bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential biotransformation ability may alter fish biodiversity in polluted waters
Authors: Franco Marco E. , Hollender Juliane , Schirmer Kristin 
Published: July 2024

AbstractDivergence in the activity of biotransformation pathways could lead to species sensitivity differences to chemical stress. To explore this hypothesis, we evaluated the biotransformation capacity of five fish species that are representatives of Swiss biodiversity assemblages and that inhabit watercourses surrounded by different land use. We report important interspecific differences regarding the presence and activity of major biotransformation pathways, such as the invasive pumpinkseed (Lepomis gibbosus) displaying micropollutant clearance between 3- and 7–fold higher than native species (e.g.Salmo trutta, Squalius cephalus) collected in the same areas. These differences were exacerbated by urban and agricultural influence, which increased biotransformation potential at the enzyme level by as much as 11-fold and micropollutant clearance by approximately 2-fold compared to biotransformation levels in areas with minimal human influence. In the context of the chemical defensome, we argue that fish with low biotransformation activity carry a greater burden on chemical stress, making them less likely to cope with additional stressors and sustain their population in competition with species with a higher biotransformation capacity.
Bifunctional probes reveal the rules of intracellular ether lipid transport
Authors: Böhlig Kristin , Iglesias-Artola Juan M. , Lennartz H. Mathilda , Link Anna C. , Drobot Björn , Nadler André 
Published: July 2024

AbstractEther glycerophospholipids bear a long chain alcohol attached via an alkyl or vinyl ether bond at thesn1position of the glycerol backbone. Emerging evidence suggests that ether lipids play a significant role in physiology and human health but their precise cellular functions remain largely unknown. Here, we introduce bifunctional ether lipid probes bearing diazirine and alkyne groups to study ether lipid biology. To interrogate the kinetics of intracellular ether lipid transport in mammalian cells we used a combination of fluorescence imaging, machine learning-assisted image analysis and mathematical modelling. We find that alkyl-linked ether lipids are transported up to twofold faster than vinyl-linked plasmalogens, suggesting that the lipid transport machinery can distinguish between linkage types differing by as little as two hydrogen atoms. We find that ether lipid transport predominantly occurs via non-vesicular pathways, with varying contributions from vesicular mechanisms between cell types. Altogether, our results suggest that differential recognition of alkyl- and vinyl ether lipids by lipid transfer proteins contributes to their distinct biological functions. In the future, the probes reported here will enable studying ether lipid biology in much greater detail through identification of interacting proteins and in-depth characterization of intracellular ether lipid dynamics.
PRAME expression in melanoma is negatively regulated by TET2-mediated DNA hydroxymethylation
Authors: Fang Rui , Vallius Tuulia , Zhang Arianna , Cura Devon Van , Alicandri Francisco , Fischer Grant , Draper Elizabeth , Xu Shuyun , Pelletier Roxanne , Katsyv Igor , Sorger Peter K. , Murphy George F. , Lian Christine G. 
Published: July 2024

ABSTRACTPreferentially Expressed Antigen in Melanoma (PRAME) and Ten-Eleven Translocation (TET) dioxygenase-mediated 5-hydroxymethylcytosine (5hmC) are emerging melanoma biomarkers. We observed an inverse correlation between PRAME expression and 5hmC levels in benign nevi, melanoma in situ, primary invasive melanoma, and metastatic melanomas via immunohistochemistry and multiplex immunofluorescence: nevi exhibited high 5hmC and low PRAME, whereas melanomas showed the opposite pattern. Single-cell multiplex imaging of melanoma precursors revealed that diminished 5hmC coincides with PRAME upregulation in premalignant cells. Analysis of TCGA and GTEx databases confirmed a negative relationship between TET2 and PRAME mRNA expression in melanoma. Additionally, 5hmC levels were reduced at the PRAME 5’ promoter in melanoma compared to nevi, suggesting a role for 5hmC in PRAME transcription. Restoring 5hmC levels via TET2 overexpression notably reduced PRAME expression in melanoma cell lines. These findings establish a function of TET2-mediated DNA hydroxymethylation in regulating PRAME expression and demonstrate epigenetic reprogramming as pivotal in melanoma tumorigenesis.TeaserMelanoma biomarker PRAME expression is negatively regulated epigenetically by TET2-mediated DNA hydroxymethylation
CO-OPTION OF NECK MUSCLES SUPPORTED THE VERTEBRATE WATER-TO-LAND TRANSITION
Authors: Heude Eglantine , Dutel Hugo , Sanchez-Garrido Frida , Prummel Karin D. , Lalonde Robert , Lam France , Mosimann Christian , Herrel Anthony , Tajbakhsh Shahragim 
Published: July 2024

ABSTRACTA major event in vertebrate evolution was the separation of the skull from the pectoral girdle and the acquisition of a functional neck, transitions which required profound developmental rearrangements of the musculoskeletal system. The neck is a hallmark of the tetrapod body plan and allows for complex head movements on land. While head and trunk muscles arise from distinct embryonic mesoderm populations, the origins of neck muscles remained elusive. Here, we combine comparative embryology and anatomy to reconstruct the mesodermal contribution to neck evolution. We demonstrate that head/trunk-connecting muscle groups have conserved mesodermal origins in fishes and tetrapods and that the neck evolved from muscle groups present in fishes. We propose that expansions of mesodermal populations into head and trunk domains during embryonic development underpinned the emergence and adaptation of the tetrapod neck. Our results provide evidence for exaptation of archetypal muscle groups in ancestral fishes, which were co-opted to acquire novel functions adapted to terrestrial lifestyle.
Patterns of neural activity in prelimbic cortex neurons correlate with attentional behavior in the rodent continuous performance test
Authors: Miranda-Barrientos Jorge , Adiraju Suhaas , Rehg Jason J. , Hallock Henry L. , Li Ye , Carr Gregory V. , Martinowich Keri 
Published: July 2024

AbstractSustained attention, the ability to focus on a stimulus or task over extended periods, is crucial for higher level cognition, and is impaired in individuals diagnosed with neuropsychiatric and neurodevelopmental disorders, including attention-deficit/hyperactivity disorder, schizophrenia, and depression. Translational tasks like the rodent continuous performance test (rCPT) can be used to study the cellular mechanisms underlying sustained attention. Accumulating evidence points to a role for the prelimbic cortex (PrL) in sustained attention, as electrophysiological single unit and local field (LFPs) recordings reflect changes in neural activity in the PrL in mice performing sustained attention tasks. While the evidence correlating PrL electrical activity with sustained attention is compelling, limitations inherent to electrophysiological recording techniques, including low sampling in single unit recordings and source ambivalence for LFPs, impede the ability to fully resolve the cellular mechanisms in the PrL that contribute to sustained attention.In vivoendoscopic calcium imaging using genetically encoded calcium sensors in behaving animals can address these questions by simultaneously recording up to hundreds of neurons at single cell resolution. Here, we usedin vivoendoscopic calcium imaging to record patterns of neuronal activity in PrL neurons using the genetically encoded calcium sensor GCaMP6f in mice performing the rCPT at three timepoints requiring differing levels of cognitive demand and task proficiency. A higher proportion of PrL neurons were recruited during correct responses in sessions requiring high cognitive demand and task proficiency, and mice intercalated non-responsive-disengaged periods with responsive-engaged periods that resemble attention lapses. During disengaged periods, the correlation of calcium activity between PrL neurons was higher compared to engaged periods, suggesting a neuronal network state change during attention lapses in the PrL. Overall, these findings illustrate that cognitive demand, task proficiency, and task engagement differentially recruit activity in a subset of PrL neurons during sustained attention.
An essential role for glial cells in postingestive nutrient sensing
Authors: Kulshrestha Divita , Koch Charlotte , Khalilov Majid , Schirmeier Stefanie 
Published: July 2024

AbstractBehavioral flexibility is an essential trait for survival of any organism. For example, choosing an appropriate food source is vital. To do so, the food’s nutritive value needs to be evaluated. Several studies have demonstrated thatDrosophila melanogasterlarvae and adults, as mammals, are able to distinguish between nutritious and non-nutritious carbohydrates independent of their taste. Several groups of neurons have been implicated in postprandial sugar sensing in adult flies (Dus et al., 2011, 2015; Miyamoto et al., 2012; Park et al., 2016; Musso et al., 2023). In larvae, neurons expressing Gr43a, a fructose receptor, have been shown to be implicated in postingestive glucose sensing (Mishra et al., 2013). How can a fructose sensor mediate glucose sensing? We show that postingestive glucose, and also sorbitol, sensing involves carbohydrate conversion into fructose via the polyol pathway in glial cells. Glia-derived fructose is subsequently sensed via Gr43a expressed in neurons, which leads to behavioral adaptation. Thus, in postingestive nutrient sensing, the glial cells play a central role in information processing and regulation of behavior.
Expanding the substrate selectivity of the fimsbactin biosynthetic adenylation domain, FbsH
Authors: Ahmed Syed Fardin , Balutowski Adam , Yang Jinping , Wencewicz Timothy A. , Gulick Andrew M. 
Published: July 2024

AbstractNonribosomal peptide synthetases (NRPSs) produce diverse natural products including siderophores, chelating agents that many pathogenic bacteria produce to survive in low iron conditions. Engineering NRPSs to produce diverse siderophore analogs could lead to the generation of novel antibiotics and imaging agents that take advantage of this unique iron uptake system in bacteria. The highly pathogenic and antibiotic-resistant bacteriaAcinetobacter baumanniiproduces fimsbactin, an unusual branched siderophore with iron-binding catechol groups bound to a serine or threonine side chain. To explore the substrate promiscuity of the assembly line enzymes, we report a structure-guided investigation of the stand-alone aryl adenylation enzyme FbsH. We report on structures bound to its native substrate 2,3-dihydroxybenzoic acid (DHB) as well as an inhibitor that mimics the adenylate intermediate. We produced enzyme variants with an expanded binding pocket that are more tolerant for analogs containing a DHB C4 modification. Wild-type and mutant enzymes were then used in anin vitroreconstitution analysis to assess the production of analogs of the final product as well as several early-stage intermediates. This analysis shows that some altered substrates progress down the fimsbactin assembly line to the downstream domains. However, analogs from alternate building blocks are produced at lower levels, indicating that selectivity exists in the downstream catalytic domains. These findings expand the substrate scope of producing condensation products between serine and aryl acids and identify the bottlenecks for chemoenzymatic production of fimsbactin analogs.
Structured flexibility in recurrent neural networks via neuromodulation
Authors: Costacurta Julia C. , Bhandarkar Shaunak , Zoltowski David M. , Linderman Scott W. 
Published: July 2024

AbstractThe goal of theoretical neuroscience is to develop models that help us better understand biological intelligence. Such models range broadly in complexity and biological detail. For example, task-optimized recurrent neural networks (RNNs) have generated hypotheses about how the brain may perform various computations, but these models typically assume a fixed weight matrix representing the synaptic connectivity between neurons. From decades of neuroscience research, we know that synaptic weights are constantly changing, controlled in part by chemicals such as neuromodulators. In this work we explore the computational implications of synaptic gain scaling, a form of neuromodulation, using task-optimized low-rank RNNs. In our neuromodulated RNN (NM-RNN) model, a neuromodulatory subnetwork outputs a low-dimensional neuromodulatory signal that dynamically scales the low-rank recurrent weights of an output-generating RNN. In empirical experiments, we find that the structured flexibility in the NM-RNN allows it to both train and generalize with a higher degree of accuracy than low-rank RNNs on a set of canonical tasks. Additionally, via theoretical analyses we show how neuromodulatory gain scaling endows networks with gating mechanisms commonly found in artificial RNNs. We end by analyzing the low-rank dynamics of trai ned NM-RNNs, to show how task computations are distributed.
Rab5 Overcomes CAR T Cell Dysfunction Induced by Tumor-Mediated CAR Capture
Authors: Gu Meidi , Carvalho Edmund J. , Read Kaitlin A. , Nardo David Padron , Riley James L. 
Published: July 2024

SUMMARYContinuous interaction between chimeric antigen receptor (CAR) T cell (CART) and tumors often result in CART dysfunction and tumor escape. We observed that tumors can take up CAR molecules, leaving CARTs without surface-expressed CARs and thus unable to kill tumors after prolonged exposure. Overexpression of Rab5 resulted in augmented clathrin-independent endocytosis, preventing loss of surface-expressed CARs, and enhanced CART activity. Interestingly, we observed membrane protrusions on the CART cell surface which disappeared after multiple tumor challenges. Rab5 maintained these protrusions after repeated tumor engagements and their presence correlated with effective tumor clearance, suggesting a link between endocytosis, membrane protrusions, and cytolytic activity.In vivo, Rab5-expressing CARTs demonstrated improved activity and were able to clear an otherwise refractory mesothelin-expressing solid cancer in humanized mice by maintaining CAR surface expression within the tumor. Thus, pairing Rab5 with CAR expression could improve the clinical efficacy of CART therapy.Highlights“CAR-jacking” occurs when surface CAR is internalized by target tumor cells.Rab5 overexpression prevents “CAR-jacking” and enhances CART function.Rab5 promotes CAR endocytic recycling and maintains membrane protrusions.Rab5-expressing CARTs exhibit enhanced therapeutic efficacy against solid tumors.
In vivoanalysis of the relationship between CP26 and qE-type NPQ via higher-orderArabidopsis cp26mutants
Authors: Walter Julia , Patel-Tupper Dhruv , Lam Lam , Ma Alexa , Taylor Georgia , Fleming Graham R. , Niyogi Krishna K. , Kromdijk Johannes 
Published: July 2024

AbstractCP26 is a monomeric minor light-harvesting complex of PSII (LHCII) protein that connects major LHCII trimers to the PSII core in photosynthetic thylakoid membranes. Previous studies have proposed that CP26 is not only involved in light harvesting but could also be involved in non-photochemical quenching (NPQ). Here, we analyzed higher-orderArabidopsis cp26mutants using biophysical and pharmacological approaches to investigate the nature of NPQ and its relationship to known NPQ regulators (PSII subunit S (PsbS), the xanthophyll-converting enzyme VDE and the pH gradient across the thylakoid membrane). Maximum PSII quantum efficiencies (Fv/Fm) and chlorophyll fluorescence lifetimes in the dark were significantly lower incp26mutants, confirming that CP26 deficiency leads to a sustained quenched state even in the absence of light. Destabilized PSII-LHCII supercomplexes as observed with native PAGE analysis are the likely cause for this pre-quenched state, without other antenna proteins being able to rescue this phenotype. Further analyses revealed thatcp26mutants exhibit modest (single mutant) to highly significant (double mutants) reductions in overall NPQ capacity, which do not directly rely on PsbS and VDE (although the effect is more pronounced when these qE components are altered) but depend on thylakoid lumen acidification and protonation of protein residues. Together, these results show that the NPQ component lacking incp26mutants acts independently of qE and qZ and is induced in a slower phase of NPQ induction that most likely relies on pH-dependent conformational changes.
Environmental context sculpts spatial and temporal visual processing in thalamus
Authors: Peelman Kayla , Haider Bilal 
Published: July 2024

SummaryBehavioral state modulates neural activity throughout the visual system1–3. This is largely due to changes in arousal that alter internal brain state4–10. Much is known about how these internal factors influence visual processing7–11, but comparatively less is known about the role of external environmental contexts12. Environmental contexts can promote or prevent certain actions13, and it remains unclear if and how this affects visual processing. Here, we addressed this question in the thalamus of awake head-fixed mice while they viewed stimuli but remained stationary in two different environmental contexts: either a cylindrical tube, or a circular running wheel that enabled locomotion. We made silicon probe recordings in the dorsal lateral geniculate nucleus (dLGN) while simultaneously measuring multiple metrics of arousal changes, so that we could control for them across contexts. We found surprising differences in spatial and temporal processing in dLGN across contexts. The wheel context (versus tube) showed elevated baseline activity, and faster but less spatially selective visual responses; however, these visual processing differences disappeared if the wheel no longer enabled locomotion. Our results reveal an unexpected influence of the physical environmental context on fundamental aspects of early visual processing, even in otherwise identical states of alertness and stillness.
Expansion of the genomic and functional diversity of global ocean giant viruses
Authors: Minch Benjamin , Moniruzzaman Mohammad 
Published: July 2024

AbstractGiant viruses (GVs) play crucial roles in the global ocean microbial food web and biogeochemistry by infecting protists. Traditionally, insights into GV ecology and functions have been limited to culture-based studies. However, recent metagenomic advances have uncovered over 1,800 new GV genomes from the world’s oceans. While this rapid increase in genomic information marks an impressive advance for the field, it is nowhere close to the extensive genomic information available for other marine entities - e.g., prokaryotes and their ‘virome’. Addressing this gap, we present 230 novel, high-quality GV genomes and 398 partial genomes from nine global ocean datasets using an open-source bioinformatic workflow we developed. Notably, we identified numerous GV genomes from the Baltic Sea, offering insights into their phylogenomics, metabolic potential, and environmental drivers in one of the largest brackish water ecosystems. We discovered new GV functions, including photosynthetic proteins, and identified a significant functional divide between the Imitervirales and Algavirales orders. Additionally, we evaluated best practices for GV genome recovery from metagenomic datasets through a case study on the Baltic Sea dataset. Our study significantly expands the marine GV genomic and functional diversity, broadening our understanding of their roles in the food web and biogeochemistry.
From greenwashing to greenbleaching: green communication and mitigating moral outrage in the context of revisited situational crisis communication theory
Authors: Selaković Marko , Ljepava Nikolina , Bagheri Noushin , Al Chami Riad 
Published: July 2024

PurposeThe purpose of the study is to examine the relevance and application of green communication in management of the risks associated with moral outrage inducing crises. The study aims to identify how green communication mitigates both crisis risks and moral outrage. Additionally, the research discusses ethical and unethical green communication practices in the context of their impact on relationships between organizations and stakeholders during the crisis.Design/methodology/approachThe study is designed as exploratory research. Available English-language journal articles and conference proceedings have been examined to investigate the role of green communications in crisis response contexts. The application of the search criteria and initial filtering yielded a total of 139 publications for further analysis. Following a detailed review and subsequent filtering, the final sample of 66 unique cases has been selected and analyzed in the context of Situational Crisis Communication Theory.FindingsThe systematic review and document analysis indicated multitude of significances of green communications in the context of the updated Situational Crisis Communication Theory. Moreover, a novel phenomenon has been identified: greenbleaching is exaggerated or fabricated usage of green communication to mitigate risks in the organizational crises caused by ESG-unrelated factors or events.Originality/valueThis study offers greenbleaching as a novel concept. Moreover, this is the first research that examines unethical green communication in the context of moral outrage inducing crises. Insights for researchers and practitioners regarding sustainability communication, green communication, and crisis communication ethics are also incorporated.
Institutional ownership and cost of equity of Chinese firms
Authors: Huang Min , Jiang Hai , Ning Zhiyuan , Tu Jun 
Published: July 2024

PurposeThe purpose of this paper is to investigate the role of institutional investors in the cost of equity for Chinese firms, especially state-owned enterprises (SOEs).Design/methodology/approachBy using data from Chinese firms with a unique state ownership structure, we provide empirical evidence on whether institutional investors can help reduce the cost of equity for SOEs and non-SOEs, respectively, and if so, identify the underlying channels.FindingsWe find that an increase in the shareholdings of institutions, especially independent institutions, can lead to a reduction in the cost of equity. This effect is particularly prominent in SOEs compared to non-SOEs. Moreover, institutional investors promote corporate social responsibility activities and innovation activities of invested firms, thereby reducing the cost of equity.Originality/valueThis paper contributes to a comprehensive understanding of the effects of institutional shareholdings with heterogeneity on the cost of equity and their influential mechanisms in the process of mixed ownership reform.