Biology subjects

Alonso, C.

Publications and source records attributed to Alonso, C..

26 records · Page 2Linked to original sources

bioRxiv2020

Identification of NPC1 as a novel SARS-CoV-2 intracellular target

Niemann-Pick type C1 (NPC1) receptor is an endosomal membrane protein that regulates intracellular cholesterol trafficking, which is crucial in the Ebola virus (EBOV) cycle. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the cell by binding of the viral spike (S) protein to the ACE2 receptor. This requires S-protein processing either by the surface transmembrane serine protease TMPRSS2 for plasma membrane fusion or cathepsin L for endosomal entry. Additional host factors are required for viral fusion at endosomes. Here, we report a novel interaction of the SARS-CoV-2 nucleoprotein (N) with the cholesterol transporter NPC1. Moreover, small molecules interfering with NPC1 that inhibit EBOV entry, also inhibited human coronavirus. Our findings suggest an important role for NPC1 in SARS-CoV-2 infection, a common strategy shared with EBOV, and a potential therapeutic target to fight against COVID-19.

microbiology↗

bioRxiv2020

Lifetime genealogical divergence within plants leads to epigenetic mosaicism in the long lived shrub Lavandula latifolia (Lamiaceae)

O_LIEpigenetic mosaicism is a possible source of within-plant phenotypic heterogeneity, yet its frequency and developmental origin remain unexplored. This study examines whether the extant epigenetic heterogeneity within long-lived Lavandula latifolia (Lamiaceae) shrubs reflects recent epigenetic modifications experienced independently by different plant parts or, alternatively, it is the cumulative outcome of a steady lifetime process. C_LIO_LILeaf samples from different architectural modules were collected from three L. latifolia plants and characterized epigenetically by global DNA cytosine methylation and methylation state of methylation-sensitive amplified fragment length polymorphism markers (MS-AFLP). Epigenetic characteristics of modules were then assembled with information on the branching history of plants. Methods borrowed from phylogenetic research were used to assess genealogical signal of extant epigenetic variation and reconstruct within-plant genealogical trajectory of epigenetic traits. C_LIO_LIPlants were epigenetically heterogeneous, as shown by differences among modules in global DNA methylation and variation in the methylation states of 6-8% of MS-AFLP markers. All epigenetic features exhibited significant genealogical signal within plants. Events of epigenetic divergence occurred throughout the lifespan of individuals and were subsequently propagated by branch divisions. C_LIO_LIInternal epigenetic diversification of L. latifolia individuals took place steadily during their development, a process which eventually led to persistent epigenetic mosaicism. C_LI

plant biology↗

bioRxiv2020

A physical theory of larval Drosophila behaviour

All animal behaviour must ultimately be governed by physical laws. As a basis for understanding the physics of behaviour in a simple system, we here develop an effective theory for the motion of the larval form of the fruitfly Drosophila melanogaster, and compare it against a quantitative analysis of the real animals behaviour. We first define a set of fields which quantify stretching, bending, and twisting along the larvas antero- posterior axis, and then perform a search in the space of possible theories that could govern the long-wavelength physics of these fields, using a simplified approach inspired by the renormalisation group. Guided by symmetry considerations and stability requirements, we arrive at a unique, analytically tractable free-field theory with a minimum of free parameters. Unexpectedly, we are able to explain a wide-spectrum of features of Drosophila larval behaviour by applying equilibrium statistical mechanics: our theory closely predicts the animals postural modes (eigenmaggots), as well as distributions and trajectories in the postural mode space across several behaviours, including peristaltic crawling, rolling, self-righting and unbiased substrate exploration. We explain the low-dimensionality of postural dynamics via Boltzmann suppression of high frequency modes, and also propose and experimentally test, novel predictions on the relationships between different forms of body deformation and animal behaviour. We show that crawling and rolling are dominated by similar symmetry properties, leading to identical dynamics/statistics in mode space, while rolling and unbiased exploration have a common dominant timescale. Furthermore, we are able to demonstrate that self-righting behaviour occurs continuously throughout substrate exploration, owing to the decoupling of stretching, bending, and twisting at low energies. Together, our results demonstrate that relatively simple effective physics can be used to explain and predict a wide range of animal behaviours.

biophysics↗

bioRxiv2020

Effects of environmental variables on the distribution of juvenile cubomedusae Carybdea marsupialis in the coastal Western Mediterranean

Relationships between environmental factors and oscillations in jellyfish abundance, especially in the early life stages, could help to interpret past increases and also predict scenarios in a changing future. For the first time, we present cubozoan spatial and temporal distributions in the earliest stages and their relationships with different factors. Abundances of Carybdea marsupialis medusae showed high interannual variability from 2008 to 2014 along the Denia coast (SE Spain, W Mediterranean). During 2015, samples were collected from 11 beaches along 17 km of coastline, 8 times from January to November in order to determine the effects of environmental factors on the distribution of juvenile C. marsupialis. Juveniles ([≤] 15 mm diagonal bell width) were present from May to July, with more sampled near shore (0 - 15 m). Most of them occurred in June when their numbers were unequal among beaches (average 0.05 ind m-3, maximum 6.71 ind m-3). We tested distributions of juveniles over time and space versus temperature, salinity, nutrients (N, P and Si), chlorophyll-a (Chl-a), and zooplankton abundance. Temperature and cladocerans (zooplankton group) were significantly positively correlated with juvenile distribution, whereas Chl-a concentration was weakly negative. By contrast, in 2014, high productivity areas (Chl-a and zooplankton) overlapped the maximum adult abundance (5.2 ind m-3). The distribution of juveniles during 2015 did not spatially coincide with the areas where ripe adults were located the previous year, suggesting that juveniles drift with the currents upon release from the cubopolyps. Our results yield important insights into the complexity of cubozoan distributions.

ecology↗

bioRxiv2019

The effect of alien species on plant-pollinator network structure across a gradient of plant species invasion

The interactions between pairs of native and alien plants via shared use of pollinators have been widely studied. Studies of invasive species effects at the community level on the other hand are still scarce. Few community level studies, however, have considered how differences in the intensity of invasion, and degree of floral trait similarity between native and invasive species, can mediated effects on native plant-pollinator communities. Here, we evaluated the effect of alien species on overall plant-pollinator network structure, and species-level network parameters, across nine coastal communities distributed along 205 km at Yucatan, Mexico that vary in alien species richness and flower abundance. We further assessed the effect of alien plant species on plant-pollinator network structure and robustness via computational simulation of native and invasive plant extinction scenarios. We did not find significant differences between native and alien species in functional floral phenotypes, the visitation rate and species composition of the pollinator community. Variation in the proportion of alien plant species and flower abundance across sites did not affect plant-pollinator networks structure. Species-level network parameters (i.e., normalized degree and nestedness contribution) did not differ between native and alien species. Furthermore, our simulation analyses revealed that alien species are functionally equivalent to native species and contribute equally to network structure and robustness. Overall, our results suggest that alien species are well integrated into native coastal plant-pollinator networks which may be facilitated by high levels of floral trait similarity and pollinator use overlap. As a result, alien species may play a similar role than that of natives in the structure and stability of native plant and pollinator communities in the studied coastal sand dune ecosystem.

ecology↗

bioRxiv2018

Familial hypercholesterolemia: a single-nucleotide variant (SNV) in mosaic at the Low density lipoprotein receptor (LDLR)

IntroductionFamilial hypercholesterolemia (FH) is most frequently caused by genetic variants in the LDLR gene. Most of LDLR pathogenic variants are missense, followed by splicing and deletion/insertions variants. Mosaicism is a genetic condition in which an individual shows more than one clone of cells with different genotypes.\n\nObjectiveMolecular characterization of a patient with hypercholesterolemia.\n\nMethodsGenetic analysis of DNA from peripheral blood and saliva was performed by NGS, sanger sequencing and pyrosequencing technologies.\n\nResultsNGS analysis detected the pathogenic variant LDLR:c.1951G>T:p.(Asp651Tyr) in 9%-12% of reads. The presence of the variant was confirmed by pyrosequencing analysis.\n\nConclusionHerein, we report the first case of a mosaic single nucleotide variant affecting the LDLR gene in a patient with familial hypercholesterolemia. As has been described for other pathologies, mosaicism could be underestimated in FH and its detection will improve with the introduction of NGS technologies in the diagnostic routine.

genetics↗

bioRxiv2017

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward

Growing evidence makes a strong case that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology from dissecting developmental processes to understanding aspects of human health and disease. In ecology, recent studies have merged ecological experimental design with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress response, adaptation to habitat, or species range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, many studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which allow for a more mechanistic understanding but have limited ecological realism. To understand the true significance of epigenetics for plant ecology and evolution, we must combine both approaches transferring knowledge and methods from model-species research to genomes of evolutionarily divergent species, and examining responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration between molecular epigeneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.

ecology↗

bioRxiv2017

Case-control study highlights a different gut microbiome in cirrhotic patients with and without hepatocellular carcinoma

BackgroundNo specific microbiome in patients with hepatocellular carcinoma (HCC) has been reported to date.\n\nAimTo compare the gut microbiome found in cirrhotic patients with and without HCC.\n\nMethodsFrom 407 patients with Child Pugh A/B cirrhosis prospectively followed, 25 with HCC (cases) were matched with 25 without HCC (wo-HCC) in a 1:1 ratio according to age, gender, etiology, Child Pugh and severity of portal hypertension. In addition results were also compared with 25 healthy subjects. Faecal stool samples were collected noninvasively, aliquoted for DNA extraction and sequenced for the V3-V4 region of the microbial 16S rRNA (Illumina MiSeq Platform).\n\nResultsThere were no significant clinical differences among cases and controls. We found a differential abundance in family members of Firmicutes with a 3-fold increased of Erysipelotrichaceae and a 5-fold decrease in family Leuconostocaceae in HCC when compared to wo-HCC controls. Genus Fusobacterium was found 5-fold decreased in HCC versus wo-HCC. The ratio bacteriodes/prevotella was increased in HCC due to the significant decrease in the genus prevotella. Genus Odoribacter and Butyricimonas were more differentialy abundant in HCC. This pattern has been previously associated with an inflammatory milieu with a putative increased activation of NOD-like receptor signalling pathways. A Random Forest model trained with differential abundant taxa correctly classifyed HCC individuals with an error of 22%.\n\nConclusionsA pattern of microbiome linked to inflammation was observed in cirrhotic patients with HCC. These findings open the discussion whether or not microbiota has a physiopathologic role in HCC development in cirrhosis.

cancer biology↗