bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformational dynamics in specialized C2H2zinc finger domains enable zinc-responsive gene repression in S. pombe
Authors: Wadhwa Vibhuti , Jamshidi Cameron , Stachowski Kye , Bird Amanda J. , Foster Mark P.
Published: September 2024

Loz1 is a zinc-responsive transcription factor in fission yeast that maintains cellular zinc homeostasis by repressing the expression of genes required for zinc uptake in high zinc conditions. Previous deletion analysis of Loz1 found a region containing two tandem C2H2zinc-fingers and an upstream “accessory domain” rich in histidine, lysine, and arginine residues to be sufficient for zinc-dependent DNA binding and gene repression. Here we report unexpected biophysical properties of this pair of seemingly classical C2H2zinc fingers. Isothermal titration calorimetry and NMR spectroscopy reveal two distinct zinc binding events localized to the zinc fingers. NMR spectra reveal complex dynamic behavior in this zinc responsive region spanning time scales from fast 10−12-10−10to slow > 100sec. Slow exchange due tocis-transisomerization of the TGERP linker results in doubling of many signals in the protein.

Conformational exchange on the 10−3s timescale throughout the first zinc finger distinguishes it from the second and is linked to weaker affinity for zinc. These findings reveal the mechanism of zinc sensing by Loz1 and illuminate how the protein’s rough free-energy landscape enable zinc sensing, DNA binding and regulated gene expression.
Stimulation of otolith irregular fibers produces a rostro-caudal gradient in activity in the vestibular nuclear complex (VNC), but not the vestibulocerebellum (VeCb)
Authors: Holt Avril Genene , King Shana , Naqvi Danial , Braun Rod D. , Bauer David S. , Anderson Marie , King William Michael
Published: September 2024

The vestibular system is important for posture, balance, motor control, and spatial orientation. Each of the vestibular end organs have specialized neuroepithelia with both regular and irregular afferents. In otolith organs, the utricle and saccule, afferents most responsive to linear jerk (jerk - derivative of acceleration) are located in the striola and project centrally to the vestibular nuclear complex (VNC) as well as the uvula and nodulus of the vestibulocerebellum (VeCb). The pattern of central neuronal activation attributed to otolith irregular afferents is relatively unknown. To address this gap, c-Fos was used as a marker of neuronal activity to map the distribution of active neurons throughout the rostro-caudal extent of the VNC and VeCb. Immunohistochemistry for c-Fos was performed to assess activation of VNC and VeCb neurons in response to a linear jerk stimulus delivered in the naso-occipital plane. Activated neurons were distributed throughout the VNC, including the lateral vestibular nucleus (LVe), magnocellular medial vestibular nucleus (MVeMC), parvocellular medial vestibular nucleus (MVePC), spinal vestibular nucleus (SpVe), and superior vestibular nucleus (SuVe). Notably, after stimulation, the MVePC exhibited the greatest number of c-Fos labeled nuclei. Significant increases in c-Fos labeling were found in mid-rostrocaudal and caudal regions of the VNC in the LVe, MVe, and SpVe. Additionally, c-Fos labeling was observed across all regions of the VeCb after jerk stimulation. Significant increases in the number of labeled nuclei were found throughout the rostro-caudal extent of the nodulus and uvula. However, jerk stimulated increases in activity for the paraflocculus were restricted to the caudal VeCb. The distribution of neuronal activity suggests that regions receiving the greatest direct otolith input exhibit the most substantial changes in response to otolith derived, irregular fiber stimulation.

Highlights

Nuclei with descending projections (LVe, MVePC, and SpVe) demonstrated the greatest change in activity after naso-occipital jerk stimulation.

Naso-occipital jerk stimulation preferentially activates caudal VNC neurons

Naso-occipital jerk stimulation activates neurons throughout the VeCb

Jerk stimulation in the naso-occipital plane has the greatest effects on activity in VNC and VeCb regions with the greatest inputs from afferents originating in gravity receptors
Functional characterization of N-acetyltransferase 10 (NAT10) in Leishmania mexicana
Authors: Rodrigues Maran Suellen , Barbosa Leite Ariely , Gomes Alves Gabriela , Souza Bonifácio Bruno , Eduardo Alves Carlos , Lourenco Moreira Paulo Otávio , Marques Panessa Giovanna , Montero do Amaral Prado Heloísa , Klippel Angélica Hollunder , Cussiol José Renato , Massirer Katlin Brauer , Rodrigues Ferreira Tiago , Sacks David , Barbiéri Clara Lúcia , Santos da Silva Marcelo , Lima do Monte-Neto Rubens , Silvio Moretti Nilmar
Published: September 2024

Leishmaniapresents a complex life cycle that involves both invertebrate and vertebrate hosts. By regulating gene expression, protein synthesis, and metabolism, the parasite can adapt to various environmental conditions. This regulation occurs mainly at the post-transcriptional level and may involve epitranscriptomic modifications of RNAs. Recent studies have shown that mRNAs in humans undergo a modification known as N4-acetylcytidine (ac4C) catalyzed by the enzyme N-acetyltransferase (NAT10), impacting mRNAs stability and translation. Here, we characterized the NAT10 homologue ofL. mexicana, finding that the enzyme exhibits all the conserved acetyltransferase domains and although failed to functionally complement the Kre33 mutant inSaccharomyces cerevisiae, hasin vitroacetyltransferase activity. We also discovered that LmexNAT10 is nuclear, and seems essential, as evidenced by unsuccessful attempts to obtain null mutant parasites. Phenotypic characterization of single-knockout parasites revealed that LmexNAT10 affects the multiplication of procyclic forms and the promastigote-amastigote differentiation. Additionally,in vivoinfection studies using the invertebrate vectorLutzomyia longipalpisshowed a delay in the parasite differentiation into metacyclics. Finally, we observed changes in the cell cycle progression and protein synthesis in the mutant parasites. Together, these results suggest that LmexNAT10 might be important for parasite differentiation, potentially by regulating ac4C levels.
Abstinence from cocaine self-administration promotes microglia pruning of astrocytes which drives cocaine-seeking behavior
Authors: Testen Anze , VanRyzin Jonathan W , Bellinger Tania J , Kim Ronald , Wang Han , Gastinger Matthew J , Witt Emily A , Franklin Janay P , Vecchiarelli Haley A , Picard Katherine , Tremblay Marie-Ève , Reissner Kathryn J
Published: September 2024

Rodent drug self-administration leads to compromised ability of astrocytes to maintain glutamate homeostasis within the brain’s reward circuitry, as well as reductions in surface area, volume, and synaptic colocalization of astrocyte membranes. However, the mechanisms driving astrocyte responses to cocaine are unknown. Here, we report that long-access cocaine self-administration followed by prolonged home cage abstinence results in decreased branching complexity of nucleus accumbens astrocytes, characterized by the loss of peripheral processes. Using a combination of confocal fluorescence microcopy and immuno-gold electron microscopy, we show that alterations in astrocyte structural features are driven by microglia phagocytosis, as labeled astrocyte membranes are found within microglia phagolysosomes. Inhibition of complement C3-mediated phagocytosis using the neutrophil inhibitory peptide (NIF) rescued astrocyte structure and decreased cocaine seeking behavior following cocaine self-administration and abstinence. Collectively, these results provide evidence for microglia pruning of accumbens astrocytes across cocaine abstinence which mediates cocaine craving.
Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids
Authors: Schmied Verena , Korkut-Demirbaş Medina , Venturino Alessandro , Siegert Sandra
Published: September 2024

Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. While human induced pluripotent stem cells (hIPSC)-derived brain organoid models have started to explore functional consequences upon viral stimulation, these models commonly lack microglia. Yet, microglia are susceptible to and promote inflammation and will influence the effects.

Here, we generate hIPSC-derived microglia precursor cells and assemble them into retinal organoids to dissect their interplay with the developing nervous system and expose them to the immunostimulant poly(I:C). We first identified successful hIPSC-derived microglia (iMG) integration into the retinal organoid at the time when the outer plexiform layer forms. To improve ganglion cell surveillance, we adapted the retinal organoid model and found that the ganglion cell number significantly decreased only with iMG presence. While poly(I:C) exposure alters the iMG phenotype, it does not hinder their interaction with ganglion cells. Furthermore, iMG significantly enhances the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure with the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens the poly(I:C)-mediated changes of the iMG phenotype and ameliorates cell proliferation. Remarkably, while poly(I:C) disrupts neuronal calcium dynamics independent of iMG, ibuprofen rescues this effect only if iMG are present. This effect depends on cyclooxygenase 1 in microglia and cyclooxygenase 2, common NSAID targets.

These findings underscore the importance of microglia in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development.
Increased listening effort and decreased speech discrimination at high presentation sound levels in acoustic hearing listeners and cochlear implant users
Authors: Huang Chengjie G. , Field Natalie A. , Latorre Marie-Elise , Anderson Samira , Goupell Matthew J.
Published: September 2024

The sounds we experience in our everyday communication can vary greatly in terms of level and background noise depending on the environment. Paradoxically, increasing the sound intensity may lead to worsened speech understanding, especially in noise. This is known as the “Rollover” phenomenon. There have been limited studies on rollover and how it is experienced differentially across aging groups, for those with and without hearing loss, as well as cochlear implant (CI) users. There is also mounting evidence that listening effort plays an important role in challenging listening conditions and can be directly quantified with objective measures such as pupil dilation. We found that listening effort was modulated by sound level and that rollover occurred primarily in the presence of background noise. The effect on listening effort was exacerbated by age and hearing loss in acoustic listeners, with greatest effect in older listeners with hearing loss, while there was no effect in CI users. The age- and hearing-dependent effects of rollover highlight the potential negative impact of amplification to high sound levels and therefore has implications for effective treatment of age-related hearing loss.
Brain-body mitochondrial distribution patterns lack coherence and point to tissue-specific and individualized regulatory mechanisms
Authors: Devine Jack , Monzel Anna S , Shire David , Rosenberg Ayelet M , Junker Alex , Cohen Alan A , Picard Martin
Published: September 2024

Energy transformation capacity is generally assumed to be a coherent individual trait driven by genetic and environmental factors. This predicts that some individuals should have high and others low mitochondrial oxidative phosphorylation (OxPhos) capacity across organ systems. Here, we test this assumption using multi-tissue molecular and enzymatic activities in mice and humans. Across up to 22 mouse tissues, neither mitochondrial OxPhos capacity nor mtDNA density were correlated between tissues (medianr= -0.01–0.16), indicating that animals with high mitochondrial capacity in one tissue can have low capacity in other tissues. Similarly, the multi-tissue correlation structure of RNAseq-based indices of mitochondrial gene expression across 45 tissues from 948 women and men (GTEx) showed small to moderate coherence between only some tissues (regions of the same brain), but not between brain-body tissue pairs in the same person (medianr= 0.01). Mitochondrial DNA copy number (mtDNAcn) also lacked coherence across organs and tissues. Mechanistically, tissue-specific differences in mitochondrial gene expression were attributable in part to i) tissue-specific activation of canonical energy sensing pathways including the transcriptional coactivator PGC-111 and the integrated stress response (ISR), and ii) proliferative activity across tissues. Finally, we identify subgroups of individuals with high mitochondrial gene expression in some tissues (e.g., heart) but low expression in others (e.g., skeletal muscle) who display different clinical phenotypic patterns. Taken together, these data raise the possibility that tissue-specific energy sensing pathways may contribute to the idiosyncratic mitochondrial distribution patterns associated with the inter-organ heterogeneity and phenotypic diversity among individuals.
Microbial magnetite oxidation via MtoAB porin-multiheme cytochrome complex inSideroxydans lithotrophicusES-1
Authors: Keffer Jessica L. , Zhou Nanqing , Rushworth Danielle D. , Yu Yanbao , Chan Clara S.
Published: September 2024

Most of Earth’s iron is mineral-bound, but it is unclear how and to what extent iron-oxidizing microbes can use solid minerals as electron donors. A prime candidate for studying mineral-oxidizing growth and pathways isSideroxydans lithotrophicusES-1, a robust, facultative iron oxidizer with multiple possible iron oxidation mechanisms. These include Cyc2 and Mto pathways plus other multiheme cytochromes and cupredoxins, and so we posit that the mechanisms may correspond to different Fe(II) sources. Here,S. lithotrophicusES-1 was grown on dissolved Fe(II)-citrate and magnetite.S. lithotrophicusES-1 oxidized all dissolved Fe2+released from magnetite, and continued to build biomass when only solid Fe(II) remained, suggesting it can utilize magnetite as a solid electron donor. Quantitative proteomic analyses ofS. lithotrophicusES-1 grown on these substrates revealed global proteome remodeling in response to electron donor and growth state and uncovered potential proteins and metabolic pathways involved in the oxidation of solid magnetite. While the Cyc2 iron oxidases were highly expressed on both dissolved and solid substrates, MtoA was only detected during growth on solid magnetite, suggesting this protein helps catalyze oxidation of solid minerals inS. lithotrophicusES-1. A set of cupredoxin domain-containing proteins were also specifically expressed during solid iron oxidation. This work demonstrated the iron oxidizerS. lithotrophicusES-1 utilized additional extracellular electron transfer pathways when growing on solid mineral electron donors compared to dissolved Fe(II).

Importance

Mineral-bound iron could be a vast source of energy to iron-oxidizing bacteria, but there is limited physiological evidence of this metabolism, and it has been unknown whether the mechanisms of solid and dissolved Fe(II) oxidation are distinct. In iron-reducing bacteria, multiheme cytochromes can facilitate iron mineral reduction, and here, we link a multiheme cytochrome-based pathway to mineral oxidation, expanding the known functionality of multiheme cytochromes. Given the growing recognition of microbial oxidation of minerals and cathodes, increasing our understanding of these mechanisms will allow us to recognize and trace the activities of mineral-oxidizing microbes. This work shows how solid iron minerals can promote microbial growth, which if widespread, could be a major agent of geologic weathering and mineral-fueled nutrient cycling in sediments, aquifers, and rock-hosted environments.
hiPSC-derived astrocytes from individuals with schizophrenia induce a dystrophic phenotype in microglial-like cells
Authors: Cardozo Pablo L. , Lee Chia-Yi , Lacerda Juliana P. S. , Fahel Júlia S. , Trindade Pablo , Vitória Gabriela , Chicaybam Leonardo , Cordeiro Rafaela C. , de Faria Isaque J. S. , Silva Nathália C. , Todjro Yaovi M. H. , Maciel Joana C. do P. , Bonamino Martin H. , Vieira Luciene B. , Cruz Breno F. , Nicolato Rodrigo , Brennand Kristen J. , Rehen Stevens K. , Ribeiro Fabíola M
Published: September 2024

Background

Neuroinflammation, particularly astrocyte reactivity, is increasingly linked to schizophrenia (SCZ). Yet, the crosstalk between astrocytes and microglia in SCZ, especially under pro-inflammatory conditions, remains unclear.

Methods

Here, we employed human induced-pluripotent stem cells to compare how astrocytes from five age-matched individuals with SCZ and five neurotypical controls, upon stimulation with TNF-α (10 ng/mL), affected microglial biology. Transcriptomics, bioinformatics and functional assays were used as readouts.

Results

TNF-□ stimulation of SCZ astrocytes, relative to their control counterparts, triggered increased mRNA expression of pro-inflammatory cytokines and CX3CL1, a chemokine involved in chemotaxis and synapse pruning. Interestingly, transcriptomic and gene set enrichment analyses revealed that reactive SCZ astrocytes promoted the downregulation of biological processes associated with immune cell proliferation and activation, phagocytosis and cell migration in induced microglial-like cells (iMGs). Under such conditions, iMGs assumed a dystrophic/senescent-like phenotype associated with accelerated transcriptional age. Functional validations showed that TNF-□-stimulated SCZ astrocytes promoted reduced synaptoneurosomes phagocytosis by iMGs. Additionally, stimulated astrocytes (control and SCZ) induced iMGs migration in a CX3CR1-dependent manner. Nevertheless, reactive SCZ astrocytes did not promote greater microglial chemotaxis, despite secreting twice as much CX3CL1 compared to stimulated control astrocytes, possibly by lowering CX3CR1 in the plasma membrane.

Conclusions

Altogether, these findings suggest that astrocytes contribute to SCZ pathology by altering normal microglial function and inducing a dystrophic phenotype.
Clustering of rRNA operons inE. coliis disrupted by σH
Authors: Ho Khang , Harshey Rasika M.
Published: September 2024

Chromosomal organization inE. colias examined by Hi-C methodology indicates that long-range interactions are sparse. Yet, spatial co-localization or ‘clustering’ of 6/7 ribosomal RNA (rrn) operons distributed over half the 4.6 Mbp genome has been captured by two other methodologies - fluorescence microscopy and Mu transposition. Our current understanding of the mechanism of clustering is limited to mapping essentialciselements. To identifytranselements, we resorted to perturbing the system by chemical and physical means and observed that heat shock disrupts clustering. Levels of σHare known to rise as a cellular response to the shock. We show that elevated expression of σHalone is sufficient to disrupt clustering, independent of heat stress. The anti-clustering activity of σHdoes not depend on its transcriptional activity but requires core-RNAP interaction and DNA-binding activities. This activity of σHis suppressed by ectopic expression of σDsuggesting a competition for core-RNAP. A query of the other five known σ factors ofE. colifound that elevated expression of FecI, the ECF σ factor that controls iron citrate transport, also perturbs clustering and is also suppressed by σD. We discuss a possible scenario for how these membrane-associated σ factors participate in clustering of distantrrnloci.
Rubisco packaging and stoichiometric composition of a native β-carboxysome
Authors: Sun Yaqi , Sheng Yuewen , Ni Tao , Ge Xingwu , Sarsby Joscelyn , Brownridge Philip J. , Li Kang , Hardenbrook Nathan , Dykes Gregory F. , Rockliffe Nichola , Eyers Claire E. , Zhang Peijun , Liu Lu-Ning
Published: September 2024

Carboxysomes are anabolic bacterial microcompartments that play an essential role in carbon fixation in cyanobacteria. This self-assembling proteinaceous organelle encapsulates the key CO2-fixing enzymes, Rubisco and carbonic anhydrase, using a polyhedral shell constructed by hundreds of shell protein paralogs. Deciphering the precise arrangement and structural organization of Rubisco enzymes within carboxysomes is crucial for understanding the formation process and overall functionality of carboxysomes. Here, we employed cryo-electron tomography and subtomogram averaging to delineate the three-dimensional packaging of Rubiscos within β-carboxysomes in the freshwater cyanobacteriumSynechococcus elongatusPCC7942 that were grown under low light. Our results revealed that Rubiscos are arranged in multiple concentric layers parallel to the shell within the β-carboxysome lumen. We also identified the binding of Rubisco with the scaffolding protein CcmM in β-carboxysomes, which is instrumental for Rubisco encapsulation and β-carboxysome assembly. Using QconCAT-based quantitative mass spectrometry, we further determined the absolute stoichiometric composition of the entire β-carboxysome. This study and recent findings on the β-carboxysome structure provide insights into the assembly principles and structural variation of β-carboxysomes, which will aid in the rational design and repurposing of carboxysome nanostructures for diverse bioengineering applications.
Differential representations for affective and informative components of reward in the striatum and hippocampus
Authors: Shen Xinxu , Wang Kainan S. , Murty Vishnu P. , Delgado Mauricio R. , Smith David V.
Published: September 2024

Receipt of a reward is composed of affective and informative components, which are often intertwined in most reward-processing and decision-making tasks. Our previous work allowed us to identify regions that were more strongly engaged for the affective and informative components of reward upon receipt (Smith et al., 2016) and showed that the ventral striatum responds to both affective and informative components of reward processing. However, the limited spatial resolution and coarse analytical approaches made it hard to understand how these different components of reward were represented in the brain, wherein similar engagement may not necessitate similar representations. In our current study, we used high-resolution functional magnetic resonance imaging (voxel size: 1.75 mm3) and representational similarity analysis to investigate the representation of affective and informative components of reward receipt in the striatum and the hippocampus, another region that is sensitive to reward information. We found a differential representation of affective and informative components of reward receipt in the striatum and the hippocampus, with no difference in representation between the two structures. However, in the dorsal striatum, we found that representations were stronger for affective rather than the informative components of reward receipt. Finally, we observed that the ventral striatum was sensitive to the predictiveness of information, such that across-run pattern similarity in the ventral striatum increased with the predictiveness of information. In sum, our results provide evidence of how affective and informative components of rewards are represented in the striatum and the hippocampus, potentially indicating a differential coding schema for the dorsal and the ventral striatum.
Development of a protein synthesis network at the sarco/endoplasmic reticulum in adult cardiac myocytes
Authors: Sandmann Christoph , Sramek Viviana , Brandenburg Sören , Uhlenkamp Dennis , Renz Marc , Meyer Bianca , Sandmann Clara , Herzog Nicole , Groß Julia , Katus Hugo A. , Lehnart Stephan E. , Völkers Mirko , Doroudgar Shirin
Published: September 2024

Introduction

The endoplasmic reticulum (ER) is the site of synthesis and folding of membrane and secretory proteins, which constitute a large fraction of the total protein output of a mammalian cell. Striated muscle cells contain a specialized membrane system known as the sarcoplasmic reticulum (SR) that controls calcium homeoastasis and contraction, however the biochemical and physiological relationship between the ER and SR and how both compartments participate in protein synthesis remains incompletely understood.

Methods

Protein quantification and imaging of selected marker proteins for ER and SR functions was performed to characterize the relationship of the ER and SR and its individual involvement in protein synthesis in neonatal and adult cardiac myocytes. Superresolution microscopy was used to examine the interaction of ribosomes and the SR in adult cardiac myocytes.

Results

Quantification of ER and SR-associated proteins of isolated ventricular cardiac myocytes showed that relative expression of ER/SR resident protein quality elements, as well as relative ribosome levels are decreased in adult cells, whereas SR-associated Ca2+handling proteins increase. Immunocytoflourescence revealed that the membrane compartment that exists in early postpartum resembles mostly the ER and decreases in postnatal development. The SR is the main membrane network that exists in the adult cardiac myocytes, replacing the ER, in all but the perinuclear region. Immunocytoflourescence staining further indicated that both networks perform overlapping but distinct, specialized functions, such as localization of excitation-contraction coupling exclusively to the SR or initiation of secretion via the classical secretory pathway mainly from the ER. Ribosomes and mRNA were localized both in close proximity to the ER and the SR of adult ventricular cardiac myocytes. Superresolution microscopy confirmed that both the ER as well as the developed SR bind ribosomes and are direct sites of protein synthesis and protein homeostasis in adult cardiac myocytes.

Conclusion

Our findings suggest molecular differentiation and structural organization of the ER/SR in cardiac muscle development, resulting in the development of a protein synthesis network at the sarco/endoplasmic reticulum in adult cardiac myocytes.
Unveil the Molecular Interplay between Aminoglycosides and Pseudouridine in IRES Translation
Authors: Zhao Yu , Xu Chong , Chen Xin , Jin Hong , Li Hong
Published: September 2024

Eukaryotic ribosomes are enriched with pseudouridine, particularly at the functional centers targeted by antibiotics. Here we investigated the roles of pseudouridine in aminoglycoside-mediated translation inhibition by comparing the structural and functional properties of the wild-type ribosomes and those lacking pseudouridine (cbf5-D95A). We showed that thecbf5-D95A ribosomes have decreased thermostability and high sensitivity to aminoglycosides. When presented with an internal ribosome entry site (IRES) RNA, elongation factor eEF2, GTP, sordarin, hygromycin B preferentially binds to thecbf5-D95A ribosomes during initiation by blocking eEF2 binding and stalls the ribosomes in a non-rotated conformation, further hindering translocation. Hygromycin B binds to the inter-subunit bridge B2a that is known to be sensitive to pseudouridine, revealing a functional link between pseudouridine and aminoglycoside inhibition. Our results suggest that pseudouridine enhances both thermostability and conformational fitness of the ribosomes, thereby influencing their susceptibility to aminoglycosides.

Highlights

Loss of pseudouridine increases cell sensitivity to aminoglycosides

Pseudouridine enhances ribosome thermostability

Hygromycin B competes with eEF2 for the non-rotated ribosome

Hygromycin B deforms the codon-anticodon duplex
Maternal adiponectin restores cholinergic vasodilation in resistance vessels from adult offspring exposed to maternal obesityin utero
Authors: Murphy Molly , Fallahi Sahand , Dumolt Jerad H. , Houck Julie A. , Vaughan Owen R. , Moore Lorna G. , Julian Colleen G. , Rosario Fredrick J. , Powell Theresa L. , Jansson Thomas , Lorca Ramón A.
Published: September 2024

Maternal obesity increases the risk of cardiovascular and metabolic disease in the offspring both during childhood and adult life. Pregnant women and mice with obesity have lower circulating levels of adiponectin (ADN) compared to lean controls. ADN is an adipokine involved in regulating energy metabolism, vascular function, and placental function. We hypothesized that offspring of obese mice have impaired resistance artery function, which can be prevented by restoration of normal circulating ADN levels in obese dams during late pregnancy. Adult female mice were fed either control or obesogenic diet and mated with control diet-fed males. Control dams received a continuous infusion of phosphate saline buffer (PBS) during late pregnancy whereas obese females received either PBS or ADN. After weaning, offspring were fed a control diet. Mesenteric arteries (MsA) were dissected from adult offspring and mounted in a wire myograph or fixed for histology. MsA responses to vasoconstrictors (phenylephrine and endothelin-1) were not different between infusion groups. However, the vasodilatory responses to acetylcholine were reduced in offspring from obese dams as compared to control-fed dams. ADN supplementation during pregnancy restored the cholinergic vasodilatory responses of resistance vessels in offspring from obese dams. These observations suggest that normalizing circulating adiponectin levels in pregnancies complicated by obesity prevents in utero programming of vascular dysfunction in the offspring.
Effects of in vitro hemolysis and repeated freeze-thaw cycles in protein abundance quantification using the SomaScan and Olink assays
Authors: Candia Julián , Fantoni Giovanna , Moaddel Ruin , Delgado-Peraza Francheska , Shehadeh Nader , Tanaka Toshiko , Ferrucci Luigi
Published: September 2024

SomaScan and Olink are the leading aptamer- and antibody-based platforms in current proteomics research, each of them capable of measuring thousands of human proteins with a broad range of endogenous concentrations. In this study, we investigated the effects of in vitro hemolysis and repeated freeze-thaw cycles in protein abundance quantification across 10,776 (11K SomaScan) and 1,472 (Olink Explore 1536) analytes, respectively. Using SomaScan, we found two distinct groups, each one consisting of 4% of all aptamers, affected by either hemolysis or freeze-thaw cycles. Using Olink, probes impacted by freeze-thaw cycles were in line with the observations from SomaScan, with 6% of analytes affected. In dramatic contrast, however, we found that nearly half of all measured Olink probes were significantly impacted by hemolysis. Moreover, by a variety of statistical approaches, we observed that Olink probes affected by hemolysis target proteins with a larger number of annotated protein-protein interactions. Given the extent of the observed nuisance effects, we propose that unbiased, quantitative methods of evaluating hemolysis, such as the hemolysis index successfully implemented in many clinical laboratories, should be adopted in proteomics studies, particularly in those using the Olink assay. We provide detailed results for each SomaScan and Olink probe in the form of extensive Supplementary Data files to be used as resources for the growing user communities of both platforms.
Diet induced mitochondrial DNA replication instability inRad51cmutant mice drives sex-bias in anemia of inflammation
Authors: Tomaszowski Karl-Heinz , Chen Yue , Roy Sunetra , Harris Momo , Zhang Jianhua , Tsai Chi-lin , Schlacher Katharina
Published: September 2024

Anemia of inflammation (AI) is a common comorbidity associated with obesity, diabetes, cardiac disease, aging, and during anti-cancer therapies. Mounting evidence illustrates that males are disproportionally affected by AI, but not why. Here we demonstrate a molecular cause for a sex-bias in inflammation. The data shows that mitochondrial DNA (mtDNA) instability induced by dietary stress causes anemia associated with inflamed macrophages and improper iron recycling in mice. These phenotypes are enhanced in mice with mutations inFanco/Rad51c, which predisposes to the progeroid disease Fanconi Anemia. The data reveals a striking sex-bias whereby females are protected. We find that estrogen acts as a mitochondrial antioxidant that reduces diet-induced oxidative stress, mtDNA replication instability and the distinctively mtDNA-dependent unphosphorylated STAT1 response. Consequently, treatment of maleRad51cmutant mice with estrogen or mitochondrial antioxidants suppresses the inflammation-induced anemia. Collectively, this study uncovers estrogen-responsive mtDNA replication instability as a cause for sex-specific inflammatory responses and molecular driver for AI.
Concurrent large-scale brain dynamics during the emotional face matching task and their relation to behavior and mental health
Authors: Korponay Cole , Cohen-Gilbert Julia E. , Kumar Poornima , Harnett Nathaniel G. , Medina Adrian A. , Forester Brent P. , Ressler Kerry J. , Beckmann Christian F. , Harper David G. , Nickerson Lisa D.
Published: September 2024

Prior investigations of emotion processing’s neural underpinnings rely ona priorimodels of brain response, obscuring detection of task-relevant neurobiological processes with complex temporal dynamics. To overcome this limitation, we applied unsupervised machine learning to functional magnetic resonance imaging data acquired during the emotional face matching task (EFMT) in healthy young adults from the Human Connectome Project (n=413; n=416 replication). Tensorial independent component analysis showed that the EFMT engages 10 large-scale brain networks – each recruiting visual association cortex in distinct temporal fashions and in tandem with diverse non-visual regions – that collectively recruit 74% of cortex, posterior cerebellum, and amygdala. Despite prominent use of the EFMT to probe negative affect and related psychopathology, EFMT-recruited networks strongly reflected individual differences in cognition but not internalizing/negative affect. Overall, we characterize a richer-than-expected tapestry of concurrent EFMT-recruited brain processes, their diverse activation dynamics, and their relations to task performance and latent mental health phenotypes.
Lifetime fitness benefits of breeding site fidelity and low costs of inbreeding permit inbreeding tolerance in an avian cooperative breeder
Authors: Shah Shailee S. , Diamond Jennifer , Barve Sahas , Cosgrove Elissa J. , Bowman Reed , Fitzpatrick John W. , Chen Nancy
Published: September 2024

Inbreeding, or breeding with close relatives, often decreases individual fitness, but mate choice in many species can increase inbreeding risk. Inbreeding is more likely in species with limited dispersal, such as cooperative breeders where non-parental individuals—often offspring from previous broods—provide parental care and frequently breed close to home. We leverage 32 years of data from a population of Florida Scrub-Jays (Aphelocoma coerulescens), an avian cooperative breeder, to investigate whether mate choice, and its lifetime fitness outcomes, affects inbreeding tolerance. We find that both sexes show a stronger preference for geographically closer rather than less related mates. While female-biased dispersal mitigates inbreeding risk when pairing for the first time, limited movement away from the breeding territory by both sexes for later pairings (following mate death or divorce) results in higher relatedness between mates than expected under random mating. Males paired with close relatives and females that move longer distances experience equivalently reduced lifetime reproductive success. Fitness benefits of breeding site fidelity and relatively low fitness costs of inbreeding thus permit inbreeding tolerance in Florida Scrub-Jays. Understanding how and why mate choice contributes to inbreeding is crucial for informed conservation action for endangered species like the Florida Scrub-Jay.
Histone deacetylase 5 in prelimbic prefrontal cortex limits context-associated cocaine seeking
Authors: Barry Sarah M. , Huebschman Jessica , Devries Derek M , McCue Lauren M , Tsvetkov Evgeny , Anderson Ethan M. , Siemsen Benjamin M. , Berto Stefano , Scofield Michael D. , Taniguchi Makoto , Penrod Rachel D. , Cowan Christopher W.
Published: September 2024

Background

Repeated cocaine use produces neuroadaptations that support drug craving and relapse in substance use disorders (SUDs). Powerful associations formed with drug-use environments can promote a return to active drug use in SUD patients, but the molecular mechanisms that control the formation of these prepotent drug-context associations remain unclear.

Methods

In the rat intravenous cocaine self-administration (SA) model, we examined the role and regulation of histone deacetylase 5 (HDAC5) in the prelimbic (PrL) and infralimbic (IL) cortices in context-associated drug seeking. To this end, we employed viral molecular tools, chemogenetics, RNA-sequencing, electrophysiology, and immunohistochemistry.

Results

In the PrL, reduction of endogenous HDAC5 augmented context-associated, but not cue-or drug prime-reinstated cocaine seeking, whereas overexpression of HDAC5 in PrL, but not IL, reduced context-associated cocaine seeking, but it had no effects on sucrose seeking. In contrast, PrL HDAC5 overexpression following acquisition of cocaine SA had no effects on future cocaine seeking. We found that HDAC5 and cocaine SA altered the expression of numerous PrL genes, including many synapse-associated genes. HDAC5 significantly increased inhibitory synaptic transmission onto PrL deep-layer pyramidal neurons, and it reduced the induction of FOS-positive neurons in the cocaine SA environment.

Conclusions

Our findings reveal an essential and selective role for PrL HDAC5 to limit associations formed in cocaine, but not sucrose, SA environments, and that it alters the PrL excitatory/inhibitory balance, possibly through epigenetic regulation of synaptic genes. These results further position HDAC5 as a key factor regulating reward-circuit neuroadaptations that underlie common relapse triggers in SUD.
A Cryptic Prophage Transcription Factor Drives Phenotypic Changes via Host Gene Regulation
Authors: Lally P. , Tierrafría V.H. , Gómez-Romero L. , Stringer A. , Collado-Vides J. , Wade J.T. , Galagan J.E.
Published: September 2024

Cryptic prophages (CPs) are elements of bacterial genomes acquired from bacteriophage that infect the host cell and ultimately become stably integrated within the host genome. While some proteins encoded by CPs can modulate host phenotypes, the potential for Transcription Factors (TFs) encoded by CPs to impact host physiology by regulating host genes has not been thoroughly investigated. In this work, we report hundreds of host genes regulated by DicC, a DNA-binding TF encoded in the Qin prophage ofEsherichia coli. We identified host-encoded regulatory targets of DicC that could be linked to known phenotypes of its induction. We also demonstrate that a DicC-induced growth defect is largely independent of other Qin prophage genes. Our data suggest a greater role for cryptic prophage TFs in controlling bacterial host gene expression than previously appreciated.
Thermal inactivation spectrum of influenza A H5N1 virus in raw milk
Authors: Nooruzzaman Mohammed , Covaleda Lina M. , Britto de Oliveira Pablo Sebastian , Martin Nicole H. , Koebel Katherine , Ivanek Renata , Alcaine Samuel D. , Diel Diego G.
Published: September 2024

The spillover of highly pathogenic avian influenza (HPAI) H5N1 virus to dairy cows and shedding of high amounts of infectious virus in milk raised public health concerns. Here, we evaluated the decay and thermal stability spectrum of HPAI H5N1 virus in raw milk. For the decay studies, HPAI H5N1 positive raw milk was incubated at different temperatures and viral titers and the thermal death time D-values were estimated. We then heat treated HPAI H5N1 virus positive milk following different thermal conditions including pasteurization and thermization conditions. Efficient inactivation of the virus was observed in all tested conditions, except for thermization at 50°C 10 min. Utilizing a submerged coil system with temperature ramp up times that resemble commercial pasteurizers, we showed that the virus was rapidly inactivated by pasteurization and most thermization conditions. These results provide important insights on the food safety measures utilized in the dairy industry.
Modulation of β-Catenin is important to promote WNT expression in macrophages and mitigate intestinal injury
Authors: Chugh Rishi Man , Bhanja Payel , Zitter Ryan , Gunewardena Sumedha , Badkul Rajeev , Saha Subhrajit
Published: September 2024

Macrophages are the major source of WNT ligands. Macrophage-derived WNT is one of the most potent regenerative signals to mitigate intestinal injury. However, regulation of WNT expression in macrophages has not been studied. In the present study, we discovered that activation of canonical β-Catenin suppresses WNT expression in macrophages. Our CHIP-seq and validation study demonstrated the involvement of β-Catenin in the transcriptional regulation of WNT expression. Genetic and pharmacological approaches to de-stabilize/inactivate β-Catenin induce WNT expression in macrophages. Extracellular vesicles (EVs) are a major career of WNT ligands. Transfusion of EVs from pre-conditioned WNT-enriched macrophages demonstrated significant regenerative benefit over native macrophage-derived EVs to mitigate radiation-induced intestinal injury. Transfusion of WNT-enriched EVs also reduces DSS-induced colitis. Our study provides substantial evidence to consider that macrophage-targeted modulation of canonical WNT signaling to induce WNT expression followed by treatment with WNT-enriched EVs can be a lead therapy against intestinal injury..

Activation of β-Catenin suppresses WNT expression in macrophages. Macrophage-targeted pharmacological modulation of canonical WNT signaling followed by adoptive transfer mitigate radiation injury in intestine. EVs from these preconditioned macrophages mitigate chemical or radiation induced intestinal injury.
Distinct Roles for SETα and SETβ in Early Cell Fate Decisions
Authors: Lim Patrick Siang Lin , Meshorer Eran
Published: September 2024

SET, the nuclear proto-oncogene, is primarily expressed as SETα in embryonic stem cells. Upon pluripotency exit, a transcriptional switch driven by alternative promoters causes SETβ to largely replace SETα expression. Functional distinctions between the two isoforms have been difficult to ascertain, partly due to the redundancy between SETα and SETβ in their protein structure and activity. In this study, we use embryonic stem cells (ESCs) with inducible SET isoform-specific expression to investigate the differences between both SET isoforms. Time-course RNA-seq analyses in SET-KO backgrounds as well as isoform-specific ChIP-seq experiments reveal regulatory functions for SETα and SETβ. Despite sharing many binding sites and binding partners, SETα has unique regulatory functions on its target genes, while SETβ downregulates FGF4. As KLF5 specifically regulates SETα, this implicates SET isoform switching at the KLF5/FGF signalling axis during primitive endoderm specification. Together, we propose a model of how distinct roles of SETα and SETβ may regulate cell identity in the early blastocyst.
DivergentPlasmodiumkinases drive MTOC, kinetochore and axoneme organisation in male gametogenesis
Authors: Yanase Ryuji , Zeeshan Mohammad , Ferguson David J. P. , Marcus Robert , Brady Declan , Bottrill Andrew R. , Holder Anthony A. , Guttery David S. , Tewari Rita
Published: September 2024

Sexual development and male gamete formation of the malaria parasite in the mosquito midgut is governed by rapid endomitosis in the activated male gametocyte. This process is highly regulated by protein phosphorylation, specifically by three divergent male-specific protein kinases (PKs): CDPK4, SRPK1 and MAP2. Here, we localise each PK during rapid male gamete formation using live-cell imaging, identify their putative substrates by immunoprecipitation, and determine the morphological consequences of their absence using ultrastructure expansion and transmission electron microscopy. Each PK has a distinct location in either the nuclear or cytoplasmic compartment. Protein interaction studies revealed that CDPK4 and MAP2 interact with key drivers of rapid DNA replication, while SRPK1 is involved in RNA translation. The absence of each PK results in severe defects in either microtubule organising centre (MTOC) organisation, kinetochore segregation or axoneme formation. This study reveals the crucial role of these PKs during endomitosis in formation of the flagellated male gamete and uncovers some of their potential substrates that drive this process.

Summary blurb

This study reveals how Plasmodium kinases regulate MTOC, axoneme and kinetochore organisation in male gametogenesis, providing key insights into potential targets for malaria transmission control.
The expansion and diversification of epigenetic regulatory networks underpins major transitions in the evolution of land plants
Authors: Petroll Romy , Papareddy Ranjith K. , Krela Rafal , Laigle Alice , Riviere Quentin , Bišová Kateřina , Mozgová Iva , Borg Michael
Published: September 2024

Epigenetic silencing is essential for regulating gene expression and cellular diversity in eukaryotes. While DNA and H3K9 methylation silence transposable elements (TEs), H3K27me3 marks deposited by the Polycomb repressive complex 2 (PRC2) silence varying proportions of TEs and genes across different lineages. Despite the major development role epigenetic silencing plays in multicellular eukaryotes, little is known about how epigenetic regulatory networks were shaped over evolutionary time. Here, we analyse epigenomes from diverse species across the green lineage to infer the chronological epigenetic recruitment of genes during land plant evolution. We first reveal the nature of plant heterochromatin in the unicellular chlorophyte microalgaChlorella sorokinianaand identify several genes marked with H3K27me3, highlighting the deep origin of PRC2-regulated genes in the green lineage. By incorporating genomic phylostratigraphy, we show how genes of differing evolutionary age occupy distinct epigenetic states in plants. While young genes tend to be silenced by H3K9 methylation, genes that emerged in land plants are preferentially marked with H3K27me3, some of which form part of a common network of PRC2-repressed genes across distantly-related species. Finally, we analyse the potential recruitment of PRC2 to plant H3K27me3 domains and identify conserved DNA-binding sites of ancient transcription factor (TF) families known to interact with PRC2. Our findings shed light on the conservation and potential origin of epigenetic regulatory networks in the green lineage, while also providing insight into the evolutionary dynamics and molecular triggers that underlie the adaptation and elaboration of epigenetic regulation, laying the groundwork for its future consideration in other eukaryotic lineages.