bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid generation and screening of transgenic black soldier fly (Hermetia illucens)
Authors: Pfitzner Chandran , Tepper Kate , Kumar Sheemal , Retief Carly , McNab Justin M , Harrell Robert A , Maselko Maciej 
Published: February 2024

AbstractBackgroundThe black soldier fly (BSF),Hermetia illucensis a widely used, and mass-produced insect that fulfils an important role in both the management of organic waste and as a component of animal feed formulations. They also have significant potential as a platform for converting organic waste into high-value proteins, and lipids for the production of biofuels. Applying synthetic biology to BSF provides even more potential for improvement through the generation of transgenic BSF to enhance animal feed, produce and fine tune high-value industrial biomolecules, and to expand their waste conversion capabilities.ResultsTo enable the rapid generation and screening of transgenic BSF, we utilised microinjections of piggyBac mRNA with donor plasmids. We have found preliminary screening of G0 BSF to identify mosaics for outcrossing can be completed less than 2 weeks after microinjection. Stable transgenic lines were reliably generated with effective transformation rates of 30-33%, and transmission of the transgene could be confirmed 3 days after outcrossing the G0 adults. We also present a protocol for identifying the location of integrated transgenes.ConclusionsThe methods presented here expedite the screening process for BSF transgenesis and further expand the toolkit for BSF synthetic biology.
The ZmHSF20–ZmHSF4–ZmCesA2 module regulates heat stress tolerance in maize
Authors: Li Ze , Li Zerui , Ji Yulong , Wang Chunyu , Wang Shufang , Shi Yiting , Le Jie , Zhang Mei 
Published: February 2024

AbstractTemperature shapes the geographical distribution and behavior of plants. Understanding the regulatory mechanisms behind plant heat response is important for developing climate-resilient crops, including maize (Zea mays). To identify transcription factors that may contribute to heat response, we generated a dataset of short- and long-term transcriptome changes following a heat treatment time course in the maize inbred line B73. Co-expression network analysis highlighted several transcription factors, including the class B2a heat shock factor ZmHSF20.ZmHsf20mutant seedlings exhibited enhanced tolerance of heat stress. Furthermore, DNA affinity purification sequencing and CUT&Tag assays demonstrated that ZmHSF20 binds the promoters ofCellulose synthase A2(ZmCesA2) and three class AHSFgenes, includingZmHSF4, repressing their transcription. We showed that ZmCesA2 and ZmHSF4 positively regulate heat response, with ZmHSF4 directly activatingZmCesA2transcription. In agreement with the transcriptome analysis, ZmHSF20 negatively modulated cellulose accumulation and repressed the expression of cell wall–related genes. Importantly, theZmHsf20 ZmHsf4double mutant exhibited decreased thermotolerance, placing ZmHSF4 downstream of ZmHSF20. Based on our results, we propose an expanded model of the heat stress response in maize, whereby ZmHSF20 lowers heat tolerance of seedlings by repressingZmHSF4andZmCesA2, thus balancing growth and defense at the seedling stage.One-sentence summaryZmHSF20, as a negative factor, acts upstream ofZmHSF4andZmCesA2, which are involved in positively regulating the cell wall development under heat stress, thereby improving maize heat tolerance.
Expectations about presence enhance the influence of content-specific expectations on low-level orientation judgements
Authors: Haarsma Joost , Kaltenmaier Aaron , Fleming Stephen M , Kok Peter 
Published: February 2024

AbstractWill something appear and if so, what will it be? Perceptual expectations can concern both the presence and content of a stimulus. However, it is unclear how these different types of expectations interact with each other in biasing perception. Here, we tested how expectations about stimulus presence and content differently affect perceptual inference. Across separate online discovery (N=110) and replication samples (N=218), participants were asked to judge both the presence and content (orientation) of noisy grating stimuli. Crucially, preceding compound cues simultaneously and orthogonally predicted both whether a grating was likely to appear as well as what its orientation would be. We found that expectations of presence interacted with expectations of content, such that the latter’s effect on discrimination was larger when a stimulus was expected to appear than when it was not. This interaction was observed both when a grating was truly presented and when participants falsely perceived one. Confidence in having seen a grating on the other hand was independently affected by presence and content expectations. Further, modelling revealed higher sensitivity in distinguishing between grating presence and absence following absence cues than presence cues, demonstrating an asymmetry between gathering evidence in favour of stimulus presence and absence. Finally, evidence for overweighted predictions being associated with hallucination-like perception was inconclusive. In sum, our results provide nuance to popular predictive processing accounts of perception by showing that expectations of presence and content have distinct but interacting roles in shaping conscious perception.
High-Performance Wide-Band Open-Source System for Acoustic Stimulation
Authors: Silva Artur , Carvalho Filipe , Cruz Bruno F. 
Published: February 2024

AbstractThe design and characterization of a low-cost, open-source auditory delivery system to deliver high performance auditory stimuli is presented. The system includes a high-fidelity sound card and audio amplifier devices with low-latency and wide bandwidth targeted for behavioral neuroscience research. The characterization of the individual devices and the entire system is performed, providing a thorough audio characterization data for varying frequencies and sound levels. The system implements the open-source Harp protocol, enabling the hardware timestamping of devices and seamless synchronization with other Harp devices.Specifications table
An egg sabotaging mechanism drives non-Mendelian transmission in mice
Authors: Clark Frances E. , Greenberg Naomi L. , Silva Duilio M.Z.A. , Trimm Emily , Skinner Morgan , Walton R Zaak , Rosin Leah F. , Lampson Michael A. , Akera Takashi 
Published: February 2024

SummaryDuring meiosis, homologous chromosomes segregate so that alleles are transmitted equally to haploid gametes, following Mendel’s Law of Segregation. However, some selfish genetic elements drive in meiosis to distort the transmission ratio and increase their representation in gametes. The established paradigms for drive are fundamentally different for female vs male meiosis. In male meiosis, selfish elements typically kill gametes that do not contain them. In female meiosis, killing is predetermined, and selfish elements bias their segregation to the single surviving gamete (i.e., the egg in animal meiosis). Here we show that a selfish element on mouse chromosome 2,R2d2, drives using a hybrid mechanism in female meiosis, incorporating elements of both male and female drivers. IfR2d2is destined for the polar body, it manipulates segregation to sabotage the egg by causing aneuploidy that is subsequently lethal in the embryo, so that surviving progeny preferentially containR2d2. In heterozygous females,R2d2orients randomly on the metaphase spindle but lags during anaphase and preferentially remains in the egg, regardless of its initial orientation. Thus, the egg genotype is either euploid withR2d2or aneuploid with both homologs of chromosome 2, with only the former generating viable embryos. Consistent with this model,R2d2heterozygous females produce eggs with increased aneuploidy for chromosome 2, increased embryonic lethality, and increased transmission ofR2d2. In contrast to a male meiotic driver, which kills its sister gametes produced as daughter cells in the same meiosis,R2d2eliminates “cousins” produced from meioses in which it should have been excluded from the egg.
UnconventionalIFNω-like genes dominate the type I IFN locus and the constitutive antiviral responses in bats
Authors: Geng Rong , Wang Qi , Yao Yu-Lin , Shen Xu-Rui , Jia Jing-Kun , Wang Xi , Zhu Yan , Li Qian , Shi Zheng-Li , Zhou Peng 
Published: February 2024

AbstractBats are the natural reservoir hosts of some viruses, some of which may spillover to humans and cause global-scale pandemics. Different to humans, bats may coexist with high pathogenic viruses without showing symptoms of diseases. As one of the most important first defenses, bat type I interferon (IFN-Is) were thought to play a role during this virus coexistence and thus were studied in recent years. However, there are arguments that whether bats have a contracted genome locus or constitutive expressed IFNs, mainly due to species-specific findings. We hypothesized that because of the lacking of pan-bat analysis, the common characters for bat IFN-Is have not been revealed yet. Here, we characterized the IFN-I locus for 9 Yangochiroptera bats and 3 Yinpterochiroptera based on the their high quality bat genomes. We also compared the basal expression for 6 bats and compared the antiviral, anti-proliferative activity and thermo-stability of a representativeRhinolophusbat IFNs. We found a dominance of unconventionalIFNω-like responses in the IFN-I system, which is unique to bats. In contrast toIFNa-dominated IFN-I loci in the majority of other mammals, bats generally have shorter IFN-I loci with more unconventionalIFNω-like genes (IFNωor relatedIFNaω), but with less or even noIFNagenes. In addition, bats generally have constitutively expressed IFNs, the highest expressed of which is more likely anIFNω-like gene. Likewise, the highly expressed IFNω-like protein also demonstrated the best antiviral activity, anti-proliferative activity or thermo-stability, as shown in a representativeRhinolophusbat species. Overall, we revealed pan-bat unique characteristics in IFN-I system, which provide insights into our understanding of the innate immunity that contribute to a special coexistence between bats and viruses.
ASTROGLIOSIS AND NEUROINFLAMMATION UNDERLIE SCOLIOSIS UPON CILIA DYSFUNCTION
Authors: Djebar Morgane , Anselme Isabelle , Pezeron Guillaume , Bardet Pierre-Luc , Cantaut-Belarif Yasmine , Eschstruth Alexis , Santos Diego López , Ribeuz Hélène Le , Jenett Arnim , Khoury Hanane , Véziers Joelle , Parmentier Caroline , Hirschler Aurélie , Carapito Christine , Bachmann-Gagescu Ruxandra , Schneider-Maunoury Sylvie , Vesque Christine 
Published: February 2024

ABSTRACTCilia defects lead to scoliosis in zebrafish, but the underlying pathogenic mechanisms are poorly understood and may diverge depending on the mutated gene. Here, we dissected the mechanisms of scoliosis onset in a zebrafish mutant for therpgrip1lgene encoding a ciliary transition zone protein.rpgrip1lmutant fish developed scoliosis with near-total penetrance but asynchronous onset in juveniles. Taking advantage of this asynchrony, we found that curvature onset was preceded by ventricle dilations and was concomitant to the perturbation of Reissner fiber polymerization and to the loss of multiciliated tufts around the subcommissural organ. Rescue experiments showed that Rpgrip1l was exclusively required infoxj1a-expressing cells to prevent axis curvature. Genetic interactions investigations ruled out Urp1/2 levels as a main driver of scoliosis inrpgrip1mutants. Transcriptomic and proteomic studies identified neuroinflammation associated with increased Annexin levels as a potential mechanism of scoliosis development inrpgrip1ljuveniles. Investigating the cell types associated withannexin2over-expression, we uncovered astrogliosis, arising in glial cells surrounding the diencephalic and rhombencephalic ventricles just before scoliosis onset and increasing with time in severity. Anti-inflammatory drug treatment reduced scoliosis penetrance and severity and this correlated with reduced astrogliosis and macrophage/microglia enrichment around the diencephalic ventricle. Mutation of thecep290gene encoding another transition zone protein also associated astrogliosis with scoliosis. Thus, we propose astrogliosis induced by perturbed ventricular homeostasis and associated with immune cell activation as a novel pathogenic mechanism of zebrafish scoliosis caused by cilia dysfunction.
Chromatin structure around long non-coding RNA (lncRNA) genes inSchistosoma mansonigonads
Authors: de Carvalho Augusto Ronaldo , Quack Thomas , Grevelding Christoph G. , Grunau Christoph 
Published: February 2024

AbstractIn this study, we employed a total of eight distinct modifications of histone proteins (H3K23ac, H3K27me3, H3K36me3, H3K4me3, H3K9ac, H3K9me3, H4K12ac, and H4K20me1) to discern the various chromatin colors encompassing lncRNA genes in both mature and immature gonads of the human parasiteSchistosoma mansoni. Our investigation revealed that these chromatin colors exhibit a tendency to aggregate based on the similarities in their metagene shapes, leading to the formation of less than six distinct clusters. Moreover, these clusters can be further grouped according to their resemblances by shape, which are co-linear with specific regions of the genes and potentially associated with transcriptional stages.
Evolutionary approaches predicted changes in transcription factors andcis-elements that associate with Kranz anatomy development in maize
Authors: Saji Angeo , Bijukumar Gopikrishnan , Nikhitha R , Thakur Vivek 
Published: February 2024

ABSTRACTC4plants are more efficient in high temperatures and less water due to unique anatomy and biochemical modifications, but critical regulator genes controlling Kranz anatomy remain undiscovered. This study aims to investigate the genes andcis-motifs that may be critical regulators in establishing and maintaining Kranz anatomy features in leaves of C4grasses by investigating candidate genes and their upstream regions fromZea maysby looking for genes with adaptive evolution in solely C4orthologs and motifs present uniquely in C4plants. Three genes out of 70 genes analyzed, namelymyb89,spb21,andereb80were observed from Maize with adaptive evolution uniquely present in multiple C4species, with the first two supported by expression data from different studies to be possibly involved in Kranz regulation, with further experimental validation required to investigate their exact roles in Kranz development. 12 motifs were found upstream of gene orthologs specific to or enriched in C4species. Three motifs upstream of IDP8537 and gras19 were found in a subset of their coexpression cluster, further suggesting their potential involvement in Kranz anatomy regulation. These novel motifs are potential additions to the limited Kranz-specific motifs and can aid in predicting new regulators after experimental validation.HIGHLIGHTIn this paper, we analyze the putative regulator sets of Kranz anatomy to discover important regulators and novelcis-regulatory elements that possibly regulate Kranz anatomy using evolutionary approaches.
Post-transcriptional control drives Aurora kinase A expression in human cancers
Authors: Cacioppo Roberta , Rad Deniz , Pagani Giulia , Gandellini Paolo , Lindon Catherine 
Published: February 2024

ABSTRACTAurora kinase A (AURKA) is a major regulator of the cell cycle. A prominent association exists between high expression of AURKA and cancer, and impairment of AURKA levels can trigger its oncogenic activity. In order to explore the contribution of post-transcriptional regulation to AURKA expression in different cancers, we carried out a meta-analysis of -omics data of 18 cancer types from The Cancer Genome Atlas (TCGA). Our study confirmed a general trend for increased AURKA mRNA in cancer compared to normal tissues and revealed that AURKA expression is highly dependent on post-transcriptional control in several cancers. Correlation and clustering analyses of AURKA mRNA and protein expression, and expression of AURKA-targetinghsa-let-7amiRNA, unveiled thathsa-let-7ais likely involved to varying extents in controlling AURKA expression in cancers. We then measured differences in the short/long ratio (SLR) of the two alternative cleavage and polyadenylation (APA) isoforms of AURKA mRNA across cancers compared to the respective healthy counterparts. We suggest that the interplay between APA andhsa-let-7atargeting of AURKA mRNA may influence AURKA expression in some cancers.hsa-let-7aand APA may also independently contribute to altered AURKA levels. Therefore, we argue that AURKA mRNA and protein expression are often discordant in cancer as a result of dynamic post-transcriptional regulation.
Predicting the direction of phenotypic difference
Authors: Gokhman David , Harris Keith D. , Carmi Shai , Greenbaum Gili 
Published: February 2024

AbstractPredicting phenotypes from genomic data is a key goal in genetics, but for most complex phenotypes, predictions are hampered by incomplete genotype-to-phenotype mapping. Here, we describe a more attainable approach than quantitative predictions, which is aimed at qualitatively predicting phenotypic differences. Despite incomplete genotype-to-phenotype mapping, we show that it is relatively easy to determine which of two individuals has a greater phenotypic value. This question is central in many scenarios, e.g., comparing disease risk between individuals, the yield of crop strains, or the anatomy of extinct vs extant species. To evaluate prediction accuracy, i.e., the probability that the individual with the greater predicted phenotype indeed has a greater phenotypic value, we developed an estimator of the ratio between known and unknown effects on the phenotype. We evaluated prediction accuracy using human data from tens of thousands of individuals from either the same family or the same population, as well as data from different species. We found that, in many cases, even when only a small fraction of the loci affecting a phenotype is known, the individual with the greater phenotypic value can be identified with over 90% accuracy. Our approach also circumvents some of the limitations in transferring genetic association results across populations. Overall, we introduce an approach that enables accurate predictions of key information on phenotypes — the direction of phenotypic difference — and suggest that more phenotypic information can be extracted from genomic data than previously appreciated.
Graphene microelectrode arrays, 4D structured illumination microscopy, and a machine learning-based spike sorting algorithm permit the analysis of ultrastructural neuronal changes during neuronal signalling in a model of Niemann-Pick disease type C
Authors: Lu Meng , Hui Ernestine , Brockhoff Marius , Trauble Jakob , Fernandez-Villegas Ana , Burton Oliver J , Lamb Jacob , Ward Edward , Hooper Philippa J , Tadbier Wadood , Laubli Nino F , Hofmann Stephan , Kaminski Clemens F , Lombardo Antonio , Kaminski Schierle Gabriele S 
Published: February 2024

AbstractSimultaneously recording network activity and ultrastructural changes of the synapse is essential for advancing our understanding of the basis of neuronal functions. However, the rapid millisecond-scale fluctuations in neuronal activity and the subtle sub-diffraction resolution changes of synaptic morphology pose significant challenges to this endeavour. Here, we use graphene microelectrode arrays (G-MEAs) to address these challenges, as they are compatible with high spatial resolution imaging across various scales as well as high temporal resolution electrophysiological recordings. Furthermore, alongside G-MEAs, we deploy an easy-to-implement machine learning-based algorithm to efficiently process the large datasets collected from MEA recordings. We demonstrate that the combined use of G-MEAs, machine learning (ML)-based spike analysis, and four-dimensional (4D) structured illumination microscopy (SIM) enables the monitoring of the impact of disease progression on hippocampal neurons which have been treated with an intracellular cholesterol transport inhibitor mimicking Niemann-Pick disease type C (NPC) and show that synaptic boutons, compared to untreated controls, significantly increase in size, which leads to a loss in neuronal signalling capacity.
Code Multiplexed Nanocapacitor Arrays for Scalable Neural Recordings
Authors: Weaver Sean , Chen Yiyang , Renz Aline , Choi Woojun , Vyza Yashwanth , Schlotter Tilman , Vulić Katarina , Kim Donghwan , Atzeni Gabriele , Momotenko Dmitry , Nakatsuka Nako , Jang Taekwang , Vörös János 
Published: February 2024

AbstractLarge scale neural recordings are redefining our understanding of the brain. However, simultaneously recording potentials from thousands of microelectrodes remains challenging. We overcome this limitation by measuring activity-induced changes in mutual capacitance. Code division multiplexing enabled simultaneous recordings of neural activity from 1,024 nanocapacitor electrodes at a density of 10k electrodes/mm.2Features of neural activityi.e., action potentials, bursts, and local field potentials were measured in recordings, benchmarking our device against the state-of-the-art.SummaryCapacitive sensing of neural activity improves the scalability, fabrication, and miniaturization of microelectrode arrays.
The assembly and efflux processes revealed byin situstructures of the ABC-type tripartite pump MacAB-TolC
Authors: Huo Tong , Zheng Wei , Yu Zhili , Wu Yaoming , Ren Qiuyu , Cao Junli , Wang Zhao , Shi Xiaodong 
Published: February 2024

AbstractThe MacAB-TolC tripartite efflux pump is widely distributed in Gram-negative bacteria, extruding antibiotics and virulence factors that lead to multidrug resistance and pathogenicity. This pump spans the cell envelope through its three components, an inner membrane ATP-binding cassette (ABC) transporter MacB, a periplasmic adaptor protein MacA, and an outer membrane protein TolC. However, the assembly process and efflux mechanism of the MacAB-TolC in cells remain unclear. Here, we resolve thein situstructures ofEscherichia coli(E. coli) MacAB-TolC efflux pump by electron cryo-tomography and subtomogram averaging. InE. coliwithout antibiotic treatment, we observe a fully assembled MacAB-TolC pump with a weak constriction density in the middle of the MacA region. WhenE. colicells were treated with erythromycin, we discovered the emergence of MacA-TolC subcomplexes, indicating flexible binding of MacB in the presence of an antibiotic substrate. This finding was further validated byin vivocrosslinking results. Together, our data present thein situassembly process of the MacAB-TolC and derive a substrate-driven working model for ABC-type tripartite pump.