bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synchronicity transitions determine connection fluctuations in a model of coupled oscillators with plasticity
Authors: Kuroki Satoshi , Mizuseki Kenji 
Published: June 2024

AbstractSleep and rest are crucial for knowledge reorganization and creativity. During these periods, synapses between neurons are plastically altered and neuronal activities are collectively synchronized, accompanied by large differences in excitation-inhibition (EI) balance. These processes are assumed to be dissimilar from the learning process during task engagement. The detailed mechanism of how synchronized neuronal activities modify neural circuits via plasticity has yet to be fully understood. The Kuramoto model is utilized to study the collective synchronization of oscillators, including neurons. We previously proposed the EI-Kuramoto model, in which the EI balance was implemented in the Kuramoto model. The model alters its synchronicity based on the EI balance of the interaction strength. In this study, we developed this EI-Kuramoto model by implementing plasticity, leading to the plastic EI-Kuramoto (pEI-Kuramoto) model. Models with high inhibition displayed desynchronized dynamics and consistent connection strengths. Models with low inhibition exhibited bistable dynamics between synchronized and desynchronized states and fluctuation of interaction strengths in middle strength connections, while the strongest connections remained stable. These results, stabilizing a few strong connections and fluctuating the other connections in low inhibition conditions, could facilitate knowledge abstraction and reorganization. Our findings shed light on how varying inhibitory effects influence network stability and coupling, offering deeper insights into synaptic networks and knowledge reshaping.
Balancing complexity, performance and plausibility to meta learn plasticity rules in recurrent spiking networks
Authors: Confavreux Basile , Agnes Everton J. , Zenke Friedemann , Sprekeler Henning , Vogels Tim P. 
Published: June 2024

AbstractSynaptic plasticity is a key player in the brain’s life-long learning abilities. However, due to experimental limitations, the mechanistic link between synaptic plasticity rules and the network-level computations they enable remain opaque. Here we use evolutionary strategies (ES) to meta-learn local co-active plasticity rules in large recurrent spiking net-works, using parameterizations of increasing complexity. We discover rules that robustly stabilize network dynamics for all four synapse types acting in isolation (E-to-E, E-to-I, I-to-E and I-to-I). More complex functions such as familiarity detection can also be included in the search constraints. However, our meta-learning strategy begins to fail for co-active rules of increasing complexity, as it is challenging to devise loss functions that effectively constrain net-work dynamics to plausible solutionsa priori. Moreover, in line with previous work, we can ﬁnd multiple degenerate solutions with identical network behaviour. As a local optimization strategy, ES provides one solution at a time and makes exploration of this degeneracy cumbersome. Regardless, we can glean the interdependecies of various plasticity parameters by considering the covariance matrix learned alongside the optimal rule with ES. Our work provides a proof of principle for the success of machine-learning-guided discovery of plasticity rules in large spiking networks, and points at the necessity of more elaborate search strategies going forward.
Eugenol loaded lipid nanoparticles derived hydrogels ameliorate psoriasis-like skin lesions by lowering oxidative stress and modulating inflammation
Authors: Keshari Roshan , Tharmatt Abhay , Pillai Mamatha M. , Chitkara Deepak , Tayalia Prakriti , Banerjee Rinti , Sen Shamik , Srivastava Rohit 
Published: June 2024

AbstractPsoriasis is a chronic T-cell-mediated autoimmune skin disorder characterized by excessive epidermal thickening, keratinocyte over-proliferation, disruption of epidermal cell differentiation, and increased blood vessel growth in the dermal layer. Despite the common use of corticosteroids in psoriasis treatment, their limited efficacy and numerous side effects pose significant challenges. This research introduces a promising alternative approach by presenting hydrogels loaded with Eugenol (EU) in combination with Carbopol 974P (EUNPGel) for potential psoriasis management. EUN-loaded lipid nanoparticles (EUNPs) exhibit superior drug loading, enhanced release kinetics, long-term stability, and the ability to scavenge reactive oxygen species (ROS). Furthermore, EUNPs have been shown to inhibit keratinocyte proliferation, induce apoptosis, and augment the uptake of IL-6-mediated inflammation in human keratinocyte cells. Application of EUNPs-loaded gels (EUNPGel) to imiquimod-induced psoriatic lesions has demonstrated effective dermal penetration, suppressing keratinocyte hyperplasia and restoring epidermal growth. This led to a remarkable reduction in the Psoriasis Area and Severity Index (PASI) score from 3. 75 to 0. 5 within five days. These findings highlight the potential of EUNPGel as an innovative nanomedicine for treating inflammation. This novel approach enhances ROS scavenging capacity, improves cellular uptake, facilitates skin penetration and retention, reduces the activity of hyperactive immune cells, and suggests potential applications for treating other immune-related disorders such as acne and atopic dermatitis.HighlightsHydrogel loaded with eugenol is an innovative alternative for psoriasis management.Superior drug loading, release kinetics, stability, and ROS scavenging capacity.Curb (human keratinocyte) HaCaT cells proliferation, induce apoptosis, lower IL-6 mediated inflammation.Effective dermal penetration and retention both in vivo and ex vivo.
Age-dependent H3K9 trimethylation by dSetdb1 impairs mitochondrial UPR leading to degeneration of olfactory neurons and loss of olfactory function inDrosophila
Authors: Muñoz-Carvajal Francisco , Sanhueza Nicole , Sanhueza Mario , Court Felipe A. 
Published: June 2024

AbstractAging is characterized by a decline in essential sensory functions, including olfaction, which is crucial for environmental interaction and survival. This decline is often paralleled by the cellular accumulation of dysfunctional mitochondria, particularly detrimental in post-mitotic cells such as neurons. Mitochondrial stress triggers the mitochondrial unfolded protein response (UPRMT), a pathway that activates mitochondrial chaperones and antioxidant enzymes. Critical to the efficacy of the UPRMTis the cellular chromatin state, influenced by the methylation of lysine 9 on histone 3 (H3K9). While it has been observed that the UPRMTresponse can diminish with an increase in H3K9 methylation, its direct impact on age-related neurodegenerative processes, especially in the context of olfactory function, has not been clearly established. UsingDrosophila,we demonstrate that an age-dependent increase in H3K9 trimethylation by the methyltransferase dSetdb1 reduces the activation capacity of the UPRMTin olfactory projection neurons leading to neurodegeneration and loss of olfactory function. Age-related neuronal degeneration was associated with morphological alterations in mitochondria and an increase in reactive oxygen species levels. Importantly, forced demethylation of H3K9 through knockdown of dSetdb1 in olfactory projection neurons restored the UPRMTactivation capacity in aged flies, and suppressed age-related mitochondrial morphological abnormalities. This in turn prevented age-associated neuronal degeneration and rescued age-dependent loss of olfactory function. Our findings highlight the effect of age-related epigenetic changes on the response capacity of the UPRMT, impacting neuronal integrity and function. Moreover, they suggest a potential therapeutic role for UPRMTregulators in age-related neurodegeneration and loss of olfactory function.
Assessment of microphytobenthos communities in the Kinzig catchment using photosynthesis-related traits, digital light microscopy and 18S-V9 amplicon sequencing
Authors: Mayombo Ntambwe Albert Serge , Dani Mimoza , Kloster Michael , Vidakovic Danijela , Buchner Dominik , Burfeid-Castellanos Andrea M. , Beszteri Bánk 
Published: June 2024

AbstractMicroalgae form an essential group of benthic organisms that respond swiftly to environmental changes. They are widely used as bioindicators of anthropogenic stressors in freshwater ecosystems. We aimed to assess the responses of microalgae communities to multiple environmental stressors in the Kinzig River catchment, home to a long-term ecological monitoring site, in Germany. We used a photosynthetic biomass proxy alongside community composition of diatoms assessed by digital light microscopy, and of microalgae by 18S-V9 amplicon sequencing, to characterise microalgae at 19 sampling sites scattered across the catchment. Our results revealed significant effects of physical and chemical factors on microalgae biomass and community compositions. We found that conductivity, water temperature and pH were the most important factors affecting microalgae community composition, as observed in both microscopy and amplicon analysis. In addition to these three variables, the effect of total phosphate on all microalgae, together with water discharge on the diatom (Bacillariophyta) communities, as assessed by amplicon analysis, may reveal taxon-specific variations in the ecological responses of different microalgal groups. Our results highlighted the complex relationship between various environmental variables and microalgae biomass and community composition. Further investigations, involving the collection of time series data, are required to fully understand the underlying biotic and abiotic parameters that influence these microalgae communities.
Rosettes in a matrix: Predicting spatial variation in density of a large felid in a forest-production mosaic
Authors: Paul Anish , Kumar Nitish , Mukherjee Tonmoy , Chhetri Amir Kumar , Kshettry Aritra 
Published: June 2024

AbstractLarge carnivores are keystone for ecosystems and flagships for conservation efforts but face severe threats globally. Protected Areas are vital for the conservation of these charismatic species along with a host of ecological processes. However, the extent and scope of protected areas for conservation of all threatened species is limited, especially in the global south. Considering larger landscapes that can be compatible with large carnivore conservation goals is an alternative approach to ensure their persistence. This study explores the potential of multi-use landscapes for the persistence of a globally threatened large felid, the leopard. This study investigated the spatial variability of leopard densities across a land-use gradient using spatially explicit capture-recapture framework in a tea-plantation dominated forest-production landscape mosaic. While the density of leopards in this landscape was estimated to be 7.96 ± 1.56 (SE) per 100 km2, significant (p=0.048, t=2.02, df=61) differences in estimates were observed between tea-plantations (11.53 ± 2.72 (SE) leopards per 100 km2) and the forested habitats (4.67 ± 2.07 (SE) per 100 km2). Densities between tea plantations and Protected Areas (a subset of the forested habitat) were found to be comparable (9.19 ± 4.55 (SE) per 100 km2). The study posits that conservation-compatible land use in landscapes shared with people can host a higher density of large felids than forested areas and that conservation planning needs to move beyond the dominant PA-centric paradigm. The study also reinforces the importance of multi-use landscapes for wildlife conservation, especially for an adaptable large felid.
Various plasmid strategies limit the effect of bacterial Restriction-Modification systems against conjugation
Authors: Dimitriu Tatiana , Szczelkun Mark D. , Westra Edze R. 
Published: June 2024

AbstractIn bacteria, genes conferring antibiotic resistance are mostly carried on conjugative plasmids, mobile genetic elements which spread horizontally between bacterial hosts. Bacteria carry defence systems which defend them against genetic parasites, but how effective these are against plasmid conjugation is poorly understood. Here, we study to what extent Restriction-Modification (RM) systems – by far the most prevalent bacterial defence systems - act as a barrier against plasmids. Using 10 different RM systems and 13 natural plasmids conferring antibiotic resistance inEscherichia coli, we uncovered variation in defence efficiency ranging from none to 105-fold protection. Further analysis revealed genetic features of plasmids that explain the observed variation in defence levels. First, the number of RM recognition sites present on the plasmids generally correlates with defence levels, with higher numbers of sites being associated with stronger defence. Secondly, some plasmids encode methylases that protect against restriction activity. Finally, we show that a high number of plasmids in our collection encode anti-restriction genes that provide protection against several types of RM systems. Overall, our results show that it is common for plasmids to encode anti-RM strategies, and that, as a consequence, RM systems form only a weak barrier for plasmid transfer by conjugation.
Cell fate plasticity of xylem-pole-pericycle inArabidopsisroots
Authors: Wang Xin , Ye Lingling , Zhang Jing , Melnyk Charles W. , Mähönen Ari Pekka 
Published: June 2024

AbstractInArabidopsisroots, xylem-pole-pericycle (XPP) cells exhibit remarkable cell fate plasticity by contributing to both lateral root (LR) and cambium formation. Despite significant progress in understanding these individual processes, the mechanism orchestrating these two fates and their effects on root architecture and secondary growth remain unclear. Here we combined lineage tracing with molecular genetics to study the fate dynamics of XPP cells. We showed that developmentally arrested lateral root primordia (LRP) that fail to emerge as lateral roots, gradually obtain cambium identity thus contributing to secondary growth. Conversely, preestablished procambium identity within XPP cells can be reverted to LR identity when simulated by auxin, an important player in LR development. This competence for auxin-induced LR formation from XPP cells, termed LR potency, however, decreases as the root matures. We found key cambium regulators play essential roles in shaping LR potency by promoting cambium activation and inhibiting LR development. Consistently, corresponding mutants with impaired cambium activity display broader LR potency. Moreover, cytokinins, essential players in cambium development, facilitate the identity transition of LRPs to cambium and reduce LR potency through key cambium regulators. Overall, our findings highlight the inherent cellular plasticity of XPP cells and elucidate how plant hormones influence root architecture and secondary growth through balancing the two cell fates of XPP cells.
Histidine limitation causes alteration in the TOR network and plant development
Authors: Guérin Amandine , Levasseur Caroline , Herger Aline , Renggli Dominik , Sotiropoulos Alexandros Georgios , Kadler Gabor , Hou Xiaoyu , Schaufelberger Myriam , Meyer Christian , Wicker Thomas , Bigler Laurent , Ringli Christoph 
Published: June 2024

ABSTRACTPlant growth depends on growth regulators, nutrient availability, and amino acids levels. The TOR (Target of Rapamycin) network senses these parameters and influences cell wall formation and expansion accordingly. Cell wall integrity and structures are surveyed and modified by a complex array of cell wall integrity sensors, including LRR-extensins (LRXs), that function as hormone receptors and help to compact cell walls. Expressing the Arabidopsis root-hair specific LRX1 without the extensin domain, which anchors the protein to the cell wall, has a negative effect on root hair development. The mechanism of this negative effect was investigated by a suppressor screen, which led to the identification of asune(suppressor of dominant-negative LRX1) mutant collection. Thesune82mutant was identified as an allele ofHISN2which encodes an enzyme essential for histidine biosynthesis. Thesune82mutation leads to reduced accumulation of histidine, and this influences the TOR network. Thesune82mutant reflects the impact of the TOR network on cell wall formation processes involving LRX proteins. It also represents an excellent tool to study the effects of reduced histidine levels on plant development, as it is a rare example of a viable partial loss-of-function allele in an essential biosynthetic pathway.HighlightPartial loss of function ofHISN2insune82results in a significant reduction in histidine content, which subsequently alters the TOR network.
Posterior parietal cortex maps progress along routes sharing the same meta-structure
Authors: Johnson Alexander B. , Nitz Douglas A. 
Published: June 2024

AbstractNeurons of posterior parietal cortex were recorded as rats performed a working memory task within a network of intersecting paths. The specific routes utilized in task performance provided opportunity to contrast responses of posterior parietal cortex sub-populations to linear and angular velocity with more complex responses that map route progress. We found evidence for the presence of posterior parietal cortex neurons that generalize in their firing patterns across routes having the same shape but opposite action series. The results indicate that posterior parietal cortex has the capacity to generalize the mapping of route progress independent of the specific actions taken to move through those routes. We suggest that such encoding can form the basis for learning the meta-structural organization of a non-random path network structure, such as that commonly found in cities.
The UPRERgoverns the cell-specific response of human dopaminergic neurons to mitochondrial stress
Authors: Heneine Jana , Colace-Sauty Claire , Zhu Christiane , Galet Benjamin , Guégan Justine , Lejeune François-Xavier , Gareau Thomas , Asfogo Noemi , Pardanaud-Glavieux Corinne , Corti Olga , Ravassard Philippe , Cheval Hélène 
Published: June 2024

AbstractMitochondrial dysfunction is thought to be central to the pathophysiology of Parkinson’s disease. The preferential vulnerability of dopaminergic (DA) neurons of thesubstantia nigra pars compactato mitochondrial stress may underlie their massive degeneration and the occurrence of motor symptoms. Using LUHMES-derived DA neurons, we demonstrated that inhibition of the mitochondrial electron transport chain resulted in a severe alteration of mitochondrial turnover, pushing the balance towards mitochondrial loss, a reduction of the maturation status of the DA population and an increased proportion of apoptotic cells. PERK-mediated Unfolded Protein Response of the Endoplasmic Reticulum (UPRER) emerged as the key coordinator of the stress response, governing the inactivation of the mitochondrial UPR (UPRmt), the initiation of mitophagy and the cell-specific expression of long non-coding RNAs (lncRNAs). Importantly, we discovered novel lncRNAs specifically expressed in human DA neurons upon stress. Among them, we showed that lnc-SLC6A15-5 contributes to the resumption of translation after mitochondrial stress.SummaryThe Unfolded Protein Response of the Endoplasmic Reticulum is induced upon stress in human dopaminergic neurons and modulates mitochondrial homeostasis and transcriptional programs including expression of long non-coding RNAs (lncRNAs). We discovered a lncRNA involved in translation resumption after stress.
Multi omics aided small RNA profiling of wheat rhizosphere and their potential targets in contrasting soils forRhizoctonia solani-AG8 suppression
Authors: Regmi Roshan , Panchal Shivangi , Hicks Marcus , Kroker Stasia , Anderson Jonathan , Vadakattu Gupta 
Published: June 2024

AbstractNext-generation sequencing helps describe microbial communities in rhizosphere environments, but understanding rhizosphere-plant interactions’ synergistic effects on plant traits and health outcomes remains challenging. This study analyses rhizosphere sRNAs’ ability to manipulate host gene targets in plants grown in suppressive (SP) and non-suppressive (NSP) soils with an integrated multi omics dataset. The results showed that rhizosphere sRNAs exhibited specific compositional features that may be important for rhizosphere-plant interaction. Small RNAs, less than 30 nt in size, were predominant in both samples, with a 5-prime bias towards cytosine enrichment, suggesting potential association with wheat specific argonauts. Mapping of sRNA reads to microbial metagenomes assembled draft genomes from SP and NSP soils showed sRNA loci were differentially expressed (DE) between the soils with contrasting disease suppressive capacities. In total, 96 and 132 non redundant rhizosphere sRNAs were abundant in SP and NSP rhizosphere communities, respectively. While 55 known bacterial sRNA loci were predicted from both SP and NSP metagenomes, 127 sRNAs originated from these loci were differentially expressed. Global wheat target prediction and functional analysis from DE rhizosphere sRNAs showed both soil type specific and common pathways. Upregulated NSP sRNAs target metabolic pathways, secondary metabolite biosynthesis, MAPK signalling, while SP sRNAs target glycerophospholipid metabolism, pathways such as polycomb repressive complex, starch/sucrose metabolism, and plant-pathogen interactions were targeted by both sets of sRNAs. This is the first study showing evidence for rhizosphere sRNAs and their corresponding plant transcripts in the context of biological disease suppression in agricultural soils.ImportanceSmall RNAs (sRNAs) have gained attention in host-microbe interactions due to their diverse roles in controlling biological processes. Studies have identified numerous sRNAs with novel functions across various organisms. Echoing growing evidence of sRNAs in different plant-microbe interaction, we show an evidence of rhizosphere sRNAs regulating wheat genes in soil disease suppression context. This understanding could significantly enhance our comprehension of gene regulation in biological functions, potentially paving the way for the development of microbiome-based methods to influence host traits. Understanding the microbiome community’s mechanisms in different environments offers opportunities to modify them for agriculture, including modifying farming practices, host genetics/immunity, and synthetic communities for disease suppression.
The differential effect of SARS-COV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage and virus evolution
Authors: Berlanga Juan José , Matamoros Tania , Pulido Miguel Rodríguez , Sáiz Margarita , Bayón Mercedes Núñez , Toribio René , Ventoso Iván 
Published: June 2024

SummaryThe non-structural protein 1 (NSP1) of SARS-CoV-2 blocks the mRNA entry channel of the 40S ribosomal subunit, causing inhibition of translation initiation and subsequent degradation of host mRNAs. However, target mRNA specificity and the way in which viral mRNAs escape NSP1-mediated degradation have not been clarified to date. Here we found that NSP1 acts as a translational switch capable of blocking or enhancing translation depending on how preinitiation complex 43S-PIC is recruited to the mRNA, whereas NSP1-mediated mRNA degradation mostly depends on codon usage bias. Thus, fast-translating mRNAs with optimal codon usage for human cells that preferentially recruit 43S-PIC by threading, showed a dramatic sensitivity to NSP1. On the contrary, slow-translating mRNAs with suboptimal codon usage and 5’ UTR that enabled slotting on 43S-PIC were resistant to or even enhanced by NSP1. Translation of SARS-CoV-2 mRNAs escapes NSP1-mediated inhibition by a proper combination of suboptimal codon usage and slotting-prone 5’ UTR that also confers efficient translation. Thus, the prevalence of non-optimal codons found in SARS-CoV-2 and other coronavirus genomes is favored by the distinctive effect that NSP1 plays on translation and mRNA stability.