The specific underlying mechanisms from typical developmental trajectory to regression features throughout life are unclear. Lack of established timelines to study the molecular, cellular, and behavioral features of regression in female mouse models is a major contributing factor. Due to random X-chromosome inactivation, female patients with Rett syndrome and female mouse models for Rett syndrome (Mecp2Heterozygous, Het) express a functional copy of wild-type MECP2 protein in approximately half of all cells. As MECP2 expression is regulated during early postnatal development and experience, we characterized the expression of wild-type MECP2 in the primary somatosensory cortex of female Het mice. Here, we report increased MECP2 levels in non-parvalbumin-positive neurons of 6-week-old adolescent Het relative to age-matched wild-type controls, while also displaying similar levels of perineuronal net expression, mild tactile sensory perception deficits, and efficient pup retrieval behavior. In contrast, 12-week-old adult Het express MECP2 at levels similar to age-matched wild-type mice, show increased perineuronal net expression in the cortex, and display significant tactile sensory perception deficits. Thus, we have identified a set of behavioral metrics and the cellular substrates to study regression during a specific time in the female Het mouse model, which coincide with changes in wild-type MECP2 expression. We speculate that the precocious increase in MECP2 expression within specific cell types of adolescent Het may provide compensatory benefits at the behavioral level, while the inability to further increase MECP2 levels leads to regressive behavioral phenotypes over time.

neuroscience↗

bioRxiv2021

Cerebellar stimulations prevent Levodopa-induced dyskinesia in mice and normalize brain activity

Chronic Levodopa therapy, the gold-standard treatment of Parkinsons Disease (PD), leads to the emergence of involuntary movements, called levodopa-induced dyskinesia (LID). Cerebellar stimulations have been shown to decrease LID severity in PD patients. Here, in order to determine how cerebellar stimulations induce LID alleviation, we performed daily short trains of optogenetic stimulations of Purkinje cells (PC) in freely moving mice. We demonstrated that these stimulations are sufficient to suppress LID or even prevent their development. This symptomatic relief is accompanied by the normalization of aberrant neuronal discharge in the cerebellar nuclei, the motor cortex and the parafascicular thalamus. Inhibition of the cerebello-parafascicular pathway counteracted the beneficial effect of cerebellar stimulations. Moreover, cerebellar stimulations reversed plasticity in D1 striatal neurons and normalized the overexpression of FosB, a transcription factor causally linked to LID. These findings demonstrate LID alleviation and prevention by daily PC stimulations, which restore the function of a wide brain motor network, and may be valuable for LID treatment.

neuroscience↗

bioRxiv2021

Additive manufactured scaffolds for bone tissue engineering: physical characterization of thermoplastic composites with functional fillers

Thermoplastic polymer - filler composites are excellent materials for bone tissue engineering (TE) scaffolds, combining the functionality of fillers with suitable load bearing ability, biodegradability, and additive manufacturing (AM) compatibility of the polymer. Two key determinants of their utility are their rheological behavior in the molten state, determining AM processability, and their mechanical load-bearing properties. We report here the characterization of both these physical properties for four bone TE relevant composite formulations with poly(ethylene oxide terephthalate) / poly(butylene terephthalate (PEOT/PBT) as a base polymer, which is often used to fabricate TE scaffolds. The fillers used were reduced graphene oxide (rGO), hydroxyapatite (HA), gentamycin intercalated in zirconium phosphate (ZrP-GTM) and ciprofloxacin intercalated in MgAl layered double hydroxide (MgAl-CFX). The rheological assessment showed that generally the viscous behavior dominated the elastic behavior (G > G) for the studied composites, at empirically determined extrusion temperatures. Coupled rheological-thermal characterization of ZrP-GTM and HA composites showed that the fillers increased the solidification temperatures of the polymer melts during cooling. Both these findings have implications for the required extrusion temperatures and bonding between layers. Mechanical tests showed that the fillers generally made the polymer stiffer but more brittle in proportion to the filler fractions. Furthermore, the elastic moduli of scaffolds did not directly correlate with the corresponding bulk material properties, implying composite-specific AM processing effects on the mechanical properties. Lastly, we show computational models to predict multi-material scaffold elastic moduli using measured single material scaffold and bulk moduli. The reported characterizations are essential for assessing the AM processability and ultimately the suitability of the manufactured scaffolds for the envisioned bone regeneration application.

bioengineering↗

bioRxiv2021

Surveillance of Shiga toxin-producing Escherichia coli associated bloody diarrhea in Argentina

In Argentina, the hemolytic uremic syndrome associated with Shiga toxin-producing Escherichia coli (STEC-HUS) infection is endemic, and reliable data about prevalence and risk factors are available since 2000. However, information about STEC-associated bloody diarrhea (BD) cases is limited. A prospective study was carried out in seven tertiary-hospitals and 18 Referral Units from different regions, aiming to determine (i) STEC-positive BD cases frequency in 714 children aged 1 to 9 years old; and (ii) rate of progression to HUS. The number and regional distribution of STEC-HUS cases assisted in the same hospitals and period was also assessed. A total of 29 (4.1%) STEC-positive BD cases were confirmed by Shiga Toxin Quik Chek (STQC) and/or mPCR. The highest frequencies were found in the Southern region (Neuquen, 8.7%; Bahia Blanca, 7.9%), in children between 12 and 23 month of age (8.8%), during summertime. Four (13.8%) cases progressed to HUS, three to five days after BD onset. Twenty-seven STEC-HUS children mainly under 5 years old (77.8%) were enrolled, 51.9% were female; 44% were Stx-positive by STQC and all by mPCR. The most common serotypes were O157:H7 and O145:H28 and prevalent genotypes were stx2a-only or associated, both among BD and HUS cases. Considering the endemic behavior of HUS and its impact on public health, it is important to have updated information about the epidemiology of the diarrheal disease for early recognition of infected patients and initiation of supportive treatment. Finally, it also gives the opportunity to respond to outbreak situations effectively and in timely manner.

microbiology↗

bioRxiv2020

Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation

Host-associated microbiomes can play important roles in the ecology and evolution of their insect hosts, but bacterial diversity in many insect groups remains poorly understood. Here we examine the relationship between host environment, host traits, and microbial diversity in three species in the ground beetle family (Coleoptera: Carabidae), a group of roughly 40,000 species that synthesize a wide diversity of defensive compounds. This study found that the ground beetle microbiome is consistent across different host food sources. We used 16S amplicon sequencing to profile three species that are phylogenetically distantly related, trophically distinct, and whose defensive chemical secretions differ: Anisodactylus similis LeConte, 1851, Pterostichus serripes (LeConte, 1875), and Brachinus elongatulus Chaudoir, 1876. Wild-caught beetles were compared to individuals maintained in the lab for two weeks on carnivorous, herbivorous, or starvation diets. Soil environment but not diet had a significant effect on bacterial diversity and composition. The three carabid species have patterns of microbial diversity similar to those previously found in other insect hosts. Metagenomic samples from two highly active tissue types -- guts, and pygidial gland secretory cells (which produce defensive compounds) -- were processed and sequenced separately from those of the remaining body. The observed similarity of the pygidial gland secretory cell microbiome across hosts suggests the possibility that it may be a conserved community, possibly due to functional interactions related to defensive chemistry. These results provide a baseline for future studies of the role of microbes in the diversification of defensive chemical biosynthesis in carabids.

ecology↗

bioRxiv2020

Haloargentinum marplatensis gen. nov., sp. nov., a novel extremely halophilic bacterium isolated from salted-ripened anchovy (Engraulis anchoita)

A facultative aerobic, Gram-negative, motile, non-endospore forming and extremely halophilic bacterium, strain 11aii{intcal}, isolated from salted-ripened anchovy, was examined using a polyphasic approach to characterize and clarify its phylogenetic and taxonomic position. Sequences of the 16S rRNA gene revealed close relationships to species of the genera Lentibacillus and Virgibacillus (94.2% similarity). The organism grew optimally in the presence of 20-35 % NaCl. The major fatty acids of strain 11aii{intcal} were C16:0 (42.1%) and anteiso-C15:0 (31.2%) and also presented iso-C16:0 (11.0%), anteiso-C17:0 (10.4%) and C18:0 (5.2%). Based on data presented here, strain 11aii{intcal} is considered to represent a novel genus and species, for which the name Haloargentinum marplatensis gen. nov. sp. nov. is proposed with the strain 11aii{intcal} as type strain.

microbiology↗

bioRxiv2020

A liquid biopsy platform for detecting gene-gene fusions as glioma diagnostic biomarkers and drug targets

Gliomas account for about 80% of all malignant brain tumours. Diagnosis is achieved by radiographic imaging followed by tumour resection, to determine tumour cell type, grade and molecular characteristics. Glioblastoma multiforme (GBM) is the most common type of glioma, and is uniformly fatal. The median survival of treated GBM patients is 12-15 months. Standard modalities of therapy are unselective and include surgery, radiation therapy and chemotherapy, while precision medicine has yet to demonstrate improvements in disease outcome. We therefore selected GBM as a model to develop a precision medicine methodology for monitoring patients using blood plasma circulating cell-free DNA (cfDNA). Currently, tumour heterogeneity, clonal diversity and mutation acquisition are the major impedances for tailoring personalized therapy in gliomas in general, and particularly in GBM. Thus, a liquid biopsy diagnostics platform based on cfDNA sequencing may improve treatment outcome for GBM patients, by guiding therapy selection. In this study, we processed from 27 patients with glioma, 27 plasma samples for cfDNA isolation and 5 tissue biopsy samples for tumour DNA isolation. From a control group of 14 healthy individuals, 14 plasma samples were processed for cfDNA isolation. In glioma patients, cfDNA concentration was elevated compared to controls. Point mutations found in glioma tissue biopsies were also found in the cfDNA samples (95% identity). Finally, we identified novel chimeric genes (gene-gene fusions) in both tumour and cfDNA samples. These fusions are predicted to alter protein interaction networks, by removing tumour suppressors and adding oncoproteins. Indeed, several of these fusions are potential drug targets, particularly, NTRK or ROS1 fusions, specifically for crizotinib analogues (like entrectinib and larotrectinib) with enhanced penetration of the central nervous system. Taken together, our results demonstrate that novel druggable targets in gliomas can be identified by liquid biopsy using cfDNA in patient plasma. These results open new perspectives and abilities of precision medicine in GBM.

cancer biology↗

bioRxiv2020

The need to harmonize insecticide resistance testing: methodology, intensity concentrations and molecular mechanisms evaluated in Aedes aegypti populations in Central America and Hispaniola

BackgroundThe Zika AIRS Project, a USAID-funded initiative worked across the Latin America and Caribbean regions from 2016 to 2019, as an emergency to contain the spread of the Zika virus. All entomological records in the target countries showed wide distribution and high abundance of Aedes aegypti populations, however the susceptibility profiles of these insects to insecticides commonly employed by vector control campaigns were in most cases incomplete or inexistent. In close collaboration with the Ministries of Health of individual countries, Zika-AIRS teams conducted insecticide susceptibility testing of an array of insecticides in A. aegypti populations of each country. Procedures applied met the standard international protocols instructed by the World Health Organization and Centers for Disease Control and Prevention. Methodology and main findingsThe insecticides tested were selected under categories such as pyrethroids, organophosphates and carbamate. Results showed A. aegypti populations displaying high and widely distributed resistance to all pyrethroids across countries, tolerance to organophosphates and full susceptibility to a carbamate. Key inconsistencies between testing methods are presented and discussed. Additionally, four kdr mutations were analyzed to detect molecular mechanisms of insecticide resistance. The screening for kdr mutations suggested the widespread nature of V1016I mutation, linked to pyrethroid resistance in A. aegypti populations distributed and sampled in the above mentioned regions. Conclusions and perspectivesThis multi-country study contributes with updated information to the public health decision-makers across Central America and the Caribbean. This study provided training and established technical networks for more effective and sustainable insecticide surveillance programs. Most but not all records of insecticide resistance in A. aegypti were consistent between methodologies, thus inconsistent issues are discussed here to call for further improvement in procedures and convey more practical guidelines for surveillance teams in countries where Aedes-borne diseases are endemic. Author summaryAt the forefront of the fight against arboviruses transmission is the insecticide-based vector control. All countries in the Latin American and Caribbean region invest valuable resources from their limited budget to acquire and implement insecticide-based tools, with non-existent or weak insecticide resistance monitoring programs. Hence, the USAID-funded Zika AIRS Project (ZAP) collaborated with the Ministries of Health of multiple countries to update the profile of susceptibility to insecticides in Aedes aegypti populations. We found widespread resistance to pyrethroid and organophosphate insecticides, which account to almost 100% of the products available to control adult mosquitoes. As we used both of World Health Organization and Centers for Disease Control and Prevention standard methods, we found many similarities and some inconsistencies in the susceptibility profiles obtained for the very same vector populations. Additionally, we obtained insight on potential molecular mechanisms of resistance across the countries, finding the kdr mutation V1016I possibly involved in loss of susceptibility. This study is the biggest cross-country update of insecticide resistance for Aedes aegypti in years, and it should be used as evidence for improving the selection of insecticides in these countries and a call for further support to maintain insecticide resistance monitoring programs.

ecology↗

bioRxiv2019

BDNF controls bidirectional endocannabinoid-plasticity at corticostriatal synapses

The dorsal striatum exhibits bidirectional corticostriatal synaptic plasticity, NMDAR- and endocannabinoids-(eCB)-mediated, necessary for the encoding of procedural learning. Therefore, characterizing factors controlling corticostriatal plasticity is of crucial importance. Brain-derived neurotrophic factor (BDNF) and its receptor, the tropomyosine receptor kinase-B (TrkB), shape striatal functions and their dysfunction deeply affect basal ganglia. BDNF/TrkB signaling controls NMDAR-plasticity in various brain structures including striatum. However, despite cross-talks between BDNF and eCBs, the role of BDNF in eCB-plasticity remains unknown. Here, we show that BDNF/TrkB signaling promotes eCB-plasticity (LTD and LTP) induced by rate-based (low-frequency stimulation) or spike-timing-based (spike-timing-dependent plasticity, STDP) paradigm in striatum. We show that TrkB activation is required for the expression and the scaling of both eCB-LTD and eCB-LTP. Using two-photon imaging of the dendritic spines combined with patch-clamp recordings, we show that TrkB activation induces an intracellular calcium boost, thus increasing eCB synthesis and release. We provide a mathematical model for the dynamics of the signaling pathways involved in corticostriatal plasticity. Finally, we show that TrkB activation allows an enlargement of the domain of expression of eCB-STDP. Our results reveal a novel role for BDNF/TrkB signaling in governing eCB-plasticity expression in striatum, and thus the engram of procedural learning.

neuroscience↗

bioRxiv2017

Spatial resource heterogeneity increases diversity and evolutionary potential

Spatial heterogeneity is believed to be an evolutionary driver of biodiversity. Variability in the distribution of resource patches can allow an environment to support a wider variety of phenotypes for selection to act upon at the ecosystem level, which may lead to more species. However, the generality of this principle has not been thoroughly tested, as the relevant adaptive dynamics occur on evolutionary timescales. We overcame this challenge by performing experiments on populations of digital organisms in the Avida Digital Evolution Platform, in which we investigated the impact of spatial resource heterogeneity on phenotypic diversity. Since an important benefit of diversity may be increased evolutionary potential, we also tracked the probability of a complex trait evolving in the context of various levels of spatial heterogeneity. We found that spatial entropy and phenotypic diversity have a strong positive correlation and this relationship is consistent across various spatial configurations. Diversity also increases evolutionary potential, but has a much smaller impact than other components of environmental composition. The most important of these components was the mean number of resources present in locations across the environment, likely owing to the importance of building blocks for the evolution of complex features. These results suggest that a general relationship exists between spatial heterogeneity and diversity, beyond the specific ecosystems and timescales in which it has previously been studied. By examining this relationship in the context of phenotypic evolution, we advance a mechanistic understanding of the resulting dynamics. Moreover, our results suggest that the likelihood of evolving various traits can be impacted by the spatial configuration of patches in which these traits are advantageous. These findings have implications for both evolutionary biology and evolutionary computation, as generating and maintaining diversity is critical to all forms of evolution.

ecology↗