bluuebunny/crossref_metadata_2025 huggingface dataset:
When most fMRI connectivity cannot be detected: insights from time course reliability
Authors: Koten Jan Willem , Manner Hans , Pernet Cyril , Schüppen Andre , Szücs Dénes , Wood Guilherme , Ioannidis John P. A.
Published: February 2024

The level of correlation between two phenomena is limited by the accuracy at which these phenomena are measured. Despite numerous group reliability studies, the strength of the fMRI connectivity correlation that can be detected given underlying within subject time course reliability remains elusive. Moreover, it is unclear how within subject time course reliability limits the robust detection of connectivity on the group level. We estimated connectivity from 50 individuals engaged in a working memory task. The grand mean connectivity of the connectome equaled r =0.41 (95% CI 0.31-0.50) for the test run and r =0.40 (95% CI 0.29-0.49) for the retest run. However, mean connectivity was reduced to r=0.09 (95% C.I. 0.03-0.16) when test-retest reliability and residual auto-correlations of single time courses were considered, suggesting that less than a quarter of the observed connectivity is reliably detectable. Null hypothesis significance testing (NHST)-based analysis revealed that within subject time course reliability markedly affects the significance levels at which paths can be detected at the group level. This was in particular the case when samples were small or connectome coordinates were randomly selected. With a sample of 50 individuals, the connectome of a test session was completely reproduced in retest sessions at P < 2.54e-6. Despite perfect group reproducibility at conservative p-values, on average only 0.81 percent of the observed connectivity could be attributed to working memory-related time course fluctuations after corrections. Time course reliability can offer valuable insights on the detectable connectivity and should be assessed more frequently in fMRI investigations.
The bispectral EEG (BSEEG) method quantifies post-operative delirium-like states in young and aged mice after head mount implantation surgery
Authors: Nishiguchi Tsuyoshi , Shibata Kazuki , Yamanishi Kyosuke , Dittrich Mia Nicole , Islam Noah Yuki , Patel Shivani , Phuong Nathan James , Marra Pedro S. , Malicoat Johnny R. , Seki Tomoteru , Nishizawa Yoshitaka , Yamanashi Takehiko , Iwata Masaaki , Shinozaki Gen
Published: February 2024

Delirium, a syndrome characterized by an acute change in attention, awareness, and cognition, is commonly observed in older adults and has multiple potential triggers, including illness, drug, trauma, and surgery. There are few quantitative monitoring methods in clinical settings. We developed the bispectral electroencephalography (BSEEG) method in clinical research that can detect the presence of and quantify the severity of delirium using a novel algorithm. In the pre-clinical model, we reported that the BSEEG method can capture a delirium-like state in mice following LPS administration. However, its application to post-operative delirium (POD) has not yet been validated in animal experiments. Therefore, this study aimed to create a POD model mouse with the BSEEG method by monitoring BSEEG scores after EEG head-mount implantation surgery throughout the recovery phase. We compared the BSEEG scores of C57BL/6J young (2-3 months old) with aged (18-19 months old) mice for quantitative evaluation of the delirium-like state after the surgery. Postoperatively, both groups showed increased BSEEG scores and a loss of regular diurnal changes in BSEEG scores every daytime and night. In young mice, BSEEG scores and regular diurnal changes recovered relatively quickly to baseline by around postoperative day 3. On the other hand, aged mice had prolonged increases in postoperative BSEEG scores and it reached steady state only after around postoperative day 8. This study suggests the BSEEG method can be utilized to quantitatively evaluate POD and also assess the effect of aging on recovery from POD in pre-clinical model.
Discovery of free glycated amines and glycated urea as potential markers of diabetic nephropathy
Authors: Shaikh Rashdajabeen Q , Das Sancharini , Chaurasiya Arvindkumar , Ashtamy MG , Sheikh Amreen B , Fernandes Moneesha , Tiwari Shalbha , Unnikrishnan AG , Kulkarni Mahesh J
Published: February 2024

The role of protein glycation in the pathogenesis of diabetes is well established. Akin to proteins, free amino acids and other small-molecule amines are also susceptible to glycation in hyperglycemic conditions and may have a role in the pathogenesis of the disease. However, the information on glycation of free amino acids and other small- molecule amines is relatively obscure. In the quest to discover small molecule glycated amines in the plasma, we have synthesized glycated amino acids, glycated creatine, and glycated urea, and by using a high-resolution accurate mass spectrometer, a mass spectral library was developed comprising the precursor and predominant fragment masses of glycated amines. Using this information, we report the discovery of glycation of free lysine, arginine, and leucine/isoleucine from the plasma of diabetic patients. This has great physiological significance as glycation of these amino acids may create their deficiency and affect vital physiological processes such as protein synthesis, cell signaling and insulin secretion. Also, these glycated amino acids could serve as potential markers of diabetes and its complications. On the other hand, accumulation of creatinine and urea in the plasma act as biomarkers of diabetic nephropathy diagnosis. For the first time, we report the detection of glycated urea in diabetes, which is confirmed by matching the precursor and fragment masses with thein vitrosynthesized glycated urea by using12C6 and13C6-glucose. Further, we quantified glycated urea detected in two forms, monoglycated urea (MGU) and diglycated urea (DGU), by a targeted mass spectrometric approach in the plasma of healthy, diabetes, and diabetic nephropathy subjects. Both MGU and DGU showed a positive correlation with clinical parameters such as blood glucose and HbA1c. Given that urea gets converted to glycated urea in hyperglycemic conditions, it is crucial to quantify MGU and DGU along with the urea for the diagnosis of diabetic nephropathy.
Selection on sporulation strategies in a metapopulation can lead to coexistence
Authors: Proulx Stephen R. , Sakal Taom , Thomasson Kelly
Published: February 2024

In constant environments the coexistence of similar species or genotypes is generally limited. In a metapopulation context, however, types that utilize the same resource but are distributed along a competition-coexistence trade-off, can coexist. Much thought in this area focuses on a generic trade-off between within-deme competitive ability and between-deme dispersal ability. We point out that the sporulation program in yeasts and other microbes can create a natural trade-off such that strains which initiate sporulation at higher rates suffer in terms of within-deme competition but benefit in terms of between deme dispersal. We develop simple metapopulation models where the within-deme behavior follows simple chemostat dynamics. We first show that the rate of sporulation determines the colonization ability of the strain, with colonization ability increasing with sporulation rate up to a point. Metapopulation stability of a single strain exists in a defined range of sporulation rates. We then use pairwise invasability plots to show that coexistence of strains with different sporulation rates generally occurs, but that the set of sporulation rates that can potentially coexist is smaller than the set that allows for stable metapopulations. We then extend our pairwise results to show how a continuous set of strains can coexist and verify our conclusions with numerical calculations. Our results show that stable variation in sporulation rates is expected under a wide range of ecological conditions.
Alpha-synuclein-induced nigrostriatal degeneration and pramipexole treatment disrupt frontostriatal plasticity
Authors: Chevalier Sarah , Decourt Mélina , Francheteau Maureen , Balbous Anaïs , Fernagut Pierre-Olivier , Benoit-Marand Marianne
Published: February 2024

BACKGROUND

Parkinson’s disease is characterized by the degeneration ofsubstantia nigra pars compacta(SNc) dopaminergic neurons, leading to motor and cognitive symptoms. Numerous cellular and molecular adaptations due to the degenerative process or dopamine replacement therapy (DRT) have been described in motor networks but little is known regarding associative basal ganglia loops.

OBJECTIVE

To investigate the contributions of nigrostriatal degeneration and pramipexole (PPX) on neuronal activity in the orbitofrontal cortex (OFC), frontostriatal plasticity and markers of synaptic plasticity.

METHODS

Bilateral nigrostriatal degeneration was induced by viral-mediated overexpression of human mutated alpha-synuclein in the SNc. Juxtacellular recordings were performed in anesthetized rats to evaluate neuronal activity in the OFC. Recordings in the dorsomedial striatum (DMS) were performed and spike probability in response to OFC stimulation was measured before and after a high frequency stimulation (HFS). Post-mortem analysis included stereological assessment of nigral neurodegeneration, BDNF and TrkB levels.

RESULTS

Nigrostriatal neurodegeneration led to altered firing patterns of OFC neurons that were restored by PPX. HFS of the OFC led to an increased spike probability in the DMS, while dopaminergic loss had an opposite effect. PPX led to a decreased spike probability following HFS in control rats and failed to counteract the effect of dopaminergic neurodegeneration. These alterations were associated with decreased levels of BDNF and TrkB.

CONCLUSIONS

Both nigral dopaminergic loss and PPX concur to alter fronstostriatal transmission, precluding adequate information processing in associative basal ganglia loops as a gateway for the development of non-motor symptoms or non-motor side-effects of DRT.
Genetic Modulation of Protein Expression in Rat Brain
Authors: Li Ling , Wu Zhiping , Guarracino Andrea , Villani Flavia , Kong Deihui , Mancieri Ariana , Zhang Aijun , Saba Laura , Chen Hao , Brozka Hana , Vales Karel , Senko Anna N. , Kempermann Gerd , Stuchlik Ales , Pravenec Michal , Prins Pjotr , Peng Junmin , Williams Robert W. , Wang Xusheng
Published: February 2024

Genetic variations in protein expression are implicated in a broad spectrum of common diseases and complex traits. However, the fundamental genetic architecture and variation of protein expression have received comparatively less attention than either mRNA or classical phenotypes. In this study, we systematically quantified proteins in the brains of a large family of rats using tandem mass tag (TMT)-based quantitative mass-spectrometry (MS) technology. We identified and quantified a comprehensive proteome of 8,119 proteins from Spontaneously Hypertensive (SHR/Olalpcv), Brown Norway with polydactyly-luxate (BN-Lx/Cub), and 29 of their fully inbred HXB/BXH progeny. Differential expression (DE) analysis identified 597 proteins with significant differences in expression between the parental strains (fold change > 2 and FDR < 0.01). We characterized 95 variant peptides by proteogenomics approach and discovered 464 proteins linked to strongcis-acting quantitative trait loci (pQTLs, FDR < 0.05). We also explored the linkage of pQTLs with behavioral phenotypes in rats and examined the sex-specific pQTLs to reveal both distinct and sharedcis-pQTLs between sexes. Furthermore, by creating a novel view of the rat pangenome, we improved the ability to pinpoint candidate genes underlying pQTL. Finally, we explored the connection between the pQTLs in rat and human disorders, underscoring the translational potential of our findings. Collectively, this work demonstrates the value of large and systematic proteo-genetic datasets in understanding protein modulation in the brain and its functional linkage to complex central nervous system (CNS) traits.
Episodic recruitment of attractor dynamics in frontal cortex reveals distinct mechanisms for forgetting and lack of cognitive control in short-term memory
Authors: Oña-Jodar Tíffany , Prat-Ortega Genís , Li Chengyu , Dalmau Josep , Compte Albert , de la Rocha Jaime
Published: February 2024

Short-term memory (STM) is prone to failure, especially during prolonged memory maintenance or under limited cognitive control. Despite predictive mechanistic frameworks based on persistent neural activity and attractor states, a direct assessment of network dynamics during multifactorial STM failure is still missing. We addressed this in a delayed-response task where mice maintained a prospective response during a long variable delay. Mice behavior episodically switched between a task-engaged state described by an attractor model, and a task-disengaged state purely determined by previous choices. During task engagement, the anterolateral motor cortex (ALM) showed delay persistent activity stably encoding correct choices, whereas the encoding reversed during the delay in error trials. In contrast, in task-disengaged phases ALM showed no clear traces of attractor dynamics and instead exhibited enhanced synchrony at ∼ 4-5Hz. Thus, ALM switches between distinct error-generating dynamics: in control-capable trials, transitions between memory attractors cause forgetting errors, whereas non-memory errors are caused by the dissociation of ALM during the mnemonic period reflecting the lack of cognitive control.
Spatial Transcriptomics in Breast Cancer Reveals Tumour Microenvironment-Driven Drug Responses and Clonal Therapeutic Heterogeneity
Authors: Jiménez-Santos María José , García-Martín Santiago , Rubio-Fernández Marcos , Gómez-López Gonzalo , Al-Shahrour Fátima
Published: February 2024

Breast cancer is a heterogeneous disease that has the highest incidence and mortality rate among cancers in women worldwide. Breast cancer patients are stratified into three clinical subtypes with different treatment strategies and prognostic values. The development of targeted therapies against the biomarkers that define these strata constitutes one of the precedents of precision oncology, which aims to provide tailored treatments to cancer patients by targeting the molecular alterations found in each tumour. Although this approach has increased patient outcomes, many treatment failure cases still exist. Drug ineffectiveness and relapse have been associated with the coexistence of several malignant subpopulations with different drug sensitivities within the same lesion, a phenomenon known as intratumor heterogeneity. This heterogeneity has been extensively studied from a tumour-centric view, but recently, it has become evident that the tumour microenvironment plays a crucial role in intratumor heterogeneity. However, few studies consider the tumour-microenvironment interplay and its influence on drug sensitivity. In this work, we predict the sensitivity of 10x Visium spatial transcriptomics data from 9 breast cancer patients to >1,200 drugs and verify different response patterns across the tumour, interphase and microenvironment regions. We uncover a sensitivity continuum from the tumour core to the periphery accompanied by a functional gradient. Moreover, we identify conserved therapeutic clusters with distinct response patterns within the tumour region. We link the specific drug sensitivities of each therapeutic cluster to different ligand-receptor interactions that underpin distinct biological functions. Finally, we demonstrate that genetically identical cancer spots may belong to different therapeutic clusters and that this therapeutic heterogeneity is related to their location at the edge or core of tumour ducts. These results highlight the importance of considering the distance to the tumour core and the microenvironment composition when identifying suitable treatments to target intratumor heterogeneity.
Accumulation of Oncogenic Mutations During Progression from Healthy Tissue to Cancer
Authors: Zhang Ruibo , Bozic Ivana
Published: February 2024

Cancers typically result from sequential accumulation of driver mutations in a previously healthy cell. Some of these mutations, such as inactivation of the first copy of a tumor suppressor gene, can be neutral, and some, like those resulting in activation of oncogenes, may provide cells with a selective growth advantage. We study a multi-type branching process that starts with healthy tissue in home-ostasis and models accumulation of neutral and advantageous mutations on the way to cancer. We provide results regarding the sizes of premalignant populations and the waiting times to the first cell with a particular combination of mutations, including the waiting time to malignancy. Finally, we apply our results to two specific biological settings: initiation of colorectal cancer and age incidence of chronic myeloid leukemia. Our model allows for any order of neutral and advantageous mutations and can be applied to other evolutionary settings.
A single E205D allele of a key P450CYP6P3is driving metabolic pyrethroid resistance in the major African malaria vectorAnopheles gambiae
Authors: Kengne-Ouafo Jonas A. , Kouamo Mersimine , Muhammad Abdullahi , Tepa Arnaud , Ntadoun Stevia , Mugenzi Leon , Tekoh Theofelix , Hearn Jack , Tchouakui Magellan , Wondji Murielle , Ibrahim Sulaiman S. , Wondji Charles S.
Published: February 2024

Deciphering the molecular drivers of insecticide resistance is paramount to extend the effectiveness of malaria vector control tools. Here, we demonstrated that the E205D amino acid change in a key metabolic resistance P450CYP6P3drives pyrethroid resistance in the major malaria vector,Anopheles gambiae. Spatio-temporal whole genome Poolseq analyses in Cameroon detected a major P450-linked locus on chromosome 2R beside the sodium channel locus.In vitrometabolism assays with recombinantly expressedCYP6P3protein revealed that the catalytic efficiency of 205D was 2.5 times higher than E205 with α-cypermethrin. Similar patterns were observed for permethrin. Overexpression of the 205D allele in transgenic flies confers higher more pyrethroids and carbamates resistance, compared to controls. A DNA-based assay further supported that theCYP6P3-205D variant strongly correlates with pyrethroid resistance in field populations (OR=26.4; P<0.0001) and that it reduces the efficacy of pyrethroid-only LLINs with homozygote RR genotype exhibiting significantly higher survival following PermaNet 3.0 exposure compared to the SS genotype (OR: 6.1, p = 0.0113). Furthermore, theCYP6P3-E205D combines with thekdrtarget-site resistance mechanisms to worsen the loss of bednet efficacy. The 205D mutation is now predominant in West and Central Africa but less abundant or absent in East and South Africa with signs of introgression withAn. coluzziiin Ghana. This study highlights the importance of P450-based resistance and designs field-applicable tools to easily track the spread of metabolic resistance and assess its impact on control interventions.

One Sentence Summary:The major obstacle to malaria control and elimination is the spread of parasite resistance to anti-malarial drugs, and mosquito resistance to insecticides. In this study, we identified a key point mutation E205D in the metabolic geneCYP6P3(cytochrome P450) conferring resistance to pyrethroids by enhancing the breakdown of insecticides used for bednets impregnation. DNA-based assays were then designed and used to determine the spread of the resistance across Africa and demonstrate that theCYP6P3-205D allele works together with the knockdown resistance in the voltage-gated Sodium channel to reduce the efficacy of insecticide-treated bednets.
Turgor and the conformational pathway for MscS recovery
Authors: Anishkin Andriy , Sukharev Sergei
Published: February 2024

The bacterial mechanosensitive channel MscS is an adaptive osmolyte release valve that cycles between closed, open, and inactivated states. Since some of these conformations are stable only in the lipid environment under specific conditions, the structures that are currently available cannot explain the entire functional cycle. Previous patch-clamp characterization has provided insights into the missing functional state by estimating protein expansion areas associated with the closed-to-open and closed-to-inactivated transitions and indicating that the closed state must be the most compact. In this paper, we model the conformational transition of MscS from the splayed conformation with the uncoupled gate to the putative compact closed state. The compaction pathway revealed in preliminary extrapolated motion simulations (ExMoS) involved an upward sliding motion of the internal TM3 barrel inside the outer sheath formed by TM1-TM2 helical pairs. This move leads to several structural changes: (1) the relocation of the characteristic kink at G113 to a new position at G121, (2) the establishment of the hydrophobic TM2-TM3 contact, (3) a new pattern of interactions with membrane lipids, and (4) the formation of stabilizing salt bridges between TM1-TM2 loops and the cytoplasmic cage domain. In the intact bacterial cell, the driving force for this upward motion is likely to be turgor pressure normal to the plane of the membrane acting on the upper hemisphere of the cage domain from the inside. Under continuing lipid synthesis in the inner leaflet of the plasma membrane, turgor pressure is also predicted to maximize the lateral pressure of lipids in the membrane, thus driving MscS compaction. Steered simulations were performed on the splayed state to mimic these effects by applying normal forces to the upper part of the cage domain and by applying lateral compression to the TM1-TM2 pairs, emulating the pressure of lipids. The structure arrived at the predicted compact state of the channel. This state was critically stabilized by displacing non-bilayer lipids from the TM2-TM3 crevices into the bilayer. We propose that the energized metabolic state of the cell generating high turgor and promoting lipid synthesis should strongly favor the compact closed state of MscS. The normal forces pressing the dome of the cage domain against the membrane may provide a common recovery mechanism for the entire family of MscS-like channels found exclusively in organisms with walled cells, which evolved to function under turgor pressure. A conversion of turgor into membrane tension under hypoosmotic cytoplasm swelling and peptidoglycan expansion will drive opposite processes of opening followed by adaptive MscS closure and inactivation.
Identifying regulators of associative learning using a protein-labelling approach inC. elegans
Authors: Rahmani Aelon , McMillen Anna , Allen Ericka , Ansaar Radwan , Poljak Anne , Chew Yee Lian
Published: February 2024

The ability to learn and form memories is critical for animals to make choices that promote their survival. The biological processes underlying learning and memory are mediated by a variety of genes in the nervous system, acting at specific times during memory encoding, consolidation, and retrieval. Many studies have utilised candidate gene approaches or random mutagenesis screens in model animals to explore the key molecular drivers for learning and memory. We propose a complementary approach to identify this network of learning regulators: the proximity-labelling tool TurboID, which promiscuously biotinylates neighbouring proteins, to snapshot the proteomic profile of neurons during learning. To do this, we expressed the TurboID enzyme in the entire nervous system ofC. elegansand exposed animals to biotin only during the training step of a gustatory associative learning paradigm. Our approach revealed hundreds of proteins specific to ‘trained’ worms, including components of molecular pathways previously implicated in learning and memory formation in multiple species. We validated several novel regulators of learning involved in neurotransmission, including cholinergic receptors (ACC-1, ACC-3, GAR-1, LGC-46) and the putative glutaminase GLNA-3. These previously uncharacterised learning regulators show a clear impact on appetitive gustatory memory, but do not appear to have a generalised role in learning. In summary, we have shown that our approach to use proximity labelling to profile the brain of a small animal during training is a feasible and effective method to advance our knowledge on the biology of learning.
Playing with the ploidy level enables to switch on and off the strict recombination control even in the vicinity ofBrassicacentromeres
Authors: Boideau Franz , Huteau Virginie , Brunet Anael , Maillet Loeiz , Coriton Olivier , Trotoux Gwenn , Lodé-Taburel Maryse , Deniot Gwenaelle , Eber Frédérique , Gilet Marie , Boutte Julien , Morice Jérôme , Falentin Cyril , Martin Olivier , Falque Matthieu , Chèvre Anne-Marie , Rousseau-Gueutin Mathieu
Published: February 2024

Meiotic recombination is a key biological process in plant evolution and breeding, as it generates novel genetic diversity at each generation. However, due to its importance in chromosome segregation and genomic stability, crossovers are highly regulated in both frequency and distribution. We previously demonstrated that this strict regulation is not a fatality and that it can be naturally modified (3.6-fold increased frequency and altered distribution) in an allotriploidBrassicahybrid (2n=3x=29; AAC), resulting from a cross betweenB. napus(2n=4x=38; AACC) andB. rapa(2n=2x=20; AA). Taking advantage of the recently updatedBrassica napusgenome assembly, which now includes the pericentromeric regions, we unambiguously demonstrated that crossovers occur in these normally cold regions in allotriploids, with the presence of crossovers as close as 375 kb from the centromere. We deciphered that this modified recombination landscape (both frequency and distribution) can be maintained in successive generations of allotriploidy, with even a slight increase of crossover frequency. We also showed that this deregulated meiotic behavior may revert back to a strictly regulated one when recovering an allotetraploid progeny in the second generation. Overall, we provide here for the first time a practical and natural way to switch on and off the tight recombination control in a polyploid crop. We also discuss the potential role of this modified regulation of recombination in polyploid speciation success.
Eco-evolutionary dynamics for finite populations and the noise-induced reversal of selection
Authors: Bhat Ananda Shikhara , Guttal Vishwesha
Published: February 2024

Theoretical studies from diverse areas of population biology have shown that demographic stochasticity can substantially impact evolutionary dynamics in finite populations, including scenarios where traits that are disfavored by natural selection can nevertheless increase in frequency through the course of evolution. Here, we analytically describe the eco-evolutionary dynamics of finite populations from demographic first principles to investigate how noise-induced effects can alter the evolutionary fate of populations in which total population size may vary stochastically over time. Starting from a generic birth-death process describing a finite population of individuals with discrete traits, we derive a set of stochastic differential equations (SDEs) that recover well-known descriptions of evolutionary dynamics such as the replicator-mutator equation, the Price equation, and Fisher’s fundamental theorem in the infinite population limit. For finite populations, our SDEs reveal how stochasticity can predictably bias evolutionary trajectories to favour certain traits, a phenomenon we call ‘noise-induced biasing’. We show that noise-induced biasing acts through two distinct mechanisms that we call the ‘direct’ and ‘indirect’ mechanisms. While the direct mechanism can be identified with classic bet-hedging theory, the indirect mechanism is a more subtle consequence of frequency and density-dependent demographic stochasticity. Our equations reveal that noise-induced biasing may lead to evolution proceeding in a direction opposite to that predicted by natural selection in the infinite population limit. By extending and generalizing some standard equations of population genetics, we thus describe how demographic stochasticity appears alongside and interacts with the more well-understood forces of natural selection and neutral drift to determine the eco-evolutionary dynamics of finite populations of non-constant size.
SCRAPPY - a single cell rapid assay of proteome perturbation in yeast uncovers a joint role of aromatic amino acids and oxidative stress in the toxicity of lipophilic nucleoside analogs
Authors: Ghazy Eslam , Bidiuk Victoria A. , Ryabov Fedor , Mitkevich Olga V. , Riabova Olga B. , Stanishevskiy Yaroslav M. , Levshin Igor B. , Alexandrova Liudmila A. , Jasko Maxim V. , Makarov Dmitriy A. , Zhgun Alexander A. , Avdanina Darya A. , Ermolyuk Anna A. , Kushnirov Vitaly V. , Egorova Anna P. , Agaphonov Michael O. , Alexandrov Alexander I.
Published: February 2024

Assaying cellular responses to antimicrobial molecules is a path to understanding modes of action of potential drugs. This is often achieved via transcriptomics and proteomics, but simple and inexpensive methods for rapid characterization are lacking. To bridge this gap, we assayed changes in the abundance of a panel of 64 “sentinel” proteins fused to GFP in the yeastSaccharomyces cerevisiaeusing flow cytometry. This method produced expected patterns for classical antifungals and allowed inference of common mechanisms between known and novel compounds. Single-cell data also revealed diverging responses in mitochondrial protein abundance in response to thiazolidine antifungals, and perturbations of the cell cycle caused by various compounds. Finally, the method provided insight into the unknown mode of action of alkylated nucleosides, which can be used against fungi residing on works of art. These substances elevate levels of proteins involved in the biosynthesis of aromatic amino acids (AAA), as well as in oxidative stress. Furthermore, deficiencies of Trp and Tyr biosynthesis increased the efficacy of these compounds, while antioxidants reduced it. Most surprisingly, antioxidant effectiveness relied on AAA biosynthesis. Thus, our approach and its possible modifications for other microbes provides an easy and reliable platform for revealing modes of action of novel compounds.
Lineage-tracing ofActa2+ cells in aged mice during lung fibrosis formation and resolution supports the lipofibroblast to myofibroblast reversible switch
Authors: Lingampally Arun , Truchi Marin , Mauduit Olivier , Delcroix Vanessa , Hadzic Stefan , Koepke Janine , Vazquez-Armendariz Ana Ivonne , Herold Susanne , Samakovlis Christos , Makarenkova Helen P , Agha Elie El , Chen Chengshui , Mari Bernard , Bellusci Saverio
Published: February 2024

Idiopathic pulmonary fibrosis (IPF) develops mostly in old man and is characterized by the irreversible accumulation of excessive extracellular matrix components by activated myofibroblasts (aMYFs) leading to lung failure. Following bleomycin administration in young mice, fibrosis formation associated with efficient resolution takes place, the later limiting the clinical relevance of this model for IPF. In young mice, we previously reported that aMYFs captured during fibrosis formation differentiate towards a lipofibroblast (LIF)-like phenotype during resolution.

In this study, we used aged mice in combination with bleomycin administration to trigger enhanced fibrosis formation and delayed resolution, as a more relevant model for IPF and examined the heterogeneity and fate of aMYFs at different time points. Alveolosphere assay were carried out to compare the alveolar resident mesenchymal niche activity for AT2 stem cells in young versus old mice. Lineage tracing of the Acta2+ aMYFs in old mice exposed to bleomycin followed by scRNAseq of the lineage-traced cells isolated during fibrosis formation and resolution was performed to delineate the heterogeneity of aMYFs during fibrosis formation and their fate during resolution. Data mining of human mesenchymal cells from IPF and control datasets were also performed to decipher the heterogeneity of aMYFs and investigate differentiation trajectories during fibrosis formation.

Our results show that alveolar resident mesenchymal cells from old mice display decreased supporting activity for AT2 stem cells. We report that aMYFs consist of four subclusters displaying unique pro-alveologenic versus pro-fibrotic profiles. Alveolar fibroblasts displaying a high LIF-like signature largely constitute both the origin and fate of aMYFs during fibrosis formation and resolution, respectively. The heterogeneity of aMYFs is conserved in humans and a significant proportion of human aMYFs displays a high LIF signature.

In conclusion, our data indicate that the cellular and molecular bases of aMYFs formation and differentiation towards the LIF phenotype are conserved between young and old mice. Importantly, our work identifies a subcluster of aMYFs that is potentially relevant for future management of IPF.
Pathologic α-Synuclein-NOD2 Interaction and RIPK2 Activation Drives Microglia-Induced Neuroinflammation in Parkinson’s Disease
Authors: Seo Bo Am , Kwon Seung-Hwan , Kim Donghoon , Kim Han-Byeol , Ma Shi-Xun , Gadhave Kundlik , Burgess Noelle , Mao Xiaobo , Rosenthal Liana S. , Redding-Ochoa Javier , Troncoso Juan C , Lee Seulki , Dawson Valina L. , Dawson Ted M. , Ko Han Seok
Published: February 2024

Pathological aggregation of α-Synuclein (α-Syn) and neuroinflammation are closely linked to Parkinson’s disease (PD). However, the specific regulators of the neuroinflammation caused by pathological α-syn remain obscure. In this study, we show that NOD2/RIPK2 signaling is a crucial regulator of neuroinflammation in PD. Pathological α-syn binds to NOD2, causing self-oligomerization and complex formation with RIPK2, leading to RIPK2 ubiquitination and activation of MAPK and NF-kB. Notably, this NOD2/RIPK2 signaling is particularly active in microglia of human PD brains and the α-Syn preformed fibril (α-Syn PFF) mouse model. Depleting NOD2 or RIPK2 reduces neuroinflammation and protects against dopamine neuron degeneration in a pathologic α-Syn mouse model by blocking the formation of neurotoxic reactive astrocytes caused by microglia activation. The discovery of NOD2/RIPK2 signaling as a key regulator of neuroinflammation in PD provides a new understanding of α-Syn-driven neuroinflammation and neurodegeneration in PD and a potential new therapeutic strategy.

Graphical Abstract

In brief

Pathological α-Synuclein (α-Syn) binds to the microglial NOD2 protein, which in turn triggers NOD2/RIPK2 complex and RIPK2 phosphorylation/ubiquitination. This process activates the NF-kB/MAPK pathways, ultimately leading to neurotoxic reactive astrocyte-induced dopaminergic neurodegeneration. Depletion of RIPK2 (RIPK2 KO) or NOD2 (NOD2) protects dopamine neurons in a mouse model of Parkinson’s disease (PD). These findings provide insights into α-Syn-driven neuroinflammation and offer potential therapeutic strategies for PD.

Highlights

NOD2/RIPK2 signaling is identified as a crucial regulator of neuroinflammation in PD.

NOD2/RIPK2 signaling is highly active in microglia in human PD brains and α-Syn PFF mouse models.

Pathological α-Syn binds to NOD2, triggering self-oligomerization and RIPK2 complex formation, leading to MAPK and NF-kB activation

Genetic depletion of NOD2 or RIPK2 reduces neuroinflammation and protects dopamine neurons by blocking the formation of neurotoxic reactive astrocytes.
The effects of clay minerals on bacterial community composition during arthropod decay
Authors: Corthésy Nora , Saleh Farid , Thomas Camille , Antcliffe Jonathan B. , Daley Allison C.
Published: February 2024

Fossilization, or the transition of an organism from the biosphere to the geosphere, is a complex mechanism involving numerous biological and geological variables. Bacteria are one of the most significant biotic players to decompose organic matter in natural environments, early on during fossilization. However, bacterial processes are difficult to characterize as many different abiotic conditions can influence bacterial efficiency in degrading tissues. One potentially important variable is the composition and nature of the sediment on which a carcass is deposited after death. We experimentally examined this by decaying the marine shrimpPalaemon variansunderwater on three different clay sediments. Samples were then analyzed using 16S ribosomal RNA sequencing to identify the bacterial communities associated with each clay system. Results show that samples decaying on the surface of kaolinite have a lower bacterial diversity than those decaying on the surface of bentonite and montmorillonite, which could explain the limited decay of carcasses deposited on this clay. However, this is not the only role played by kaolinite, as a greater proportion of gram-negative over gram-positive bacteria is observed in this system. Gram-positive bacteria are generally thought to be more efficient at recycling complex polysaccharides such as those forming the body walls of arthropods. This is the first experimental evidence of sediments shaping an entire bacterial community. Such interaction between sediments and bacteria might have contributed to arthropods’ exquisite preservation and prevalence in kaolinite-rich Lagerstätten of the Cambrian Explosion.
A difficult coexistence: resolving the iron-induced nitrification delay in groundwater filters
Authors: Corbera-Rubio Francesc , Kruisdijk Emiel , Malheiro Sofia , Leblond Manon , Verschoor Liselotte , van Loosdrecht Mark C.M. , Laureni Michele , van Halem Doris
Published: February 2024

Rapid sand filters (RSF) are an established and widely applied technology for the removal of dissolved iron (Fe2+) and ammonium (NH+) in groundwater treatment. Most often, biological NH+oxidation is delayed and starts only upon complete Fe2+depletion. However, the mechanism(s) responsible for the inhibition of NH+oxidation by Fe2+or its oxidation (by)products remains elusive, hindering further process control and optimization. We used batch assays, lab-scale columns, and full-scale filter characterizations to resolve the individual impact of the main Fe2+oxidizing mechanisms and the resulting products on biological NH+oxidation. Modelling of the obtained datasets allowed to quantitatively assess the hydraulic implications of Fe2+oxidation. Dissolved Fe2+and the reactive oxygen species formed as byproducts during Fe2+oxidation had no direct effect on nitrification. The Fe3+oxides on the sand grain coating, commonly assumed to be the main cause for inhibited nitrification, seemed instead to enhance nitrification by providing additional surface area for biofilm growth. Modelling allowed to exclude mass transfer limitations induced by accumulation of iron flocs and consequent filter clogging as the cause for delayed nitrification. We unequivocally identify the inhibition of NH+oxidizing organisms by the Fe3+flocs generated during Fe2+oxidation as the main cause for the commonly observed nitrification delay. The addition of Fe3+flocs inhibited NH+oxidation both in batch and column tests, and the removal of Fe3+flocs by backwashing completely re-established the NH+removal capacity, suggesting that the inhibition is reversible. In conclusion, our findings not only identify the iron form that causes the inhibition, albeit the biological mechanism remains to be identified, but also highlight the ecological importance of iron cycling in nitrifying environments.

Graphical abstract

Highlight

Dissolved Fe2+and reactive oxygen species do not affect NH+oxidation

Fe oxide coating aids sand grain colonization by NH+-oxidizing bacteria

Fe3+flocs inhibit NH+oxidation by reducing the nitrifying capacity of AOB

Changes in transport patterns due to clogging do not play a major role in NH+oxidation

The inhibition of NH4+oxidation is reversible and reduced by backwashing
Adaptive predictor-set linear model: an imputation-free method for linear regression prediction on datasets with missing values
Authors: Jiménez Benjamin Planterose , Kayser Manfred , Vidaki Athina , Caliebe Amke
Published: February 2024

Linear regression (LR) is vastly used in data analysis for continuous outcomes in biomedicine and epidemiology. Despite its popularity, LR is incompatible with missing data, which frequently occur in health sciences. For parameter estimation, this short-coming is usually resolved by complete-case analysis or imputation. Both workarounds, however, are inadequate for prediction, since they either fail to predict on incomplete records or ignore missingness-induced reduction in prediction accuracy and rely on (unrealistic) assumptions about the missing mechanism. Here, we derive adaptive predictor-set linear model (aps-lm), capable of making predictions for incomplete data without the need for imputation. It is derived by using a predictor-selection operation, the Moore-Penrose pseudoinverse and the reduced QR-decomposition. aps-lm is an LR generalization that inherently handles missing values. It is applied on a reference dataset, where complete predictors and outcome are available, and yields a set of privacy-preserving parameters. In a second stage, these are shared for making predictions of the outcome on external datasets with missing entries for predictors without imputation. Moreover, aps-lm computes prediction errors that account for the pattern of missing values even under extreme missingness. We benchmark aps-lm in a simulation study. aps-lm showed greater prediction accuracy and reduced bias compared to popular imputation strategies under a wide range of scenarios including variation of sample size, goodness-of-fit, missing value type and covariance structure. Finally, as a proof-of-principle, we apply aps-lm in the context of epigenetic aging clocks, linear models that predict a person’s biological age from epigenetic data with promising clinical applications.
Causal Discovery Analysis Reveals Insights into Psychosis Proneness, Brain Function, and Environmental Factors among Young Individuals
Authors: Sahin-Ilikoglu Tuba , Ma Sisi , Kummerfeld Erich , Rawls Eric , Tan Hao Yang , Toulopoulou Timothea
Published: February 2024

Background

Experiencing symptoms of psychosis, such as delusions and hallucinations, are observed in general, nonclinical populations. These experiences are sometimes described as psychosis proneness (PP) and potentially part of the psychosis continuum. The directional relationships among various factors contributing to psychosis proneness and its interactions, encompassing both environmental and neural mechanisms, lack comprehensive description. We aimed to identify targets to prevent psychosis proneness and its interactions by characterizing pathways using causal discovery analysis (CDA).

Methods

Participants were 194 healthy adolescent and young adult twin and sibling pairs aged between 14-24 years from Türkiye. They completed comprehensive assessments evaluating sociodemographic status, environmental risk, general intelligence, self-schema, PP, and working memory (WM) performance during fMRI (37 variables). CDA was applied, a novel machine learning algorithm, to understand the causal relationships of PP.

Results

The analysis identified negative self-schema as having the largest causal effect among all assessments in PP [Effect size (ES)= 0.55]. Secondly, social cohesion and trust (SC&T) had a protective causal effect on PP [ES= −0.18]. Lastly, PP was identified as a direct cause of greater activation in DLPFC (BA9a-BA46v) during manipulation in the WM (ES= 0.14).

Conclusions

CDA provides directionality of the 37 variables which were not presented earlier. The findings highlight the significance of negative self-schema and SC&T in the general population with PP, emphasizing the potential for preventive interventions targeting these factors. These findings also suggest a role for DLPFC as a potential target in this regard. To our knowledge, this is the first study using data-driven analysis to model causal mechanisms in PP in the general population.
The Co-Evolution of Jawed Vertebrates and Interferon Regulatory Factor 5 Generates Unique Inflammation and Innate Immunity
Authors: Hubing Vanessa , Marquis Avery , Ziemann Chanasei , Moriyama Hideaki , Moriyama Etsuko N. , Zhang Luwen
Published: February 2024

The emergence of jaws in early vertebrates introduced a novel feeding apparatus and potent oral defenses but also increased the risk of physical injury and pathogen exposure. Innate immunity and inflammation constitute the body’s first line of defense against invading microbes and tissue damage, aiming to eliminate threats and restore internal homeostasis. Interferon regulatory factor 5 (IRF5) plays a critical role in orchestrating innate immunity and inflammation by regulating the transcription of genes that encode type I interferons (IFNs) and pro-inflammatory cytokines. Despite this, the evolution of IRF5 has remained poorly understood. We have identified the IRF5 and IRF6 genes in cartilaginous fish, including sharks. As cartilaginous fish represent one of the oldest surviving jawed vertebrate lineages, the presence of these genes suggests the genes have ancient origins potentially dating back hundreds of millions of years to early jawed vertebrates. Furthermore, our analysis shows that IRF5 has conserved nuclear export sequences and phosphorylation sites for activation throughout evolution from cartilaginous fish to humans, indicating these regulatory elements evolved early and have been maintained across jawed vertebrates. Additionally, the shift in subcellular localization of IRF5 from nucleus to cytosol, and of other interferon related IRFs, aligns with functional enhancements of IRFs in innate immunity and the emergence of IFNs across jawed vertebrates. This analysis implies that the evolution of jaws may have driven the emergence of new IRF members, the expansion of their functions, and the development of a unique inflammation and innate immune system.
Development of a whole-cell biosensor for ethylene oxide and ethylene
Authors: Moratti Claudia F. , Yang Sui Nin Nicholas , Scott Colin , Coleman Nicholas V.
Published: February 2024

Ethylene and ethylene oxide are widely used in the chemical industry, and ethylene is also important for its role in fruit ripening. Better sensing systems would assist risk management of these chemicals. Here, we characterise the ethylene regulatory system inMycobacteriumstrain NBB4 and use these genetic parts to create a biosensor. The regulatory genesetnR1andetnR2and cognate promoter Petnwere combined with a fluorescent reporter gene (fuGFP) in aMycobacteriumshuttle vector to create plasmid pUS301-EtnR12P. Cultures ofM. smegmatismc2-155(pUS301-EtnR12P) gave a fluorescent signal in response to ethylene oxide with a detection limit of 0.2 µM (9 ppb). By combining the epoxide biosensor cells with another culture expressing the ethylene monooxygenase, the system was converted into an ethylene biosensor. The co-culture was capable of detecting ethylene emission from banana fruit. These are the first examples of whole-cell biosensors for epoxides or aliphatic alkenes. This work also resolves long-standing questions concerning the regulation of ethylene catabolism in bacteria.