bluuebunny/crossref_metadata_2025_split huggingface dataset:
Apolar mode of gastrulation leads to the formation of polarized larva in a marine hydroid,Dynamena pumila
Authors: Vetrova Alexandra A. , Lebedeva Tatiana S. , Saidova Aleena A. , Kupaeva Daria M. , Kraus Yulia A. , Kremnyov Stanislav V. 
Published: February 2021

AbstractBackgroundIn almost all metazoans examined to this respect, the axial patterning system based on canonical Wnt (cWnt) signaling operates throughout the course of development. In most metazoans, gastrulation is polar, and embryos develop morphological landmarks of axial polarity, such as blastopore under control/regulation from Wnt signaling. However, in many cnidarian species, gastrulation is morphologically apolar. The question remains whether сWnt signaling providing the establishment of a body axis controls morphogenetic processes involved in apolar gastrulation.ResultsIn this study, we focused on the embryonic development ofDynamena pumila, a cnidarian species with apolar gastrulation. We thoroughly described cell behavior, proliferation, and ultrastructure and examined axial patterning in the embryos of this species. We revealed that the first signs of morphological polarity appear only after the end of gastrulation, while molecular prepatterning of the embryo does exist during gastrulation. We have shown experimentally that inD. pumila,the morphological axis is highly robust against perturbations in cWnt activity.ConclusionOur results suggest that morphogenetic processes are uncoupled from molecular axial patterning during gastrulation inD. pumila. Investigation ofD. pumilamight significantly expand our understanding of the ways in which morphological polarization and axial molecular patterning are linked in Metazoa.
Sensory and cognitive factors affecting multi-digit touch: a perceptual and modeling study
Authors: Arslanova Irena , Takamuku Shinya , Gomi Hiroaki , Haggard Patrick 
Published: February 2021

AbstractWhilst everyday interactions with objects often involve multiple tactile contacts, integration of tactile signals remains poorly understood. Here we characterise the integration process of tactile motion on multiple fingerpads. Across four experiments, participantsaveragedthe direction of two simultaneous tactile motion trajectories delivered to different fingerpads. Averaging performance differed between within- and between-hands in terms of sensitivity and precision but was unaffected by somatotopic proximity between stimulated fingers. The sensitivity to the average direction was influenced by the discrepancy between individual motion signals, but only for within-hand conditions. This was explained by a model, in which the ‘virtually leading finger’ received a higher perceptual weighting. Precision was greater in between-hand compared to within-hand conditions. While biased weighting accounted for differences in sensitivity, it was not sufficient to explain the difference in precision, implying additional sensory limitations during within-hand integration. We suggest that unimanual integration is limited and thus exploits a ‘natural’ cognitive prior involving a single object moving relative to the hand to maximise information gain.Author summaryTactile stimulation is always on. Yet little is known about how the brain combines widespread tactile inputs for perception. Most tactile studies emphasize a single point of tactile stimulation (e.g., location or intensity of a static stimulus) and minimal units of tactile perception (e.g., acuity or selectivity). However, our daily interactions with the world involve encoding spatially and temporally extended tactile signals. Perceiving tactile objects and events as coherent entities requires the somatosensory system to aggregate tactile afferent signals across separate skin regions (i.e., separate digits). Across four experiments we asked participants toaveragedirection of two tactile motion trajectories delivered simultaneously to two different fingerpads, either on the same, or on different hands. Our results show strong integration between multiple tactile inputs, but subject to limitations for inputs delivered within a hand. Our model suggests that tactile inputs are weighted according to an integrative model of hand-object interaction that operates within-hands on purely geometric information to prioritise ‘novel’ information from a ‘virtually leading finger’ (VLF).
Development of a label-free microfluidic impedimetric immunoassay for anti-SPAG16 antibody
Authors: Froyen T , Vreys F , Slaets L , Somers V , Thoelen R 
Published: February 2021

ABSTRACTA recently found biomarker regarding multiple sclerosis, namely the anti-SPAG16 antibody (Ab), could be a potential way for early detection, prognosis and diagnosis of said autoimmune disease. Merging electrochemical analysis with a microfluidic system is a novel approach, which avoids the use of labelling steps as seen in traditional ELISA immunoassays. In this study, aluminium interdigitated electrodes on polystyrene-coated PET foils were implemented in a microfluidic flow cell to bind and detect SPAG16 Abs by impedimetric measurements. The coated PET foils showed a clear affinity for the fusion protein SPAG16-THIO and thioredoxin (THIO). Determining sensitivity and specificity of antibody-antigen binding using a microfluidic ELISA immunoassay has revealed the test to be unreliable by showing no linear pattern of a dilution series of the standard and producing skewed inconsistent results. The impedimetric analysis showed opposite results of what one would expect. The systems efficiency is in need to be revised and optimised before undergoing actual diagnostic tests. Further advancement could be done by reducing leakage, securing a more stable entrance for injection and circumventing the occurence of air bubbles in the wells.SAMENVATTINGMultiple sclerosis (MS) is een auto-immune ziekte, gekenmerkt door inflammatie van het centraal zenuwstelsel en demyelinisatie van axonen. Een recent gevonden proteïne, namelijk het anti-SPAG16 antilichaam, is bewezen een biomerker te zijn voor MS. Met behulp van een elektrochemisch analytisch systeem gecombineerd met microfluidica zou men anti-SPAG16 antilichamen kunnen opsporen voor vroegtijdige detectie, prognose en diagnose. Het grote voordeel tegenover traditionele ELISA testen is het elimineren vanlabellingstappen waardoor de immunoassay goedkoper en gebruiksvriendelijk wordt. In deze studie werden overlappende aluminium elektrodes op polystyreen-gecoate PET-plaatjes geïmplementeerd in een microfluidische flow cell voor binding en detectie van anti-SPAG16 antilichamen door middel van impedimetrische metingen. De gecoate PET-plaatjes vertonen een duidelijke affiniteit voor 0,1 μg/ml SPAG16 en THIO. Het bepalen van sensitiviteit en specificiteit van antilichaam-antigen binding, gebruikmakende van een ELISA immunoassays, gaf aan dat de test onbetrouwbaar is doordat geen duidelijk patroon voor standaardoplossingen zichtbaar was en resultaten vertekend en inconsistent bleken te zijn. De impedimetrische analyse vertoonde tevens onbetrouwbare resultaten, waarbij een omgekeerd effect werd geobserveerd van wat er in theorie zou moeten gebeuren. De efficiëntie van het systeem moet herzien en geoptimaliseerd worden voordat men het voor diagnostische testen kan gebruiken. Verdere vorderingen zouden gerealiseerd kunnen worden door lekkages te reduceren, steviger bevestigen van de PDMS-ingang en de ontwikkeling van luchtbellen in de wells te vermijden.
Evolution of thermal physiology alters the projected range of threespine stickleback under climate change
Authors: Wuitchik Sara J.S. , Mogensen Stephanie , Barry Tegan N. , Paccard Antoine , Jamniczky Heather A. , Barrett Rowan D.H. , Rogers Sean M. 
Published: February 2021

AbstractSpecies distribution models (SDMs) are widely used to predict range shifts but could be unreliable under climate change scenarios because they do not account for evolution. The thermal physiology of a species is a key determinant of range and thus incorporating thermal trait evolution into SDMs might be expected to alter projected ranges. We identified a genetic basis for physiological and behavioural traits that evolve in response to temperature change in natural populations of threespine stickleback(Gasterosteus aculeatus).Using these data, we created geographic range projections using a mechanistic niche area approach under two climate change scenarios. Under both scenarios, trait data was either static (‘no evolution’ models), allowed to evolve at observed evolutionary rates (‘evolution’ models), or allowed to evolve at a rate of evolution scaled by the trait variance that is explained by quantitative trait loci (QTL; ‘scaled evolution’ models). We show that incorporating these traits and their evolution substantially altered the projected ranges for a widespread panmictic marine population, with over 7-fold increases in area under climate change projections when traits are allowed to evolve. Evolution-informed SDMs should improve the precision of forecasting range dynamics under climate change, and aid in their application to management and the protection of biodiversity.
A pipeline to detect the relationship between transposable elements and adjacent genes in host genomes
Authors: Caroline Meguerditchian , Ayse Ergun , Veronique Decroocq , Marie Lefebvre , Quynh-Trang Bui 
Published: February 2021

AbstractUnderstanding the relationship between transposable elements (TEs) and their closest positional genes in the host genome is a key point to explore their potential role in genome evolution. Transposable elements can regulate and affect gene expression not only because of their mobility within the genome but also because of their transcriptional activity. A comprehensive knowledge of structural organization between transposable elements and neighboring genes is important to study TE functional role in gene regulation. We implemented a pipeline to display the relationship between the distribution of TEs and adjacent genes in host genomes. Our tool is freely available here:https://github.com/marieBvr/TEs_genes_relationship_pipeline.
Multilamellar mesoporous silica nanoparticles using a cationic co-surfactant dual-templating method
Authors: Froyen Timo , Geysmans Niels , Vounckx Ulrique , Hardy An 
Published: February 2021

ABSTRACTThe utility of mesoporous silica nanoparticles (MSNs) has been repeatedly proven in a wide range of biomedical applications. The general morphology of these particles is easily modifiable by various post-grafting possibilities and adjustments within the surfactant-based template. The synthesis of multilamellar vesicular silica nanoparticles has led to the discovery of beneficial attributes regarding said particles. Depending on the synthesis process, various parameters are affected including packaging capacity, stability, drug adsorption and release. This research focused on synthesis and characterization of multilamellar MSNs using a cationic-cationic co-surfactant templating route testing various ratios of cetyltrimethylammonium bromide (CTAB) and didodecyldimethylammonium bromide (DDAB). TEM imaging showed clear differences in size and morphology between the different samples, and was further characterized by BET and BJH analysis. All multilamellar nanoparticles did exhibit a similar pore size distribution and overall gradual release of drug contents. However, the degree of drug adsorption and overtime drug release was clearly influenced by the number of layers of the MSNs, proving the utility of adjusting the template. Further experiments could be conducted to validate the utility of beta-cyclodextrin as a template regulator and to investigate both biocompatibility and biodegradability of the multilamellar MSNs.
Wolbachiain the spittlebugProsapia ignipectus:Variable infection frequencies, but no apparent effect on host reproductive isolation
Authors: Wheeler Timothy B. , Thompson Vinton , Conner William R. , Cooper Brandon S. 
Published: February 2021

AbstractAnimals serve as hosts for complex communities of microorganisms, including endosymbionts that live inside their cells.Wolbachiabacteria are perhaps the most common endosymbionts, manipulating host reproduction to propagate. ManyWolbachiacause intense cytoplasmic incompatibility (CI) that promotes their spread to high and relatively stable frequencies.Wolbachiathat cause weak or no CI tend to persist at intermediate, often variable, frequencies.Wolbachiacould also contribute to host reproductive isolation (RI), although current support for such contributions is limited to a few systems. To test forWolbachiafrequency variation and effects on host RI, we sampled several localProsapia ignipectus(Fitch)(Hemiptera: Cercopidae) spittlebug populations in the northeastern USA over two years, including closely juxtaposed Maine populations with different monomorphic color forms, “black” and “lined”. We discovered a group-BWolbachia(wPig) infectingP. ignipectusthat diverged from group-AWolbachia—likemodelwMel andwRi strains inDrosophila—6to 46 MYA. Populations of the sister speciesProsapia bicincta(Say) from Hawaii and Florida are uninfected, suggesting thatP. ignipectusacquiredwPig after their initial divergence.wPig frequencies were generally high and variable among sites and between years. While phenotypingwPig effects on host reproduction is not currently feasible, thewPig genome contains three divergent sets of CI loci, consistent with highwPig frequencies. Finally, Maine monomorphic black and monomorphic lined populations ofP. ignipectusshare bothwPig and mtDNA haplotypes, implying no apparent effect ofwPig on the maintenance of this morphological contact zone. We hypothesizeP. ignipectusacquiredwPig horizontally as observed for manyDrosophilaspecies, and that significant CI and variable transmission produce high but variablewPig frequencies.
FrozenChicken: Promoting the meta-analysis of chicken microarray data
Authors: Duarte Isabel , Liber Marta , Magno Ramiro , Andrade Raquel P. 
Published: February 2021

AbstractThe FrozenChicken RData package, contains the frozen vectors for the commercially available (in situ oligonucleotide) Affymetrix Chicken Genome Array (GEO platform id GPL3213). This package will promote, simplify, and ease the meta-analysis of chicken microarray data by the research community studying vertebrate development using the chick model organism. The package is freely available inhttps://github.com/iduarte/FrozenChicken. (*Equal contribution.)
Description and analysis of glycosidic residues in the largest open natural products database
Authors: Schaub Jonas , Zielesny Achim , Steinbeck Christoph , Sorokina Maria 
Published: February 2021

AbstractNatural products (NP), biomolecules produced by living organisms, inspire the pharmaceutical industry and research due to their structural characteristics and the substituents from which they derive their activities. Glycosidic residues are frequently present in NP structures and have particular pharmacokinetic and pharmacodynamic importance as they improve their solubility and are often involved in molecular transport, target specificity, ligand-target interactions and receptor binding. The COlleCtion of Open Natural prodUcTs (COCONUT) is currently the largest open database of NP and therefore a suitable starting point for the detection and analysis of the diversity of glycosidic residues in NP. In this work, we report and describe the presence of circular, linear, terminal and non-terminal glycosidic units in NP, together with their importance in drug discovery.
Physiological and transcriptomic variability indicative of differences in key functions within a single coral colony
Authors: Drake Jeana L. , Malik Assaf , Popovits Yotam , Yosef Oshra , Shemesh Eli , Stolarski Jarosław , Tchernov Dan , Sher Daniel , Mass Tali 
Published: February 2021

AbstractPolyps in different locations on individual stony coral colonies experience variation in numerous environmental conditions including flow and light, potentially leading to transcriptional and physiological differences across the colony. Here, we describe high-resolution physiological measurements and differential gene expression from multiple locations within a single colony ofStylophora pistillata, aiming to relate these to environmental gradients across the coral colony. We observed broad transcriptional responses in both the host and photosymbiont in response to height above the substrate, cardinal direction, and, most strongly, location along the branch axis. Specifically, several key physiological processes in the host appear more active toward branch tips including several metabolic pathways, toxin production for prey capture or defense, and biomolecular mechanisms of biomineralization. Further, the increase in gene expression related to these processes toward branch tips is conserved betweenS. pistillataandAcroporaspp. The photosymbiont appears to respond transcriptionally to relative light intensity along the branch and due to cardinal direction. These differential responses were observed across the colony despite its genetic homogeneity and likely inter-polyp communication. While not a classical division of labor, each part of the colony appears to have distinct functional roles related to polyps’ differential exposure to environmental conditions.
Genome-wide survey of odorant-binding proteins in the dwarf honey beeApis florea
Authors: Mam Bhavika , Karpe Snehal , Sowdhamini Ramanathan 
Published: February 2021

AbstractOdorant binding proteins (OBPs) in insects bind to volatile chemical cue and help in their binding to odorant receptors. The odor coding hypothesis states that OBPs may bind with specificity to certain volatiles and aid the insect in various behaviours. Honeybees are eusocial insects with complex behaviour that requires olfactory inputs. Here, we have identified and annotated odorant binding proteins from the genome of the dwarf honey bee,Apis floreausing an exhaustive homology-based bioinformatic pipeline and analyzed the evolutionary relationships between the OBP subfamilies. Our study suggests that Minus-C subfamily may have diverged from the Classic subfamily of odorant binding proteins in insects.
The impact of invader number on whole community invasions in biomethane-producing communities
Authors: Sierocinski Pawel , Pascual Jesica Soria , Padfield Daniel , Salter Mike , Buckling Angus 
Published: February 2021

AbstractMicrobes can invade as whole communities, but the ecology of whole community invasions are poorly understood. Here, we investigate how invader frequency affects the composition and function of invaded laboratory methanogenic communities. An invading community was equally successful at establishing itself in a resident community regardless of initial invader frequency, which varied between 0.01 and 10%. Invasion resulted in enhanced biogas production (to the level of the pure invading community), but only when invader frequency was 1% or greater. This inconsistency between invasion success and changes in function can be explained by a lower number of invading taxa (but not individuals) at lower initial invader frequencies, and an important functional role of the taxa that were absent. Our results highlight that whole community invasion ecology cannot simply be extrapolated from our understanding of single species invasions. Moreover, we show that methane production can be enhanced by invading poorly performing reactors with a better performing community at levels that may be practical in industrial settings.
Decisive Role of Polymer-BSA Interactions in Biofilm Substrates on ‘Philicity’ and EPS Composition
Authors: Sinha Suparna Dutta , Choudhuri Madhumita , Basu Tania , Gupta Debkishore , Datta Alokmay 
Published: February 2021

AbstractFormation of extracellular polymeric substances (EPS) is a crucial step for bacterial biofilm growth. Dependence of EPS composition on the growth substrate and the conditioning of the latter is thus of primary importance. Here, we present results of studies on the growth of biofilms of two different strains each, of the Gram negative bacteriaEscherichia coliandKlebsiella pneumoniae, on four polymers used commonly in indwelling medical devices – Polyethene, Polypropylene, Polycarbonate, and Polytetrafluoroethylene immersed in Bovine Serum Albumin (BSA) for 24 hrs. The polymer substrates are studied before and after immersing in BSA for 9 hrs and 24 hrs, using contact angle measurement (CAM) and Field Emission Scanning Electron Microscopy (FE-SEM) to extract, respectively, the ‘philicity’ (defined asϕ≡sin(θ-90°), whereθis contact angle of the liquid on the solid at a particular temperature and ambient pressure) and spatial Hirsch parameterH(defined from the relation,F(r)~r2H, whereF(r)is the mean squared density fluctuation at the sample surface).H=, <0.5 or >0.5 signifies no correlation, anti-correlation, and correlation, respectively. The substrates are seen to transform from large hydrophobicity to near amphiphilicity with the formation of BSA conditioning surface layer, and theH-values distinguish the length scales of ~ 100 nm, 500 nm, and 2000 nm, with the anti-correlation increasing with length scale. Biofilms grown on the BSA-covered surfaces are studied with CAM, FE-SEM, Fourier Transform Infrared (FTIR) and Surface Enhanced Raman Spectroscopy (SERS). Most notably, theϕ-values areindependentof the bacterial species and strain butdependenton the polymer, as is also shown strikingly by both types of spectra, whileH-values show some bacterial variation. Thus, the EPS composition and consequently the wetting properties of the corresponding bacterial biofilms seems to be decided by the interaction of the conditioning BSA layer with a specific polymer used as the growth substrate.