bluuebunny/crossref_metadata_2025_split huggingface dataset:
Roots of coastal plants stabilize carbon fixed by marine algae
Authors: Hellige Inga , Mundanatt Aman Akeerath , Massing Jana C. , Hehemann Jan-Hendrik 
Published: December 2024

AbstractCoastal vegetated ecosystems are key-nature based solutions in climate change mitigations. Mangroves, seagrass meadows and saltmarshes contribute to carbon sequestration not only through the storage of biomass and sediments, but also through the secretion of dissolved organic carbon over their root system. Macro- and microalgae release most of their produced organic carbon as exudates, exported away from their origin, leading to underrepresentation of their contribution in blue carbon assessments. Here, we analysed 93 sediment cores of coastal vegetated ecosystems from temperate to tropical regions. We used polysaccharides as bioindicators of carbon sequestration to trace carbon from source to sink in different ecosystems. By binding of specific monoclonal antibodies, algal-derived polysaccharides were detected in sediments of coastal vegetated ecosystems. The relative abundance of the main building blocks of polysaccharides, monosaccharides was consistent across all 93 sediment cores, with no significant differences, despite the varying ecosystems and locations. Our findings suggest that the restoration of plant ecosystems, fixing carbon, protecting coasts and enhance biodiversity should also be enumerated for the stored carbon from distant donors. Hence carbon sequestration is a collective or synergistic process of different photosynthetic organisms.Significance statementCoastal vegetated ecosystems are vital for climate change mitigation, sequestering carbon through biomass, sediments and the integration of organic carbon from external sources such as algae. By using polysaccharides as bioindicators, this study reveals that algal-derived carbon is preserved in sediment across diverse ecosystems, emphasizing the synergistic role of multiple photosynthetic organisms in carbon sequestration. This finding indicates that coastal vegetated ecosystems accept, accrete and stabilize carbon from different and distant donors and highlights the collective contribution of these ecosystems to global carbon storage.
Connectivity in the human and the monkey brain probes causal involvement of the fornix in Mild Cognitive Impairment and Alzheimer’s Disease
Authors: Pelekanos Vassilis , Warrington Shaun , Premereur Elsie , de Boer Jessica , Sotiropoulos Stamatios N. , Mitchell Anna S. ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: December 2024

AbstractAlzheimer’s disease (AD) is characterised by memory loss and severe deficits in cognitive function associated with neural degeneration in a network of brain regions. However, little is known about those regions’ connectivity patterns and how that differs from mild cognitive impairment (MCI) or healthy aging. To address that, we used diffusion-weighted MRI to determine connectivity across 11 key memory-related regions and their unique set of connections (connectivity fingerprints) to 14 white matter (WM) tracts. One WM tract particularly important for memory, and attractive target for therapeutic interventions in AD, is the fornix. However, determining fornix-specific contributions to memory deficits or therapeutic benefits is difficult, partly because the fornix carries numerous subcortical and cortical projections. To explore that, we additionally examined MRI-derived connectivity across homologous structures in non-human primates before and after fornix transections. We report several important findings. First, that connectivity between the hippocampus and the anterior thalamus (ATh) is strongly compromised in cognitive decline, as is fornix integrity. We also found strong reductions in the hippocampus-fornix and ATh-fornix connectivity in AD, demonstrating that fingerprint divergence across groups in hippocampal CA1 and ATh can identify differences between people with AD and MCI. In AD, we observed also elevated connectivity between WM tracts and the hippocampus or the ATh, suggesting a compensatory mechanism, which, importantly, depends on a viable fornix. We finally demonstrate that certain thalamic nuclei and hippocampal subfields link through the retrosplenial cortex in both species, highlighting its potential role as an alternative target for interventions in memory disorders.
MEG signals reveal arm posture coding and intrinsic movement plans in parietofrontal cortex
Authors: Blohm Gunnar , Cheyne Douglas O. , Crawford J. Douglas 
Published: December 2024

AbstractMovement planning processes must account for body posture to accurately convert sensory signals into movement plans. While movement plans can be computed relative to the world (extrinsic), intrinsic muscle commands tuned for current limb posture are ultimately needed to execute spatially accurate movements. The whole-brain topology and dynamics of this process are largely unknown. Here, we use high spatiotemporal resolution magnetoencephalography (MEG) in humans combined with a Pro-/Anti-wrist pointing task with 2 opposing forearm postures to investigate this question. First, we computed cortical source activity in 16 previously identified bilateral cortical areas (Alikhanian, et al., Frontiers in Neuroscience 2013). We then contrasted oscillatory activity related to opposing wrist postures to find posture coding and test when and where extrinsic and intrinsic motor codes occurred. We found a distinct pair of overlapping networks coding for posture (predominantly in γ band) vs. posture-specific movement plans (α and β). Some areas (e.g., pIPS) only showed extrinsic motor coding, and others (e.g., AG) only showed intrinsic coding, but the majority showed both types of codes. In the latter case, intrinsic codes appeared slightly before extrinsic codes and persisted in parallel across different cortical areas. These findings are consistent with two cortical networks for 1) direct feed-forward sensorimotor transformations to intrinsic muscle coordinates (for rapid control) and 2) computations of extrinsic spatial coordinates, possibly for use in higher-level aspects of visually-guided action, such as spatial updating and internal performance monitoring.Significance statement / author summaryIt is thought that the brain incorporates posture into extrinsic spatial codes to compute intrinsic (muscle-centered) motor commands, but the whole-brain temporal dynamics of this process is unknown. Here we employed human magneto-encephalography (MEG) to track this process across 16 bilateral cortical sites. We identified two, largely overlapping subnetworks for posture-dependent intrinsic codes, and extrinsic spatial coding. Surprisingly, the direct transformation from sensorimotor coordinates to intrinsic commandsprecededthe appearance of extrinsic codes, suggesting that extrinsic motor codes are derived from intrinsic codes for higher-level cognitive purposes.
A signal of temporal integration in the human auditory brain: psychological insights, EEG evidence, and clinical application
Authors: Xu Haoxuan , Huang Qianyue , Song Peirun , Zhai Yuying , Du Xinyu , Ye Hangting , Bao Xuhui , Mehmood Ishrat , Tanigawa Hisashi , Niu Wanqiu , Tu Zhiyi , Chen Pei , Zhang Tingting , Zhang Lingling , Zhao Xuan , Zhang Li , Wen Wanshun , Cao Liyu , Xiongjie Yu 
Published: December 2024

AbstractTemporal integration, the process by which the auditory system combines sound information over a curtain period to form a coherent auditory object, is essential for coherent auditory perception, yet its neural mechanisms remain underexplored. We use a “transitional click train” paradigm, which concatenates two click trains with slightly differing inter-click intervals (ICIs), to investigate temporal integration in the human cortex. Using a 64-channel electroencephalogram (EEG), we recorded responses from 42 healthy participants exposed to regular and irregular transitional click trains and conducted change detection tasks. Regular transitional click trains elicited significant change responses in the human cortex, indicative of temporal integration, whereas irregular trains did not. These neural responses were modulated by ICI length, ICI contrast, and regularity. Behavioral data mirrored EEG findings, showing enhanced detection for regular conditions compared to irregular conditions and pure tones. Furthermore, variations in change responses were associated with decision-making processes. Temporal continuity was critical, as introducing gaps between click trains diminished both behavioral and neural responses. In clinical assessments, 22 coma patients exhibited diminished or absent change responses, effectively distinguishing them from healthy individuals. Our findings identify distinct neural markers of temporal integration and highlight the potential of transitional click trains for clinical diagnostics.
Reproducible Brain Entropy (BEN) Alterations During Rumination
Authors: Lu Jue , Song Donghui , Chang Da , Wang Ze 
Published: December 2024

AbstractRumination, characterized by recurrent and repetitive thinking, is closely associated with mental disorders such as depression. However, the neural mechanisms underlying this mental state remain poorly understood. In this study, we use a relatively novel neuroimaging analysis method-Brain Entropy (BEN) to quantitatively assess the irregularity, disorder, and complexity of brain activity, providing new insights into the neural mechanisms of rumination.We utilized a publicly available MRI dataset from three different scanners. The dataset included 41 healthy adult participants who completed identical fMRI tasks on IPCASGE, PKUGE, and PKUSIEMENS scanners. The time interval between the two visits was 22.0 ± 14.6 days. The fMRI session included four runs: resting state, sad memory, rumination, and distraction. Whole brain voxel-wise BEN differences of task state and resting state, rumination and sad memory, distraction and sad memory, and rumination and distraction were tested and overlap regions after thresholded (p<0.05) across the three scanners were identified as exhibiting significant differences.The results demonstrate distinct alterations in BEN across mental states. Compared to the sad memory condition, decreased BEN was found in the visual cortex (VC) during rumination and decreased BEN in the posterior cingulate cortex/precuneus (PCC/PCu) during distraction. However, when compared to distraction, rumination showed increased BEN in the PCC/PCu. These findings suggest that rumination involves heightened internal focus and reduced processing of external environmental information. This study highlights BEN as a valuable metric for elucidating the neural mechanisms underlying rumination and its role in depression.
Evolution of plasticity and character displacement in a fluctuating environment
Authors: Chevin Luis-Miguel , Chauhan Lakshya 
Published: December 2024

AbstractSpecies that compete for the same resource may undergo ecological character displacement (CD), where the phenotype of each species evolves to deviate from its optimum in the absence of competition. As most environments are not static, interspecific competition is likely to occur in environments that fluctuate over time, which can also cause the evolution of phenotypic plasticity for traits mediating the competition. We use a quantitative genetic model to study theoretically how a randomly fluctuating environment and evolution of plasticity influence the outcome of ecological CD between two competing species. We show that environmental fluctuations make the conditions for CD more stringent, requiring stronger competitive selection relative to stabilizing selection. This occurs because environmental fluctuations reduces the average population size, and thereby competition intensity. Evolving plasticity can restore CD by buffering the impact of environmental fluctuations through phenotypic tracking, to a degree that depends on environmental predictability. Somewhat paradoxically, competition that favors phenotypic divergence among species can cause convergent CD in plasticity, when this reduces the load caused by fluctuations in phenotypic divergence. Our results shed light on how competition influence evolution of the fundamental niche in a fluctuating environment.
Soil bacterial neutral lipid fatty acids: Markers for carbon storage or necromass?
Authors: Gorka Stefan , Canarini Alberto , Schmidt Hannes , Kaiser Christina 
Published: December 2024

AbstractCarbon storage is a common strategy of soil microbes to cope with resource fluctuations. Fungi use neutral lipids (triacylglycerols, TAGs) for storage, which can be quantified via their derived fatty acids (NLFAs). NLFAs specific to bacteria can also be abundant in soils, but are rarely analysed as soil bacteria are assumed to not store TAGs. Instead, bacterial NLFAs are thought to derive from degraded phospholipids (diacylglycerols, DAGs), and thus indicate bacterial necromass, but this interpretation lacks evidence. In this perspective, we synthesise knowledge from the literature and our own experimental results on the origin of soil bacterial NLFAs. In sum, we provide evidence that bacterial NLFAs are predominantly derived from TAGs used for carbon storage: (1) Several pure culture studies provide evidence for TAG production in selected bacterial isolates. (2) Screening of genomes showed that wax ester synthase/diacylglycerol acyltransferases, which mediate the last step of TAG synthesis, are abundant in bacterial isolates from soil, suggesting a widespread genetic capability to produce TAGs. (3) We experimentally created conditions of excess labile carbon by adding isotopically labelled glucose to soil. Glucose-13C was rapidly allocated into bacterial NLFAs, with higher relative enrichment than phospholipid-derived fatty acids, indicating storage. (4) DAGs are not necessarily produced—and may only be intermediate compounds—during phospholipid degradation. We conclude that soil bacterial NLFAs are mainly derived from storage compounds, but a potential contribution from degraded phospholipids needs further validation. Isotopic labelling could resolve this, making NLFAs a valuable biomarker for microbial storage compounds in soil.HighlightsBacterial NLFAs originate from triacylglycerols (TAGs) or degraded phospholipidsNeutral lipids are not necessarily produced during phospholipid degradationSoil bacteria have the genetic potential to produce TAGs for storageRapid transfer of excess glucose-13C into soil bacterial NLFAs suggests storageBacterial NLFAs are markers for carbon storage rather than necromass
The phosphorylation of Pak1 by Erk1/2 for cell migration requires Arl4D acting as a scaffolding protein
Authors: Chang Ting-Wei , Lin Ming-Chieh , Yu Chia-Jung , Lee Fang-Jen S. 
Published: December 2024

AbstractActivation of extracellular signal-regulated kinases 1 and 2 (Erk1/2) at the plasma membrane typically results in their translocation to other intracellular sites for substrate targeting. This targeting requires scaffolding proteins to bring Erk1/2 and their substrates together. In the case of platelet-derived growth factor (PDGF)-induced signaling that activates Erk1/2 to phosphorylate Pak1 for cell migration, Erk1/2 remain at the plasma membrane. Thus, it has been unclear in this case whether a scaffolding protein is needed for substrate targeting by Erk1/2. The small GTPase Arf-like protein (Arl) 4D also promotes cell migration by targeting Pak1 to the plasma membrane. However, as this recruitment also results in the phosphorylation of Pak1, it has been unclear how this phosphorylation is achieved. Furthermore, because both Erk1/2 and Arl4D promote the role of Pak1 in cell migration, the relationship between these two processes has also been unclear. Addressing these outstanding questions, we show that Arl4D acts as a scaffolding protein by recruiting Erk1/2 and Pak1 to the plasma membrane for their assembly into a protein complex. Our findings identify Arl4D as a novel regulator of Erk1/2, reveal a conserved role for scaffolding proteins in substrate targeting by Erk1/2, as well as uncovering a previously unknown interplay among Arl4D, Erk1/2, and Pak1. Moreover, as all these factors are known to be involved in cell migration, we have shed new mechanistic insights into how this fundamental cellular process occurs.
KlebPhaCol: A community-driven resource for Klebsiella research identified a novel gut phage order associated with the human gut
Authors: Rothschild-Rodriguez Daniela , Lambon Kai S. , Latka Agnieszka , Costa Ana Rita , Mantzouratou Anna , King Claire , Boeckaerts Dimitri , Sheridan Elizabeth , Merrick Francesca , Drobniewski Francis , Angelis Ilaria De , Saeed Kordo , Sutton J. Mark , Wand Matthew E. , Andrew Michael , Hedges Morgen , Brouns Stan J. J. , Haas Pieter-Jan , Kushwaha Simran Krishnakant , Lawson Sophie T. , Fordham Stephen M.E. , Lee Yan-Jiun , Wu Yi , Briers Yves , Weigele Peter R. , Nobrega Franklin L. 
Published: December 2024

AbstractThe growing threat of multidrug-resistantKlebsiella pneumoniae, coupled with its role in gut colonisation, has intensified the search for new treatments, including bacteriophage therapy. Despite increasing documentation ofKlebsiella-targeting phages, clinical applications remain limited, with key phage-bacteria interactions still poorly understood. A major obstacle is fragmented access to well-characterised phage-bacteria pairings, restricting the collective advancement of therapeutic and mechanistic insights. To address this gap, we created the Klebsiella Phage Collection (KlebPhaCol), an open-source resource comprising 53 phages and 74Klebsiellaisolates, all fully characterised. These phages span five families – including a novel order,Felixvirales, associated with the human gut – and target 27 sequence types (including ST258, ST11, ST14) and 28 capsular-locus types (including KL1 and KL2), across sixKlebsiellaspecies. Freely accessible atwww.klebphacol.org, KlebPhaCol invites the scientific community to both use and contribute to this resource, fostering collaborative research and a deeper understanding ofKlebsiella-phage interactions beyond therapeutic use.
Molecular Correlates of Glycine Receptor Activity in Human β Cells
Authors: Gomes Amanda Schukarucha , Ellis Cara E. , Spigelman Aliya F. , Santos Theodore dos , Maghera Jasmine , Suzuki Kunimasa , MacDonald Patrick E. 
Published: December 2024

AbstractObjectivesGlycine acts in an autocrine positive feedback loop in human β cells through its ionotropic receptors (GlyRs). In type 2 diabetes (T2D), islet GlyR activity is impaired by unknown mechanisms. We sought to investigate if the GlyR dysfunction in T2D is replicated by hyperglycemiaper se, and to further characterize its action in β cells and islets.MethodsGlyR-mediated currents were measured using whole-cell patch-clamp in human β cells from donors with or without T2D, or after high glucose (15 mM) culture. We also correlated glycine-induced current amplitude with transcript expression levels through patch-seq. The expression of the GlyR α1, α3, and β subunit mRNA splice variants was compared between islets from donors with and without T2D, and after high glucose culture. Insulin secretion from human islets was measured in the presence or absence of the GlyR antagonist strychnine.ResultsAlthough gene expression of GlyRs was decreased in T2D islets, and β cell GlyR-mediated currents were smaller, we found no evidence for a shift in GlyR subunit splicing. Glycine-induced currents are also reduced after 48 hours culture of islets from donors without diabetes in high glucose, where we also find the reduction of the α1 subunit expression, but an increase in the α3 subunit. We discovered that glycine-evoked currents are highly heterogeneous amongst β cells, inversely correlate with donor HbA1c, and are significantly correlated to the expression of 92 different transcripts and gene regulatory networks (GRNs) that include CREB3(+), RREB1(+) and ZNF697(+). Finally, glucose-stimulated insulin secretion is decreased in the presence of the GlyR antagonist strychnine.ConclusionsWe demonstrate that glucose can modulate GlyR expression, and that the current decrease in T2D is likely due to the receptor gene expression downregulation, and not a change in transcript splicing. Moreover, we define a previously unknown set of genes and regulons that are correlated to GlyR-mediated currents and could be involved in GlyR downregulation in T2D.HighlightsGlycine-evoked currents in β cells are lower in T2D and after high glucose cultureGlyR gene expression is reduced in T2D, with no shift in splice variant expressionGlyR inhibition with strychnine decreases insulin secretionWe define transcripts and gene regulatory networks correlated to glycine-induced currents
Rescue of bacterial motility using two and three-species FliC chimeras
Authors: Scadden Jacob , Pandit Divyangi , Ridone Pietro , Sowa Yoshiyuki , Baker Matthew AB 
Published: December 2024

AbstractThe bacterial flagellar filament acts as a propeller to drive most bacterial swimming. The filament is made of flagellin, known as FliC inEscherichia coli, Salmonella TyphimuriumandPseudomonas aeruginosa. FliC consists of four domains, the highly conserved core D0 and D1 domains and the hypervariable outer D2 and D3 domains. The size and structure of the outer domains varies, being completely absent in some bacterial species. Here we sought to identify outer domains from various species which were compatible such that they could form functional filaments to drive motility. We calculated a phylogeny of 211 representative flagellin amino acid sequences and generated two outer domain deleted variants and six chimericfliCmutants using domains from E. coli,Salmonella Typhimurium, P. aeruginosa,Collimonas fungivorans, Helicobacter mustelae andMesorhizobiumsp. ORS3359. Four of the chimericfliCmutants rescued motility in afliCdisrupted strain, all of which contained theSalmonella TyphimuriumD2 domain. Overall, we demonstrate the interchangeability of the outer domains, in particular that domains from different species can be interchanged to form functional filaments that propel bacterial swimming.
Conserved effectors underpin the virulence of liverwort-isolatedPseudomonasin divergent plants
Authors: Robinson Kayla , Buric Lucia , Grenz Kristina , Chia Khong-Sam , Hulin Michelle T. , Ma Wenbo , Carella Philip 
Published: December 2024

ABSTRACTPlant pathogenicPseudomonasspecies naturally antagonize a diverse range of flowering plants. While emerging research demonstrates that isolates belonging to theP. syringaespecies complex colonize diverse hosts, the extent to which these bacteria naturally infect non-flowering plants like the model liverwortMarchantia polymorpharemains unclear. Here, we identify natural associations betweenPseudomonas viridiflavaand the liverwortMarchantia polymorpha. Pseudomonasbacteria isolated from diseased liverworts in the wild successfully re-infectedM. polymorphain pure culture conditions, producing highin plantabacterial densities and causing prominent tissue maceration. Comparative genomic analysis ofMarchantia-associatedP. viridiflavaidentified core virulence machinery like the type-III secretion system (T3SS) and conserved effectors (AvrE and HopM1) that were essential for liverwort infection. Disease assays performed inNicotiana benthamianafurther confirmed that liverwort-associatedP. viridiflavainfect flowering plants in an effector-dependent manner. Our work highlightsP. viridiflavaas an effective broad host pathogen that relies on conserved virulence factors to manipulate evolutionarily divergent host plants.