Miracle-dz/UniFAR-FTUs huggingface dataset:
Circadian protein regulation in the green lineage I. A phospho-dawn of protein modification anticipates light onset in the picoeukaryote O. tauri

Diel regulation of protein levels and protein modification had been less studied than transcript rhythms. Here, we compare transcriptome data under light-dark cycles to partial proteome and phosphoproteome data, assayed using shotgun mass-spectrometry, from the alga Ostreococcus tauri, the smallest free-living eukaryote. 10% of quantified proteins but two-thirds of phosphoproteins were rhythmic. Mathematical modelling showed that light-stimulated protein synthesis can account for the observed clustering of protein peaks in the daytime. Prompted by night-peaking and apparently dark-stable proteins, we also tested cultures under prolonged darkness, where the proteome changed less than under the diel cycle. The dark-stable, prasinophyte-specific proteins were also reported to accumulate when O. tauri formed lipid droplets. In the phosphoproteome, 39% of rhythmic phospho-sites reached peak levels just before dawn. This anticipatory phosphorylation suggests that a clock-regulated phospho-dawn prepares green cells for daytime functions. Acid-directed and proline-directed protein phosphorylation sites were regulated in antiphase, implicating the clock-related, casein kinases 1 and 2 in phase-specific regulation, alternating with the CMGC protein kinase family. Understanding the dynamic phosphoprotein network should be facilitated by the minimal kinome and proteome of O. tauri. The data are available from ProteomeXchange, with identifiers PXD001734, PXD001735 and PXD002909. This submission updates a previous version, posted on bioRxiv on 4th April 2018, as https://www.biorxiv. org/content/10.1101/287862v1 Highlight The phosphorylation of most protein sites was rhythmic under light-dark cycles, and suggested circadian control by particular kinases. Day-peaking, rhythmic proteins likely reflect light-stimulated protein synthesis in this microalga.
Mitogenomic investigation reveals a cryptic lineage of Crocodylus in Cuba

The American crocodile, Crocodylus acutus (Cuvier, 1807), is the most widely distributed crocodylian in the Americas, and coexists with the endemic and critically endangered Cuban crocodile, Crocodylus rhombifer Cuvier, 1807. Although these species are morphologically distinguishable, previous studies have shown that they are more genetically related to each other than either of them are to continental C. acutus. Here, we characterize the mitochondrial genome of Cuban C. acutus and analyze the resulting data relative to previously published whole mitochondrial genomes to reconstruct patterns of variation and phylogenetic placement within Crocodylus. We sequenced 13,776 basepairs, representing 82% of the entire genome including five (COI, COII, ATP8, ND3, ND4L) of the 13 protein-coding genes and 16 of the 22 tRNAs. Independent gene analysis of nucleotide diversity and genetic distance of Tamura-Nei demonstrated that the 16S rRNA, 12S rRNA, and COI genes are the most conserved in Crocodylus, while ND6 was the most variable (approximately 9%). Phylogenetic analysis confirmed that Cuban C. acutus forms a well-supported sister relationship with C. rhombifer, in contrast to continental C. acutus that clusters with Crocodylus intermedius Graves, 1819. The results are consistent with the hypothesis that Antillean C. acutus represents a cryptic lineage with genetic divergence at the species level. The ability to fully evaluate the taxonomic status of the Caribbean lineage of C. acutus still requires more comprehensive population samplings across the range as well as nuclear DNA sequence data. Of more immediate consequence, our results provide important information to be integrated into current Crocodylus conservation strategies in Cuba.
The physiology of alien chloroplasts: light adaptation mechanisms in cytoplasmic hybrids of the Solanaceae family.

The investigation presented here is of a new plant model for photosynthesis research. The plant’s novelty is a hybrid cytoplasm which was engineered to contain the nuclear genome of Nicotiana tabacum (tobacco) and the chloroplast genome of Hyoscyamus niger (henbane). For photosynthesis research the implications of cytoplasmic hybridisation centre on the nuclear and chloroplast encoded pigmentprotein complexes of the photosynthetic machinery in the thylakoid membrane of the chloroplast. We investigate how the energy input from nuclear-encoded light harvesting complexes to the chloroplast-encoded core complexes is regulated in the cybrid plants, when light limits or exceeds photochemical capacity. When light limited, the phenomenon of state transitions (ST) serves to redress the imbalance of light input at PSI and PSII. In excess light, non-photochemical quenching (NPQ) mechanisms are activated in order to safely dissipate potentially harmful energy that has been absorbed by the system. Our investigation at first indicated that the cybrid plants had a greater capacity for NPQ compared to wildtype N. tabacum and H. niger. LHCII aggregation, xanthopyll cycle activity and PsbS were investigated for a possible reasons for the increase. However no difference or contradictory evidence was found. NPQ measurements were repeated and showed large variability and no significant difference in NPQ capacity compared to the wildtype parent species. The reason for the variability in the cybrid results could not be resolved but is suggested to be due to heightened environmental sensitivity. STs were found to be consistently inhibited in cybrids. Investigation of cybrid LHC isoelectric points and molecular weight revealed novelties. LHCs were then subjected to proteomic analysis that indicated possible truncation at the N-terminus, and thus the possible removal of a phosphorylation site that crucial for the initiation of ST. We also investigate the ability of the Nt(Hn) cybrid to adjust to high and low intensity light environments in terms of acclimation at the level of the whole plant, leaf, tissue, cell, chloroplast, thylakoid membrane, pigment, and electron transport rates.
The cross-modal effects of packaging glossiness on haptic perception

Submitted by Gemma Davies on Thu, 06/25/2015 14:02 Titre The cross-modal effects of packaging glossiness on haptic perception Type de publication Communication Type Communication avec actes dans un congrès Année 2015 Langue Anglais Date du colloque 19-21/06/2015 Titre du colloque Advances in Consumer Research, Asia Pacific Conference Auteur Cloonan, Caroline [1], Briand-Decre, Gwenaëlle [2] Pays Chine Ville Hong Kong URL de la notice http://okina.univ-angers.fr/publications/ua13052 [3]
Detection of epistatic interactions with Random Forest

In order to elucidate the influence of genetic factors on phenotype variation, non-additive genetic interactions (i.e., epistasis) have to be taken into account. However, there is a lack of methods that can reliably detect such interactions, especially for quantitative traits. Random Forest was previously recognized as a powerful tool to identify the genetic variants that regulate trait variation, mainly due to its ability to take epistasis into account. However, although it can account for interactions, it does not specifically detect them. Therefore, we propose three approaches that extract interactions from a Random Forest by testing for specific signatures that arise from interactions, which we termed ’paired selection frequency’, ’split asymmetry’, and ’selection asymmetry’. Since they complement each other for different epistasis types, an ensemble method that combines the three approaches was also created. We evaluated our approaches on multiple simulated scenarios and two different real datasets from different Saccharomyces cerevisiae crosses. We compared them to the commonly used exhaustive pair-wise linear model approach, as well as several two-stage approaches, where loci are pre-selected prior to interaction testing. The Random Forest-based methods presented here generally outperformed the other methods at identifying meaningful genetic interactions both in simulated and real data. Further examination of the results for the simulated and real datasets established how interactions are extracted from the Random Forest, and explained the performance differences between the methods. Thus, the approaches presented here extend the applicability of Random Forest for the genetic mapping of biological traits. Author summary The genetic mechanisms underlying biological traits are often complex, involving the effects of multiple genetic variants. Interactions between these variants, also called epistasis, are also common. The machine learning algorithm Random Forest can be used to study genotype-phenotype relationships, by using genetic variants to predict the phenotype. One of Random Forest’s strengths is its ability to implicitly model interactions. However, Random Forest does not give any information about which predictors specifically interact, i.e. which variants are in epistasis. Here, we developed three approaches that identify interactions in a Random Forest. We demonstrated their ability to detect genetic interactions using simulations and real data from Saccharomyces cerevisiae. Our Random Forest-based methods generally outperformed several other commonly used approaches at detecting epistasis. This study contributes to the long-standing problem of extracting information about the underlying model from a Random Forest. Since Random Forest has many applications outside of genetic association, this work represents a valuable contribution to not only genotype-phenotype mapping research, but also other scientific applications where interactions between predictors in a Random Forest might be of interest.
Tumour-stroma Signalling in Cancer Cell Motility and Metastasis

The tumour-associated stroma, consisting of fibroblasts, inflammatory cells, vasculature and extracellular matrix proteins, plays a critical role in tumour growth, but how it regulates cancer cell migration and metastasis is poorly understood. The Wnt-planar cell polarity (PCP) pathway regulates convergent extension movements in vertebrate development. However, it is unclear whether this pathway also functions in cancer cell migration. In addition, the factors that mobilize long-range signalling of Wnt morphogens, which are tightly associated with the plasma membrane, have yet to be completely characterized. Here, I show that fibroblasts secrete membrane microvesicles of endocytic origin, termed exosomes, which promote tumour cell protrusive activity, motility and metastasis via the exosome component Cd81. In addition, I demonstrate that fibroblast exosomes activate autocrine Wnt-PCP signalling in breast cancer cells as detected by the association of Wnt with Fzd receptors and the asymmetric distribution of Fzd-Dvl and Vangl-Pk complexes in exosome-stimulated cancer cell protrusive structures. Moreover, I show that Pk expression in breast cancer cells is essential for fibroblast-stimulated cancer cell metastasis. Lastly, I reveal that trafficking in cancer cells promotes tethering of autocrine Wnt11 to fibroblast exosomes. These studies further our understanding of the role of iii the tumour-associated stroma in cancer metastasis and bring us closer to a more targeted approach for the treatment of cancer spread.
Unravelling the evolutionary origins of biogeographic assemblages

Floristic and faunal diversity fall within species assemblages that can be grouped into distinct biomes or ecoregions. Understanding the origins of such biogeographic assemblages helps illuminate the processes shaping present‐day diversity patterns and identifies regions with unique or distinct histories. While the fossil record is often sparse, dated phylogenies can provide a window into the evolutionary past of these regions. Here, we present a novel phylogenetic approach to investigate the evolutionary origins of present‐day biogeographic assemblages and highlight their conservation value.
Reproductive life history characteristics of invasive red lionfish (Pterois volitans) in the northern Gulf of Mexico

With invasive lionfish (Pterois spp.) increasing throughout the western North Atlantic Ocean and Gulf of Mexico (GOM), it is important to define life history characteristics to help understand the invasion and potential effects on receiving ecosystems. Although some aspects of reproduction are known elsewhere in the invaded range, little is known in the northern GOM [nGOM; Florida Keys (24.66°N) to south Texas (26.00°N)]. In the present study, gonadosomatic index (GSI) calculations were based on 4527 red lionfish Pterois volitans (Linnaeus, 1758) specimens (April 2012–March 2015). Male and female GSI peaked from May to October, corresponding with macroscopic gonadal assessments of reproductively active females. Histological examination of ovaries from 355 females found they were spawning capable during all months. Males (n = 211) were spawning capable in all months except March, the only month in which no actively spawning females were present. A significantly higher percentage of reproductively active females was found from May to December. Lionfish reached 50% maturity at a small size (166.6 mm TL, females; 145.2 mm TL, males). Mean relative batch fecundity (n = 71) was 92 eggs g–1 gonad-free body weight (GFBW) and was highest in August (207 eggs g–1 GFBW). The population spawning frequency was estimated to be every 2.5 d over 11 mo in the nGOM, corresponding to a maximum potential annual output of 2,332,490 eggs for an average sized (188.6 g) female. These reproductive characteristics are similar to invasive lionfish in tropical waters, although nGOM reproductive output appears higher. Our results represent the most comprehensive reproductive data on lionfish in their invaded range, and provide a baseline for management in the nGOM.
Use of constructed coarse woody debris corridors in a clearcut by American martens (Martes americana) and their prey

American martens (Martes americana) are typically associated with mature coniferous forests because they provide overhead cover and coarse woody debris (CWD) that martens require for protection and hunting. Therefore, clearcuts are considered poor marten habitat because they contain no overhead cover and relatively little CWD. We examined the efficacy of retaining CWD and constructing CWD corridors in a recently harvested clearcut to promote the use of the area by martens and small mammals, a major prey resource. We installed remote cameras in corridors, the surrounding clearcut and forest to monitor the distribution of martens and small mammals. Martens and red squirrels did not use CWD corridors more frequently than clearcut areas in summer; forest-floor small mammals, however, used corridors approximately three times as frequently as other habitats (x² = 13.374, P = 0.001). Marten presence was positively associated with mature, dense forest and long pieces of CWD. In winter, red squirrels used corridors more frequently than other clearcut areas, and limited data suggested that martens preferred the corridors to other clearcut areas. Consequently, we recommend that forest managers retain CWD and construct CWD corridors within clearcuts to provide small mammal habitat, and to enhance marten habitat.
Can opportunistically collected Citizen Science data fill a data gap for habitat suitability models of less common species?

Opportunistically collected species observations contributed by volunteer reporters are increasingly available for species and regions for which systematically collected data are not available. However, it is unclear if they are suitable to produce reliable habitat suitability models (HSMs), and hence if the species–habitat relationships found and habitat suitability maps produced can be used with confidence to advice conservation management and address basic and applied research questions. We evaluated HSMs with opportunistically collected observations against HSMs with systematically collected observations. We enhanced the opportunistically collected presence‐only data by adding inferred species absences. To obtain inferred absences, we asked individual reporters about their identification skills and if they reported certain species consistently and combined this information with their observations. We evaluated several HSM methods using a forest bird species, Siberian jay (Perisoreus infaustus), in Sweden: logistic regression with inferred absences, two versions of MaxEnt, a model combining presence–absence with presence‐only observations and a Bayesian site‐occupancy‐detection model. All HSM methods produced nationwide habitat suitability maps of Siberian jay that agreed well with systematically collected observations (AUC: 086–0.88) and were very similar to a habitat suitability map produced from the HSM with systematically collected observations (Spearman rho: 0.94–0.98). At finer geographical scales there were differences among methods. At finer scale, the resulting habitat suitability maps from logistic regression with inferred absences agreed better with results from systematically collected observations than other methods. The species–habitat relationships found with logistic regression also agreed well with those found from systematically collected data and with prior expectations based on the species ecology. Synthesis and application. For many regions and species, systematically collected data are not available. By using inferred absences from high‐quality, opportunistically collected contributions of few very active reporters in logistic regression we obtained HSMs that produced results similar to those from a systematic survey. Adding high‐quality inferred absences to opportunistically collected data is likely possible for many less common species across various organism groups. Well‐performing HSMs are important to facilitate applications such as spatial conservation planning and prioritization, monitoring of invasive species, understanding species habitat requirements or climate change studies.
Effect of hypoxia-inducing ions on chondrogenic differentiation in adipose derived mesenchymal stem cells within alginate matrix

Cartilage is a highly organized tissue with complex biomechanical properties, but since it has a poor intrinsic capacity of self-healing, injuries at this site usually lead to several problems, often ending in disabling symptoms. Although, different approaches have been proposed, even now cartilage repair represents a great challenge for orthopaedic surgeons (1, 2). One of the promising approach is given from tissue engineering, employing the combination of biomaterials and cell therapy to develop new therapeutic strategies. In this paper, we describe the behaviour of human adipose derived mesenchymal stem cells encapsulated into Ca/Co alginate beads as potential chondrogenic inducing biomaterial tacking advance on the synergy between alginate matrix and Co+2 ions without employing other expensive growth factors such as TGFbs or BMPs. The expression of chondrogenic markers such as sox9, collagen type II, and versican was investigated by Real Time PCR and Western blotting analysis. The expression of hif1mRNA was investigated to check the capability of Co+2 ions to induce a chemical hypoxia. Real Time PCR and WB data reveal a different cells behaviour on chondrogenic marker expression. In conclusion, the synergic effect of alginate and Co+2 ions can represent a valid strategy for chondrogenic differentiation of stem cells.
Thresholding of sensory inputs by extrasynaptic glutamate receptors in olfactory bulb glomeruli

The mammalian olfactory bulb has presented a challenging system for understanding information processing, in part because the bulb largely lacks the topographical ordering of neurons that promotes processes such as lateral inhibition. Here we have used dual and triple-cell recordings in rodent bulb slices combined with ultrastructural methods to provide the first experimental evidence for a processing mechanism circumventing this problem that operates at the level of single glomeruli, the bulb’s odorant receptor-specific modules. A key feature is non-traditional, extrasynaptic glutamatergic signaling derived from excitatory interneurons and what it means for the local balance between excitation (E) and inhibition (I). We found that the distinct dynamic properties of extrasynaptic excitation versus synaptic inhibition create a thresholding effect whereby only strong stimuli produce a favorable E/I balance enabling an output. This single-glomerulus threshold could have a number of important functions during natural odor responses, for example enhancing stimulus tuning.
Some Physiological and Biological Studies on Reuterin Production from Lactobacillus reuteri

Lactic Acid Bacteria (LAB) can be used as food preservatives to improve food stability and safety. This is due to its ability to produce antimicrobial substances which can inhibit the growth of the food poisoning organisms. LAB produce antimicrobial compounds named bacteriocins. This study focused on bacteriocin named reuterin which produced from Lactobacillus reuteri strain and its optimal production condition. The metabolite L. reuteri bacteriocin (reuterin) was extracted and the antimicrobial activity was evaluated against some hospitalized bacterial and fungal pathogens. The reuterin producing L. reuteri exhibited the highest inhibition zone (22.2, 22.5 and 22.7 mm) against E. coli, Staphylococcus aureus and Candida albicans, respectively, when grown on optimized condition, i.e., growth on 2% glucose, soy bean (sb) or yeast extract as nitrogen source, all MRS salts medium and inoculated by 21 × 108 cfu/ml, pH 6.5 at 37°C for 24 hr anaerobically. This study gave us the possibility to use reuterin as food preservative to control pathogenic microorganisms and food spoilage.
Role of crumbs and bazooka in the organization and distribution of DE-cadherin in Drosophila embryo

Les tissus epitheliaux sont des couches de cellules adherentes qui servent de barrieres entre differents compartiments morphologiques et procurent un transport directionnel de molecules. L’action cooperative de plusieurs determinants de la polarite gouverne l’identite et la morphogenese specifiques de ces domaines : 1) le cytosquelette d’actomyosine, 2) les jonctions adherentes (AJs) basees sur la E-cadherine et 3) les complexes de polarite conserves au cours de l’evolution. Une perte de l’adherence via la DE-cadherine (DE-Cad) conduit a des defauts de polarite apico-basale, tandis que la localisation apicale de DE-Cad necessite les proteines de polarite Crumbs (Crb) et Bazooka (Baz) (L’homologue de Par3 chez la mouche). Notablement, DE-Cad forme des amas qui co-localisent partiellement avec les amas de Baz, generent l’adhesion intercellulaire et transmettent la tension. Les mecanismes impliques dans le controle de la taille, le nombre, la repartition et la dynamique des amas de DE-Cad restent peu connus.J’ai etudie le role de Crumbs et Baz dans la regulation de la distribution fine de DE-Cad. J’ai montre que Crb controle la distribution macroscopique de DE-Cad, au moins, partiellement via Baz. En generant des mutations de Baz sur des sites regulateurs varies grâce a de la transgenese specifique de site et en utilisant de la microscopie en temps reel quantitative, j’ai montre que Crb agit via le domaine d’oligomerisation CR1 et le site Ser980 de Baz afin d’ajuster les niveaux de DE-Cad. Remarquablement, j’ai aussi revele que le domaine d’oligomerisation de Baz est inutile a la formation d’amas Baz-DE-Cad et j’ai caracterise la reciprocite de l’interaction DE-Cad-Baz.