bluuebunny/crossref_metadata_2025 huggingface dataset:
Variability in the phytoplankton response to upwelling across an iron limitation mosaic within the California Current System
Authors: Lin YuanYu , Torano Olivia , Whitehouse Logan , Pierce Emily , Till Claire P. , Hurst Matthew , Freiberger Robert , Mellett Travis , Maldonado Maria T. , Guo Jian , Sutton Mariam , Zeitz David , Marchetti Adrian
Published: September 2023

Coastal upwelling currents such as the California Current System (CCS) comprise some of the most productive biological systems on the planet. Diatoms, a distinct taxon of phytoplankton, dominate these upwelling events in part due to their rapid response to nutrient entrainment. In this region, they may also be limited by the micronutrient iron (Fe), an important trace element primarily involved in photosynthesis and nitrogen assimilation. The mechanisms behind how diatoms physiologically acclimate to the different stages of the upwelling conveyor belt cycle with respect to Fe limitation remains largely uncharacterized. Here, we explore their physiological and metatranscriptomic response to the upwelling cycle with respect to the Fe limitation mosaic that exists in the CCS. Subsurface, natural plankton assemblages that would potentially seed surface blooms were examined over wide and narrow shelf regions. The initial biomass and physiological state of the phytoplankton community had a large impact on the overall response to simulated upwelling. Following on-deck incubation under varying Fe physiological states, our results suggest that diatoms quickly dominated the blooms by “frontloading” nitrogen assimilation genes prior to upwelling. However, diatoms subjected to induced Fe limitation exhibited reductions in carbon and nitrogen uptake and decreasing biomass accumulation. Simultaneously, they exhibited a distinct gene expression response which included increased expression of Fe-starvation induced proteins and decreased expression of nitrogen assimilation and photosynthesis genes. These findings may have significant implications for upwelling events in future oceans, where changes in ocean conditions are projected to amplify the gradient of Fe limitation in coastal upwelling regions.
Exposure to aldehyde cherry e-liquid flavouring and its vape by-product disrupts pulmonary surfactant biophysical function
Authors: Martin Alexia , Tempra Carmelo , Yu Yuefan , Liekkinen Juho , Thakker Roma , Lee Hayoung , de Santos Moreno Berta , Vattulainen Ilpo , Rossios Christos , Javanainen Matti , Bernardino de la Serna Jorge
Published: September 2023

Over the last decade there has been a surge in vaping device usage, especially among adolescents, raising concerns for potentially related lung damage. Notoriously, there have been many e-cigarette or vaping-related lung injury (EVALI) cases resulting in hospitalisations and deaths. Although the vaping component vitamin E acetate has been linked to a large proportion of EVALI cases resulting in its widespread banning, one fifth of the cases remain unexplained. Furthermore, the overall long-term impact of vaping on respiratory health is poorly understood. A likely driver behind EVALI is pulmonary surfactant disruption, as it is the first point of contact for any inhaled toxicant in the alveoli, and abnormalities of its function are linked to some symptoms presented in EVALI cases. Aberrant biophysical function of the surfactant results in alveolar surface tension increase, causing alveolar collapse. Vaping chemicals with the potential to disrupt surfactant function must be hydrophobic molecules able to interact with surfactant components at the alveolar air–liquid interface. Recent findings have recorded the synthesis of highly hydrophobic acetal by-products of the base vaping chemical propylene glycol and common flavouring aldehydes, including the cherry flavouring benzaldehyde, not identified in preliminary e-liquid safety tests. This study provides evidence that benzaldehyde and its by-product, benzaldehyde propylene glycol acetal, have the potential to significantly disrupt surfactant biophysical functionviainteractions with surfactant proteins SP-B and/or SP-C, which may provide stable interactions within the surfactant film by forming associations with the sublayer of surfactant three-dimensional structure present at high lateral compression,i.e., expiration breathing. Data also suggest considerable vaping chemical loss to the experimental subphase, indicating potential further implications to the alveolar epithelial layer beneath.
NF-κB dependent expression of A20 controls IKK repression of RIPK1 dependent cell death in activated T cells
Authors: Layzell Scott , Barbarulo Alessandro , Seddon Benedict
Published: September 2023

The Inhibitor of Kappa B Kinase (IKK) complex is a critical regulator of canonical NF-κB activation. More recently, RIPK1 has also been identified as a phosphorylation target of the IKK complex, resulting in repression of extrinsic cell death pathways. Our previous work shows that normal thymocyte development is exclusively reliant on repression of TNF triggered cell death pathways by IKK, and that NF-κB signalling is in fact redundant for development. The role of IKK signalling in activated T cells is unclear. To investigate this, we analysed activation of IKK2 deficient TCR transgenic T cells with cognate peptide. While early activation events were normal, proliferation of blasts was impaired. Surprisingly, cell cycle progression in IKK2 KO T cells was unperturbed. Instead, dividing cells were more sensitive to apoptosis triggered by extrinsic cell death pathways, since inhibition of RIPK1 kinase activity almost completely rescued cell survival. Transcriptomic analysis of activated IKK2 deficient T cells revealed defective expression of several NF-κB targets, including Tnfaip3, that encodes A20, a negative regulator of NF-κB in T cells. To test whether A20 expression was required to protect IKK2 deficient T cells from cell death, we generated mice with T cells lacking both A20 and IKK2. Conditional deletion of bothIkk2andTnfaip3in T cells resulted in near complete ablation of peripheral naïve T cells, in contrast to mice lacking one or other gene. Strikingly, this phenotype was completely reversed by inhibition of RIPK1 kinase activity in vivo. Therefore, our data suggests that IKK signalling in T cells protects against RIPK1 dependent death, both by direct phosphorylation of RIPK1 and through NF-κB mediated induction of A20, that we identify for the first time as a modulator of RIPK1 function in T cells.
Gene regulatory Networks Reveal Sex Difference in Lung Adenocarcinoma
Authors: Saha Enakshi , Guebila Marouen Ben , Fanfani Viola , Fischer Jonas , Shutta Katherine H. , Mandros Panagiotis , DeMeo Dawn L. , Quackenbush John , Lopes-Ramos Camila M.
Published: September 2023

Lung adenocarcinoma (LUAD) has been observed to have significant sex differences in incidence, prognosis, and response to therapy. However, the molecular mechanisms responsible for these disparities have not been investigated extensively. Sample-specific gene regulatory network methods were used to analyze RNA sequencing data from non-cancerous human lung samples from The Genotype Tissue Expression Project (GTEx) and lung adenocarcinoma primary tumor samples from The Cancer Genome Atlas (TCGA); results were validated on independent data. We observe that genes associated with key biological pathways including cell proliferation, immune response and drug metabolism are differentially regulated between males and females in both healthy lung tissue, as well as in tumor, and that these regulatory differences are further perturbed by tobacco smoking. We also uncovered significant sex bias in transcription factor targeting patterns of clinically actionable oncogenes and tumor suppressor genes, includingAKT2andKRAS. Using differentially regulated genes between healthy and tumor samples in conjunction with a drug repurposing tool, we identified several small-molecule drugs that might have sex-biased efficacy as cancer therapeutics and further validated this observation using an independent cell line database. These findings underscore the importance of including sex as a biological variable and considering gene regulatory processes in developing strategies for disease prevention and management.
Cooperative Membrane Binding of HIV-1 Matrix Proteins
Authors: Banerjee Puja , Monje-Galvan Viviana , Voth Gregory A.
Published: September 2023

The HIV-1 assembly process begins with a newly synthesized Gag polyprotein being targeted to the inner leaflet of the plasma membrane of the infected cells to form immature viral particles. Gag-membrane interactions are mediated through the myristoylated(Myr) N-terminal matrix (MA) domain of Gag which eventually multimerize on the membrane to form trimers and higher-order oligomers. The study of the structure and dynamics of peripheral membrane proteins like MA has been challenging for both experimental and computational studies due to the complex dynamics of protein-membrane interactions. Although the roles of anionic phospholipids (PIP2, PS) and the Myr group in the membrane targeting and stable membrane binding of MA are now well-established, the cooperative interactions between MA monomers and MA-membrane still remain elusive. Our present study focuses on the membrane binding dynamics of a higher-order oligomeric structure of MA protein (a dimer of trimers), which has not been explored before. Employing time-lagged independent component analysis (tICA) to our microsecond-long trajectories, we investigate conformational changes of the matrix protein induced by membrane binding. Interestingly, the Myr switch of a MA monomer correlates with the conformational switch of adjacent monomers in the same trimer. Together, our findings suggest that MA trimerization facilitates Myr insertion, but MA trimer-trimer interactions in the lattice of immature HIV-1 particles can hinder the same. Additionally, local lipid density patterns of different lipid species provide a signature of the initial stage of lipid-domain formation upon membrane binding of the protein complex.

TOC
Prrx1-driven LINC complex disruption in vivo reduces osteoid deposition but not bone quality after voluntary wheel running
Authors: Birks Scott , Howard Sean , Wright Christian S. , O’Rourke Caroline , Day Elicza A. , Lamb Alexander J. , Walsdorf James R. , Lau Anthony , Thompson William R. , Uzer Gunes
Published: September 2023

The Linker of Nucleoskeleton and Cytoskeleton (LINC) complex serves to connect the nuclear envelope and the cytoskeleton, influencing cellular processes such as nuclear arrangement, architecture, and mechanotransduction. The role LINC plays in mechanotransduction pathways in bone progenitor cells has been well studied; however, the mechanisms by which LINC complexes governin vivobone formation remain less clear. To bridge this knowledge gap, we established a murine model disrupting LINC using transgenic Prx-Cre mice and floxed Tg(CAG-LacZ/EGFP-KASH2) mice. Prx-Cre mice express the Cre recombinase enzyme controlled by the paired-related homeobox gene-1 promoter (Prrx1), a pivotal regulator of skeletal development. Prx-Cre animals have been widely used in the bone field to target bone progenitor cells. Tg(CAG-LacZ/EGFP-KASH2) mice carry a lox-stop-lox flanked LacZ gene allowing for the overexpression of an EGFP-KASH2 fusion protein via cre recombinase mediated deletion of the LacZ cassette. This disrupts endogenous Nesprin-Sun binding in a dominant negative manner disconnecting nesprin from the nuclear envelope. By combining these lines, we generated a Prrx1(+) cell-specific LINC disruption model to study its impact on the developing skeleton and subsequently exercise-induced bone accrual. The findings presented here indicate Prx-driven LINC disruption (PDLD) cells exhibit no change in osteogenic and adipogenic potential compared to controlsin vitronor are there bone quality changes when compared to in sedentary animals at 8 weeks. While PDLD animals displayed increased voluntary running activity andPrrx1(+) cell-specific LINC disruption abolished the exercise-induced increases in osteoid volume and surface after a 6-week exercise intervention, no other changes in bone microarchitecture or mechanical properties were found.
The lactonase BxdA mediates metabolic adaptation of maize root bacteria to benzoxazinoids
Authors: Thoenen Lisa , Kreuzer Marco , Florean Matilde , Mateo Pierre , Züst Tobias , Giroud Caitlin , Rouyer Liza , Gfeller Valentin , Notter Matheus D. , Knoch Eva , Hapfelmeier Siegfried , Becker Claude , Schandry Niklas , Robert Christelle A. M. , Köllner Tobias G. , Bruggmann Rémy , Erb Matthias , Schlaeppi Klaus
Published: September 2023

Root exudates contain secondary metabolites that affect the plant’s root microbiome. How microbes cope with these bioactive compounds, and how this ability shapes root microbiomes remain largely unknown. We investigated how maize root bacteria metabolise benzoxazinoids, the main specialised metabolites of maize. Diverse and abundant bacteria metabolised the major compound (6-methoxy-benzoxazolin-2-one, MBOA) in the maize rhizosphere to 2-amino-7-methoxyphenoxazin-3-one (AMPO). By contrast, bacteria isolated from Arabidopsis, which does not produce benzoxazinoids, were unable to metabolise MBOA. AmongMicrobacteriastrains, this differential metabolisation allowed to identify a conserved gene cluster containing the lactonasebxdA. BxdA converts MBOA to AMPO in vitro and we show that this capacity provided bacteria a growth benefit under carbon-limiting conditions. Together these results reveal that maize root bacteria - through BxdA - are metabolically adapted to the benzoxazinoids of their host. We propose that metabolic adaptation to plant-specialised compounds shapes root bacterial communities across the plant kingdom.
Structural insights into abscisic acid exporter AtABCG25
Authors: Xin Jian , Zhou Yeling , Qiu Yichun , Geng He , Wang Yuzhu , Song Yi , Liang Jiansheng , Yan Kaige
Published: September 2023

Cellular hormone homeostasis is essential for the precise spatial and temporal signaling responses and plant fitness. Abscisic acid (ABA) plays pivotal roles in orchestrating various developmental and stress responses and confers fitness benefits over ecological and evolutionary timescales in terrestrial plants. Cellular ABA levels is regulated by complex processes including biosynthesis, catabolism, and transport. AtABCG25 is the first identified ABA exporter through genetic screen which affects diverse ABA responses. Resolving the structure basis of ABCG25 in ABA exporting is critical for further manipulating ABA homeostasis and plant fitness. We utilized cryo-electron microscopy to elucidate the structural dynamics of AtABCG25, and successfully characterized different states including apo AtABCG25, ABA-bound AtABCG25 and ATP-bound AtABCG25(E232Q). Notably, AtABCG25 forms a homodimer, featuring a deep, slit-like cavity in the transmembrane domain. The critical residues in the cavity where ABA binds are precisely characterized. Moreover, ATP binding triggers the closure of nucleotide-binding domains and conformational transitions in the transmembrane domains. Collectively, these findings provide valuable insights into the intricate substrate recognition and transport mechanisms of ABA exporter ABCG25, paving the way towards genetical manipulating of ABA homeostasis and plant fitness.
Differential Modulation of Polycomb-Associated Histone Marks by cBAF, pBAF, and gBAF Complexes
Authors: Bergwell Mary , Park JinYoung , Kirkland Jacob G.
Published: September 2023

Chromatin regulators are a group of proteins that can alter the physical properties of chromatin to make it more or less permissive to transcription by modulating another protein’s access to a specific DNA sequence through changes in nucleosome occupancy or histone modifications at a particular locus. Mammalian SWI/SNF complexes (mSWI/SNF) are a group of ATPase-dependent chromatin remodelers that alter chromatin states. In mouse embryonic stem cells (mESCs), there are three primary forms of mSWI/SNF: canonical BAF (cBAF), polybromo-associated BAF (pBAF), and GLTSCR-associated BAF (gBAF or ncBAF). While cBAF and gBAF contain the SS18 protein subunit, pBAF lacks SS18. Previous studies used a novel dCas9-mediated inducible recruitment (FIRE-Cas9) of mSWI/SNF complexes via SS18 to theNkx2.9locus.Nkx2.9is a developmentally regulated gene that requires mSWI/SNF for transcriptional activation during neural differentiation. However, in mESCs,Nkx2.9is bivalent, meaning nucleosomes at the locus have both active and polycomb-associated repressive modifications. Upon recruitment of SS18-containing complexes, polycomb-associated histone marks are removed, followed by transcriptional activation ofNkx2.9. However, since both cBAF and gBAF share the SS18 subunit, it is unclear whether one or both complexes oppose the polycomb repressive marks. The ability of pBAF to do the same also remains unknown. In this study, we used unique subunits to recruit each of the three complexes to the Nkx2.9 locus individually. Here, we show that cBAF most effectively opposes polycomb repressive marks atNkx2.9, leading to transcriptional activation of the gene. Recruitment of cBAF complexes leads to a significant loss of the polycomb repressive-2 H3K27me3 and polycomb repressive-1 H2AK119ub histone marks, whereas gBAF and pBAF do not. Moreover, nucleosome occupancy alone cannot explain the loss of these marks. Our results demonstrate that cBAF has a unique role in the direct opposition of polycomb-associated histone modifications that gBAF and pBAF do not share.

Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104

Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, 73104
Single-Cell Profiling Reveals a Naive-Memory Relationship between CD56brightand Adaptive Human Natural Killer Cells
Authors: Panjwani M. Kazim , Grassmann Simon , Sottile Rosa , Le Luduec Jean-Benoît , Kontopoulos Theodota , van der Ploeg Kattria , Sun Joseph C. , Hsu Katharine C.
Published: September 2023

Development of antigen-specific memory upon pathogen exposure is a hallmark of the adaptive immune system. While natural killer (NK) cells are considered part of the innate immune system, humans exposed to the chronic viral pathogen cytomegalovirus (CMV) often possess a distinct NK cell population lacking in individuals who have not been exposed, termed “adaptive” NK cells. To identify the “naïve” population from which this “memory” population derives, we performed phenotypic, transcriptional, and functional profiling of NK cell subsets. We identified immature precursors to the Adaptive NK cells that are equally present in both CMV+ and CMV-individuals, resolved an Adaptive transcriptional state distinct from most mature NK cells and sharing a common gene program with the immature CD56brightpopulation, and demonstrated retention of proliferative capacity and acquisition of superior IFNγ production in the Adaptive population. Furthermore, we distinguish the CD56brightand Adaptive NK populations by expression of the transcription factor CXXC5, positioning these memory NK cells at the inflection point between innate and adaptive lymphocytes.
Direct ionic stress sensing and mitigation by the transcription factor NFAT5
Authors: Khandwala Chandni B. , Sarkar Parijat , Schmidt H. Broder , Ma Mengxiao , Kinnebrew Maia , Pusapati Ganesh V. , Patel Bhaven B. , Tillo Desiree , Lebensohn Andres M. , Rohatgi Rajat
Published: September 2023

Homeostatic control of intracellular ionic strength is essential for protein, organelle and genome function, yet mechanisms that sense and enable adaptation to ionic stress remain poorly understood in animals. We find that the transcription factor NFAT5 directly senses solution ionic strength using a C-terminal intrinsically disordered region. Both in intact cells and in a purified system, NFAT5 forms dynamic, reversible biomolecular condensates in response to increasing ionic strength. This self-associative property, conserved from insects to mammals, allows NFAT5 to accumulate in the nucleus and activate genes that restore cellular ion content. Mutations that reduce condensation or those that promote aggregation both reduce NFAT5 activity, highlighting the importance of optimally tuned associative interactions. Remarkably, human NFAT5 alone is sufficient to reconstitute a mammalian transcriptional response to ionic or hypertonic stress in yeast. Thus NFAT5 is both the sensor and effector of a cell-autonomous ionic stress response pathway in animal cells.
Single-Cell Analysis Reveals Cryptic Prophage Protease LfgB ProtectsEscherichia coliDuring Oxidative Stress by Cleaving Antitoxin MqsA
Authors: Fernández-García Laura , Gao Xinyu , Battisti Michael E. , Kirigo Joy , García-Contreras Rodolfo , Tomas Maria , Guo Yunxue , Wang Xiaoxue , Wood Thomas K.
Published: September 2023

Although toxin/antitoxin (TA) systems are ubiquitous, beyond phage inhibition and mobile element stabilization, their role in host metabolism is obscure. One of the best-characterized TA systems is MqsR/MqsA ofEscherichia coli, which has been linked previously to protecting this gastrointestinal species during the stress it encounters from the bile salt deoxycholate as it colonizes humans. However, some recent whole-population studies have challenged the role of toxins such as MqsR in bacterial physiology, since themqsRAlocus is induced over a hundred-fold during stress, but a phenotype was not found upon its deletion. Here, we investigate further the role MqsR/MqsA by utilizing single cells and demonstrate that upon oxidative stress, the TA system MqsR/MqsA has a heterogeneous effect on the transcriptome of single cells. Furthermore, we discovered that MqsR activation leads to induction of the poorly-characterizedyfjXY ypjJ yfjZFoperon of cryptic prophage CP4-57. Moreover, deletion ofyfjYmakes the cells sensitive to H2O2, acid, and heat stress, and this phenotype was complemented. Hence, we recommendyfjYbe renamed tolfgB(less fatalitygeneB). Critically, MqsA represseslfgBby binding the operon promoter, and LfgB is a protease that degrades MqsA to derepressrpoSand facilitate the stress response. Therefore, the MqsR/MqsA TA system facilitates the stress response through cryptic phage protease LfgB.
Construction and reconfiguration of dynamic DNA origami assemblies with coiled-coil patches and patterns
Authors: Teng T. , Bernal-Chanchavac J. , Stephanopoulos N. , Castro C.E.
Published: September 2023

DNA origami nanodevices achieve programmable structure and tunable mechanical and dynamic properties by leveraging the sequence specific interactions of nucleic acids. Previous advances have also established DNA origami as a useful building block to make well-defined micron-scale structures through hierarchical self-assembly, but these efforts have largely leveraged the structural features of DNA origami. The tunable dynamic and mechanical properties also provide an opportunity to make assemblies with adaptive structure and properties. Here we report the integration of DNA origami hinge nanodevices and coiled-coil peptides into hybrid reconfigurable assemblies. With the same dynamic device and peptide interaction, we make multiple higher order assemblies by organizing clusters of peptides (i.e. patches) or arranging single peptides (i.e. patterns) on the surfaces of DNA origami to control the relative orientation of devices. We use coiled-coil interactions to construct circular and linear assemblies whose structure and mechanical properties can be modulated with DNA-based actuation. Actuation of linear assemblies leads to micron scale motions and ∼2.5-10-fold increase in bending stiffness. Our results provide a foundation for stimulus responsive hybrid assemblies that can adapt their structure and properties in response to nucleic acid, peptide, protein, or other triggers.
Rhythm Receptive Fields in Striatum of Mice Executing Complex Continuous Movement Sequences
Authors: Hirokane Kojiro , Nakamura Toru , Terashita Takuma , Kubota Yasuo , Hu Dan , Yagi Takeshi , Graybiel Ann M. , Kitsukawa Takashi
Published: September 2023

By the use of a novel experimental system, the step-wheel, we investigated the neural underpinnings of complex and continuous movements. We recorded neural activities from the dorsolateral striatum and found neurons sensitive to movement rhythm parameters. These neurons responded to specific combinations of interval, phase, and repetition of movement, effectively forming what we term “rhythm receptive fields.” Some neurons even responsive to the combination of movement phases of multiple body parts. In parallel, cortical recordings in sensorimotor areas highlighted a paucity of neurons responsive to multiple parameter combinations, relative to those in the striatum. These findings have implications for comprehending motor coordination deficits seen in brain disorders including Parkinson’s disease. Movement encoding by rhythm receptive fields should streamline the brain’s capacity to encode temporal patterns, help to resolve the degrees of freedom problem. Such rhythm fields hint at the neural mechanisms governing effective motor control and processing of rhythmic information.
Acetylcholine signaling in the medial prefrontal cortex mediates the ability to learn an active avoidance response following learned helplessness training
Authors: Abdulla Zuhair I. , Mineur Yann S. , Crouse Richard B. , Etherington Ian M. , Yousuf Hanna , Na Jessica J. , Picciotto Marina R.
Published: September 2023

Increased brain levels of acetylcholine (ACh) are observed in subsets of patients with depression and increasing ACh levels chronically can precipitate stress-related behaviors in humans and animals. Conversely, optimal ACh levels are required for cognition and memory. We hypothesize that ACh signaling is important for encoding both appetitive and stress-relevant memories, but that excessive increases in ACh result in a negative encoding bias in which memory formation of a stressful event is aberrantly strengthened, potentially contributing to the excessive focus on negative experience that could lead to depressive symptoms. The medial prefrontal cortex (mPFC) is critical to control the limbic system to filter exteroceptive cues and stress-related circuits. We therefore evaluated the role of ACh signaling in the mPFC in a learned helplessness task in which mice were exposed to repeated inescapable stressors followed by an active avoidance task. Using fiber photometry with a genetically-encoded ACh sensor, we found that ACh levels in the mPFC during exposure to inescapable stressors were positively correlated with later escape deficits in an active avoidance test in males, but not females. Consistent with these measurements, we found that both pharmacologically- and chemogenetically-induced increases in mPFC ACh levels resulted in escape deficits in both male and female mice, whereas chemogenetic inhibition of ACh neurons projecting to the mPFC improved escape performance in males, but impaired escape performance in females. These results highlight the adaptive role of ACh release in stress response, but also support the idea that sustained elevated ACh levels contribute to maladaptive behaviors. Furthermore, mPFC ACh signaling may contribute to depressive symptomology differentially in males and females.
Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA
Authors: Finocchio Giada , Koopal Balwina , Potocnik Ana , Heijstek Clint , Jinek Martin , Swarts Daan C.
Published: September 2023

In both prokaryotic and eukaryotic innate immune systems, TIR domains function as NADases that degrade the key metabolite NAD+or generate signaling molecules. Catalytic activation of TIR domains requires oligomerization, but how this is achieved varies in distinct immune systems. In theShortprokaryoticArgonaute (pAgo)/TIR-APAZ (SPARTA) immune system, TIR NADase activity is triggered upon guide RNA-mediated recognition of invading DNA by an unknown mechanism. Here, we describe cryo-EM structures of SPARTA in the inactive monomeric and target DNA-activated tetrameric states. The monomeric SPARTA structure reveals that in the absence of target DNA, a C-terminal tail of TIR-APAZ occupies the nucleic acid binding cleft formed by the pAgo and TIR-APAZ subunits, suppressing SPARTA activation. In the active tetrameric SPARTA complex, guide RNA-mediated target DNA binding displaces the C-terminal tail and induces conformational changes in pAgo that facilitate SPARTA-SPARTA dimerization. Concurrent release and rotation of one TIR domain allow it to form a composite NADase catalytic site with the other TIR domain within the dimer, and generate a self-complementary interface that mediates cooperative tetramerization. Combined, this study provides critical insights into the structural architecture of SPARTA and the molecular mechanism underlying target DNA-dependent oligomerization and catalytic activation.

KEY POINTS

Inactive monomeric SPARTA is autoinhibited by the C-terminal tail of TIR-APAZ

Target DNA recognition causes C-terminal tail release, pAgo restructuring, and dimerization

TIR domain rotation enables catalytic activation and cooperative tetramer formation
The lipid Gb3 promotes germinal center B cell responses and anti-viral immunity
Authors: Sharma Pankaj , Zhang Xiaolong , Ly Kevin , Zhang Yuxiang , Hu Yu , Ye Adam Yongxin , Hu Jianqiao , Kim Ji Hyung , Lou Mumeng , Wang Chong , Celuzza Quinton , Kondo Yuji , Furukawa Keiko , Bundle David R. , Furukawa Koichi , Alt Frederick W. , Winau Florian
Published: September 2023

Influenza viruses escape immunity due to rapid antigenic evolution, which requires vaccination strategies that allow for broadly protective antibody responses. Here, we demonstrate that the lipid globotriaosylceramide (Gb3) expressed on germinal center (GC) B cells is essential for the production of high-affinity antibodies. Mechanistically, Gb3 binds and disengages CD19 from its chaperone CD81 for subsequent translocation to the B cell receptor (BCR) complex to trigger signaling. Abundance of Gb3 amplifies the PI3-kinase/Akt/Foxo1 pathway to drive affinity maturation. Moreover, this lipid regulates MHC-II expression to increase diversity of T follicular helper (Tfh) and GC B cells reactive with subdominant epitopes. In influenza infection, Gb3 promotes broadly reactive antibody responses and cross-protection. Thus, we show that Gb3 determines affinity as well as breadth in B cell immunity and propose this lipid as novel vaccine adjuvant against viral infection.

One Sentence Summary

Gb3 abundance on GC B cells selects antibodies with high affinity and broad epitope reactivities, which are cross-protective against heterologous influenza infection.
Unveiling fetal brain changes in congenital diaphragmatic hernia: hypoxic injury with loss of progenitor cells, neurons, and oligodendrocytes
Authors: Biouss George , Antounians Lina , Aguet Julien , Kopcalic Katarina , Fakhari Nikan , Baranger Jerome , Mertens Luc , Villemain Olivier , Zani Augusto
Published: September 2023

Congenital diaphragmatic hernia (CDH) is a birth defect characterized by incomplete closure of the diaphragm, herniation of abdominal organs into the chest, and compression of the lungs and the heart. Besides complications related to pulmonary hypoplasia, 1 in 4 survivors develop neurodevelopmental impairment, whose etiology remains unclear. Using a fetal rat model of CDH, we demonstrated that the compression exerted by herniated organs on the mediastinal structures results in decreased brain perfusion on ultrafast ultrasound, cerebral hypoxia with compensatory angiogenesis, mature neuron and oligodendrocyte loss, and activated microglia. In CDH fetuses, apoptosis was prominent in the subventricular and subgranular zones, areas that are key for neurogenesis. We validated these findings in the autopsy samples of four human fetuses with CDH compared to age- and sex-matched controls. This study reveals the molecular mechanisms and cellular changes that occur in the brain of fetuses with CDH and creates opportunities for therapeutic targets.
Wavelet transform analysis reveals differences between patients with impaired left ventricular systolic function and healthy individuals
Authors: Gruszecki Marcin , Kaufmann Damian , Świątczak Michał , Młodziński Krzysztof , Neary J. Patrick , Singh Jyotpal , Rumiński Jacek , Daniłowicz-Szymanowicz Ludmiła
Published: September 2023

Background

Despite continuous progress in medical treatment, heart failure (HF) is the leading cause of hospitalizations with a high all-cause mortality in patients. Patients with a left ventricular ejection fraction (LVEF) below 50% are characterized by the highest risk of cardiovascular complications. The objective of this study was to examine how LVEF below 50% and aging impact cardiovascular physiology.

Methods

Sixteen males with physician diagnosed coronary artery disease and LVEF = 42 ± 6% (age 62 ± 6 years, BMI 29.1 ± 3.8kg/m2) and 10 healthy controls (9 male and 1 female, age 28.5 ± 9.1 years, BMI = 24.1 ± 1.2kg/m2) were recruited in our study. Finger photoplethysmography for blood pressure (BP) and electrocardiogram (ECG) were recorded while participants rested in a supine position. Wavelet transformations were used to analyze the amplitudes, phase coherence and phase difference of BP and ECG. The frequency intervals were separated as follows: I (0.6-2Hz), II (0.145– 0.6Hz), III (0.052–0.145Hz), and IV (0.021–0.052Hz).

Results

HF patients showed a decrease (p<0.05) in BP wavelet amplitude intervals III and IV in comparison to controls, and interval I for ECG. A decrease in phase coherence (p<0.01) at interval I is also found in HF patients compared to controls.

Conclusions

A decrease in smooth muscle cell activity and smooth muscle autonomic innervation (intervals III and IV) contributions to BP, along with a decrease in cardiac activity as shown by the wavelet amplitude in ECG, suggests altered BP and ECG function in aging HF patients. Furthermore, a decrease in the cardiac interval represents an impairment in the BP and ECG relationship in HF patients. The wavelet transform has the potential to expand our understanding of LVEF and improve diagnostic procedures and patient prognosis.
Incorporating Nanopore Sequencing into a Diverse Diagnostic Toolkit for Incontinentia Pigmenti
Authors: Ahting Simone , Popp Denny , Oppermann Henry , Strehlow Vincent , Fasshauer Maria , Popp Bernt , Karnstedt Maike , Schumann Isabell
Published: September 2023

Background

Incontinentia pigmenti (IP) is a rare, hereditary multisystemic disorder affecting 1.2 in 100,000 live births, predominantly females. Conventional genetic analyses through short-read sequencing are complicated in case of IP due to the presence of a highly homologous pseudogene. Traditionally, long-range PCR is employed in order to overcome this challenge, however, detection of skewed X-Inactivation can also aid in correctly assign a variant toIKBKG.

Methods

We employed a comprehensive multi-method approach, incorporating whole-exome sequencing (WES), long-range PCR, RT-PCR, X-inactivation analysis, and nanopore sequencing of genomic DNA, to identify and accurately phase a small heterozygous deletion NM_001099857.5:c.363_367del, p.(Leu122Glyfs*14) to theIKBKGgene in a family affected with IP.

Results

The deletion was initially detected through WES and skewed X-inactivation was observed in both the proband and her mother. Long-range PCR specific toIKBKGwas utilized to verify that the variant is located inIKBKGand not in its highly homologous pseudogene. On RNA level, the variant was undetectable, suggesting nonsense-mediated decay (NMD) of the transcript containing the variant. We further utilized nanopore sequencing not only to pinpoint and accurately map the variant to theIKBKGgene but also to analyze methylation status of both alleles. This allowed us to confirm the skewed X-inactivation, with the variant-carrying allele found to be predominantly inactivated.

Conclusion

Nanopore sequencing serves as a valuable tool in genetic diagnosis, enabling the precise localization of the variant in either the gene or the pseudogene. Furthermore, in females with skewed X-inactivation, this method facilitates the determination of whether the variant is predominantly located on the activated or inactivated X-chromosome.
Generative AI Mitigates Representation Bias and Improves Model Fairness Through Synthetic Health Data
Authors: Marchesi Raffaele , Micheletti Nicolo , Kuo Nicholas I-Hsien , Barbieri Sebastiano , Jurman Giuseppe , Osmani Venet
Published: September 2023

Representation bias in health data can lead to unfair decisions and compromise the generalisability of research findings. As a consequence, underrepresented subpopulations, such as those from specific ethnic backgrounds or genders, do not benefit equally from clinical discoveries. Several approaches have been developed to mitigate representation bias, ranging from simple resampling methods, such as SMOTE, to recent approaches based on generative adversarial networks (GAN). However, generating high-dimensional time-series synthetic health data remains a significant challenge. In response, we devised a novel architecture (CA-GAN) that synthesises authentic, high-dimensional time series data. CA-GAN outperforms state-of-the-art methods in a qualitative and a quantitative evaluation while avoiding mode collapse, a serious GAN failure. We perform evaluation using 7535 patients with hypotension and sepsis from two diverse, real-world clinical datasets. We show that synthetic data generated by our CA-GAN improves model fairness in Black patients as well as female patients when evaluated separately for each subpopulation. Furthermore, CA-GAN generates authentic data of the minority class while faithfully maintaining the original distribution of data, resulting in improved performance in a downstream predictive task.
Detection of TRAF1‐ALK fusion in skin lesions of systemic ALK+ anaplastic large cell lymphoma initially involving the skin and the draining lymph node
Authors: Norimatsu Yuta , Akatsuka Taro , Matsuoka Akari , Hamada Toshihisa , Mori Ichiro , Shiomi Takayuki , Mori Naoki , Onishi Kayoko , Togashi Yuki , Inoue Norihito , Takeuchi Kengo , Sugaya Makoto
Published: September 2023

A case of cytoplasmic anaplastic lymphoma kinase (ALK)‐positive anaplastic large cell lymphoma (ALCL) initially involving the skin in a 44‐year‐old Japanese female is reported. The patient had a hemorrhagic erythematous tumor on the right thigh without any systemic symptoms. Pathology showed diffuse infiltration of CD30‐positive anaplastic large cells positive for epithelial membrane antigen and cytoplasmic ALK. The right inguinal lymph node showed infiltration of tumor cells in the marginal sinus. Only 2 weeks after radiation therapy, the patient developed multiple subcutaneous nodules and lung involvement. Even after subsequent multichemotherapy sessions, cutaneous recurrence occurred. Literature review of cytoplasmic ALK‐positive ALCL initially involving in the skin revealed that skin lesions were mostly seen in the extremities and that half of the cases developed extracutaneous lesions. Radiation and chemotherapy were effective for most cases. Inverse RT‐PCR identified a tumor necrosis factor receptor‐associated factor (TRAF)1‐ALK fusion in our case. Most reported cases with this translocation experienced repeated changes in chemotherapy, suggesting poorer prognosis. Although ALK‐positive ALCL generally responds well to chemotherapy, the presence of a TRAF1‐ALK fusion may suggest resistance to treatment. Detection of fusion partners of ALK is important for predicting clinical courses and deciding treatment options.
A diagnosis of the primary difference betweenEuroForMixandSTRmix™
Authors: Buckleton John , Susik Mateusz , Curran James M. , Cheng Kevin , Taylor Duncan , Bright Jo‐Anne , Kelly Hannah , Wivell Richard
Published: September 2023

There is interest in comparing the output, principally the likelihood ratio, from the two probabilistic genotyping software EuroForMix (EFM) and STRmix™. Many of these comparison studies are descriptive and make little or no effort to diagnose the cause of difference. There are fundamental differences between EFM and STRmix™ that are causative of the largest set of likelihood ratio differences. This set of differences is for false donors where there are many instances ofLRs just above or below 1 for EFM that give much lowerLRs in STRmix™. This is caused by the separate estimation of parameters such as allele height variance and mixture proportion using MLE underHpandHafor EFM. This can result in very different estimations of these parameters underHpandHa. It results in a departure from calibration for EFM in the region ofLRs just above and below 1.
Evaluation of facial nerve perineural spread from cutaneous squamous cell carcinoma using 3T MR neurography
Authors: Schachtel Michael JC , Panizza Benedict J , Gandhi Mitesh
Published: September 2023

Introduction

Perineural spread (PNS) is a rare but potentially fatal consequence of cutaneous squamous cell carcinoma (cSCC) of the head and neck. We aimed to evaluate the accuracy of 3T MR neurography in detecting and defining the extent of facial nerve (VII) PNS from cSCC, and highlight characteristic radiological features in peripheral branches to improve early diagnosis.

Methods

Single‐institution retrospective review of 38 patients with clinical, radiological, and/or histopathological findings consistent with VII PNS from cSCC who underwent pre‐operative 3T MR neurography.

Results

Compared to histopathology (gold standard), 3T MR neurography had a sensitivity of 89% and positive predictive value of 97%. In true‐positive cases (n = 33), zonal extent was correctly identified in 100%. Seventy‐nine% had simultaneous trigeminal nerve (V) PNS, mostly involving the auriculotemporal branch of the mandibular nerve (64%). When the causative lesion was absent (n = 23), the extra‐temporal VII demonstrated asymmetrical enhancement alone (n = 6), bulky expansion (n = 8), or extra‐neural spread (n = 9). Peripheral VII branch involvement, particularly the buccal and zygomatic, was readily identified using known anatomical landmarks.

Conclusion

3T MR neurography is highly accurate in evaluating VII PNS from cSCC, and thus should be specifically requested by physicians if suspicious for disease. Coexistent V PNS was common, highlighting the need to examine V branches to allow complete treatment planning. The unique radiological patterns identified showcases disease progression. As early detection improves patient outcomes, the radiologist must look for peripheral VII involvement in specific anatomical areas, which is within the capabilities of 3T MR neurography.
The Necessity of Moving Averages in Dynamic Linear Regression Models
Authors: Vande Kamp Garrett N. , Jordan Soren
Published: September 2023

Consensus from the debate over lagged dependent variables in dynamic linear regression models advises that including enough lags of the dependent and independent variables will fully model autocorrelation in the error term. But this approach fails to account for a long‐neglected source of autocorrelation in the error term—moving averages—which cannot be represented with a finite number of lags. Approximating moving averages results in either inconsistent or inefficient estimates of relevant quantities of interest, a claim demonstrated here via Monte Carlo simulations and three empirical demonstrations. Ultimately, we argue that moving averages should be a standard part of dynamic analysis and offer guidance for incorporating them into various modeling strategies.
When a synonymous mutation breaks the silence in a thalassaemia patient
Authors: Gorivale M. , Sawant P. , Kargutkar N. , Hariharan P. , Thaker P. , Chiddarwar A. , Nadkarni A.
Published: September 2023

Synonymous mutations were considered to lack functional roles in human diseases; however, distinguishing deleterious synonymous mutations from benign ones is still a challenge. In this article, we identified a deleterious synonymous mutation β‐codon 16 (C>T). HBB: c.51C>T, in compound heterozygous form with known β‐thalassaemia mutation patients who clinically presented as non‐transfusion‐dependent thalassaemia (NTDT). A total of 9 families with 11 compound heterozygous index cases were reported. In the heterozygous state, codon 16 (C>T) mutation results in borderline HbA2 (3.18 ± 0.36%) and slightly reduced RBC indices (RBCs: 4.73 ± 0.75 × 106/μL, Hb: 12.26 ± 2.60 g/dL, MCV: 79.48 ± 8.40 fL, MCH: 25.95 ± 4.15 pg). The compound heterozygous patients showed elevated HbA2 (5.98 ± 1.17%) and HbF (12.75 ± 7.51%) and presented clinically as NTDT with a mean Hb of 6.95 ± 1.29 g/dL. Many of them were dependent on few transfusions and had mild splenomegaly. Of the 11 patients, 5 (45.4%) were treated with hydroxyurea. This study highlights the clinical significance of synonymous mutation, when inherited with other β‐thalassaemia mutations leading to the phenotype of NTDT. Thus, the study would help to improve screening protocols for β‐thalassaemia carriers, which will ultimately improve the prevention programme.
Multi‐phasic eGFR trajectory during follow up and long‐term graft failure after kidney transplantation
Authors: Rahamimov Ruth , Agur Timna , Zingerman Boris , Bielopolski Dana , Steinmetz Tali , Nesher Eviatar , Hanniel Iddo , Rozen‐Zvi Benaya
Published: September 2023

Background

The prevailing assumption is that following kidney transplantation the pattern of kidney function decline is consistent. Nevertheless, numerous factors leading to graft loss may emerge, altering the trajectory of kidney function. In this study, we aim to assess alterations in estimated glomerular filtration rate (eGFR) trajectory over an extended period of follow‐up and examine its correlation with graft survival.

Methods

We calculated eGFR using all creatinine values available from 1‐year post transplantation to the end of follow‐up. For pattern analysis, we used a piecewise linear model.

Results

Nine hundred eighty‐eight patients were included in the study. After a median follow‐up of 5.2 years, 297 (30.1%) patients had a multi‐phasic eGFR trajectory. Change in eGFR trajectory was associated with increased risk for graft failure (HR 7.15, 95% CI 5.17–9.89, p < .001), longer follow‐up time, younger age, longer cold ischemia time, high prevalence of acute rejection, longer hospitalization and a lower initial eGFR. Of the 988 patients included in the study, 494 (50.0%) had a mono‐phasic stable trajectory, 197 (19.9%) had a mono‐phasic decreasing trajectory, 184 (18.6%) had bi‐phasic decreasing trajectory (initial stability and then decline, 46(4.7%) had a bi‐phasic stabilized (initial decline and then stabilization) and 67(6.8%) had a more complex trajectory (tri‐phasic). Out of the total 144 patients who experienced graft loss, the predominant pattern was a bi‐phasic decline characterized by a bi‐linear trajectory (66 events, 45.8%).

Conclusions

Changes in eGFR trajectory during long‐term follow‐up can serve as a valuable tool for assessing the underlying mechanisms contributing to graft loss.