bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotypic trade-off between appetitive and aversive capacities in honeybees
Authors: Junca Pierre , Garnery Lionel , Sandoz Jean-Christophe 
Published: July 2019

AbstractHoney bees can learn both appetitive and aversive associations, using two olfactory conditioning protocols. Appetitive conditioning of the proboscis extension response (PER) involves associating an odor, the conditioned stimulus (CS) with a sucrose solution, the unconditioned stimulus (US). Conversely, aversive conditioning of the sting extension response (SER) involves associating the odor CS with an electric or thermal shock US. Here, we investigated the relationship between bees’ appetitive and aversive learning capacities at the individual level and the influence of bees’ genotype. As learning performance was shown to depend on an individuals’ sensitivity to the US, we systematically measured four different traits in each individual bee: sensitivity to sucrose, PER learning performance with a sucrose US, sensitivity to temperature, SER learning with a temperature US. First, we confirmed for both conditioning types that learning performance correlates with US responsiveness. Second, we found a trade-off between appetitive and aversive learning performances: bees that were better appetitive learners (and had a lower sucrose US threshold) learned less efficiently in the aversive conditioning (and had a higher temperature US threshold). Because the honey bee queen typically mates with 15–20 males, the workers from a honey bee hive belong to as many different patrilines, allowing for the search of the genetic determinism of cognitive abilities. Using microsatellite analysis, we show that a genetic determinism underlies the trade-off between appetitive and aversive capacities, with appetitively vs aversively biased patrilines. The honey bee hive thus appears as a genetically structured cognitive community.
Bionanocomposites based on chitosan intercalation in designed swelling high-charged micas
Authors: Alba María D. , Cota Agustín , Osuna Francisco J. , Pavón Esperanza , Perdigón Ana C. , Raffin Florian 
Published: July 2019

AbstractBionanocomposites based on layered inorganic components, as clays, and polymers of biological origin, as chitosan, have a major impact in medical and environmental fields, being economical and environmentally friendly materials. Na-Mn micas (n = 2 and 4) with controlled surface charge, high cation exchange capacity and swelling behaviour, are attractive inorganic composite components that exhibit improved adsorption properties compared to other inorganic solids which makes them potentially useful for bionanocomposites. The goal of this research was to explore the potential use of those synthetic brittle micas to form eco-friendly bionanocomposites with chitosan biopolymer. Hence, chitosan-mica bionanocomposites were prepared by ion-exchange reaction between chitosan solution and synthetic high charge mica. X-ray diffraction, Fourier transform infrared spectroscopy, thermal analysis, MAS-NMR spectroscopy and zeta-potential have been employed for bionanocomposites characterization. The results showed that the adsorption of chitosan is effective, although a chitosan portion remains in the outer surface being hydrogen-bonded to the tetrahedral sheet of the silicate.
A 4-cyano-3-methylisoquinoline inhibitor of Plasmodium falciparum growth targets the sodium efflux pump PfATP4
Authors: Gilson Paul R. , Kumarasingha Rasika , Thompson Jennifer , Zhang Xinxin , Penington Jocelyn Sietsma , Kalhor Robabeh , Bullen Hayley E. , Lehane Adele M. , Dans Madeline G. , de Koning-Ward Tania F. , Holien Jessica K. , Soares da Costa Tatiana P. , Hulett Mark D. , Buskes Melissa J. , Crabb Brendan S. , Kirk Kiaran , Papenfuss Anthony T. , Cowman Alan F. , Abbott Belinda M. 
Published: July 2019

AbstractWe developed a novel series of antimalarial compounds based on a 4-cyano-3-methylisoquinoline. Our lead compound MB14 achieved modest inhibition of the growth in vitro of the human malaria parasite, Plasmodium falciparum. To identify its biological target we selected for parasites resistant to MB14. Genome sequencing revealed that all resistant parasites bore a single point S374R mutation in the sodium (Na+) efflux transporter PfATP4. There are many compounds known to inhibit PfATP4 and some are under preclinical development. MB14 was shown to inhibit Na+ dependent ATPase activity in parasite membranes, consistent with the compound targeting PfATP4 directly. PfATP4 inhibitors cause swelling and lysis of infected erythrocytes, attributed to the accumulation of Na+ inside the intracellular parasites and the resultant parasite swelling. We show here that inhibitor-induced lysis of infected erythrocytes is dependent upon the parasite protein RhopH2, a component of the new permeability pathways that are induced by the parasite in the erythrocyte membrane. These pathways mediate the influx of Na+ into the infected erythrocyte and their suppression via RhopH2 knockdown limits the accumulation of Na+ within the parasite hence protecting the infected erythrocyte from lysis. This study reveals a role for the parasite-induced new permeability pathways in the mechanism of action of PfATP4 inhibitors.
In Silico Identification of Novel Biomarkers and Development of New Rapid Diagnostic Tests for the Filarial Parasites Mansonella perstans and Mansonella ozzardi
Authors: Poole C. B. , Sinha A. , Ettwiller L. , Apone L. , McKay K. , Panchapakesa V. , Lima N. F. , Ferreira M. U. , Wanji S. , Carlow C. K. S. 
Published: July 2019

AbstractMansonelliasis is a widespread yet neglected tropical infection of humans in Africa and South America caused by the filarial nematodes, Mansonella perstans, M. ozzardi, M. rodhaini and M. streptocerca. Clinical symptoms are non-distinct and diagnosis mainly relies on the detection of microfilariae in skin or blood. Species-specific DNA repeat sequences have been used as highly sensitive biomarkers for filarial nematodes. We have developed a bioinformatic pipeline to mine Illumina reads obtained from sequencing M. perstans and M. ozzardi genomic DNA for new repeat biomarker candidates which were used to develop loop-mediated isothermal amplification (LAMP) diagnostic tests. The M. perstans assay based on the Mp419 repeat has a limit of detection of 0.1 pg, equivalent of 1/1000th of a microfilaria, while the M. ozzardi assay based on the Mo2 repeat can detect as little as 0.01 pg. Both LAMP tests possess remarkable species-specificity as they did not amplify non-target DNAs from closely related filarial species, human or vectors. We show that both assays perform successfully on infected human samples. Additionally, we demonstrate the suitability of Mp419 to detect M. perstans infection in Culicoides midges. These new tools are field deployable and suitable for the surveillance of these understudied filarial infections.
Topologically correct central projections of tetrapod inner ear afferents require Fzd3
Authors: Duncan Jeremy S. , Fritzsch Bernd , Houston Douglas W. , Ketchum Elizabeth M. , Kersigo Jennifer , Deans Michael R. , Elliott Karen L. 
Published: July 2019

AbstractInner ear sensory afferent connections establish sensory maps between the inner ear hair cells and the vestibular and auditory nuclei to allow vestibular and sound information processing. While molecular guidance of sensory afferents to the periphery has been well studied, molecular guidance of central projections from the ear is only beginning to emerge. Disorganized central projections of spiral ganglion neurons in a Wnt/PCP pathway mutant,Prickle1, suggest the Wnt/PCP pathway plays a role in guiding cochlear afferents to the cochlear nuclei in the hindbrain, consistent with known expression of the Wnt receptor,Frizzled3(Fzd3) in inner ear neurons. We therefore investigated the role of Wnt signaling in central pathfinding inFzd3mutant mice andFzd3morpholino treated frogs and found aberrant central projections of vestibular afferents in both cases. Ear transplantations from knockdown to controlXenopusshowed that it is theFzd3expressed within the ear that mediates this guidance. Also, cochlear afferents ofFzd3mutant mice lack the orderly topological organization observed in controls. Quantification ofFzd3expression in spiral ganglion neurons show a gradient of expression withFzd3being higher in the apex than in the base. Together, these results suggest that a gradient ofFzd3in inner ear afferents directs projections to the correct dorsoventral column within the hindbrain.
Multimetal bioremediation and biomining by a combination of new aquatic strains of Mucor hiemalis
Authors: Hoque Enamul , Fritscher Johannes 
Published: July 2019

AbstractHere we describe a unique microbial biotechnology for simultaneous bioremediation and biomining of twelve ionic metals overcoming the obstacles of multimetal toxicity to microbes. After a thorough search of key microorganisms in microbiomes of many sulfidic springs in Bavaria (Germany) over an area of 200 km2, we found three new strains EH8, EH10 and EH11 of Mucor hiemalis physiologically compatible and capable of multimetal-remediation and enrichment. We combined the multimetal-resistance, hyper-accumulation and elicitation power of EH8, EH10 and EH11 to develop a novel biotechnology for simultaneous removal, fractionation and enrichment of metal ions. As a first step we showed the intracellular fixing and deposition of mercury as nanospheres in EH8’s sporangiospores. Scanning Electron Microscopy-Energy-Dispersive X-Ray analysis revealed binding and precipitation of other applied metal ions as spherical nano-particles (~50–100 nm) at the outer electro-negative cellwall-surface of EH8, EH10 and EH11 sporangiospores. Microbiomes, germinated spores and dead insoluble cellwalls of these strains removed >81–99% of applied Al, Cd, Co, Cr, Cu, Hg, Ni, Pb, U, and Zn simultaneously and furthermore enriched precious Ag, Au and Ti from water all within 48 h, demonstrating the potential of new biotechnologies for safe-guarding our environment from metal pollution and concentrating precious diluted, ionic metals.
Pretreatment with probiotic Enterococcus faecium NCIMB 11181 ameliorates necrotic enteritis-induced intestinal barrier injury in broiler chickens
Authors: Wu Yuanyuan , Zhen Wenrui , Geng Yanqiang , Wang Zhong , Guo Yuming 
Published: July 2019

AbstractThe dysfunction of tight-junction integrity caused by necrotic enteritis (NE) is associated with decreased nutrient absorption and gut injury in broiler chickens. Although probiotic Enterococcus faecium (E. faecium) has been reported to possess immune-regulatory characteristics and can prevent diarrhea in pigs, very little information exists in relation to the specific regulatory impact of E. faecium NCIMB 11181 on NE-induced intestinal barrier injury of broiler chickens. This study was conducted to investigate the protective effects of probiotic E. faecium NCIMB 11181 on NE-induced intestinal barrier injury in broiler chickens. The study also aimed to elucidate the mechanisms that underpin these protective effects. One hundred and eighty Arbor Acres (AA) broiler chicks (one day old) were randomly assigned using a 2 × 2 factorial arrangement into two groups fed different levels of dietary E. faecium NCIMB 11181 (0 or 2 × 108 CFU/kg of diet) and two disease-challenge groups (control or NE challenged). The results showed that NE induced body weight loss, intestinal lesions, and histopathological inflammation, as well as intestinal-cell apoptosis. These symptoms were alleviated following the administration of probiotic E. faecium NCIMB 11181. Pretreatment with probiotic E. faecium NCIMB 11181 significantly upregulated the expression of the Claudin-1 gene encoding a tight-junction protein. Claudin-1 and HSP70 protein expression were also increased in the jejunum regardless of NE infection. Furthermore, NE-infected birds fed with E. faecium displayed notable increases in MyD88, NF-κB, iNOS, PI3K, GLP-2, IL-1β, IL-4, and HSP70 mRNA expression. E. faecium NCIMB 11181 administration also significantly improved the animals’ intestinal microbial composition regardless of NE treatment. These findings indicated that addition of E. faecium NCIMB 11181 to poultry feed is effective in mitigating NE-induced gut injury, possibly by strengthening intestinal mucosal barrier function, as well as modulating gut microflora and intestinal mucosal immune responses.
Some environmental and biological determinants of coral richness, resilience and reef building in Galápagos (Ecuador)
Authors: Riegl Bernhard , Johnston Matthew , Glynn Peter W. , Keith Inti , Rivera Fernando , Vera-Zambrano Mariana , Banks Stuart , Feingold Joshua , Glynn Peter J. 
Published: July 2019

AbstractThroughout the Galápagos, differences in coral reef development and coral population dynamics were evaluated by monitoring populations from 2000–2019, and environmental parameters (sea temperatures, pH, NO3−, PO43−) from 2015–19. The chief goal was to explain apparent coral community differences between the northern (Darwin and Wolf) and southern (Sta. Cruz, Fernandina, San Cristóbal, Española, Isabela) islands. Site coral species richness was highest at Darwin and Wolf. In the three most common coral taxa, a declining North (N)-South (S) trend in colony sizes existed for Porites lobata and Pocillopora spp., but not for Pavona spp. Frequent coral recruitment was observed in all areas. Algal competition was highest at Darwin, but competition by bioeroding sea urchins and burrowing fauna (polychaete worms, bivalve mollusks) increased from N to S with declining coral skeletal density. A biophysical model suggested strong connectivity among southern islands with weaker connectivity to Wolf and even less to Darwin. Also, strong connectivity was observed between Darwin and Wolf, but from there only intermittently to the south. From prevailing ocean current trajectories, coral larvae from Darwin and Wolf drift primarily towards Malpelo and Cocos Islands, some reaching Costa Rica and Colombia. Mean temperature, pH, and PO43− declined from N to S. Strong thermocline shoaling, especially in the warm season, was observed at most sites. A single environmental factor could not explain the variability in observed coral community characteristics, with minimum temperature, pH and nutrient levels the strongest determinants. Thus, complex environmental determinants combined with larval connectivity patterns may explain why the northern Galápagos Islands (Darwin, Wolf) have higher coral richness and cover and also recover more rapidly than central/southern islands after region-wide disturbances. These northern islands are therefore potentially of critical conservation importance as important reservoirs of regional coral biodiversity and source of larvae.
Spring constant and sensitivity calibration of FluidFM micropipette cantilevers for force spectroscopy measurements
Authors: Nagy Ágoston G. , Kámán Judit , Horváth Róbert , Bonyár Attila 
Published: July 2019

AbstractThe fluidic force microscope (FluidFM) can be considered as the nanofluidic extension of the atomic force microscope (AFM). This novel instrument facilitates the experimental procedure and data acquisition of force spectroscopy (FS) and is also used for the determination of single-cell adhesion forces (SCFS) and elasticity. FluidFM uses special probes with an integrated nanochannel inside the cantilevers supported by parallel rows of pillars. However, little is known about how the properties of these hollow cantilevers affect the most important parameters which directly scale the obtained spectroscopic data: the inverse optical lever sensitivity (InvOLS) and the spring constant (k). The precise determination of these parameters during calibration is essential in order to gain reliable, comparable and consistent results with SCFS. Demonstrated by our literature survey, the standard error of previously published SCFS results obtained with FluidFM ranges from 11.8% to 50%. The question arises whether this can be accounted for biological diversity or may be the consequence of improper calibration. Thus the aim of our work was to investigate the calibration accuracy of these parameters and their dependence on: (1) the aperture size (2, 4 and 8 µm) of the hollow micropipette type cantilever; (2) the position of the laser spot on the back of the cantilever; (3) the substrate used for calibration (silicon or polystyrene). It was found that both the obtained InvOLS and spring constant values depend significantly on the position of the laser spot. Apart from the theoretically expectable monotonous increase in InvOLS (from the tip to the base of the cantilever, as functions of the laser spot’s position), we discerned a well-defined and reproducible fluctuation, which can be as high as ±30%, regardless of the used aperture size or substrate. The calibration of spring constant also showed an error in the range of −13/+20%, measured at the first 40 µm of the cantilever. Based on our results a calibration strategy is proposed and the optimal laser position which yields the most reliable spring constant values was determined and found to be on the first pair of pillars. Our proposed method helps in reducing the error introduced via improper calibration and thus increases the reliability of subsequent cell adhesion force or elasticity measurements with FluidFM.
Identification and Characterization of Genetic Determinants of Isoniazid and Rifampicin Resistance in Mycobacterium tuberculosis in Southern India
Authors: Munir Asma , Kumar Narender , Ramalingam Suresh Babu , Tamilzhalagan Sembulingam , Shanmugam Siva Kumar , Palaniappan Alangudi Natarajan , Nair Dina , Priyadarshini Padma , Natarajan Mohan , Tripathy Srikanth , Ranganathan Uma Devi , Peacock Sharon J. , Parkhill Julian , Blundell Tom L. , Malhotra Sony 
Published: July 2019

AbstractDrug-resistant tuberculosis (TB), one of the leading causes of death worldwide, arises mainly from spontaneous mutations in the genome of Mycobacterium tuberculosis. There is an urgent need to understand the mechanisms by which the mutations confer resistance in order to identify new drug targets and to design new drugs. Previous studies have reported numerous mutations that confer resistance to anti-TB drugs, but there has been little systematic analysis to understand their genetic background and the potential impacts on the drug target stability and/or interactions. Here, we report the analysis of whole-genome sequence data for 98 clinical M. tuberculosis isolates from a city in southern India. The collection was screened for phenotypic resistance and sequenced to mine the genetic mutations conferring resistance to isoniazid and rifampicin. The most frequent mutation among isoniazid and rifampicin isolates was S315T in katG and S450L in rpoB respectively. The impacts of mutations on protein stability, protein-protein interactions and protein-ligand interactions were analysed using both statistical and machine-learning approaches. Drug-resistant mutations were predicted not only to target active sites in an orthosteric manner, but also to act through allosteric mechanisms arising from distant sites, sometimes at the protein-protein interface.
Alcohol Consumption During Pregnancy and Risk of Placental Abnormality: The Japan Environment and Children’s Study
Authors: Ohira Satoshi , Motoki Noriko , Shibazaki Takumi , Misawa Yuka , Inaba Yuji , Kanai Makoto , Kurita Hiroshi , Shiozawa Tanri , Nakazawa Yozo , Tsukahara Teruomi , Nomiyama Tetsuo ,   The Japan Environment & Children’s Study (JECS) Group, Kawamoto Toshihiro , Saito Hirohisa , Kishi Reiko , Yaegashi Nobuo , Hashimoto Koichi , Mori Chisato , Ito Shuichi , Yamagata Zentaro , Inadera Hidekuni , Kamijima Michihiro , Nakayama Takeo , Iso Hiroyasu , Shima Masayuki , Hirooka Yasuaki , Suganuma Narufumi , Kusuhara Koichi , Katoh Takahiko 
Published: July 2019

AbstractThere have been no large nationwide birth cohort studies examining for the effects of maternal alcohol use during pregnancy on placental abnormality. This study searched for associations between alcohol consumption and the placental abnormalities of placenta previa, placental abruption, and placenta accreta using the fixed dataset of a large national birth cohort study commencing in 2011 that included 80,020 mothers with a singleton pregnancy. The presence of placental abnormalities and potential confounding factors were recorded, and multiple logistic regression analysis was employed to search for correlations between maternal alcohol consumption during pregnancy and placental abnormalities. The overall rate of prenatal drinking until the second/third trimester was 2.7% (2,112). The prevalence of placenta previa, placental abruption, and placenta accreta was 0.58% (467), 0.43% (342), and 0.20% (160), respectively. After controlling for potential confounding factors, maternal alcohol use during pregnancy was significantly associated with the development of placenta accreta (OR 3.10, 95%CI 1.69-5.44). In conclusion, this large nationwide survey revealed an association between maternal drinking during pregnancy and placenta accreta, which may lead to excessive bleeding during delivery.
Ultra-fast genome comparison for large-scale genomic experiments
Authors: Pérez-Wohlfeil Esteban , Diaz-del-Pino Sergio , Trelles Oswaldo 
Published: July 2019

AbstractIn the last decade, a technological shift in the bioinformatics field has occurred: larger genomes can now be sequenced quickly and cost effectively, resulting in the computational need to efficiently compare large and abundant sequences. Furthermore, detecting conserved similarities across large collections of genomes remains a problem. The size of chromosomes, along with the substantial amount of noise and number of repeats found in DNA sequences (particularly in mammals and plants), leads to a scenario where executing and waiting for complete outputs is both time and resource consuming. Filtering steps, manual examination and annotation, very long execution times and a high demand for computational resources represent a few of the many difficulties faced in large genome comparisons. In this work, we provide a method designed for comparisons of considerable amounts of very long sequences that employs a heuristic algorithm capable of separating noise and repeats from conserved fragments in pairwise genomic comparisons. We provide software implementation that computes in linear time using one core as a minimum and a small, constant memory footprint. The method produces both a previsualization of the comparison and a collection of indices to drastically reduce computational complexity when performing exhaustive comparisons. Last, the method scores the comparison to automate classification of sequences and produces a list of detected synteny blocks to enable new evolutionary studies.