bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cranial implant for stabilizing whole-cell patch-clamp recordings in behaving rodents
Authors: Dacre Joshua , Sanchez-Rivera Michelle , Schiemann Julia , Currie Stephen , Ammer Julian J. , Duguid Ian 
Published: February 2023

AbstractBackgroundIn vivopatch-clamp recording techniques provide access to the sub- and suprathreshold membrane potential dynamics of individual neurons during behavior. However, maintaining recording stability throughout behavior is a significant challenge, and while methods for head restraint are commonly used to enhance stability, behaviorally related brain movement relative to the skull can severely impact the success rate and duration of whole-cell patch-clamp recordings.New methodWe developed a low-cost, biocompatible, and 3D-printable cranial implant capable of locally stabilizing brain movement, while permitting equivalent access to the brain when compared to a conventional craniotomy.ResultsExperiments in head-restrained behaving mice demonstrate that the cranial implant can reliably reduce the amplitude and speed of brain displacements, significantly improving the success rate of recordings across repeated bouts of motor behavior.Comparison with existing methodsOur solution offers an improvement on currently available strategies for brain stabilization. Due to its small size, the implant can be retrofitted to most in vivo electrophysiology recording setups, providing a low cost, easily implementable solution for increasing intracellular recording stability in vivo.ConclusionsBy facilitating stable whole-cell patch-clamp recordings in vivo, biocompatible 3D printed implants should accelerate the investigation of single neuron computations underlying behavior.
ABCH2 transporter in the first line of defense protects malaria vectors from pyrethroids
Authors: Kefi Mary , Balabanidou Vasileia , Sarafoglou Chara , Charamis Jason , Lycett Gareth , Ranson Hilary , Gouridis Giorgos , Vontas John 
Published: February 2023

AbstractContact insecticides are primarily used for the control ofAnophelesmalaria vectors. These chemicals penetrate mosquito legs and other appendages, the first barrier to reaching their neuronal targets. An ATP-Binding Cassette transporter from the H family (ABCH2) is highly expressed inAnopheles coluzziilegs, and further induced upon insecticide exposure. RNAi-mediated silencing of the ABCH2 caused a significant increase in deltamethrin mortality compared to control mosquitoes, coincident with a corresponding increase in14C-deltamethrin penetration. RT-qPCR analysis and immunolocalization revealed that ABCH2 is mainly localized in the legs and head appendages, and more specifically, the apical part of appendage epidermis, underneath the cuticle. To unravel the molecular mechanism underlying the role of ABCH2 in modulating pyrethroid toxicity, two hypotheses were investigated: An indirect role, based on the orthology with other insect ABCH transporters involved with lipid transport and deposition of CHC lipids inAnopheleslegs which may increase cuticle thickness, slowing down the penetration rate of deltamethrin; or the direct pumping of deltamethrin out of the organism. Evaluation of the leg cuticular hydrocarbon (CHC) content showed that this was not affected by ABCH2 silencing, indicating this transporter in is not associated with the transport of leg CHCs. Homology-based modeling suggested that the ABCH2 half-transporter adopts a physiological homodimeric state, in line with its ability to hydrolyze ATPin vitrowhen expressed on its own in insect cells. Docking analysis revealed a deltamethrin pocket on the homodimeric transporter. Furthermore, deltamethrin-induced ATP hydrolysis in ABCH2-expressing cell membranes, further supports that deltamethrin is indeed a ABCH2 substrate. Overall, our findings pinpoint ABCH2 as a key regulator of deltamethrin toxicity.
Two waves of evolution in the rodent pregnancy-specific glycoprotein (PSG) gene family lead to structurally diverse PSGs
Authors: Kammerer Robert , Zimmermann Wolfgang 
Published: February 2023

ABSTRACTThe evolution of pregnancy-specific glycoproteins (PSGs) within the CEA gene family of primates correlates with the evolution of hemochorial placentation about 45 Myr ago. Thus, we hypothesized that hemochorial placentation with intimate contact between fetal cells and maternal immune cells favors the evolution and expansion of PSGs. With only a few exceptions, all rodents have hemochorial placentas thus the question arises whether PSGs evolved in most rodent genera.Analyzing genomic data of 94 rodent species we could identify PSGs only in three families of the suborder Myomorpha (characteristic species in brackets) namely in the Muridae (mouse), Cricetidae (hamster) and Nesomyidae (giant pouched rat) families. No PSGs were detected in the suborders Anomaluromorpha (springhare), Castorimorpha (beaver), Hystricognatha (guinea pig) and Sciuromorpha (squirrel). Thus, PSGs evolved only recently in Myomorpha shortly upon their most recent common ancestor (MRCA) has coopted the retroviral genes syncytin-A and syncytin-B which enabled the evolution of the three-layered trophoblast. This may suggest that the evolution ofPsgsin rodents may have been favored by the challenge of the newly invented architecture of the maternal-fetal interface. In addition, a second hallmark of rodent PSG evolution seems to be the translocation of genes from the CEA gene family locus into a unique genomic region. Rodents without PSGs do not have any CEA-related genes in this locus. In contrast, rodent species in which PSGs evolved have lost ITAM-encoding CEACAM genes indicating that such a gene was translocated and thereby destroyed to form the new rodent PSG locus. This locus contains at least onePsgandCeacam9indicating that one of them was the founder gene of rodentPsgs. These genes are composed of various numbers of IgV-like domains (N domains) and one carboxy-terminal IgC-like domain of the A2-type. In a second wave of gene amplification in the PSG locus a gene encoding a protein composed of two N domain gave rise to four genes in mice (Ceacam11-14). In light of the divergent structure of PSGs in various mammalian species, we hypothesized that theCeacam11-14encode also functional PSGs and indeed we found that they are preferentially expressed by spongiotrophoblast cells, likePsggenes.
Comparing the transmission of carbapenemase-producing and extended-spectrum beta-lactamase-producingEscherichia colibetween broiler chickens
Authors: Dankittipong Natcha , Alderliesten Jesse B. , Van den Broek Jan , Dame-Korevaar M. Anita , Brouwer Michael S. M. , Velkers Francisca C. , Bossers Alex , de Vos Clazien J. , Wagenaar Jaap A. , Stegeman J. Arjan , Fischer Egil A. J. 
Published: February 2023

AbstractThe emergence of carbapenemase-producingEnterobacteriaceae(CPE) is a threat to public health, because of their resistance to clinically important carbapenem antibiotics. The emergence of CPE in meat-producing animals is particularly worrying because consumption of meat contaminated with resistant bacteria similar to CPE, such as extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, contributed to colonization in humans worldwide. Currently, no data on the transmission of CPE in livestock is available. We performed a transmission experiment to quantify the transmission of CPE between broilers to fill this knowledge gap and to compare the transmission rates of CPE and other antibiotic-resistantE. coli.A total of 180 Ross 308 broiler chickens were distributed on the day of hatch (day 0) over 12 pens. On day 5, half of the chickens in each pen were orally inoculated with 5·102colony-forming units of CPE, ESBL, or chloramphenicol-resistantE. coli(catA1). Amoxicillin drinking water treatment was given twice daily in 6 of the 12 pens from days 2 to 6 to evaluate the effect of antibiotic treatment on the transmission rates. Cloacal swabs of all animals were taken to determine the number of infectious broilers. We used a Bayesian hierarchical model to quantify the transmission of theE. colistrains.E. colican survive in the environment and serve as a reservoir. Therefore, the susceptible-infectious transmission model was adapted to account for the transmission of resistant bacteria from the environment. In addition, the caecal microbiome was analyzed on day 5 and at the end of the experiment on day 14 to assess the relationship between the caecal microbiome and the transmission rates.The transmission rates of CPE were 52 – 68 per cent lower compared to ESBL and catA1, but it is not clear if these differences were caused by differences between the resistance genes or between theE. colistrains. Differences between the groups in transmission rates and microbiome diversity did not correspond to each other, indicating that differences in transmission rates were probably not caused by major differences in the community structure in the caecal microbiome. Amoxicillin treatment from day 2 to 6 increased the transmission rate more than three-fold in all inoculums. It also increased alpha-diversity compared to untreated animals on day 5, but not on day 14, suggesting only a temporary effect.Future research could incorporate more complex transmission models with different species of resistant bacteria into the Bayesian hierarchical model.
Alpha-synuclein oligomers activate NFAT proteins modulating synaptic homeostasis and apoptosis
Authors: Sant’Anna Ricardo , Robbs Bruno K , de Freitas Júlia Araújo , dos Santos Patrícia Pires , König Annekatrin , Outeiro Tiago Fleming , Foguel Debora 
Published: February 2023

AbstractSoluble oligomeric forms of alpha-synuclein (aSyn-O) are believed to be one of the main toxic species in Parkinson’s disease (PD) leading to degeneration. aSyn-O can induce Ca2+influx, over activating downstream pathways leading to PD phenotype. Calcineurin (CN), a phosphatase regulated by Ca2+levels, activates NFAT transcription factors that are involved in the regulation of neuronal plasticity, growth and survival. Here, we investigate NFAT’s role in neuronal degeneration induced by aSyn-O. aSyn-O are toxic to neurons leading to cell death, loss of neuron ramification and reduction of synaptic proteins which are reversed by CN inhibition with ciclosporin-A or VIVIT, a NFAT specific inhibitor. aSyn-O induce NFAT nuclear translocation and transactivation. We found that aSyn-O modulates the gene involved in the maintenance of synapses, synapsin 1 (Syn 1). Syn1 mRNA and protein and synapticpunctaare drastically reduced in cells treated with aSyn-O which are reversed by NFAT inhibition. For the first time a direct role of NFAT in aSyn-O-induced toxicity andSyn1gene regulation was demonstrated, enlarging our understanding of the pathways underpinnings synucleinopathies.
Observation of coordinated cotranscriptional RNA folding events
Authors: Szyjka Courtney E. , Strobel Eric J. 
Published: February 2023

AbstractRNA begins to fold as it is transcribed by an RNA polymerase. Consequently, RNA folding is constrained by the direction and rate of transcription. Understanding how RNA folds into secondary and tertiary structures therefore requires methods for determining the structure of cotranscriptional folding intermediates. Cotranscriptional RNA chemical probing methods accomplish this by systematically probing the structure of nascent RNA that is displayed from RNA polymerase. Here, we have developed a concise, high-resolution cotranscriptional RNA chemical probing procedure calledTranscriptionElongationComplex RNA structureprobing-Multilength (TECprobe-ML). We validated TECprobe-ML by replicating and extending previous analyses of ZTP and fluoride riboswitch folding, and mapped the folding pathway of a ppGpp-sensing riboswitch. In each system, TECprobe-ML identified coordinated cotranscriptional folding events that mediate transcription antitermination. Our findings establish TECprobe-ML as an accessible method for mapping cotranscriptional RNA folding pathways.
Pathways to cultural adaptation: the coevolution of cumulative culture and social networks
Authors: Smolla Marco , Akçay Erol 
Published: February 2023

AbstractHumans have adapted to an immense array of ecologies by accumulating culturally transmitted knowledge and skills. Culture accumulates in at least two ways: via more distinct cultural traits, or via improvements of existing cultural trait. A trade-off is expected between these owing to the fact that social learning opportunities are finite and social learning often requires multiple exposures. Furthermore, what kind of culture accumulates depends on, and coevolves with, the social structure of societies. Here we show that the coevolution of social networks for learning and cumulative culture results in two distinct pathways to cultural adaptation: highly connected populations with high proficiency but low cultural trait diversity vs. sparsely connected populations with low proficiency but more cultural trait diversity. Importantly, we show there is a general conflict between group-level payoffs, which is maximised in highly connected groups that attain high proficiency, and individual level selection, which favours disconnection. This conflict emerges from the interaction of social learning with population structure and causes populations to cycle between the two cultural and network states. The same conflict creates a paradox where improving individual innovation rates lowers the payoffs of groups. Finally, we explore how populations navigate these two pathways in heterogeneous and changing environments, and show that high heterogeneity in payoffs and slow rate of environmental change favours high proficiency, while fast rate of environmental change favours more trait diversity. We also find that the proficiency pathway to cultural adaptation is favoured with increased population size, but only in slow changing environments. Our results uncover previously unrecognised trade-offs and tensions in the coevolutionary dynamics of cumulative culture and social structure, with broad implications for human social evolution.
Internalization-Responsive Nano-PLGA For Image-Guided Photodynamic Therapy Against HER2-Positive Breast Cancer
Authors: Sogomonyan Anna S. , Deyev Sergey M. , Shipunova Victoria O. 
Published: February 2023

AbstractOncotheranostic nanoagents are powerful artificial tools that significantly outperform traditional antitumor therapies. Among the wide variety of nanoagents, polymer nanoparticles have proven to be one of the most successful candidates for translation into clinical practice. Here we developed an oncotheranostic platform that is based on poly(lactic-co-glycolic acid) nanoparticles and possesses red/green light dual-activated diagnostic/therapeutic properties for targeted photodynamic therapy of HER2-positive aggressive breast cancer. PLGA nanoparticles were loaded with a red light-activated dye Nile Blue with pronounced solvatochromic properties for diagnostic applications and with a green light-activated photodynamic sensitizer Rose Bengal for photodynamic therapy. Targeted delivery was ensured by the non-covalent decoration of nanoparticles with anti-HER2 antibodies, which can be readily adapted for large-scale biotechnological production.In vitroandin vivostudies proved the effectiveness of red light-mediated HER2-specific imaging and green light-induced cytotoxicity of anti-HER2 PLGA. Interestingly, these particles fluoresced only after cellular internalization, which minimizes background signals inside the organism, thus facilitating real-time diagnostics. The particles allowed efficient and selective visualization of the HER2-positive primary tumor node and metastases spread and led to complete remission in BALB/c Nu/Nu mice with the HER2-positive xenografts after a single session of photodynamic therapy.
Zebra finches use brightness cues for gap selection in flight
Authors: Borsier Emma , Taylor Graham K. 
Published: February 2023

AbstractFlying animals that are adapted to life in cluttered environments require effective and robust guidance mechanisms to avoid collisions. Birds and insects use optic flow cues to avoid obstacles when flying, but these are only generated by self-motion and are likely to be used in conjunction with other cues such as visual contrast between foreground and background objects. Orchid bees use a strategy based on relative brightness to find clear paths through dense environments. To investigate the possibility that birds use a similar strategy, we presented zebra finchesTaeniopygia guttatawith symmetric or asymmetric brightness distributions behind the aperture of a tunnel and recorded their flight through it. The background brightness conditions influenced both the birds’ decision to enter the tunnel and their flight direction upon exit. Zebra finches were more likely to initiate flight through the tunnel if they could see a bright background through its aperture and were more likely to fly to the bright side on exiting the tunnel. We found no evidence of a centring response during gap negotiation; instead, the zebra finches entered the tunnel by turning tightly around its near edge. These results hint at a possible pre-planning of the trajectories before the onset of flight.
CryoPPP: A Large Expert-Labelled Cryo-EM Image Dataset for Machine Learning Protein Particle Picking
Authors: Dhakal Ashwin , Gyawali Rajan , Wang Liguo , Cheng Jianlin 
Published: February 2023

AbstractCryo-electron microscopy (cryo-EM) is currently the most powerful technique for determining the structures of large protein complexes and assemblies. Picking single-protein particles from cryo-EM micrographs (images) is a key step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though the emerging machine learning-based particle picking can potentially automate the process, its development is severely hindered by lack of large, high-quality, manually labelled training data. Here, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for single protein particle picking and analysis to address this bottleneck. It consists of manually labelled cryo-EM micrographs of 32 non-redundant, representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). It includes 9,089 diverse, high-resolution micrographs (∼300 cryo-EM images per EMPIAR dataset) in which the coordinates of protein particles were labelled by human experts. The protein particle labelling process was rigorously validated by both 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of machine learning and artificial intelligence methods for automated cryo-EM protein particle picking. The dataset and data processing scripts are available athttps://github.com/BioinfoMachineLearning/cryoppp
In-vivo subdermal implant in the alpha-Gal knockout mice model for the assessment of bioprosthetic heart valve calcification rate before and after a polyphenols-based treatment
Authors: Naso Filippo , Colli Andrea , Zilla Peter , Calafiore Antonio Maria , Lotan Chaim , Padalino Massimo A , Sturaro Giulio , Gandaglia Alessandro , Spina Michele 
Published: February 2023

ABSTRACTRationaleThe presence of preformed antibodies against αGal in the human lead to opsonization of the implanted bioprosthetic heart valve (BHV), leading to deterioration and calcification. Murine subcutaneous implantation of BHVs leaflets has been widely used for testing the efficacy of anti-calcification treatments, however, unlike the situation in humans, leaflets implanted into a murine model will not be able to elicit an αGal immune response because both donor and recipient species constitutively express the epitope.ObjectiveThis study evaluates the calcium deposition on commercial BHV using a new humanized murine αGal knockout (KO) animal model. Furtherly, the anti-calcification efficacy of a polyphenol-based treatment was deeply investigated.Methods and ResultsBy using CRISPR/Cas9 approach an αGal KO mouse was created and used for the evaluation of the calcific propensity of original and polyphenols-treated BHV by subcutaneous implantation. The calcium quantification was carried out by plasma analysis; the immune response evaluation was performed by histology and immunological assays. Anti-αGal antibodies level in KO mice increases at least double after 2 months of implantation of original commercial BHV compared to WT mice, conversely, the polyphenols-based treatment seems to effectively mask the antigen to the KO mice’s immune system. Commercial leaflets explanted after 1 month from KO mice showed a four-time increased calcium deposition than what was observed on that explanted from WT. Polyphenol treatment prevents calcium deposition by over 99% in both KO and WT animals.ConclusionsThe implantation of commercial BHV leaflets significantly stimulates the KO mouse immune system resulting in massive production of anti-Gal antibodies and the exacerbation of the αGal-related calcific effect if compared with the WT mouse. The polyphenol-based treatment applied in this investigation showed an unexpected ability to inhibit the recognition of BHV xenoantigens by circulating antibodies completely preventing calcific depositions compared to the untreated counterpart.
Machined silicon traps for capturing novel bacterial communities and strainsin-situ
Authors: Romero Santiveri Clara , Vineis Joseph H. , Martins Sofia , Calaza Carlos , Gaspar João , Bowen Jennifer L. , Goluch Edgar D. 
Published: February 2023

AbstractWe tested the feasibility of a novel machined silicon nanopore enrichment device to recover individual microbial taxa from anaerobic sediments. Unlike other environmental isolation devices that have multiple entry points for bacteria or require the sample to be manually placed inside of a culturing chamber, our silicon device contains 24 precisely sized and spaced nanopores, each of which is connected to one culturing well, thereby providing only one entry point for bacteria. The culturing wells allow nutrient transport, so the bacteria that enter continue to experience their natural chemical environment, allowing collection of microbes without manipulating the environment. The device was deployed in marsh sediment and subsequently returned to the laboratory for bacterial culturing and analysis. 16S rRNA marker gene and metagenomic sequencing was used to quantify the number of different microbial taxa cultured from the device. The 16S rRNA sequencing results indicate that each well of the device contained between 1 and 62 different organisms from several taxonomic groups, including likely novel taxa. We also sequenced the metagenome from 8 of the 24 wells, enabling the reconstruction of 56 metagenomic assembled genomes (MAGs), and 44 of these MAGs represented non-redundant genome reconstructions. These results demonstrate that our novel silicon nanofluidic device can be used for isolating and culturing consortia containing a small number of microbial taxa from anaerobic sediments, which can be very valuable in determining their physiological potential.ImportanceThere are very few methods that can remove a few bacterial cells from a complex environment and keep the cells alive so that they can propagate sufficiently to be analyzed in a laboratory. Such methods are important to develop because the physiological functions of individual species of bacteria are often unknown, cannot be determined directly in the complex sample, and many bacterial cells cannot be grown outside of their natural environment. A novel bacterial isolation device has been made tested in a salt marsh. The results show that the device successfully isolated small groups of bacterial species from the incredibly diverse surroundings. The communities of bacteria were easily removed from the device in the laboratory and analyzed.