bluuebunny/crossref_metadata_2025_split huggingface dataset:
SECRET AGENT O-GlcNAcylates hundreds of proteins involved in diverse cellular processes in Arabidopsis
Authors: Shrestha Ruben , Karunadasa Sumudu , Grismer Tara , Reyes Andres , Xu Shou-Ling 
Published: September 2023

AbstractO-GlcNAcylation is a critical post-translational modification of proteins observed in both plants and animals and plays a key role in growth and development. While considerable knowledge exists about over 3000 substrates in animals, our understanding of this modification in plants remains limited. Unlike animals, plants possess two putative homologs: SECRET AGENT (SEC) and SPINDLY (SPY), with SPY also exhibiting O-fucosylation activity. To investigate SEC’s role as a major O-GlcNAc transferase in plants, we utilized LWAC enrichment and SILIA labeling, quantifying at both MS1 and MS2 levels. Our findings reveal a significant reduction in O-GlcNAc levels in thesecmutant, indicating SEC’s critical role in mediating O-GlcNAcylation. Through a comprehensive approach, combining HCD and EThcD fragmentation with substantial fractionations, we expanded our GlcNAc profiling, identifying 436 O-GlcNAc targets, including 227 new targets. The targets span diverse cellular processes, suggesting broad regulatory functions of O-GlcNAcylation. The expanded targets also enabled exploration of crosstalk between O-GlcNAcylation and O-fucosylation. We also examined EThcD fragmentation for site assignment. This report advances our understanding of O-GlcNAcylation in plants, facilitating further research in this field.
A modular circuit architecture coordinates the diversification of courtship strategies inDrosophila
Authors: Coleman Rory T. , Morantte Ianessa , Koreman Gabriel T. , Cheng Megan L. , Ding Yun , Ruta Vanessa 
Published: September 2023

SummaryIdentifying a mate is a central imperative for males of most species but poses the challenge of distinguishing a suitable partner from an array of potential male competitors or females of related species. Mate recognition systems are thus subject to strong selective pressures, driving the rapid coevolution of female sensory cues and male sensory preferences. Here we leverage the rapid evolution of female pheromones across theDrosophilagenus to gain insight into how males coordinately adapt their detection and interpretation of these chemical cues to hone their mating strategies. While in someDrosophilaspecies females produce unique pheromones that act to attract and arouse their conspecific males, the pheromones of most species are sexually monomorphic such that females possess no distinguishing chemosensory signatures that males can use for mate recognition. By comparing several close and distantly-relatedDrosophilaspecies, we reveal thatD. yakubamales have evolved the distinct ability to use a sexually-monomorphic pheromone, 7-tricosene (7-T), as an excitatory cue to promote courtship, a sensory innovation that enablesD. yakubamales to court in the dark thereby expanding their reproductive opportunities. To gain insight into the neural adaptations that enable 7-T to act as an excitatory cue, we compared the functional properties of two key nodes within the pheromone circuits ofD. yakubaand a subset of its closest relatives. We show that the instructive role of 7-T inD. yakubaarises from concurrent peripheral and central circuit changes: a distinct subpopulation of sensory neurons has acquired sensitivity to 7-T which in turn selectively signals to a distinct subset of P1 neurons in the central brain that trigger courtship behaviors. Such a modular circuit organization, in which different sensory inputs can independently couple to multiple parallel courtship control nodes, may facilitate the evolution of mate recognition systems by allowing males to take advantage of novel sensory modalities to become aroused. Together, our findings suggest how peripheral and central circuit adaptations can be flexibly linked to underlie the rapid evolution of mate recognition and courtship strategies across species.
Multiplexed CRISPR gene editing in primary human islet cells with Cas9 ribonucleoprotein
Authors: Bevacqua Romina J. , Zhao Weichen , Merheb Emilio , Kim Seung Hyun , Marson Alexander , Gloyn Anna L. , Kim Seung K. 
Published: September 2023

SummarySuccessful genome editing in primary human islets could reveal features of the genetic regulatory landscape underlying β cell function and diabetes risk. Here, we describe a CRISPR-based strategy to interrogate functions of predicted regulatory DNA elements using electroporation of a complex of Cas9 ribonucleoprotein (Cas9 RNP) and guide RNAs into primary human islet cells. We successfully targeted coding regions including thePDX1exon 1, and non-coding DNA linked to diabetes susceptibility. CRISPR/Cas9 RNP approaches revealed genetic targets of regulation by DNA elements containing candidate diabetes risk SNPs, including anin vivoenhancer of theMPHOSPH9gene. CRISPR/Cas9 RNP multiplexed targeting of twocis-regulatory elements linked to diabetes risk inPCSK1, which encodes an endoprotease crucial for insulin processing, also demonstrated efficient simultaneous editing ofPCSK1regulatory elements, resulting in impaired β cellPCSK1regulation and insulin secretion. Multiplex CRISPR/Cas9 RNP provides powerful approaches to investigate and elucidate human islet cell gene regulation in health and diabetes.
Using theE. coliAlleleome in Strain Design
Authors: Phaneuf Patrick , Jarczynska Zofia D. , Kandasamy Vijayalakshmi , Chauhan Siddharth , Feist AM , Palsson Bernhard O. 
Published: September 2023

AbstractLeveraging observed variants in strain design is a promising technique for creating strains with specific properties. Adaptive laboratory evolution (ALE) experiments generate variants that enhance fitness under specific conditions and can contribute to application-specific strain designs. Further, the wild-type (WT) coding alleleome of an organism, the complete set of its genes’ WT alleles, can provide an additional amount and diversity of variants not yet accessible from the aggregation of ALE experiment results. This study used both an ALE mutation database (3093 genomes) and a large set of WT genomes (12,661 genomes) to explore the sequence solution space of genes involved in tolerance to 10 conditions of industrial importance. To accomplish this, ALE variants for 22 genes previously identified as potentially important for industrial chemical tolerance were collected and supplemented with all available variants from the WT coding alleleome. A total of 4879 variants were reintroduced and used in 10 selection experiments. Both ALE and WT contributed highly enriched variants, where the enrichment and benefits depended on the conditions, genes, and gene product regions. The results also revealed that variants not originating from the initial experiment could potentially confer substantially greater benefits. Additionally, ALE and WT variants rarely overlapped on AA positions, but their clustering did coincide with where highly enriched variants were ultimately located. For genes primarily hosting potential gain-of-function variations, substitutions predicted to have a conservative impact frequently outperformed more radical substitutions. Case studies demonstrated that maximizing the amount of variants enabled easier identification of variant trends, which in turn can be used to better understand areas and characteristics of genes that can be feasibly varied, representing what could be thought of as a genome design variable. The combination of ALE and WT variants is a promising approach for use in future projects to better constrain and ultimately achieve practical coverage in the exploration of feasible sequence solution space.Visual Abstract
Young Eurasian Scops Owls produce individually distinctive vocalizations
Authors: Grieco Fabrizio 
Published: September 2023

AbstractVocal distinctiveness is expected to occur more often in colonial-breeding species as the parents need to recognize their offspring in a large group of conspecifics. In this study, I examined the food-begging calls of the young of a territorial nocturnal raptor, the Scops Owl, shortly before and after fledging. The calls showed complex spectral structure not described in previous studies. I found a high degree of repeatability in many acoustic features, particularly call duration, spectral centre of gravity, and spectral skewness. Discriminant analysis assigned 52.7% of the calls to the correct individual, and 69.1% when restricting analysis within broods. The calculated information capacity HSwas 4.69 bits. Differences in acoustic features between siblings appeared before fledging and could be detected over up to ten days despite temporal variation. The results suggest that the vocalizations of young Scops Owls could potentially act as identity signals. However, the functional significance of acoustic signatures remains unclear. A few hypotheses are discussed. Call distinctiveness could simply reflect the development of vocal individuality typical of the adults; it could help parents recognize their offspring preventing misdirected parental care when breeding density is high; it could mediate preferential feeding; or it could be used by siblings communicating between each other. Further studies are needed to determine whether parents and offspring assess identity signals in vocalizations.
Description of a new genus of thePectobacteriaceaefamily isolated from lake water in France;Prodigiosinella aquatilisgen. nov. sp. nov. includes two subspeciesProdigiosinella aquatilissubsp.aquatilisssp. nov. andProdigiosinella aquatilissubsp.natabilisssp. nov
Authors: Hugouvieux-Cotte-Pattat Nicole , Flandrois Jean-Pierre , Briolay Jérôme , Reverchon Sylvie , Brochier-Armanet Céline 
Published: September 2023

ABSTRACTThePectobacteriaceaefamily comprises plant pathogens able to provoke diverse diseases, including plant maceration due to the production of pectinases disrupting the plant cell wall. To better understand their natural diversity, a survey of pectinolytic bacteria was performed in lakes of the French region La Camargue near the Mediterranean Sea. Sixteen atypical pectinolytic isolates were obtained from brackish water of three lakes. The genome of six isolates was sequenced; their size is around 4.8 to 5.0 Mb, including a plasmid of 59 to 61 kb; their G+C values range from 49.1 to 49.3 mol%. Phylogenetic analyses indicated that the novel strains formed a new clade ofPectobacteriaceae, separate from previously described genera of this family. These analyses suggested also thatAcerihabitansdoes not belong toPectobacteriaceaeand should be reclassified in theBruguierivoracaceaefamily, whileSymbiopectobacteriumcould be a truePectobacteriaceaemember. Based on phenotypic, genomic and phylogenetic characteristics, we propose the creation of a new genus with the nameProdigiosinellagen. nov. Both the phenotypic and phylogenetic analyses separated the strains into two distinct subgroups. However, the DNA–DNA relatedness values revealed a close relationship between the two groups, supporting their appurtenance to the same species. Thus, it is proposed to classify them as two subspecies ofProdigiosinella aquatilissp. nov., for which we propose the nameProdigiosinella aquatilissubsp.aquatilisssp. nov. (LS101T= CFBP 8826T= LMG 32072T) andProdigiosinella aquatilissubsp.natabilisssp. nov. (CE70T= CFBP 9054T= LMG 32867T).
Corticotropin releasing factor alters the functional diversity of accumbal cholinergic interneurons
Authors: Ingebretson Anna E. , Alonso-Caraballo Yanaira , Razidlo John A. , Lemos Julia C. 
Published: September 2023

AbstractCholinergic interneurons (ChIs) provide the main source of acetylcholine in the striatum and have emerged as a critical modulator of behavioral flexibility, motivation, and associative learning. In the dorsal striatum, ChIs display heterogeneous firing patterns. Here, we investigated the spontaneous firing patterns of ChIs in the nucleus accumbens (NAc) shell, a region of the ventral striatum. We identified four distinct ChI firing signatures: regular single-spiking, irregular single-spiking, rhythmic bursting, and a mixed-mode pattern composed of bursting activity and regular single spiking. ChIs from females had lower firing rates compared to males and had both a higher proportion of mixed-mode firing patterns and a lower proportion of regular single-spiking neurons compared to males. We further observed that across the estrous cycle, the diestrus phase was characterized by higher proportions of irregular ChI firing patterns compared to other phases. Using pooled data from males and females, we examined how the stress-associated neuropeptide corticotropin releasing factor (CRF) impacts these firing patterns. ChI firing patterns showed differential sensitivity to CRF. This translated into differential ChI sensitivity to CRF across the estrous cycle. Furthermore, CRF shifted the proportion of ChI firing patterns toward more regular spiking activity over bursting patterns. Finally, we found that repeated stressor exposure altered ChI firing patterns and sensitivity to CRF in the NAc core, but not the NAc shell. These findings highlight the heterogeneous nature of ChI firing patterns, which may have implications for accumbal-dependent motivated behaviors.New and NoteworthyChIs within the dorsal and ventral striatum can exert a huge influence on network output and motivated behaviors. However, the firing patterns and neuromodulation of ChIs within the ventral striatum, specifically the NAc shell, are understudied. Here we report that NAc shell ChIs have heterogenous ChI firing patterns that are labile and can be modulated by the stress-linked neuropeptide CRF and by the estrous cycle.
Neurological Imprints of Boys’ Love Culture: Shaping Sexual Orientation Identity in the Digital Age’s Young females
Authors: Ao Na , Jiang Xiaowei , Chen Yanan , Chen Yingying , Niu Huihui , Hu Shuoyan 
Published: September 2023

AbstractWith the omnipresence of social media, Boys’ Love (BL) culture has found a burgeoning audience among young females. While this cultural phenomenon offers a platform for self-expression to some, its potential implications remain underexplored. This study investigates whether immersion in BL culture impacts the process of young females forming self-recognition and identification of sexual orientation. Employing an fNIRS-based experiment focusing on the prefrontal cortex, we compared the neurological responses of young females within and outside the BL media cocoon when exposed to sexuality-related stimuli. Our findings revealed significant neural differences in the experimental group viewing BL images compared to the control group. These results provide fresh insights into how BL content may shape our cognition and attitudes, emphasizing the need for guidance in content consumption among young females.
Simple ways to avoid collecting highly137Cs-contaminatedAralia elatabuds
Authors: Sakai Masaru , Watanabe Mirai , Koshikawa Masami Kanao , Tanaka Asuka , Takahashi Akiko , Takechi Seiichi , Takagi Mai , Tsuji Takashi , Tsuji Hideki , Takeda Toshimasa , Jo Jaeick , Tamaoki Masanori , Hayashi Seiji 
Published: September 2023

AbstractCollection and cooking of wild vegetables have provided seasonal enjoyments for Japanese local people as provisioning and cultural ecosystem services. However, the Fukushima Daiichi Nuclear Power Plant accident in March 2011 caused extensive radiocesium contamination of wild vegetables. Restrictions on commercial shipments of wild vegetables have been in place for the last 10 years. Some species, including buds ofAralia elata, are currently showing radiocesium concentrations both above and below the Japanese reference level for food (100 Bq/kg), suggesting that there are factors decreasing and increasing the137Cs concentration. Here, we evaluated easy-to-measure environmental variables (dose rate at the soil surface, organic soil layer thickness, slope steepness, and presence/absence of decontamination practices) and the137Cs concentrations of 40A. elatabuds at 38 locations in Fukushima Prefecture to provide helpful information on avoiding collecting highly contaminated buds. The137Cs concentrations inA. elatabuds increased significantly with increases in the dose rate at the soil surface. Meanwhile, the137Cs concentration inA. elatabuds were not reduced by decontamination practices. These findings suggest that measuring the latest dose rate at the soil surface at the base ofA. elataplants is a helpful way to avoid collecting buds with higher137Cs concentrations and aid in the management of species in polluted regions.
The discovery of an evolutionarily conserved enhancer within the MYEOV locus suggests an unexpected role for this non-coding region in cancer
Authors: Davidson Brigid SA , Arcila-Galvis Juliana Estefania , Trevisan-Herraz Marco , Mikulasova Aneta , Brackley Chris A , Russell Lisa J , Rico Daniel 
Published: September 2023

AbstractThemyeloma overexpressedgene (MYEOV) has been proposed to be a proto-oncogene due to high RNA transcript levels found in multiple cancers, including myeloma, breast, lung, pancreas and esophageal cancer. The presence of an open reading frame (ORF) in humans and other primates suggests protein-coding potential. Yet, we still lack evidence of a functional MYEOV protein. It remains undetermined howMYEOVoverexpression affects cancerous tissues. In this work, we show thatMYEOVhas originated and may still function as an enhancer, possibly regulatingCCND1. Firstly,MYEOV3’ end enhancer activity was confirmed in humans using publicly available ATAC-STARR-seq data, performed on B-cell-derived GM12878 cells. We detected enhancer histone marks H3K4me1 and H3K27ac overlappingMYEOVin multiple healthy human tissues, which include B cells, liver and lung tissue. The analysis of 3D genome datasets revealed chromatin interactions between theMYEOV-3’-enhancer and the proto-oncogeneCCND1. BLAST searches and multi-sequence alignments results showed that this human enhancer element is conserved from the amphibians/amniotes divergence, with a 273 bp conserved region also found in all mammals, and even in chickens, and it consistently located near the correspondingCCND1orthologues. Furthermore, we observed conservation of active enhancer state in theMYEOVorthologues of four non-human primates, dog, rat and mouse. When studying this homologous region in mice, where the ORF ofMYEOVis absent, we not only observed an enhancer chromatin state but also found interactions between the mouse enhancer homolog andCcnd1using 3D-genome interaction data. This is similar to the interaction observed in humans and, interestingly, coincides with CTCF binding sites in both species. Taken together, this suggests thatMYEOVis a primate-specific gene with ade novoORF that originated at an evolutionarily older enhancer region. This deeply conserved enhancer element is possibly regulatingCCND1in both humans and mice, opening the possibility of studyingMYEOVregulatory functions in cancer using non-primate animal models.
One-carbon metabolism nutrients impact the interplay between DNA methylation and gene expression in liver, enhancing protein synthesis in Atlantic Salmon
Authors: Saito Takaya , Espe Marit , Vikeså Vibeke , Bock Christoph , Thomsen Tårn H. , Adam Anne-Catrin , Fernandes Jorge M.O. , Skjaerven Kaja H. 
Published: September 2023

AbstractSupplementation of one-carbon (1C) metabolism micronutrients, which include B-vitamins and methionine, is essential for the healthy growth and development of Atlantic salmon (Salmo salar). However, the recent shift towards non-fish meal diets in salmon aquaculture has led to the need for reassessments of recommended micronutrient levels. Despite the importance of 1C metabolism in growth performance and various cellular regulations, the molecular mechanisms affected by these dietary alterations are less understood.To investigate the molecular effect of 1C nutrients, we analysed gene expression and DNA methylation using two types of omics data: RNA sequencing (RNA-seq) and reduced-representation bisulfite sequencing (RRBS). We collected liver samples at the end of a feeding trial that lasted 220 days through the smoltification stage, where fish were fed three different levels of four key 1C nutrients: methionine, vitamin B6, B9, and B12.Our results indicate that the dosage of 1C nutrients significantly impacts genetic and epigenetic regulations in the liver of Atlantic salmon, particularly in biological pathways related to protein synthesis. The interplay between DNA methylation and gene expression in these pathways may play an important role in the mechanisms underlying growth performance affected by 1C metabolism.Author SummaryAtlantic salmon rely on one-carbon (1C) metabolism micronutrients like B-vitamins and methionine, which they acquire through their diets. Small pelagic fish are the primary source in the wild, but finding sustainable alternatives such as plants, insects, and algae is challenging as salmon aquaculture expands. Adjusting nutrient levels when changing base ingredients further complicates the task. Understanding the molecular mechanisms affected by these micronutrients is crucial for aquaculture sustainability.In this study, we investigated the molecular effects of 1C metabolism micronutrients on Atlantic salmon. Liver samples from salmon fed varying levels of key 1C nutrients over a 220-day trial were analysed using RNA sequencing (RNA-seq) and reduced-representation bisulfite sequencing (RRBS) to assess gene expression and DNA methylation, respectively.Our results revealed significant impacts of 1C nutrient dosage on genetic and epigenetic regulations in the salmon liver, particularly in protein synthesis pathways. The interplay between DNA methylation and gene expression in these pathways influences growth performance under 1C metabolism.Uncovering molecular changes resulting from dietary alterations provides valuable insights to optimize nutritional requirements in salmon aquaculture, supporting sustainable production and welfare of this important species.
Neuroectoderm phenotypes in a human stem cell model of O-GlcNAc transferase intellectual disability
Authors: Murray Marta , Davidson Lindsay , Ferenbach Andrew T. , Lefeber Dirk , van Aalten Daan M. F. 
Published: September 2023

AbstractMost intellectual disabilities are caused by monogenic variation. Mutations in the O-GlcNAc transferase (OGT) gene have recently been linked to a novel congenital disorder of glycosylation (OGT-CDG), involving symptoms of possible neuroectodermal origin. To test the hypothesis that pathology is linked to defects in differentiation during early embryogenesis, we developed an OGT-CDG induced pluripotent stem cell lines together with isogenic controls generated by CRISPR/Cas9 gene-editing. Although the OGT-CDG variant leads to a significant decrease in OGT and O-GlcNAcase protein levels, there were no changes in differentiation potential or stemness. However, differentiation into ectoderm resulted in significant differences in O-GlcNAc homeostasis. Further differentiation to neuronal stem cells revealed differences in morphology between patient and control lines, accompanied by disruption of the O-GlcNAc pathway. This suggests a critical role for O-GlcNAcylation in early neuroectoderm architecture, with robust compensatory mechanisms in the earliest stages of stem cell differentiation.