bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic andN-glycomic comparison of synthetic and bovine whey proteins and their effect on human gut microbiomes
Authors: Bolino Matthew , Duman Hatice , Avcı İzzet , Kayili Hacı Mehmet , Petereit Juli , Zundel Chandler , Salih Bekir , Karav Sercan , Frese Steven A. 
Published: September 2024

AbstractAdvances in food production systems and customer acceptance have led to the commercial launch of dietary proteins produced via modern biotechnological approaches as alternatives to traditional agricultural sources. At the same time, a deeper understanding of how dietary components interact with the gut microbiome has highlighted the importance of understanding the nuances underpinning diet-microbiome interactions. Novel food proteins with distinct post-translational modifications resulting from their respective production systems have not been characterized, nor how they may differ from their traditionally produced counterparts. To address this, we have characterized the protein composition andN-glycome of a yeast-synthesized whey protein ingredient isolated from commercially available ice cream and compared this novel ingredient to whey protein powder isolate derived from bovine milk. We found that despite strong similarities in protein composition, theN-glycome significantly differs between these protein sources, reflecting the biosynthetic machinery of the production systems. Further, the composition profile and diversity of proteins found in the synthetic whey protein were lower relative to bovine whey protein, despite both being predominantly composed of β-lactoglobulin. Finally, to understand whether these differences inN-glycome profiles affected the human gut microbiome, we tested these proteins in anin vitrofecal fermentation model. We found that the two whey protein sources generated significant differences among three distinct microbial compositions, which we hypothesize is a product of differences inN-glycan composition and degradation by these representative microbial communities. This work highlights the need to understand how differences in novel biotechnological systems affect the bioactivity of these proteins, and how these differences impact the human gut microbiome.
Development of a cell-permeable Biotin-HaloTag ligand to explore functional differences between protein variants across cellular generations
Authors: Yadav Anoop Kumar , Jadhav Abhijeet S. , Szczepanik Pawel , Fagherazzi Paolo , Kabelka Ivo , Vácha Robert , Svenda Jakub , Polasek-Sedlackova Hana 
Published: September 2024

SUMMARYHaloTag technology represents a versatile tool for studying proteins. Fluorescent HaloTag ligands employed in sequential labeling led to the discovery of distinct protein variants for histones, cohesins, and MCM complexes. Nonetheless, an efficient biochemical approach to separate the distinct protein variants to study their biological functions is missing. Principally being a gap in technology, the HaloTag toolbox lacks affinity ligands displaying good cell permeability and efficient affinity capture. Here, we describe the design, synthesis, and validation of a new cell-permeable Biotin-HaloTag ligand, which allows rapid labeling of Halo-tagged proteins in live cells and their efficient separation using streptavidin pull-down. Our work outlines how to use the herein-developed affinity ligand in sequential labeling to biochemically separate distinct protein variants and study their biological properties. The approach holds immense potential for addressing fundamental questions concerning essential cellular processes, including genome duplication and chromatin maintenance.
Microcystin shapes theMicrocystisphycosphere through community filtering and by influencing cross-feeding interactions
Authors: Große Rebecca , Heuser Markus , Teikari Jonna E. , Ramakrishnan Dinesh K. , Abdelfattah Ahmed , Dittmann Elke 
Published: September 2024

AbstractThe cyanobacteriumMicrocystiscauses harmful algal blooms (cyanoHABs) that pose a major threat to human health and ecosystem services, particularly due to the prevalence of the potent hepatotoxin microcystin. With their pronounced EPS layer,Microcystiscolonies also serve as a hub for heterotrophic phycosphere bacteria. Here, we tested the hypothesis that the genotypic plasticity in its ability to produce microcystin influences the composition and assembly of theMicrocystisphycosphere microbiome. In an analysis of individual colonies of a naturalMicrocystisbloom, we observed a significantly reduced richness of the community in the presence of microcystin biosynthesis genes. A subsequent synthetic community experiment with 21 heterotrophic strains in co-cultivation with either the wild-type strainM. aeruginosaPCC 7806 or the microcystin-free mutant ΔmcyBrevealed not only a tug-of-war between phototrophic and heterotrophic bacteria, but also a reciprocal dominance of two isolates of the genusSphingomonasandFlavobacterium. In contrast, anAgrobacteriumisolate thrived equally well in both consortia. In substrate utilization tests,Sphingomonasshowed the strongest dependence onMicrocystisexudates with a clear preference for the wild-type strain. Genome sequencing revealed a high potential for complementary cross-feeding, particularly for theAgrobacteriumandSphingomonasisolates but no potential for microcystin degradation. We postulate that strain-specific functional traits, such as the ability to perform photorespiration and to produce vitamin B12, play a crucial role in the cross-feeding interactions, and that microcystin is one of the determining factors in theMicrocystisphycosphere due to its interference with inorganic carbon metabolism.
The binary protein interactome mapping of theGiardia lambliaproteasome lid reveals extra proteasomal functions of GlRpn11
Authors: Das Ankita , Ray Atrayee , Chaudhuri Nibedita Ray , Mukherjee Soumyajit , Dastidar Shubhra Ghosh , Ghosh Alok , Ganguly Sandipan , Jana Kuladip , Sarkar Srimonti 
Published: September 2024

AbstractGiardia lambliadoes not encode Rpn12 and Sem1, two proteins crucial for assembling the proteasome lid. To understand how the interactions between the giardial proteasome lid subunits may have changed to compensate for their absence, we used the yeast two-hybrid assay to generate a binary protein interaction map of theGiardialid subunits. Most interactions within theGiardiaproteasome lid are stronger than those within theSaccharomyces cerevisiaelid. These may compensate for the absence of Rpn12 and Sem1. A notable exception was the weaker interaction between GlRpn11 and GlRpn8, compared to the strong interaction between Rpn11-Rpn8 of yeast. The Rpn11-Rpn8 dimer provides a platform for lid assembly and their interaction involves the insertion of a methionine residue of Rpn11 into a hydrophobic pocket of Rpn8. Molecular modeling indicates that GlRpn8’s pocket is wider, reconciling the experimental observation of its weak interaction with GlRpn11. This weaker interaction may have evolved to support extra proteasomal functions of GlRpn11, which localizes to multiple subcellular regions where other proteasome subunits have not been detected. One such location is the mitosome. Functional complementation in yeast shows that GlRpn11 can influence mitochondrial function and distribution. This, together with its mitosomal localization, indicates that GlRpn11 functions at the mitosome. Thus, this parasite’s proteasome lid has a simpler subunit architecture and structural attributes that may support dual functionalities for GlRpn11. Such parasite-specific proteasome features could provide new avenues for controlling the transmission ofGiardia.1Graphical AbstractHighlightsGiardiagenome does not encode two proteasomal lid subunits: Rpn12 and Sem1Unique interactions within the lid may compensate for the absence of these twoGlRpn8:GlRpn11 weakly interacts to support GlRpn11’s extra-proteasomal distributionGlRpn11 localizes at mitosomes, OZ of VD, and to the VFPThe 182-218 fragment of GlRpn11 may regulate mitosomal function
An efficient pipeline for creating metagenomic-assembled genomes from ancient oral microbiomes
Authors: Standeven Francesca J. , Dahlquist-Axe Gwyn , Speller Camilla F. , Meehan Conor J. , Tedder Andrew 
Published: September 2024

AbstractMetagenomic-assembled genomes (MAGs) are difficult to recover from ancient DNA (aDNA) due to substantial fragmentation, degradation, and multi-source contamination. These complexities associated with aDNA raise concerns about whether bioinformatic tools intended for interpreting modern DNA are suitable for reconstructing ancient MAGs. Using simulated modern and ancient data, we investigated: 1) how using binning tools designed for modern DNA affects our ability to effectively construct MAGs from ancient genomes; 2) the performance of three different binning tools for aDNA samples; and 3) whether a ‘one size fits all’ approach is suitable for ancient metagenomics. We established that binning tools for modern DNA performed efficiently on simulated modern and ancient DNA. When applied to ‘real’ archaeological DNA spanning 5000 years, we retrieve high-confidence MAGs in most cases.
Stable and dynamic gene expression patterns over diurnal and developmental timescales inArabidopsis thaliana
Authors: Redmond Ethan J , Ronald James , Davis Seth J , Ezer Daphne 
Published: September 2024

SummaryDevelopmental processes are known to be circadian regulated in plants. For instance, the circadian clock regulates genes involved in the photoperiodic flowering pathway and the initiation of leaf senescence. Furthermore, signals which entrain the circadian clock, such as energy availability, are known to vary in strength over plant development. However, diurnal oscillations of the Arabidopsis transcriptome have typically been measured in seedlings.We collected RNA-seq data from Arabidopsis leaves over developmental and diurnal timescales, concurrently: every 4 hours per day, on 3 separate days after a synchronised vegetative-to-reproductive transition. Gene expression varied more over the developmental timescale than on the diurnal timescale, including genes related to a key energy sensor: the Sucrose non-fermenting-1-related protein kinase (SnRK1) complex.Moreover, regulatory targets of core clock genes displayed changes in rhythmicity and amplitude of expression over development. Cell-type-specific expression showed diurnal patterns that varied in amplitude, but not phase, over development. Some previously identified qRT-PCR housekeeping genes display undesirable levels of variation over both timescales. We identify which common qRT-PCR housekeeping genes are most stable across developmental and diurnal timescales.In summary, we establish the patterns of circadian transcriptional regulation over plant development, demonstrating how diurnal patterns of expression change over developmental timescales.
Integrated Transcriptome and Metabolome Analyses Reveal the Mechanism Regulating Bulbil Initiation and Development inCystopteris chinensis
Authors: Yu An , Chen Xiaohong , Xi Wenkai , Zhao Xia , Wang Yazhu , Gong Zhihong , Zhou Xiaofeng 
Published: September 2024

AbstractCystopteris chinensisis an endangered fern endemic to China, which only has a small wild population due to its poor reproductive ability. However, we recently found that it can produce bulbils on its pinnule to generate new plants but the molecular mechanism underlying this unique phenomenon remained unknown. In this study, we have identified four distinct stages in the initiation and development of bulbils based on morphological and anatomical observation. We performed transcriptome and metabolome analyses on the collected samples at each stage. Through KEGG enrichment analysis, it was found that the phytohormone signal transduction, starch and sucrose metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis pathways play a significant role in regulating bulbil initiation and development. Specifically, the involvement of three phytohormones and sugar substances was identified in the process of bulbil initiation. Our study provides the first detailed observation of the bulbils inC. chinensisand explains their initiation and development at the molecular level. However, more in-depth studies are needed to discover the functions of key genes controlling the formation of bulbils to conserve the endangeredC. chinensispopulation.
Eco-toxicity of different agricultural tank-mix adjuvants
Authors: Roessink Ivo , Boerwinkel Marie-Claire , Sijs Rick , Hoffman Hanne , Specker Jan Christof , Bonn Daniel 
Published: September 2024

AbstractAdjuvants are often used to improve the efficiency of plant protection products. However, there is concern that these compounds themselves might result in ecotoxicological effects. To investigate this concern, we compare the toxicity of different agricultural tank-mix adjuvants for two standard test organisms, i.e. the water fleaDaphnia magnaand the honey beeApis mellifera. Daphnia trials comprised tests at 1, 5 and 20 times the normal prescribed label dosage. It is found that at 48h, the novel polymer-based adjuvant Squall is significantly less harmful toD. magnacompared to traditional surfactant or oil-based adjuvants. ForA. mellifera, we tested topical exposure to label-rate, five and twenty times label-rate. After 96h exposure to polymer- and oil based adjuvants no statistically significant harmful effects were observed. The trisiloxane-based adjuvants, however, did significantly increase bee mortality at higher dose rates, indicating a higher toxicity of these specific compounds.
Viral-mediated Oct4 overexpression and inhibition of Notch signaling synergistically induce neurogenic competence in mammalian Müller glia
Authors: Le Nguyet , Awad Sherine , Palazzo Isabella , Hoang Thanh , Blackshaw Seth 
Published: September 2024

AbstractRetinal Müller glia in cold-blooded vertebrates can reprogram into neurogenic progenitors to replace neurons lost to injury, but mammals lack this ability. While recent studies have shown that transgenic overexpression of neurogenic bHLH factors and glial-specific disruption of NFI family transcription factors and Notch signaling induce neurogenic competence in mammalian Müller glia, induction of neurogenesis in wildtype glia has thus far proven elusive. Here we report that viral-mediated overexpression of the pluripotency factorOct4(Pou5f1) induces transdifferentiation of wildtype mouse Müller glia into bipolar neurons, and synergistically stimulates glial-derived neurogenesis in parallel with Notch loss of function. Single cell multiomic analysis shows thatOct4overexpression leads to widespread changes in gene expression and chromatin accessibility, inducing activity of both the neurogenic transcription factor Rfx4 and the Yamanaka factors Sox2 and Klf4. This study demonstrates that viral-mediated overexpression of Oct4 induces neurogenic competence in wildtype retinal Muller glia, identifying mechanisms that could be used in cell-based therapies for treating retinal dystrophies.
RFX3 is essential for the development and maturation of human pancreatic islets derived from pluripotent stem cells
Authors: Memon Bushra , Aldous Noura , Elsayed Ahmed K. , Ijaz Sadaf , Hayat Sikander , Abdelalim Essam M. 
Published: September 2024

AbstractRFX3 in human pancreatic islet development has not been explored. This study aims to investigate the function of RFX3 in human pancreatic islet development using human islet organoids derived from iPSCs, hypothesizing that RFX3 regulates human islet cell differentiation. We generatedRFX3knockout (RFX3KO) iPSC lines using CRISPR/Cas9 and differentiated them into pancreatic islet organoids. Various techniques were employed to assess gene expression, cell markers, apoptosis, proliferation, and glucose-stimulated insulin secretion. Single-cell RNA sequencing (scRNA-seq) datasets from hESC-derived pancreatic islets were re-analyzed to investigateRFX3expression in specific cell populations at various developmental stages. Furthermore, bulk RNA sequencing was conducted to further assess transcriptomic changes. RFX3 was found to be highly expressed in pancreatic endocrine cell populations within pancreatic progenitors (PPs), endocrine progenitors (EPs), and mature islet stages derived from iPSCs. scRNA-seq further confirmed RFX3 expression across different endocrine cell clusters during differentiation.RFX3loss disrupted pancreatic endocrine gene regulation, reduced hormone-secreting islet cells, and impaired beta-cell function and insulin secretion. Despite a significant reduction in pancreatic islet hormones, the pan-endocrine marker CHGA remained unchanged at both EP and islet stages, likely due to an increase in enterochromaffin cells (ECs). This was supported by our findings of high EC marker expression inRFX3KO EPs and islets. In addition,RFX3loss led to smaller islet organoids, elevated TXNIP levels, and increased apoptosis in EPs and islets. These findings underscore the crucial role of RFX3 in regulating human islet cell differentiation and its role in suppressing enterochromaffin cell specification. These insights into RFX3 function have implications for understanding islet biology and potential diabetes susceptibility.
Dynamic phosphorylation of Hcm1 promotes fitness in chronic stress
Authors: Conti Michelle M. , Bail Jillian P. , Li Rui , Zhu Lihua Julie , Benanti Jennifer A. 
Published: September 2024

SummaryCell survival depends upon the ability to adapt to changing environments. Environmental stressors trigger an acute stress response program that rewires cell physiology, downregulates proliferation genes and pauses the cell cycle until the cell adapts. Here, we show that dynamic phosphorylation of the yeast cell cycle-regulatory transcription factor Hcm1 is required to maintain fitness in chronic stress. Hcm1 is activated by cyclin dependent kinase (CDK) and inactivated by the phosphatase calcineurin (CN) in response to stressors that signal through increases in cytosolic Ca2+. Expression of a constitutively active, phosphomimetic Hcm1 mutant reduces fitness in stress, suggesting Hcm1 inactivation is required. However, a comprehensive analysis of Hcm1 phosphomutants revealed that Hcm1 activity is also important to survive stress, demonstrating that Hcm1 activity must be toggled on and off to promote gene expression and fitness. These results suggest that dynamic control of cell cycle regulators is critical for survival in stressful environments.
Cortico-hippocampal interactions underlie schema-supported memory encoding in older adults
Authors: Huang Shenyang , Bogdan Paul C. , Howard Cortney M. , Gillette Kirsten , Deng Lifu , Welch Erin , McAllister Margaret L. , Giovanello Kelly S. , Davis Simon W. , Cabeza Roberto 
Published: September 2024

AbstractAlthough episodic memory is typically impaired in older adults (OAs) compared to young adults (YAs), this deficit is attenuated when OAs can leverage their rich semantic knowledge, such as their knowledge of schemas. Memory is better for items consistent with pre-existing schemas and this effect is larger in OAs. Neuroimaging studies have associated schema use with the ventromedial prefrontal cortex (vmPFC) and hippocampus (HPC), but most of this research has been limited to YAs. This fMRI study investigated the neural mechanisms underlying how schemas boost episodic memory in OAs. Participants encoded scene-object pairs with varying congruency, and memory for the objects was tested the following day. Congruency with schemas enhanced object memory for YAs and, more substantially, for OAs. FMRI analyses examined how cortical modulation of HPC predicted subsequent memory. Congruency-related vmPFC modulation of left HPC enhanced subsequent memory in both age groups, while congruency-related modulation from angular gyrus (AG) boosted subsequent memory only in OAs. Individual differences in cortico-hippocampal modulations indicated that OAs preferentially used their semantic knowledge to facilitate encoding via an AG-HPC interaction, suggesting a compensatory mechanism. Collectively, our findings illustrate age-related differences in how schemas influence episodic memory encoding via distinct routes of cortico-hippocampal interactions.
Ventrolateral prefrontal cortex in macaques guides decisions in different learning contexts
Authors: Fujimoto Atsushi , Elorette Catherine , Fujimoto Satoka H. , Fleysher Lazar , Russ Brian E. , Rudebeck Peter H. 
Published: September 2024

AbstractFlexibly adjusting our behavioral strategies based on the environmental context is critical to maximize rewards. Ventrolateral prefrontal cortex (vlPFC) has been implicated in both learning and decision-making for probabilistic rewards, although how context influences these processes remains unclear. We collected functional neuroimaging data while rhesus macaques performed a probabilistic learning task in two contexts: one with novel and another with familiar visual stimuli. We found that activity in vlPFC encoded rewards irrespective of the context but encoded behavioral strategies that depend on reward outcome (win-stay/lose-shift) preferentially in novel contexts. Functional connectivity between vlPFC and anterior cingulate cortex varied with behavioral strategy in novel learning blocks. By contrast, connectivity between vlPFC and mediodorsal thalamus was highest when subjects repeated a prior choice. Furthermore, pharmacological D2-receptor blockade altered behavioral strategies during learning and resting-state vlPFC activity. Taken together, our results suggest that multiple vlPFC-linked circuits contribute to adaptive decision-making in different contexts.
Generation of an inducible destabilized-domain Cre mouse line to target disease associated microglia
Authors: Henningfield Caden M. , Kwang Nellie , Tsourmas Kate Inman , Neumann Jonathan , Kawauchi Shimako , Swarup Vivek , MacGregor Grant R. , Green Kim N. 
Published: September 2024

SummaryThe function of microglia during progression of Alzheimer’s disease (AD) can be investigated using mouse models that enable genetic manipulation of microglial subpopulations in a temporal manner. We developed a mouse strain that expresses destabilized-domain Cre recombinase (DD-Cre) from theCst7locus (Cst7DD-Cre) and tested this in 5xFAD amyloidogenic, Ai14 tdTomato cre-reporter line mice. Dietary administration of trimethoprim to induce DD-Cre activity produces long-term labeling in disease associated microglia (DAM) without evidence of leakiness, with tdTomato-expression restricted to cells surrounding plaques. Using this model, we found that DAMs are a subset of plaque-associated microglia (PAMs) and their transition to DAM increases with age and disease stage. Spatial transcriptomic analysis revealed that tdTomato+ cells show higher expression of disease and inflammatory genes compared to other microglial populations, including non-labeled PAMs. This model should allow inducible cre-loxP targeting of DAMs, without leakiness.HighlightsWe developed a new mouse strain which specifically enables recombination of loxP sites in disease associated microglia (DAMs) and can be used to manipulate DAM-gene expression.DAMs represent a subset of plaque associated microglia (PAMs), and DAM expression increases with disease progression.Spatial transcriptomic analyses reveal that DAMs have higher expression of disease and inflammatory genes compared to other PAMs.