bluuebunny/crossref_metadata_2025 huggingface dataset:
Mutations associated with neuropsychiatric conditions delineate functional brain connectivity dimensions contributing to autism and schizophrenia
Authors: Moreau Clara A. , Urchs Sebastian G. W. , Kuldeep Kumar , Orban Pierre , Schramm Catherine , Dumas Guillaume , Labbe Aurélie , Huguet Guillaume , Douard Elise , Quirion Pierre-Olivier , Lin Amy , Kushan Leila , Grot Stephanie , Luck David , Mendrek Adrianna , Potvin Stephane , Stip Emmanuel , Bourgeron Thomas , Evans Alan C. , Bearden Carrie E. , Bellec Pierre , Jacquemont Sebastien
Published: October 2020

16p11.2 and 22q11.2 Copy Number Variants (CNVs) confer high risk for Autism Spectrum Disorder (ASD), schizophrenia (SZ), and Attention-Deficit-Hyperactivity-Disorder (ADHD), but their impact on functional connectivity (FC) remains unclear. Here we report an analysis of resting-state FC using magnetic resonance imaging data from 101 CNV carriers, 755 individuals with idiopathic ASD, SZ, or ADHD and 1,072 controls. We characterize CNV FC-signatures and use them to identify dimensions contributing to complex idiopathic conditions. CNVs have large mirror effects on FC at the global and regional level. Thalamus, somatomotor, and posterior insula regions play a critical role in dysconnectivity shared across deletions, duplications, idiopathic ASD, SZ but not ADHD. Individuals with higher similarity to deletion FC-signatures exhibit worse cognitive and behavioral symptoms. Deletion similarities identified at the connectivity level could be related to the redundant associations observed genome-wide between gene expression spatial patterns and FC-signatures. Results may explain why many CNVs affect a similar range of neuropsychiatric symptoms.
Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance
Authors: Herold Malte , Martínez Arbas Susana , Narayanasamy Shaman , Sheik Abdul R. , Kleine-Borgmann Luise A. K. , Lebrun Laura A. , Kunath Benoît J. , Roume Hugo , Bessarab Irina , Williams Rohan B. H. , Gillece John D. , Schupp James M. , Keim Paul S. , Jäger Christian , Hoopmann Michael R. , Moritz Robert L. , Ye Yuzhen , Li Sujun , Tang Haixu , Heintz-Buschart Anna , May Patrick , Muller Emilie E. L. , Laczny Cedric C. , Wilmes Paul
Published: October 2020

The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.
Single-cell transcriptomics identifies divergent developmental lineage trajectories during human pituitary development
Authors: Zhang Shu , Cui Yueli , Ma Xinyi , Yong Jun , Yan Liying , Yang Ming , Ren Jie , Tang Fuchou , Wen Lu , Qiao Jie
Published: October 2020

The anterior pituitary gland plays a central role in regulating various physiological processes, including body growth, reproduction, metabolism and stress response. Here, we perform single-cell RNA-sequencing (scRNA-seq) of 4113 individual cells from human fetal pituitaries. We characterize divergent developmental trajectories with distinct transitional intermediate states in five hormone-producing cell lineages. Corticotropes exhibit an early intermediate state prior to full differentiation. Three cell types of the PIT-1 lineage (somatotropes, lactotropes and thyrotropes) segregate from a common progenitor coexpressing lineage-specific transcription factors of different sublineages. Gonadotropes experience two multistep developmental trajectories. Furthermore, we identify a fetal gonadotrope cell subtype expressing the primate-specific hormone chorionic gonadotropin. We also characterize the cellular heterogeneity of pituitary stem cells and identify a hybrid epithelial/mesenchymal state and an early-to-late state transition. Here, our results provide insights into the transcriptional landscape of human pituitary development, defining distinct cell substates and subtypes and illustrating transcription factor dynamics during cell fate commitment.
A streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics
Authors: Fang Pan , Ji Yanlong , Silbern Ivan , Doebele Carmen , Ninov Momchil , Lenz Christof , Oellerich Thomas , Pan Kuan-Ting , Urlaub Henning
Published: October 2020

Regulation of protein N-glycosylation is essential in human cells. However, large-scale, accurate, and site-specific quantification of glycosylation is still technically challenging. We here introduce SugarQuant, an integrated mass spectrometry-based pipeline comprising protein aggregation capture (PAC)-based sample preparation, multi-notch MS3 acquisition (Glyco-SPS-MS3) and a data-processing tool (GlycoBinder) that enables confident identification and quantification of intact glycopeptides in complex biological samples. PAC significantly reduces sample-handling time without compromising sensitivity. Glyco-SPS-MS3 combines high-resolution MS2 and MS3 scans, resulting in enhanced reporter signals of isobaric mass tags, improved detection of N-glycopeptide fragments, and lowered interference in multiplexed quantification. GlycoBinder enables streamlined processing of Glyco-SPS-MS3 data, followed by a two-step database search, which increases the identification rates of glycopeptides by 22% compared with conventional strategies. We apply SugarQuant to identify and quantify more than 5,000 unique glycoforms in Burkitt’s lymphoma cells, and determine site-specific glycosylation changes that occurred upon inhibition of fucosylation at high confidence.
Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration
Authors: Rhoné Bénédicte , Defrance Dimitri , Berthouly-Salazar Cécile , Mariac Cédric , Cubry Philippe , Couderc Marie , Dequincey Anaïs , Assoumanne Aichatou , Kane Ndjido Ardo , Sultan Benjamin , Barnaud Adeline , Vigouroux Yves
Published: October 2020

Climate change is already affecting agro-ecosystems and threatening food security by reducing crop productivity and increasing harvest uncertainty. Mobilizing crop diversity could be an efficient way to mitigate its impact. We test this hypothesis in pearl millet, a nutritious staple cereal cultivated in arid and low-fertility soils in sub-Saharan Africa. We analyze the genomic diversity of 173 landraces collected in West Africa together with an extensive climate dataset composed of metrics of agronomic importance. Mapping the pearl millet genomic vulnerability at the 2050 horizon based on the current genomic-climate relationships, we identify the northern edge of the current areas of cultivation of both early and late flowering varieties as being the most vulnerable to climate change. We predict that the most vulnerable areas will benefit from using landraces that already grow in equivalent climate conditions today. However, such seed-exchange scenarios will require long distance and trans-frontier assisted migrations. Leveraging genetic diversity as a climate mitigation strategy in West Africa will thus require regional collaboration.
A role for tectorial membrane mechanics in activating the cochlear amplifier
Authors: Nankali Amir , Wang Yi , Strimbu Clark Elliott , Olson Elizabeth S. , Grosh Karl
Published: October 2020

The mechanical and electrical responses of the mammalian cochlea to acoustic stimuli are nonlinear and highly tuned in frequency. This is due to the electromechanical properties of cochlear outer hair cells (OHCs). At each location along the cochlear spiral, the OHCs mediate an active process in which the sensory tissue motion is enhanced at frequencies close to the most sensitive frequency (called the characteristic frequency, CF). Previous experimental results showed an approximate 0.3 cycle phase shift in the OHC-generated extracellular voltage relative the basilar membrane displacement, which was initiated at a frequency approximately one-half octave lower than the CF. Findings in the present paper reinforce that result. This shift is significant because it brings the phase of the OHC-derived electromotile force near to that of the basilar membrane velocity at frequencies above the shift, thereby enabling the transfer of electrical to mechanical power at the basilar membrane. In order to seek a candidate physical mechanism for this phenomenon, we used a comprehensive electromechanical mathematical model of the cochlear response to sound. The model predicts the phase shift in the extracellular voltage referenced to the basilar membrane at a frequency approximately one-half octave below CF, in accordance with the experimental data. In the model, this feature arises from a minimum in the radial impedance of the tectorial membrane and its limbal attachment. These experimental and theoretical results are consistent with the hypothesis that a tectorial membrane resonance introduces the correct phasing between mechanical and electrical responses for power generation, effectively turning on the cochlear amplifier.
Codon optimization with deep learning to enhance protein expression
Authors: Fu Hongguang , Liang Yanbing , Zhong Xiuqin , Pan ZhiLing , Huang Lei , Zhang HaiLin , Xu Yang , Zhou Wei , Liu Zhong
Published: October 2020

Heterologous expression is the main approach for recombinant protein production ingenetic synthesis, for which codon optimization is necessary. The existing optimization methods are based on biological indexes. In this paper, we propose a novel codon optimization method based on deep learning. First, we introduce the concept of codon boxes, via which DNA sequences can be recoded into codon box sequences while ignoring the order of bases. Then, the problem of codon optimization can be converted to sequence annotation of corresponding amino acids with codon boxes. The codon optimization models for Escherichia Coli were trained by the Bidirectional Long-Short-Term Memory Conditional Random Field. Theoretically, deep learning is a good method to obtain the distribution characteristics of DNA. In addition to the comparison of the codon adaptation index, protein expression experiments for plasmodium falciparum candidate vaccine and polymerase acidic protein were implemented for comparison with the original sequences and the optimized sequences from Genewiz and ThermoFisher. The results show that our method for enhancing protein expression is efficient and competitive.
Cardiovascular adaptation to simulated microgravity and countermeasure efficacy assessed by ballistocardiography and seismocardiography
Authors: Rabineau Jeremy , Hossein Amin , Landreani Federica , Haut Benoit , Mulder Edwin , Luchitskaya Elena , Tank Jens , Caiani Enrico G. , van de Borne Philippe , Migeotte Pierre-François
Published: October 2020

Head-down bed rest (HDBR) reproduces the cardiovascular effects of microgravity. We tested the hypothesis that regular high-intensity physical exercise (JUMP) could prevent this cardiovascular deconditioning, which could be detected using seismocardiography (SCG) and ballistocardiography (BCG). 23 healthy males were exposed to 60-day HDBR: 12 in a physical exercise group (JUMP), the others in a control group (CTRL). SCG and BCG were measured during supine controlled breathing protocols. From the linear and rotational SCG/BCG signals, the integral of kinetic energy ($$iK$$

iK

) was computed on each dimension over the cardiac cycle. At the end of HDBR, BCG rotational $$iK$$

iK

and SCG transversal $$iK$$

iK

decreased similarly for all participants (− 40% and − 44%, respectively, p < 0.05), and so did orthostatic tolerance (− 58%, p < 0.01). Resting heart rate decreased in JUMP (− 10%, p < 0.01), but not in CTRL. BCG linear $$iK$$

iK

decreased in CTRL (− 50%, p < 0.05), but not in JUMP. The changes in the systolic component of BCG linear iK were correlated to those in stroke volume and VO2 max (R = 0.44 and 0.47, respectively, p < 0.05). JUMP was less affected by cardiovascular deconditioning, which could be detected by BCG in agreement with standard markers of the cardiovascular condition. This shows the potential of BCG to easily monitor cardiac deconditioning.
High-field superconductivity in C-doped MgB2 bulk samples prepared by a rapid synthesis route
Authors: Matera D. , Bonura M. , Černý R. , McKeown Walker S. , Buta F. , LeBoeuf D. , Chaud X. , Giannini E. , Senatore C.
Published: October 2020

The upper critical field sets the thermodynamic limit to superconductivity. A big gap is present between the upper-critical-field values measured in MgB2 polycrystalline bulk superconductors and those of thin films, where values as high as ~ 50 T have been achieved at 4.2 K. Filling this gap would unlock the potential of MgB2 for magnet applications. This work presents the results of an extensive experimental campaign on MgB2 bulk samples, which has been guided by a Design of Experiment. We modeled the dependence of the upper critical field on the main synthesis parameters and established a new record (~ 35 T at 4.2 K) preparing C-doped bulk samples by a non-conventional rapid-synthesis route. This value appears to be an upper boundary for the upper critical field in bulk samples. Structural disorder in films seems to act selectively on one of the two bands where superconductivity in MgB2 takes place: this enhances the upper critical field while reducing the critical temperature only by few Kelvins. On the other hand, the critical temperature in bulk samples decreases monotonically when structural disorder increases, and this imposes a limit to the maximum achievable upper critical field.
Riparian and in-channel habitat properties linked to dragonfly emergence
Authors: O’Malley Zoë G. , Compson Zacchaeus G. , Orlofske Jessica M. , Baird Donald J. , Curry R. Allen , Monk Wendy A.
Published: October 2020

In freshwater ecosystems, habitat alteration contributes directly to biodiversity loss. Dragonflies are sentinel species that are key invertebrate predators in both aquatic (as larvae) and terrestrial ecosystems (as adults). Understanding the habitat factors affecting dragonfly emergence can inform management practices to conserve habitats supporting these species and the functions they perform. Transitioning from larvae to adults, dragonflies leave behind larval exoskeletons (exuviae), which reveal information about the emergent population without the need for sacrificing living organisms. Capitalizing on Atlantic Canada’s largest freshwater wetland, the Grand Lake Meadows (GLM) and the associated Saint John/Wolastoq River (SJWR), we studied the spatial (i.e., across the mainstem, tributary, and wetland sites) and temporal (across 3 years) variation in assemblages of emergent dragonflies (Anisoptera) and assessed the relative contribution of aquatic and terrestrial factors structuring these assemblages. The GLM complex, including the lotic SJWR and its tributaries and associated lentic wetlands, provided a range of riparian and aquatic habitat variability ideal for studying dragonfly emergence patterns across a relatively homogenous climatic region. Emergent dragonfly responses were associated with spatial, but not temporal, variation. Additionally, dragonfly communities were associated with both aquatic and terrestrial factors, while diversity was primarily associated with terrestrial factors. Specific terrestrial factors associated with the emergence of the dragonfly community included canopy cover and slope, while aquatic factors included water temperature, dissolved oxygen, and baseflow. Our results indicate that management of river habitats for dragonfly conservation should incorporate riparian habitat protection while maintaining aquatic habitat and habitat quality.
Multiple mutations in the EPSPS and ALS genes of Amaranthus hybridus underlie resistance to glyphosate and ALS inhibitors
Authors: García Maria J. , Palma-Bautista Candelario , Vazquez-Garcia José G. , Rojano-Delgado Antonia M. , Osuna María D. , Torra Joel , De Prado Rafael
Published: October 2020

Amaranthus hybridus is one of the main weed species in Córdoba, Argentina. Until recently, this weed was effectively controlled with recurrent use of glyphosate. However, a population exhibiting multiple resistance (MR2) to glyphosate and imazamox appeared in a glyphosate resistant (GR) soybean field, with levels of resistance up to 93 and 38-fold higher to glyphosate and imazamox, respectively compared to the susceptible (S) population. In addition to imidazolinones, MR2 plants showed high resistance levels to sulfonylamino-carbonyl (thio) benzoates and moderate resistance to sulfonylureas and triazolopyrimidines. Multiple amino acid substitutions were found in both target genes, acetolactate synthase (ALS) and 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), responsible for conferring high herbicides resistance levels in this A. hybridus population. In the case of EPSPS, the triple amino acid substitution TAP-IVS was found. In addition, MR2 plants also showed increased EPSPS gene expression compared to susceptible plants. A Ser653Asn substitution was found in the ALS sequence of MR2, explaining the pattern of cross-resistance to the ALS-inhibitor herbicide families found at the ALS enzyme activity level. No other mutations were found in other conserved domains of the ALS gene. This is the first report worldwide of the target site resistance mechanisms to glyphosate and ALS inhibitors in multiple herbicide resistance Amaranthus hybridus.
Health system utilization before age 1 among children later diagnosed with autism or ADHD
Authors: Engelhard Matthew M. , Berchuck Samuel I. , Garg Jyotsna , Henao Ricardo , Olson Andrew , Rusincovitch Shelley , Dawson Geraldine , Kollins Scott H.
Published: October 2020

Children with autism spectrum disorder (ASD) or attention deficit hyperactivity disorder (ADHD) have 2–3 times increased healthcare utilization and annual costs once diagnosed, but little is known about their utilization patterns early in life. Quantifying their early health system utilization could uncover condition-specific health trajectories to facilitate earlier detection and intervention. Patients born 10/1/2006–10/1/2016 with ≥ 2 well-child visits within the Duke University Health System before age 1 were grouped as ASD, ADHD, ASD + ADHD, or No Diagnosis using retrospective billing codes. An additional comparison group was defined by later upper respiratory infection diagnosis. Adjusted odds ratios (AOR) for hospital admissions, procedures, emergency department (ED) visits, and outpatient clinic encounters before age 1 were compared between groups via logistic regression models. Length of hospital encounters were compared between groups via Mann–Whitney U test. In total, 29,929 patients met study criteria (ASD N = 343; ADHD N = 1175; ASD + ADHD N = 140). ASD was associated with increased procedures (AOR = 1.5, p < 0.001), including intubation and ventilation (AOR = 2.4, p < 0.001); and outpatient specialty care, including physical therapy (AOR = 3.5, p < 0.001) and ophthalmology (AOR = 3.1, p < 0.001). ADHD was associated with increased procedures (AOR = 1.41, p < 0.001), including blood transfusion (AOR = 4.7, p < 0.001); hospital admission (AOR = 1.60, p < 0.001); and ED visits (AOR = 1.58, p < 0.001). Median length of stay was increased after birth in ASD (+ 6.5 h, p < 0.001) and ADHD (+ 3.8 h, p < 0.001), and after non-birth admission in ADHD (+ 1.1 d, p < 0.001) and ASD + ADHD (+ 2.4 d, p = 0.003). Each condition was associated with increased health system utilization and distinctive patterns of utilization before age 1. Recognizing these patterns may contribute to earlier detection and intervention.
New fossil from mid-Cretaceous Burmese amber confirms monophyly of Liadopsyllidae (Hemiptera: Psylloidea)
Authors: Drohojowska Jowita , Szwedo Jacek , Müller Patrick , Burckhardt Daniel
Published: October 2020

Amecephala pusillagen. et sp. nov. is described and illustrated on the basis of a well-preserved female psyllid (Liadopsyllidae) in a piece of Cretaceous Myanmar amber. The new genus differs from other members of Liadopsyllidae in details of the antennae and forewings. For the first time, the presence of a circumanal ring is documented for Mesozoic psyllids. Based on differences in the length of female terminalia, it is suggested that Liadopsyllidae may have displayed a diversified oviposition biology. As far as known, Liadopsyllidae lack a pulvillus, a putative autapomorphy supporting the monophyly of Liadopsyllidae. An identification key to genera and an annotated checklist of known Liadopsyllidae species are provided. New synonyms and combinations are proposed and the status of the subfamily Miralinae is discussed.
Propagation of optically tunable coherent radiation in a gas of polar molecules
Authors: Gładysz Piotr , Wcisło Piotr , Słowik Karolina
Published: October 2020

Coherent, optically dressed media composed of two-level molecular systems without inversion symmetry are considered as all-optically tunable sources of coherent radiation in the microwave domain. A theoretical model and a numerical toolbox are developed to confirm the main finding: the generation of low-frequency radiation, and the buildup and propagation dynamics of such low-frequency signals in a medium of polar molecules in a gas phase. The physical mechanism of the signal generation relies on the permanent dipole moment characterizing systems without inversion symmetry. The molecules are polarized with a DC electric field yielding a permanent electric dipole moment in the laboratory frame; the direction and magnitude of the moment depend on the molecular state. As the system is resonantly driven, the dipole moment oscillates at the Rabi frequency and, hence, generates microwave radiation. We demonstrate the tuning capability of the output signal frequency with the drive amplitude and detuning. We find that even though decoherence mechanisms such as spontaneous emission may damp the output field, a scenario based on pulsed illumination yields a coherent, pulsed output of tunable temporal width. Finally, we discuss experimental scenarios exploiting rotational levels of gaseous ensembles of heteronuclear diatomic molecules.
Heat-responsive and time-resolved transcriptome and metabolome analyses of Escherichia coli uncover thermo-tolerant mechanisms
Authors: Kim Sinyeon , Kim Youngshin , Suh Dong Ho , Lee Choong Hwan , Yoo Seung Min , Lee Sang Yup , Yoon Sung Ho
Published: October 2020

Current understanding of heat shock response has been complicated by the fact that heat stress is inevitably accompanied by changes in specific growth rates and growth stages. In this study, a chemostat culture was successfully performed to avoid the physico-chemical and biological changes that accompany heatshock, which provided a unique opportunity to investigate the full range of cellular responses to thermal stress, ranging from temporary adjustment to phenotypic adaptation at multi-omics levels. Heat-responsive and time-resolved changes in the transcriptome and metabolome of a widely used E. coli strain BL21(DE3) were explored in which the temperature was upshifted from 37 to 42 °C. Omics profiles were categorized into early (2 and 10 min), middle (0.5, 1, and 2 h), and late (4, 8, and 40 h) stages of heat stress, each of which reflected the initiation, adaptation, and phenotypic plasticity steps of the stress response. The continued heat stress modulated global gene expression by controlling the expression levels of sigma factors in different time frames, including unexpected downregulation of the second heatshock sigma factor gene (rpoE) upon the heat stress. Trehalose, cadaverine, and enterobactin showed increased production to deal with the heat-induced oxidative stress. Genes highly expressed at the late stage were experimentally validated to provide thermotolerance. Intriguingly, a cryptic capsular gene cluster showed considerably high expression level only at the late stage, and its expression was essential for cell growth at high temperature. Granule-forming and elongated cells were observed at the late stage, which was morphological plasticity occurred as a result of acclimation to the continued heat stress. Whole process of thermal adaptation along with the genetic and metabolic changes at fine temporal resolution will contribute to far-reaching comprehension of the heat shock response. Further, the identified thermotolerant genes will be useful to rationally engineer thermotolerant microorganisms.
Identification of quantitative trait loci associated with canopy temperature in soybean
Authors: Bazzer Sumandeep K. , Purcell Larry C.
Published: October 2020

A consistent risk for soybean (Glycine max L.) production is the impact of drought on growth and yield. Canopy temperature (CT) is an indirect measure of transpiration rate and stomatal conductance and may be valuable in distinguishing differences among genotypes in response to drought. The objective of this study was to map quantitative trait loci (QTLs) associated with CT using thermal infrared imaging in a population of recombinant inbred lines developed from a cross between KS4895 and Jackson. Heritability of CT was 35% when estimated across environments. QTL analysis identified 11 loci for CT distributed on eight chromosomes that individually explained between 4.6 and 12.3% of the phenotypic variation. The locus on Gm11 was identified in two individual environments and across environments and explained the highest proportion of phenotypic variation (9.3% to 11.5%) in CT. Several of these CT loci coincided with the genomic regions from previous studies associated with canopy wilting, canopy temperature, water use efficiency, and other morpho-physiological traits related with drought tolerance. Candidate genes with biological function related to transpiration, root development, and signal transduction underlie these putative CT loci. These genomic regions may be important resources in soybean breeding programs to improve tolerance to drought.
Behavioral and neurophysiological taste responses to sweet and salt are diminished in a model of subclinical intestinal inflammation
Authors: Pittman David W. , Dong Guangkuo , Brantly Alexandra M. , He Lianying , Nelson Tyler S. , Kogan Schuyler , Powell Julia , McCluskey Lynnette Phillips
Published: October 2020

There is strong evidence for gut-taste bud interactions that influence taste function, behavior and feeding. However, the effect of gut inflammation on this axis is unknown despite reports of taste changes in gastrointestinal (GI) inflammatory conditions. Lipopolysaccharide (LPS), an inflammatory stimulus derived from gram-negative bacteria, is present in the normal GI tract and levels increase during high-fat feeding and gut infection and inflammation. Recordings from the chorda tympani nerve (CT), which transmits taste information from taste buds on the anterior tongue to the brain, previously revealed a transient decrease in sucrose responses in mice that ingest LPS during a single overnight period. Here we test the effect of acute or chronic, weekly LPS gavage on licking behavior and CT responses. Using brief-access testing, rats treated with acute LPS and mice receiving acute or chronic LPS decreased licking responses to sucrose and saccharin and to NaCl in mice. In long-term (23 h) tests chronic LPS also reduced licking responses to saccharin, sucrose, and NaCl in mice. Neurophysiological recordings from the CT supported behavioral changes, demonstrating reduced responses to sucrose, saccharin, acesulfame potassium, glucose and NaCl in acute and chronic LPS groups compared to controls. Chronic LPS significantly elevated neutrophils in the small intestine and colon, but LPS was not detected in serum and mice did not display sickness behavior or lose weight. These results indicate that sweet and salt taste sensitivity could be reduced even in asymptomatic or mild localized gut inflammatory conditions such as inflammatory bowel disease.
Fecal microbiota transplantation from warthog to pig confirms the influence of the gut microbiota on African swine fever susceptibility
Authors: Zhang Jinya , Rodríguez Fernando , Navas Maria Jesus , Costa-Hurtado Mar , Almagro Vanessa , Bosch-Camós Laia , López Elisabeth , Cuadrado Raul , Accensi Francesc , Pina-Pedrero Sonia , Martínez Jorge , Correa-Fiz Florencia
Published: October 2020

African swine fever virus (ASFV) is the causative agent of a devastating hemorrhagic disease (ASF) that affects both domestic pigs and wild boars. Conversely, ASFV circulates in a subclinical manner in African wild pigs, including warthogs, the natural reservoir for ASFV. Together with genetic differences, other factors might be involved in the differential susceptibility to ASF observed among Eurasian suids (Sus scrofa) and African warthogs (Phacochoerus africanus). Preliminary evidence obtained in our laboratory and others, seems to confirm the effect that environmental factors might have on ASF infection. Thus, domestic pigs raised in specific pathogen-free (SPF) facilities were extremely susceptible to highly attenuated ASFV strains that were innocuous to genetically identical domestic pigs grown on conventional farms. Since gut microbiota plays important roles in maintaining intestinal homeostasis, regulating immune system maturation and the functionality of the innate/adaptive immune responses, we decided to examine whether warthog fecal microbiota transplantation (FMT) to domestic pigs affects host susceptibility to ASFV. The present work demonstrates that warthog FMT is not harmful for domestic weaned piglets, while it modifies their gut microbiota; and that FMT from warthogs to pigs confers partial protection against attenuated ASFV strains. Future work is needed to elucidate the protective mechanisms exerted by warthog FMT.
Adjustments of cardiac mitochondrial phenotype in a warmer thermal habitat is associated with oxidative stress in European perch, Perca fluviatilis
Authors: Pichaud Nicolas , Ekström Andreas , Breton Sophie , Sundström Fredrik , Rowinski Piotr , Blier Pierre U. , Sandblom Erik
Published: October 2020

Mitochondria are playing key roles in setting the thermal limits of fish, but how these organelles participate in selection mechanisms during extreme thermal events associated with climate warming in natural populations is unclear. Here, we investigated the thermal effects on mitochondrial metabolism, oxidative stress, and mitochondrial gene expression in cardiac tissues of European perch (Perca fluviatilis) collected from an artificially heated ecosystem, the “Biotest enclosure”, and an adjacent reference area in the Baltic sea with normal temperatures (~ 23 °C and ~ 16 °C, respectively, at the time of capture in summer). Fish were sampled one month after a heat wave that caused the Biotest temperatures to peak at ~ 31.5 °C, causing significant mortality. When assayed at 23 °C, Biotest perch maintained high mitochondrial capacities, while reference perch displayed depressed mitochondrial functions relative to measurements at 16 °C. Moreover, mitochondrial gene expression ofnd4(mitochondrial subunit of complex I) was higher in Biotest fish, likely explaining the increased respiration rates observed in this population. Nonetheless, cardiac tissue from Biotest perch displayed higher levels of oxidative damage, which may have resulted from their chronically warm habitat, as well as the extreme temperatures encountered during the preceding summer heat wave. We conclude that eurythermal fish such as perch are able to adjust and maintain mitochondrial capacities of highly aerobic organs such as the heart when exposed to a warming environment as predicted with climate change. However, this might come at the expense of exacerbated oxidative stress, potentially threatening performance in nature.
Prediction of genome-wide effects of single nucleotide variants on transcription factor binding
Authors: Carrasco Pro Sebastian , Bulekova Katia , Gregor Brian , Labadorf Adam , Fuxman Bass Juan Ignacio
Published: October 2020

Single nucleotide variants (SNVs) located in transcriptional regulatory regions can result in gene expression changes that lead to adaptive or detrimental phenotypic outcomes. Here, we predict gain or loss of binding sites for 741 transcription factors (TFs) across the human genome. We calculated ‘gainability’ and ‘disruptability’ scores for each TF that represent the likelihood of binding sites being created or disrupted, respectively. We found that functional cis-eQTL SNVs are more likely to alter TF binding sites than rare SNVs in the human population. In addition, we show that cancer somatic mutations have different effects on TF binding sites from different TF families on a cancer-type basis. Finally, we discuss the relationship between these results and cancer mutational signatures. Altogether, we provide a blueprint to study the impact of SNVs derived from genetic variation or disease association on TF binding to gene regulatory regions.
Rapid production of SARS-CoV-2 receptor binding domain (RBD) and spike specific monoclonal antibody CR3022 in Nicotiana benthamiana
Authors: Rattanapisit Kaewta , Shanmugaraj Balamurugan , Manopwisedjaroen Suwimon , Purwono Priyo Budi , Siriwattananon Konlavat , Khorattanakulchai Narach , Hanittinan Oranicha , Boonyayothin Wanuttha , Thitithanyanont Arunee , Smith Duncan R. , Phoolcharoen Waranyoo
Published: October 2020

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the ongoing global outbreak of coronavirus disease (COVID-19) which is a significant threat to global public health. The rapid spread of COVID-19 necessitates the development of cost-effective technology platforms for the production of vaccines, drugs, and protein reagents for appropriate disease diagnosis and treatment. In this study, we explored the possibility of producing the receptor binding domain (RBD) of SARS-CoV-2 and an anti-SARS-CoV monoclonal antibody (mAb) CR3022 in Nicotiana benthamiana. Both RBD and mAb CR3022 were transiently produced with the highest expression level of 8 μg/g and 130 μg/g leaf fresh weight respectively at 3 days post-infiltration. The plant-produced RBD exhibited specific binding to the SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2). Furthermore, the plant-produced mAb CR3022 binds to SARS-CoV-2, but fails to neutralize the virus in vitro. This is the first report showing the production of anti-SARS-CoV-2 RBD and mAb CR3022 in plants. Overall these findings provide a proof-of-concept for using plants as an expression system for the production of SARS-CoV-2 antigens and antibodies or similar other diagnostic reagents against SARS-CoV-2 rapidly, especially during epidemic or pandemic situation.
Distribution, characteristics of extracellular polymeric substances of Phanerochaete chrysosporium under lead ion stress and the influence on Pb removal
Authors: Li Ningjie , Liu Jie , Yang Rui , Wu Lei
Published: October 2020

The distribution, characteristics of extracellular polymeric substances (EPS) of Phanerochaete chrysosporium under Pb2+ stress and the influence on Pb removal were investigated. Polysaccharides was found to be the main composition in both soluble EPS (SEPS) and bounded EPS (BEPS). More polysaccharides and protein in BEPS were detected with the increased Pb2+ concentration. The ratio of Pb amount distributed in BEPS to the total Pb removed by the fungal biomass gradually decreased from 91.66 to 61.27% in group with 50 mg/L of initial Pb2+, but kept at about 35% or 25% in groups with higher Pb2+. It implies that BEPS played a certain role in the lead removal process, and the role of BEPS was relatively more important in the removal of lower concentration of Pb2+ and in the initial period of Pb removal. With FTIR analysis and Pb2+ adsorption experiment, more effective functional groups and better Pb2+ adsorption capacity was demonstrated in BEPS than in SEPS. SEM–EDS analysis demonstrated that part of Pb immobilized in BEPS was in the form of Pb precipitation. The increased molecular weight in SEPS and more polysaccharides in BEPS were probably beneficial for the adhesion of Pb precipitation.
Antimicrobial photodynamic activity of gallium-substituted haemoglobin on silver nanoparticles
Authors: Morales-de-Echegaray Ana V. , Lin Lu , Sivasubramaniam Badhu , Yermembetova Aiganym , Wang Qi , Abutaleb Nader S. , Seleem Mohamed N. , Wei Alexander
Published: October 2020

Methicillin-resistantStaphylococcus aureus(MRSA), a major scourge in skin and soft-tissue infections, expresses surface-bound haemoprotein receptors that can be exploited for the targeted delivery of photosensitizers.
Retraction: Aqueous synthesis of human serum albumin-stabilized fluorescent Au/Ag core/shell nanocrystals for highly sensitive and selective sensing of copper(ii)
Authors: Ross Philippa
Published: October 2020

Retraction of ‘Aqueous synthesis of human serum albumin-stabilized fluorescent Au/Ag core/shell nanocrystals for highly sensitive and selective sensing of copper(ii)’ by Rijun Gui et al., Analyst, 2013, 138, 7197–7205, DOI: 10.1039/C3AN01397A.
Retraction: Facile synthesis of quantum dots/mesoporous silica/quantum dots core/shell/shell hybrid microspheres for ratiometric fluorescence detection of 5-fluorouracil in human serum
Authors: Ross Philippa
Published: October 2020

Retraction of ‘Facile synthesis of quantum dots/mesoporous silica/quantum dots core/shell/shell hybrid microspheres for ratiometric fluorescence detection of 5-fluorouracil in human serum’ by Rijun Gui et al., Analyst, 2013, 138, 5956–5964, DOI: 10.1039/C3AN01089A
Retraction: Upconversion luminescent logic gates and turn-on sensing of glutathione based on two-photon excited quantum dots conjugated with dopamine
Authors: Kelly Richard
Published: October 2020

Retraction of ‘Upconversion luminescent logic gates and turn-on sensing of glutathione based on two-photon excited quantum dots conjugated with dopamine’ by Rijun Gui et al., Chem. Commun., 2014, 50, 14847–14850, DOI: 10.1039/C4CC06181K.
Self-assembly of a highly stable and active Co3O4/H-TiO2 bulk heterojunction with high-energy interfacial structures for low temperature CO catalytic oxidation
Authors: Xu Zehai , Yin Qingchuan , Li Xiong , Meng Qin , Xu Lusheng , Lv Boshen , Zhang Guoliang
Published: October 2020

Self-assembly of a highly stable and active Co3O4/H-TiO2 bulk heterojunction with high-energy interfacial structures was realized for low temperature CO catalytic oxidation.
Surface defect-rich g-C3N4/TiO2 Z-scheme heterojunction for efficient photocatalytic antibiotic removal: rational regulation of free radicals and photocatalytic mechanism
Authors: Ning Pei , Chen Huayu , Pan Jianhui , Liang Junhui , Qin Laishun , Chen Da , Huang Yuexiang
Published: October 2020

Surface defect engineering was employed to introduce two different surface defect structures (i.e., nitrogen vacancies on g-C3N4 and oxygen vacancies on TiO2) on the surface of g-C3N4/TiO2 for efficient photocatalytic antibiotic removal.
Rh promoted In2O3 as a highly active catalyst for CO2 hydrogenation to methanol
Authors: Dostagir Nazmul Hasan MD , Thompson Coogan , Kobayashi Hirokazu , Karim Ayman M. , Fukuoka Atsushi , Shrotri Abhijit
Published: October 2020

Atomically dispersed Rh promoted the activity of In2O3 for methanol formation from CO2, inducing strong CO2 adsorption and enhanced formate formation.
Retraction: A facile cation exchange-based aqueous synthesis of highly stable and biocompatible Ag2S quantum dots emitting in the second near-infrared biological window
Authors: Shore Andrew
Published: October 2020

Retraction of ‘A facile cation exchange-based aqueous synthesis of highly stable and biocompatible Ag2S quantum dots emitting in the second near-infrared biological window’ by Rijun Gui et al., Dalton Trans., 2014, 43, 16690–16697, DOI: 10.1039/C4DT00699B.
Comparative study of DHA-enriched phosphatidylcholine and EPA-enriched phosphatidylcholine on ameliorating high bone turnoverviaregulation of the osteogenesis-related Wnt/β-catenin pathway in ovariectomized mice
Authors: Fu Meng , Tian Yingying , Zhang Tianqi , Zhan Qiping , Zhang Lei , Wang Jingfeng
Published: October 2020

This study comparatively investigated the effects of DHA-PC and EPA-PC on osteogenesisviaregulating Wnt/β-catenin pathway.
Molecular-scale thermoelectricity: as simple as ‘ABC’
Authors: Ismael Ali , Al-Jobory Alaa , Wang Xintai , Alshehab Abdullah , Almutlg Ahmad , Alshammari Majed , Grace Iain , Benett Troy L. R. , Wilkinson Luke A. , Robinson Benjamin J. , Long Nicholas J. , Lambert Colin
Published: October 2020

If the Seebeck coefficient of single molecules or self-assembled monolayers could be predicted from measurements of their conductance–voltage (G–V) characteristics alone, then the difficult experimental task of measuring their thermoelectric properties could be avoided.
Construction of series-wound architectures composed of metal–organic framework-derived hetero-(CoFe)Se2 hollow nanocubes confined into a flexible carbon skeleton as a durable sodium storage anode
Authors: Ma Xiaoqing , Chen Jie , Zhao Wenxi
Published: October 2020

Metal chalcogenides with structural pulverization/degradation and intrinsic low electrical conductivity trigger the challenging issues of serious capacity fading and inferior rate capability upon repeated de-/sodiation cycling.
Isolation of DNA aptamers targeting N-cadherin and high-efficiency capture of circulating tumor cells by using dual aptamers
Authors: Gao Tian , Ding Pi , Li Wenjing , Wang Zhili , Lin Qiao , Pei Renjun
Published: October 2020

Isolation of anti-N-cadherin DNA aptamers and high-efficiency capture of circulating tumor cells using dual aptamers targeting EpCAM and N-cadherin.
Facile synthesis of norbornene–ethylene–vinyl acetate/vinyl alcohol multiblock copolymers by the olefin cross-metathesis of polynorbornene with poly(5-acetoxy-1-octenylene)
Authors: Denisova Yulia I. , Roenko Alexey V. , Adzhieva Olga A. , Gringolts Maria L. , Shandryuk Georgiy A. , Peregudov Alexander S. , Finkelshtein Eugene Sh. , Kudryavtsev Yaroslav V.
Published: October 2020

New norbornene−ethylene–vinyl acetate/vinyl alcohol multiblock copolymers are synthesized via the olefin cross-metathesis reaction of polynorbornene with poly(5-acetoxy-1-octenylene) followed by CC bond hydrogenation and acetoxy group deprotection.
Rational molecular design of anion exchange membranes functionalized with alicyclic quaternary ammonium cations
Authors: Pham Thanh Huong , Allushi Andrit , Olsson Joel S. , Jannasch Patric
Published: October 2020

Piperidine-based cations tethered to ether-free polymer membranes via the 4-position instead of the conventional 1(N)-position show significantly improved thermal and alkaline stability while retaining high hydroxide conductivity.
Cellulose-based polyacetals by direct and sensitized photocationic ring-opening polymerization of levoglucosenyl methyl ether
Authors: Kaya Kerem , Debsharma Tapas , Schlaad Helmut , Yagci Yusuf
Published: October 2020

Polyacetal homopolymers and block copolymers are produced by photochemically initiated cationic ring-opening polymerization (CROP).
Optical-switchable energy transfer controlled by multiple-responsive turn-on fluorescence via metal–ligand and host–guest interactions in diarylethene-based [2]pseudo-rotaxane polymers
Authors: Singh Ravinder , Xiao Chi-Chong , Wei Chong-Lun , Ho Feng-Cheng , Khang Trang Manh , Gouda Chinmayananda , Wu Tung-Kung , Li Yaw-Kuen , Wei Kung-Hwa , Lin Hong-Cheu
Published: October 2020

Multi-responsive and optically-active diarylethene (DAE)-based [2]pseudo-rotaxane polymers were prepared via host–guest interactions of Zn2+ coordinated with two terpyridyl ligands bearing crown-ethers as an energy donor host and DAE containing two ammonium salts as an acceptor guest.
Acetone-derived luminescent polymer dots: a facile and low-cost synthesis leads to remarkable photophysical properties
Authors: Mucha Sebastian G. , Firlej Lucyna , Bantignies Jean-Louis , Żak Andrzej , Samoć Marek , Matczyszyn Katarzyna
Published: October 2020

Acetone-derived polymer dots (PDs) have been fabricated, according to a base-mediated synthesis route at room temperature. As-obtained hydrophobic and hydrophilic PDs revealed a strong greenish-blue emission due to the crosslink-enhanced effect.
Self-template formation of porous Co3O4hollow nanoprisms for non-enzymatic glucose sensing in human serum
Authors: Ge Danhua , Yang Yunqi , Ni Xiao , Dong Jinnan , Qiu Qianying , Chu Xue-Qiang , Chen Xiaojun
Published: October 2020

Co3O4hollow nanoprisms based non-enzymatic glucose sensor were prepared by a self-template process, exhibiting wide linear range, good selectivity and stability, which can directly monitoring blood glucose without any dilution pretreatment.
Simultaneous determination of methadone and morphine at a modified electrode with 3D β-MnO2nanoflowers: application for pharmaceutical sample analysis
Authors: Akbari Sedigheh , Jahani Shohreh , Foroughi Mohammad Mehdi , Hassani Nadiki Hadi
Published: October 2020

Electrochemical sensor based on β-MnO2nanoflower-modified glassy carbon electrode for the simultaneous detection of methadone and morphine was fabricated.
Vilsmeier reagent, NaHSe and diclofenac acid chloride: one-pot synthesis of a novel selenoindolinone with potent anticancer activity
Authors: Ruberte Ana Carolina , Aydillo Carlos , Sharma Arun K. , Sanmartín Carmen , Plano Daniel
Published: October 2020

An effective and straightforward synthesis of 3-seleno functionalized indolinone (5) involving Vilsmeier reagent is presented.
Amphipathic helical peptide-based fluorogenic probes for a marker-free analysis of exosomes based on membrane-curvature sensing
Authors: Sato Yusuke , Kuwahara Kazuki , Mogami Kenta , Takahashi Kenta , Nishizawa Seiichi
Published: October 2020

Fluorogenic probes based on membrane curvature sensing-amphipathic helical peptides have been developed for a marker-free exosome analysis.
Synthesis of aryl azide chain-end functionalized N-linked glycan polymers and their photo-labelling of specific protein
Authors: Chan Ka Keung , Lei Qiaoshi , Tang Jinshan , Sun Xue-Long
Published: October 2020

We report a straightforward synthesis of aryl azide chain-end functionalized N-linked glycan polymers and its application for affinity-assisted photo-labelling of specific protein.
Understanding the geometric diversity of inorganic and hybrid frameworks through structural coarse-graining
Authors: Nicholas Thomas C. , Goodwin Andrew L. , Deringer Volker L.
Published: October 2020

A coarse-graining approach enables structural comparisons across vastly different chemical spaces, from inorganic polymorphs to hybrid framework materials.
Unusual light-driven amplification through unexpected regioselective photogeneration of five-membered azaheterocyclic AIEgen
Authors: Li Qiyao , Gong Junyi , Li Ying , Zhang Ruoyao , Wang Haoran , Zhang Jianquan , Yan He , Lam Jacky W. Y. , Sung Herman H. Y. , Williams Ian D. , Kwok Ryan T. K. , Li Min-Hui , Wang Jianguo , Tang Ben Zhong
Published: October 2020

A multifunctional, AIE-based, fused five-membered azaheterocycle is photogenerated with light-driven amplification to combat the photobleaching issue and fabricate display materials.
Layer-by-layer assembly of inorganic–organic molybdovanadogermanic (GeMoV)-polyluminol composite electrodes for capacitive charge storage
Authors: N'Diaye Jeanne , Siddiqui Shaheer , Pak Kin Long (Thomas) , Lian Keryn
Published: October 2020

Synergy between a redox active polymer and a polyoxometalate leading to an extended voltage window and capacitive charge storage.