bluuebunny/crossref_metadata_2025 huggingface dataset:
Reengineering the specificity of the highly selective Clostridium botulinum protease via directed evolution
Authors: Dyer Rebekah P. , Isoda Hariny M. , Salcedo Gabriela S. , Speciale Gaetano , Fletcher Madison H. , Le Linh Q. , Liu Yi , Brami-Cherrier Karen , Malik Shiazah Z. , Vazquez-Cintron Edwin J. , Chu Andrew C. , Rupp David C. , Jacky Birgitte P. S. , Nguyen Thu T. M. , Katz Benjamin B. , Steward Lance E. , Majumdar Sudipta , Brideau-Andersen Amy D. , Weiss Gregory A.
Published: June 2022

The botulinum neurotoxin serotype A (BoNT/A) cuts a single peptide bond in SNAP25, an activity used to treat a wide range of diseases. Reengineering the substrate specificity of BoNT/A’s protease domain (LC/A) could expand its therapeutic applications; however, LC/A’s extended substrate recognition (≈ 60 residues) challenges conventional approaches. We report a directed evolution method for retargeting LC/A and retaining its exquisite specificity. The resultant eight-mutation LC/A (omLC/A) has improved cleavage specificity and catalytic efficiency (1300- and 120-fold, respectively) for SNAP23 versus SNAP25 compared to a previously reported LC/A variant. Importantly, the BoNT/A holotoxin equipped with omLC/A retains its ability to form full-length holotoxin, infiltrate neurons, and cleave SNAP23. The identification of substrate control loops outside BoNT/A’s active site could guide the design of improved BoNT proteases and inhibitors.
Effects of active, inactive, and derivatives of Akkermansia muciniphila on the expression of the endocannabinoid system and PPARs genes
Authors: Ghaderi Farinaz , Sotoodehnejadnematalahi Fattah , Hajebrahimi Zahra , Fateh Abolfazl , Siadat Seyed Davar
Published: June 2022

This study aimed to investigate the effects of active and heat-inactivated forms of Akkermansia muciniphila, bacterium-derived outer membrane vesicles (OMVs), and cell-free supernatant on the transcription of endocannabinoid system (ECS) members, including cannabinoid receptors 1 and 2 (CB1 and CB2), fatty acid amide hydrolase (FAAH), and peroxisome proliferator-activated receptors (PPARs) genes (i.e., α, β/δ, and δ) in Caco-2 and HepG-2 cell lines. After the inoculation of A. muciniphila in brain heart infusion enriched medium, OMVs and cell-free supernatant were extracted. For the investigation of the effects of bacteria and its derivatives on the expression of ECS and PPARs genes, the aforementioned cells were treated by active and heat-inactivated bacteria, OMVs, and cell-free supernatant. Quantitative real-time polymerase chain reaction analysis revealed that both forms of the bacterium, bacterial-derived OMVs, and cell-free supernatant could affect the expression of CB1, CB2, FAAH, and PPARs genes (i.e., α, β/δ, and δ) significantly (P < 0.05). Considering the engagement of the aforementioned genes in metabolic pathways, it might be suggested that both forms of the bacterium, OMVs, and cell-free supernatant might have the potential to serve as a probiotic, paraprobiotic, and postbiotic candidate to prevent obesity, metabolic disorders, and liver diseases.
Filamentous crystal growth in organic liquids and selection of crystal morphology
Authors: Yashima Takumi , Tani Marie , Kurita Rei
Published: June 2022

Filamentous crystals such as whisker crystals are often seen not only in metallic liquids, but also in organic liquids and solutions. They are interesting as reinforce materials. However, it remains challenging to induce filamentous crystals due to an incomplete understanding of the mechanisms behind their formation. In this paper, we investigate filamentous crystal growth in viscous organic liquids. It is found that filamentous crystals grow via an extraordinary dynamical path, where the molecules locally evaporate to bubbles and then redeposite to the tip of growing crystalline filaments. We also succeeded in controlling whether filamentous or faceted crystal growth is selected by inducing or suppressing the bubbles.
Genetic structure of American bullfrog populations in Brazil
Authors: Jorgewich-Cohen Gabriel , Toledo Luís Felipe , Grant Taran
Published: June 2022

Non-native species are a major problem affecting numerous biomes around the globe. Information on their population genetics is crucial for understanding their invasion history and dynamics. We evaluated the population structure of the non-native American bullfrog, Aquarana catesbeiana, in Brazil on the basis of 324 samples collected from feral and captive groups at 38 sites in seven of the nine states where feral populations occur. We genotyped all samples using previously developed, highly polymorphic microsatellite loci and performed a discriminant analysis of principal components together with Jost’s D index to quantify pairwise differentiation between populations. We then amplified 1,047 base pairs of the mitochondrial cytochrome b (cytb) gene from the most divergent samples from each genetic population and calculated their pairwise differences. Both the microsatellite and cytb data indicated that bullfrogs comprise two populations. Population grouping 1 is widespread and possesses two cytb haplotypes. Population grouping 2 is restricted to only one state and possesses only one of the haplotypes from Population grouping 1. We show that there were two imports of bullfrogs to Brazil and that there is low genetic exchange between population groupings. Also, we find that there is no genetic divergence among feral and captive populations suggesting continuous releases. The limited genetic variability present in the country is associated to the small number of introductions and founders. Feral bullfrogs are highly associated to leaks from farms, and control measures should focus on preventing escapes using other resources than genetics, as feral and captive populations do not differ.
Implementation of sodium alginate-Fe3O4 to localize undiagnosed small pulmonary nodules for surgical management in a preclinical rabbit model
Authors: Zhang Zhi-xuan , Lv Lu , Shi Ai-hua , Li Yun-hao , Wang Tian-ren , Guo Yuan-hang , Hu Bao-juan , Yan Xiao-peng , Fu Jun-ke , Ma Feng , Wang Hao-hua , Lv Yi , Zhang Yong
Published: June 2022

Many methods are used to locate preoperative small pulmonary nodules. However, deficiencies of complications and success rates exist. We introduce a novel magnetic gel for small pulmonary nodules localization in rabbit model, and furtherly evaluate its safety and feasibility. Rabbits were used as the experimental objects. A magnetic gel was used as a tracer magnet, mixed as sodium alginate-Fe3O4 magnetic fluid and calcium gluconate solution. In short-term localization, a coaxial double-cavity puncture needle was applied to inject the gel into the lung after thoracotomy, and a pursuit magnet made of Nd-Fe-B permanent magnetic materials was used to attract the gel representing location of the nodule. In long-term localization, the gel was injected under X-ray guidance. Imaging changes to the lung were observed under X-ray daily. Thoracotomy was performed to excise tissue containing the gel, and hematoxylin–eosin staining was used to observe the tissue on postoperative days 1, 3, 5, and 7. Observe tissues morphology of heart, liver, spleen, and kidney in the same way. The gel was formed after injection and drew lung tissue to form a protrusion from the lung surface under the applied magnetic field. No complication was observed. The shape and position of the gel had not changed when viewed under X-ray. Pathological analysis showed the gel had a clear boundary without diffusion of magnetic fluid. All tissues retained good histologic morphology and no magnetic fluid was observed. Our study preliminarily suggested that the technique using sodium alginate-Fe3O4 magnetic gel to locate small pulmonary nodules with guidance of X-ray, and to search for them under an applied magnetic field during the operation is safe and feasible.
Risk factors associated with the infection of sheep with Dichelobacter nodosus
Authors: Storms Julia , Wirth Anna , Vasiliadis Danae , Jores Jörg , Kuhnert Peter , Distl Ottmar
Published: June 2022

Ovine footrot is a highly contagious foot disease caused by the gram-negative bacterium Dichelobacter nodosus (D. nodosus). In a recent report, we showed a prevalence of 42.9% D. nodosus positive swabs across Germany. In this follow-up study, we used real-time PCR results for D. nodosus and footrot scores of 9297 sheep from 208 flocks and collated these data with survey data on herd and animal characteristics and herd management. The aims of the present study were to investigate herd and animal factors associated with D. nodosus infection and footrot scores in individual sheep. Multivariable analyses with generalized mixed models showed that month of recording, breed, herdbook membership, use of antibiotics, and footbaths in the past 3–10 years, signs of footrot in the past 12 months and flock environment of the sheep, modelled as a random farm effect within region, were significant risk factors. Among the 21 different breeds, Romney had the lowest risk of D. nodosus infection, while Swifter had the highest risk and German Merino and German White Heath were the next breeds at highest risk of D. nodosus infection. The variance between farms in the prevalence of D. nodosus was large and accounted for 84% of the total variance in the mixed model analysis. We conclude that specific and as yet unknown effects influencing D. nodosus infections in flocks, as well as breed and weather, are the most important effects on D. nodosus infection in sheep, pointing towards the need to establish adequate infection control at farm level.
Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations
Authors: Shimizu Masahiro , Okuda Aya , Morishima Ken , Inoue Rintaro , Sato Nobuhiro , Yunoki Yasuhiro , Urade Reiko , Sugiyama Masaaki
Published: June 2022

Solving structural ensembles of flexible biomolecules is a challenging research area. Here, we propose a method to obtain possible structural ensembles of a biomolecule based on small-angle X-ray scattering (SAXS) and molecular dynamics simulations. Our idea is to clip a time series that matches a SAXS profile from a simulation trajectory. To examine its practicability, we applied our idea to a multi-domain protein ER-60 and successfully extracted time series longer than 1 micro second from trajectories of coarse-grained molecular dynamics simulations. In the extracted time series, the domain conformation was distributed continuously and smoothly in a conformational space. Preferred domain conformations were also observed. Diversity among scattering curves calculated from each ER-60 structure was interpreted to reflect an open-close motion of the protein. Although our approach did not provide a unique solution for the structural ensemble of the biomolecule, each extracted time series can be an element of the real behavior of ER-60. Considering its low computational cost, our approach will play a key role to identify biomolecular dynamics by integrating SAXS, simulations, and other experiments.
Coplanar embedding of multiple 3D cell models in hydrogel towards high-throughput micro-histology
Authors: Heub Sarah , Navaee Fatemeh , Migliozzi Daniel , Ledroit Diane , Boder-Pasche Stéphanie , Goldowsky Jonas , Vuille-Dit-Bille Emilie , Hofer Joëlle , Gaiser Carine , Revol Vincent , Suter-Dick Laura , Weder Gilles
Published: June 2022

Standardised and high-throughput methods have been developed for the production and experimental handling of some 3D in vitro models. However, adapted analytical tools are still missing for scientists and researchers to fully exploit the potential of complex cellular models in pre-clinical drug testing and precision medicine. Histology is the established, cost-effective and gold standard method for structural and functional tissue analysis. However, standard histological processes are challenging and costly to apply to 3D cell models, as their small size often leads to poor alignment of samples, which lowers analysis throughput. This body of work proposes a new approach: HistoBrick facilitates histological processing of spheroids and organoids by enabling gel embedding of 3D cell models with precise coplanar alignment, parallel to the sectioning plane, thus minimising the loss of sample material. HistoBrick’s features are compatible with automation standards, potentially allowing automated sample transfer from a multi-well plate to the gel device. Moreover, HistoBrick’s technology was validated by demonstrating the alignment of HepG2 cultured spheroids measuring 150–200 µm in diameter with a height precision of ± 80 µm. HistoBrick allows up to 96 samples to be studied across minimal sections, paving the way towards high-throughput micro-histology.
Natural 2D layered mineral cannizzarite with anisotropic optical responses
Authors: Dasgupta Arindam , Yang Xiaodong , Gao Jie
Published: June 2022

Cannizzarite is a naturally occurring mineral formed by van der Waals (vdW) stacking of alternating layers of PbS-like and Bi2S3-like two-dimensional (2D) materials. Although the PbS-type and Bi2S3-type 2D material layers are structurally isotropic individually, the forced commensuration between these two types of layers while forming the heterostructure of cannizzarite induces strong structural anisotropy. Here we demonstrate the mechanical exfoliation of natural cannizzarite mineral to obtain thin vdW heterostructures of PbS-type and Bi2S3-type atomic layers. The structural anisotropy induced anisotropic optical properties of thin cannizzarite flakes are explored through angle-resolved polarized Raman scattering, linear dichroism, and polarization-dependent anisotropic third-harmonic generation. Our study establishes cannizzarite as a new natural vdW heterostructure-based 2D material with highly anisotropic optical properties for realizing polarization-sensitive linear and nonlinear photonic devices for future on-chip optical computing and optical information processing.
Splitting tensile strength and microstructure of xanthan gum-treated loess
Authors: Jiang Tong , Zhao Jin-di , Zhang Jun-ran
Published: June 2022

The tensile strength of loess is closely related to geological disasters. As eco-friendly materials, biopolymers have an excellent strengthening effect on the mechanical properties of soil. The effect of different initial dry densities and xanthan gum (XG) contents on the microstructure and mechanical behavior of XG-treated loess was studied with a series of microscopic tests and splitting tensile tests based on the particle image velocimetry technique. The results show that the XG became concentrated and agglomerated during dehydration, forming bridge links between soil particles and covering their surfaces. The XG-treated loess had a significant concentration of micropores and mesopores, with greater peak pore size distribution values than untreated loess. The specimens’ load–displacement curves with different XG contents and initial dry densities showed strain-softening. The displacement vector field indicated that specimens’ primary cracks were radial–vertical, and the secondary cracks were well-developed. The strain-softening phenomenon was more significant with increased XG content and initial dry density, and the specimens’ splitting tensile strength and brittleness increased. XG treatment gave the soils stronger cementation and a denser structure, helping to increase strength and brittleness. This research provides a scientific basis and practical experience for applying XG in geotechnical engineering.
Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum
Authors: De Vivo Mattia , Lee Hsin-Han , Huang Yu-Sin , Dreyer Niklas , Fong Chia-Ling , de Mattos Felipe Monteiro Gomes , Jain Dharmesh , Wen Yung-Hui Victoria , Mwihaki John Karichu , Wang Tzi-Yuan , Machida Ryuji J. , Wang John , Chan Benny K. K. , Tsai Isheng Jason
Published: June 2022

High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing of six gastropod mitogenomes (Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata) from a graduate level biodiversity course. The students were able to produce mitogenomes from sampling to annotation using existing protocols and programs. Approximately 4 Gb of sequence was produced from 16 Flongle and one MinION flow cells, averaging 235 Mb and N50 = 4.4 kb per flow cell. Five of the six 14.1–18 kb mitogenomes were circlised containing all 13 core protein coding genes. Additional Illumina sequencing revealed that the ONT assemblies spanned over highly AT rich sequences in the control region that were otherwise missing in Illumina-assembled mitogenomes, but still contained a base error of one every 70.8–346.7 bp under the fast mode basecalling with the majority occurring at homopolymer regions. Our findings suggest that the portable MinION device can be used to rapidly produce low-cost mitogenomes onsite and tailored to genomics-based training in biodiversity research.
Increased erosion of high-elevation land during late Cenozoic: evidence from detrital thermochronology off-shore Greenland
Authors: Olivetti Valerio , Cattò Silvia , Zattin Massimiliano
Published: June 2022

Mountain regions at high altitudes show deeply incised glacial valleys that coexist with a high-standing low-relief landscape, whose origin is largely debated. Whether the plateaus contributed to sediment production during the late Cenozoic is a currently debated issue in glacial geomorphology and paleoclimatology. In this study, we used detrital apatite fission-track dating of marine sediments to trace provenance and spatial variation in focused erosion over the last 7 million years. The decomposition of age distributions into populations reveals that, moving upwards through the sections, two young populations get younger, while two older populations get progressively older. We interpreted these trends as the effect of glacial erosion on the valley floors and an increased sediment contribution from the high elevations. To test this hypothesis, we compared the measured ages with synthetic age distributions, which represented a change in the elevation of focused erosion. We conclude that the central-eastern Greenland region is the main source of sediments, and in addition to enhanced valley incision, sediments have also been sourced from progressively higher elevations since 7 Ma. The ageing trend provides an unusual case in detrital thermochronology and a strong evidence that intensified Quaternary glaciations amplify the erosional process both in valley bottoms and at high elevations.
Correlations of FRMD7 gene mutations with ocular oscillations
Authors: Huang Lijuan , Zhou Yunyu , Chen Wencong , Lin Ping , Xie Yan , He Kaiwen , Zhang Shasha , Wu Yuyu , Li Ningdong
Published: June 2022

Mutations in the FERM domain containing 7 (FRMD7) gene have been proven to be responsible for infantile nystagmus (IN). The purpose of this study is to investigate FRMD7 gene mutations in patients with IN, and to evaluate the nystagmus intensity among patients with and without FRMD7 mutations. The affected males were subdivided into three groups according to whether or not having FRMD7 mutations and the types of mutations. Fifty-two mutations were detected in FRMD7 in 56 pedigrees and 34 sporadic patients with IN, including 28 novel and 24 previous reported mutations. The novel identified mutations further expand the spectrum of FRMD7 mutations. The parameters of nystagmus intensity and the patients’ best corrected visual acuity were not statistically different among the patients with and without identified FRMD7 mutations, and also not different among patients with different mutant types. The FERM-C domain, whose amino acids are encoded by exons 7, 8 and 9, could be the harbor region for most mutations. Loss-of-function is suggested to be the common molecular mechanism for the X-linked infantile nystagmus.
Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes
Authors: Chan Abigail Hui En , Saralamba Naowarat , Saralamba Sompob , Ruangsittichai Jiraporn , Chaisiri Kittipong , Limpanont Yanin , Charoennitiwat Vachirapong , Thaenkham Urusa
Published: June 2022

Next-generation sequencing technologies have accelerated the pace of helminth DNA metabarcoding research, enabling species detection in bulk community samples. However, finding suitable genetic markers with robust species-level resolution and primers targeting a broad species range among parasitic helminths are some of the challenges faced. This study aimed to demonstrate the potential use of the mitochondrial 12S and 16S rRNA genes for parasitic helminth (nematodes, trematodes, cestodes) DNA metabarcoding. To demonstrate the robustness of the 12S and 16S rRNA genes for DNA metabarcoding, we determined the proportion of species successfully recovered using mock helminth communities without environment matrix and mock helminth communities artificially spiked with environmental matrices. The environmental matrices are human fecal material, garden soil, tissue, and pond water. Our results revealed the robustness of the mitochondrial rRNA genes, through the high sensitivity of the 12S rRNA gene, and the effectiveness of the 12S and 16S primers targeting platyhelminths. With the mitochondrial rRNA genes, a broad range of parasitc helminths were successfully detected to the species level. The potential of the mitochondrial rRNA genes for helminth DNA metabarcoding was demonstrated, providing a valuable gateway for future helminth DNA metabarcoding applications like helminth detection and biodiversity studies.
Identification of miRNAs of Strongyloides stercoralis L1 and iL3 larvae isolated from human stool
Authors: Pomari Elena , Malerba Giovanni , Veschetti Laura , Franceschi Alessandra , Moron Dalla Tor Lucas , Deiana Michela , Degani Monica , Mistretta Manuela , Patuzzo Cristina , Ragusa Andrea , Mori Antonio , Bisoffi Zeno , Buonfrate Dora
Published: June 2022

Strongyloidiasis is a neglected tropical disease caused by the soil-transmitted nematode by Strongyloides stercoralis, that affects approximately 600 million people worldwide. In immunosuppressed individuals disseminated strongyloidiasis can rapidly lead to fatal outcomes. There is no gold standard for diagnosing strongyloidiasis, and infections are frequently misdiagnosed. A better understanding of the molecular biology of this parasite can be useful for example for the discovery of potential new biomarkers. Interestingly, recent evidence showed the presence of small RNAs in Strongyloididae, but no data was provided for S. stercoralis. In this study, we present the first identification of miRNAs of both L1 and iL3 larval stages of S. stercoralis. For our purpose, the aims were: (i) to analyse the miRNome of L1 and iL3 S. stercoralis and to identify potential miRNAs of this nematode, (ii) to obtain the mRNAs profiles in these two larval stages and (iii) to predict potential miRNA target sites in mRNA sequences. Total RNA was isolated from L1 and iL3 collected from the stool of 5 infected individuals. For the miRNAs analysis, we used miRDeep2 software and a pipeline of bio-informatic tools to construct a catalog of a total of 385 sequences. Among these, 53% were common to S. ratti, 19% to S. papillosus, 1% to Caenorhabditis elegans and 44% were novel. Using a differential analysis between the larval stages, we observed 6 suggestive modulated miRNAs (STR-MIR-34A-3P, STR-MIR-8397-3P, STR-MIR-34B-3P and STR-MIR-34C-3P expressed more in iL3, and STR-MIR-7880H-5P and STR-MIR-7880M-5P expressed more in L1). Along with this analysis, we obtained also the mRNAs profiles in the same samples of larvae. Multiple testing found 81 statistically significant mRNAs of the total 1553 obtained (FDR < 0.05; 32 genes expressed more in L1 than iL3; 49 genes expressed more in L3 than iL1). Finally, we found 33 predicted mRNA targets of the modulated miRNAs, providing relevant data for a further validation to better understand the role of these small molecules in the larval stages and their valuein clinical diagnostics.
Rapid but specific perceptual learning partially explains individual differences in the recognition of challenging speech
Authors: Banai Karen , Karawani Hanin , Lavie Limor , Lavner Yizhar
Published: June 2022

Perceptual learning for speech, defined as long-lasting changes in speech recognition following exposure or practice occurs under many challenging listening conditions. However, this learning is also highly specific to the conditions in which it occurred, such that its function in adult speech recognition is not clear. We used a time-compressed speech task to assess learning following either brief exposure (rapid learning) or additional training (training-induced learning). Both types of learning were robust and long-lasting. Individual differences in rapid learning explained unique variance in recognizing natural-fast speech and speech-in-noise with no additional contribution for training-induced learning (Experiment 1). Rapid learning was stimulus specific (Experiment 2), as in previous studies on training-induced learning. We suggest that rapid learning is key for understanding the role of perceptual learning in online speech recognition whereas longer training could provide additional opportunities to consolidate and stabilize learning.
Cell type matching in single-cell RNA-sequencing data using FR-Match
Authors: Zhang Yun , Aevermann Brian , Gala Rohan , Scheuermann Richard H.
Published: June 2022

Reference cell atlases powered by single cell and spatial transcriptomics technologies are becoming available to study healthy and diseased tissue at single cell resolution. One important use of these data resources is to compare cell types from new dataset with cell types in the reference atlases to evaluate their phenotypic similarities and differences, for example, for identifying novel cell types under disease conditions. For this purpose, rigorously-validated computational algorithms are needed to perform these cell type matching tasks that can compare datasets from different experiment platforms and sample types. Here, we present significant enhancements to FR-Match (v2.0)—a multivariate nonparametric statistical testing approach for matching cell types in query datasets to reference atlases. FR-Match v2.0 includes a normalization procedure to facilitate cross-platform cluster-level comparisons (e.g., plate-based SMART-seq and droplet-based 10X Chromium single cell and single nucleus RNA-seq and spatial transcriptomics) and extends the pipeline to also allow cell-level matching. In the use cases evaluated, FR-Match showed robust and accurate performance for identifying common and novel cell types across tissue regions, for discovering sub-optimally clustered cell types, and for cross-platform and cross-sample cell type matching.
TGR5 agonists induce peripheral and central hypersensitivity to bladder distension
Authors: Caldwell Ashlee , Grundy Luke , Harrington Andrea M. , Garcia-Caraballo Sonia , Castro Joel , Bunnett Nigel W. , Brierley Stuart M.
Published: June 2022

The mechanisms underlying chronic bladder conditions such as interstitial cystitis/bladder pain syndrome (IC/BPS) and overactive bladder syndrome (OAB) are incompletely understood. However, targeting specific receptors mediating neuronal sensitivity to specific stimuli is an emerging treatment strategy. Recently, irritant-sensing receptors including the bile acid receptor TGR5, have been identified within the viscera and are thought to play a key role in neuronal hypersensitivity. Here, in mice, we identify mRNA expression of TGR5 (Gpbar1) in all layers of the bladder as well as in the lumbosacral dorsal root ganglia (DRG) and in isolated bladder-innervating DRG neurons. In bladder-innervating DRG neurons Gpbar1 mRNA was 100% co-expressed with Trpv1 and 30% co-expressed with Trpa1. In vitro live-cell calcium imaging of bladder-innervating DRG neurons showed direct activation of a sub-population of bladder-innervating DRG neurons with the synthetic TGR5 agonist CCDC, which was diminished in Trpv1−/− but not Trpa1−/− DRG neurons. CCDC also activated a small percentage of non-neuronal cells. Using an ex vivo mouse bladder afferent recording preparation we show intravesical application of endogenous (5α-pregnan-3β-ol-20-one sulphate, Pg5α) and synthetic (CCDC) TGR5 agonists enhanced afferent mechanosensitivity to bladder distension. Correspondingly, in vivo intravesical administration of CCDC increased the number of spinal dorsal horn neurons that were activated by bladder distension. The enhanced mechanosensitivity induced by CCDC ex vivo and in vivo was absent using Gpbar1−/− mice. Together, these results indicate a role for the TGR5 receptor in mediating bladder afferent hypersensitivity to distension and thus may be important to the symptoms associated with IC/BPS and OAB.
Glutamine and norepinephrine in follicular fluid synergistically enhance the antioxidant capacity of human granulosa cells and the outcome of IVF-ET
Authors: Wang Lulu , Zhou Chengliang , Sun Junyan , Zhang Qiuwan , Lai Dongmei
Published: June 2022

An increasing number of studies demonstrate that changes in neurotransmitters metabolic levels in follicular fluid are directly related to oocyte maturation, fertilization, the quality of embryo and pregnancy rates. However, the relationship between the intra-follicular neurotransmitters and the function of granulosa cells (GCs), and the outcome of in vitro fertilization-embryo transfer (IVF-ET) is not clear. Human follicular fluid and cumulus GCs were harvested from large follicles obtained from patients undergoing IVF. Neurotransmitters and steroid hormones in follicular fluid were measured through liquid chromatography-tandem mass spectrometry (LC–MS/MS) and high-performance liquid chromatography-mass spectrometry (HPLC–MS/MS). Based on the content of glutamine (Gln) in follicular fluid, the samples were divided into two groups: high Gln level group and low Gln level group. The expression of proliferation-, steroidogenesis- and antioxidant-related genes in GCs was detected by qRT-PCR. In vitro, KGN cells were used to further verify the effects of Gln and NE on GCs function. Primary and secondary outcomes were the number of mature and retrieved oocytes, and the ratio of high-quality embryos, respectively. Gln (46.75 ± 7.74 μg/mL) and norepinephrine (NE, 0.20 ± 0.07 μg/mL) were abundant neurotransmitters in follicular fluid, and exhibited a significantly positive correlation (R = 0.5869, P < 0.005). In high Gln level group, the expression of proliferation, steroidogenesis and antioxidant-related genes in GCs were higher than those in low Gln level group, and the contents of estriol and E2 in follicular fluid were more abundant. Moreover, the concentrations of Gln and NE in follicular fluid showed significantly positive correlation with IDH1 expression in GCs (R = 0.3822, R = 0.4009, P < 0.05). Importantly, a significantly positive correlation was observed between IDH1 expression in GCs and the ratio of higher-quality/cleaved embryos (R = 0.4480, P < 0.05). In vitro studies further demonstrated that Gln and NE played synergistically function in improving GCs proliferation and E2 production by upregulating IDH1 expression. These data demonstrate that Gln and NE in follicular fluid might play significant positive roles in GCs function, and may be potential predictors for selecting optimal quality oocytes and evaluating the quality of embryonic development.
Bee pollen in zebrafish diet affects intestinal microbiota composition and skin cutaneous melanoma development
Authors: Di Chiacchio Isabela M. , Gómez-Abenza Elena , Paiva Isadora M. , de Abreu Danilo J. M. , Rodríguez-Vidal Juan Francisco , Carvalho Elisângela E. N. , Carvalho Stephan M. , Solis-Murgas Luis David , Mulero Victoriano
Published: June 2022

Bee pollen is recommended as dietary supplement due to immunostimulating functions including antioxidant, anti-inflammatory and anti-carcinogenic properties. Nevertheless, the effectiveness of such properties is still not well understood. As diet can be associated with animal performance, microbiota modulation and potentially factor for cancer, this study aimed to analyze if bee pollen could influence growth, gut microbial and skin cutaneous melanoma development in zebrafish. Control diets based on commercial flakes and Artemia were compared with the same diet supplemented with bee pollen. Fish weight gain, increased length, intestinal bacteria metagenomics analysis, serum amyloid A gene expression and cutaneous melanoma transplantation assays were performed. Bee pollen affected microbiota composition and melanoma development. Differential abundance revealed higher abundance in the control group for Aeromonadaceae family, Aeromonas and Pseudomonas genus, A. sobria, A. schubertii, A. jandaei and P. alcaligenes species compared with pollen diet group. Pollen group presented higher abundance for Chromobacterium genus and for Gemmobacter aquaticus, Flavobacterium succinicans and Bifidobacterium breve compared with control group. Unexpectedly, fish fed with bee pollen showed higher tumor growth rate and larger tumor size than control group. This is the first study to report intestinal microbial changes and no protective cancer properties after bee pollen administration.
Demographic characteristics shape patterns of dawn swarming during roost switching in tree-dwelling Daubenton’s bat
Authors: Ružinská Romana , Lőbbová Denisa , Kaňuch Peter
Published: June 2022

Frequent roost switching in fission–fusion societies of tree-dwelling bats is closely associated with swarming behaviour entailing ritualised night-time displays around the roost tree and/or at the roost entrance to signal its actual location, particularly immediately prior to sunrise. However, effects of demographic characteristics of individuals in this social behaviour remain unanswered. Using passive integrated transponders (PIT) and automatic readers, we recorded swarming activity of members of a Daubenton’s bat (Myotis daubentonii) maternity colony in the vicinity of their roosts. In total, 59,622 activity events of 281 PIT-tagged individuals were recorded on ten monitored roosts during three summer seasons. We found a gradual increase of swarming activity from midnight to sunrise in old adult females, whereas young females and juveniles primarily swarmed later at dawn. We attribute this difference to the learning status of younger bats, which are not yet able to perform a defined pattern of swarming activity, whereas older bats likely take a more active role in signalling the position of the roost. Old males exhibited the least swarming activity at maternity roosts, which mostly occurred between crepuscular periods, presumably due to their solitary lives. A negative correlation between genetic distance and swarming activity suggests an important role of kinship in the formation of the maternity colony as well as group cohesion during roost switching.
Comprehensive analysis of KCTD family genes associated with hypoxic microenvironment and immune infiltration in lung adenocarcinoma
Authors: Shi Yuan-Xiang , Zhang Wei-Dong , Dai Peng-Hui , Deng Jun , Tan Li-Hong
Published: June 2022

To obtain novel insights into the tumor biology and therapeutic targets of LUAD, we performed a comprehensive analysis of the KCTD family genes. The expression patterns and clinical significance of the KCTD family were identified through multiple bioinformatics mining. Moreover, the molecular functions and potential mechanisms of differentially expressed KCTDs were evaluated using TIMER 2.0, cBioPortal, GeneMANIA, LinkedOmics and GSEA. The results indicated that the mRNA and protein expression levels of KCTD9, KCTD10, KCTD12, KCTD15 and KCTD16 were significantly decreased in LUAD, while those of KCTD5 were significantly increased. High KCTD5 expression was significantly associated with advanced tumor stage, lymph node metastasis, TP53 mutation and poor prognosis. In addition, KCTD5 was positively correlated with CD8 + T cell, neutrophil, macrophage and dendritic cell infiltration. Additionally, KCTDs demonstrate promising prospects in the diagnosis of LUAD. Importantly, high KCTD5 expression was enriched in signaling pathways associated with the malignant progression of tumors, including the inflammatory response, the IL6/JAK/STAT3 signaling pathway, EMT and hypoxia. Further association analysis showed that KCTD5 was positively correlated with hypoxia-related genes such as HIF1. Overall, KCTDs can be used as molecular targets for the treatment of LUAD, as well as effective molecular biomarkers for diagnosis and prognosis prediction.
Information-optimal local features automatically attract covert and overt attention
Authors: Castellotti Serena , Montagnini Anna , Del Viva Maria Michela
Published: June 2022

In fast vision, local spatial properties of the visual scene can automatically capture the observer’s attention. We used specific local features, predicted by a constrained maximum-entropy model to be optimal information-carriers, as candidate “salient features''. Previous studies showed that participants choose these optimal features as “more salient” if explicitly asked. Here, we investigated the implicit saliency of these optimal features in two attentional tasks. In a covert-attention experiment, we measured the luminance-contrast threshold for discriminating the orientation of a peripheral gabor. In a gaze-orienting experiment, we analyzed latency and direction of saccades towards a peripheral target. In both tasks, two brief peripheral cues, differing in saliency according to the model, preceded the target, presented on the same (valid trials) or the opposite side (invalid trials) of the optimal cue. Results showed reduced contrast thresholds, saccadic latencies, and direction errors in valid trials, and the opposite in invalid trials, compared to baseline values obtained with equally salient cues. Also, optimal features triggered more anticipatory saccades. Similar effects emerged in a luminance-control condition. Overall, in fast vision, optimal features automatically attract covert and overt attention, suggesting that saliency is determined by information maximization criteria coupled with computational limitations.
Clusterin exacerbates interleukin-1β-induced inflammation via suppressing PI3K/Akt pathway in human fibroblast-like synoviocytes of knee osteoarthritis
Authors: Ungsudechachai Tachatra , Honsawek Sittisak , Jittikoon Jiraphun , Udomsinprasert Wanvisa
Published: June 2022

This study aimed to examine, a multifaceted chaperon-like protein exerting anti-inflammatory action, clusterin (CLU), mRNA and protein levels in the systemic and local joint environment of knee osteoarthritis (OA) patients and to determine whether CLU inhibited interleukin (IL)-1β-induced inflammation in knee OA fibroblast-like synoviocytes (FLSs) through modulating phosphatidylinositol-3-kinase (PI3K)/Akt signaling pathway. CLU protein and mRNA expressions in the synovium and its protein levels in plasma and synovial fluid of knee OA patients were measured using immunohistochemistry, real-time PCR, and ELISA, respectively. Anti-inflammatory effect of CLU was further elucidated in knee OA FLSs treated with IL-1β in the absence or presence of CLU, CLU alone, or PI3K inhibitor (LY294002) along with IL-1β and CLU. In a clinical study, compared with knee OA patients without synovitis, CLU protein and mRNA were expressed in the synovium of knee OA patients with synovitis, especially those with high-grade, consistent with analyses of its plasma and synovial fluid levels. CLU mRNA and protein levels were both associated with synovitis severity. An in vitro study uncovered that CLU significantly alleviated IL-1β-induced overproduction of nitric oxide and IL-6 in knee OA FLSs. Furthermore, CLU significantly attenuated inflammation and extracellular matrix degradation induced by IL-1β via down-regulating expressions of IL-6, nuclear factor kappa B, and matrix metalloproteinase-13. Mechanistically, CLU significantly impeded IL-1β-induced Akt phosphorylation in knee OA FLSs, in line with addition of LY294002 along with IL-1β and CLU. These findings suggest that CLU may have potential as a novel therapeutic target for synovitis and cartilage destruction in knee OA.
Microgeophysics and geomatics data integration reveals the internal fracturing conditions of the statue of Ramses II (Museo Egizio, Torino, Italy)
Authors: Colombero Chiara , Dabove P. , Grasso N. , Khosro Anjom F. , Pace F. , Aicardi S.
Published: June 2022

The combined acquisition of 3D ultrasonic tomography and radar scans is growing for cultural heritage diagnostics. Both methods proved to be efficient in the detection and location of fractures and weaknesses within the investigated artefacts. Although the two techniques are widely applied together, an integrated approach for data interpretation is still missing. We present the results of radar and ultrasonic prospections carried out on the statue of the young Ramses II, an absolute masterpiece of the Egyptian art preserved in the collection of the Museo Egizio of Torino (Italy). Geophysical results are incorporated within the 3D model of the statue retrieved from total station measurements, ground-based and handheld laser scanning. A data integration approach is then proposed for the joint interpretation of the geophysical results, exploiting the final ultrasonic velocity model and radar attribute analysis (i.e. local dissimilarity computation) to define a combined damage index. The proposed methodology is efficient in fracture detection and location and improves the readability of the final results also for non-expert geophysical interpreters, offering guidance to the museum for preservation and restoration of the masterpiece.
Ecohydrological effects of water conveyance in a disconnected river in an arid inland river basin
Authors: Chen Yaning , Chen Yapeng , Zhu Chenggang , Wang Yang , Hao Xingming
Published: June 2022

Water system management is a worldwide challenge, especially in arid and semi-arid regions. Ecological water conveyance projects aim to raise the groundwater table, thereby saving natural vegetation and curbing ecological deterioration. Since 2000, these projects have been implemented in the arid zone of northwest China, with generally successful outcomes. Taking a portion of the lower reaches of the Tarim River as the study area, this paper analyzes in detail the ecohydrological effects which have occurred since the launching of artificial water conveyance 20 years ago. The results show that the groundwater table in the upper, middle and lower segments of the Tarim River’s lower reaches has been raised on average 4.06, 4.83 and 5.13 m, respectively, while the area of surface water bodies connected to those sections has expanded from 49.00 km2 to 498.54 km2. At the same time, Taitema Lake, which is the terminal lake of the Tarim River, has been revived and now boasts a water area of 455.27 km2. Other findings indicate that the surface ecological response is extremely sensitive and that the area of natural vegetation has expanded to 1423 km2. Furthermore, the vegetation coverage, vegetation index (NDVI), and Net Primary Productivity (NPP) have increased by 132 km2, 0.07 and 7.6 g C m−2, respectively, and the Simpson dominance, McIntosh evenness, and Margalef richness indices have risen by 0.33, 0.35 and 0.49, respectively, in the monitored sample sites. As well, the carbon sink area has expanded from 1.54% to 7.8%. Given the increasing intensity of the occurrence of extreme hydrological events and successive dry years, similar ecological water conveyance projects should be considered elsewhere in China and in other parts of the world. The water conveyance scheme has generally proven successful and should be optimized to enhance the benefits of ecological water conveyance under water resource constraints.
Identification of ferroptosis-related genes for overall survival prediction in hepatocellular carcinoma
Authors: Luo Lianxiang , Yao Xinyue , Xiang Jing , Huang Fangfang , Luo Hui
Published: June 2022

Ferroptosis is a novel type of cell death depending on iron and is strongly related to the development of tumors. Hepatocellular carcinoma (HCC) is a malignancy with high incidence. Despite some reports demonstrating the relation between ferroptosis-related genes and HCC, more details have not been excavated. In the present study, we collected and analyzed HCC patients' datasets from the TCGA-LIHC project and ICGC portal, respectively. Through the bioinformatic methods, we screened 126 differentially expressed genes. Then a prognostic model was established with four genes (GPX2, MT3, PRDX1, and SRXN1). PRDX1 is the hub gene of the prognosis model and has a high expression in hepatocellular carcinoma tumor tissue and cell lines. We further found that silencing PRDX1 increased the accumulation of ferrous ions and lipid peroxidation accumulation in HEPG2 cells and promoted ferroptosis in hepatocellular carcinoma. In conclusion, the study demonstrated the four-gene signature can be used to predict HCC prognosis. It also revealed the potential function of the ferroptosis-related gene PRDX1 in HCC, which can be a biomarker of the prediction for HCC outcome.
Nanomechanical probing and strain tuning of the Curie temperature in suspended Cr2Ge2Te6-based heterostructures
Authors: Šiškins Makars , Kurdi Samer , Lee Martin , Slotboom Benjamin J. M. , Xing Wenyu , Mañas-Valero Samuel , Coronado Eugenio , Jia Shuang , Han Wei , van der Sar Toeno , van der Zant Herre S. J. , Steeneken Peter G.
Published: June 2022

Two-dimensional magnetic materials with strong magnetostriction are attractive systems for realizing strain-tuning of the magnetization in spintronic and nanomagnetic devices. This requires an understanding of the magneto-mechanical coupling in these materials. In this work, we suspend thin Cr2Ge2Te6 layers and their heterostructures, creating ferromagnetic nanomechanical membrane resonators. We probe their mechanical and magnetic properties as a function of temperature and strain by observing magneto-elastic signatures in the temperature-dependent resonance frequency near the Curie temperature, TC. We compensate for the negative thermal expansion coefficient of Cr2Ge2Te6 by fabricating heterostructures with thin layers of WSe2 and antiferromagnetic FePS3, which have positive thermal expansion coefficients. Thus we demonstrate the possibility of probing multiple magnetic phase transitions in a single heterostructure. Finally, we demonstrate a strain-induced enhancement of TC in a suspended Cr2Ge2Te6-based heterostructure by 2.5 ± 0.6 K by applying a strain of 0.026% via electrostatic force.