bluuebunny/crossref_metadata_2025 huggingface dataset:
The polyadenylation landscape afterin vivolong-term potentiation in the rat brain
Authors: Gumińska Natalia , Pauzin Francois P , Kuźniewska Bożena , Miłek Jacek , Wardaszka Patrycja , Krawczyk Paweł S. , Mroczek Seweryn , Jeleń Sebastian , Pagenhart Patrick U. , Bramham Clive R. , Dziembowski Andrzej , Dziembowska Magdalena
Published: June 2024

Local protein synthesis in neurons is vital for synaptic plasticity, yet the regulatory mechanisms, particularly cytoplasmic polyadenylation, are not fully understood. This study employed nanopore sequencing to examine transcriptomic responses in rat hippocampi duringin vivolong-term potentiation (LTP) and in synaptoneurosomes afterin vitrostimulation. Our long-read transcriptomic dataset allows for detailed analysis of mRNA 3′-ends, poly(A) tail lengths, and composition. We observed dynamic shifts in polyadenylation site preference post-LTP induction, with significant poly(A) tail lengthening restricted to transcriptionally induced mRNAs. Poly(A) tails of these genes showed increased non-adenosine abundance. In synaptoneurosomes, chemical stimulation led to shortening of poly(A) tails on preexisting mRNAs, indicating translation-induced deadenylation. Additionally, we discovered a group of neuronal transcripts with poly(A) tails abundant in non-adenosine residues. These tails are semi-templated and derived from extremely adenosine-rich 3′UTRs. This study provides a comprehensive overview of mRNA 3′-end dynamics during LTP, offering insights into post-transcriptional regulation in neuronal activation.
Noise induces intercellular Ca2+signaling waves and the unfolded protein response in the hearing cochlea
Authors: Park Yesai , Li Jiang , Ismail Mohamad Noura , Matthews Ian R. , Santra Peu , Sherr Elliott H. , Chan Dylan K.
Published: June 2024

Exposure to loud noise is a common cause of acquired hearing loss. Disruption of subcellular calcium homeostasis and downstream stress pathways in the endoplasmic reticulum and mitochondria, including the unfolded protein response, have been implicated in the pathophysiology of noise-induced hearing loss. However, studies on the association between calcium homeostasis and stress pathways has been limited due to limited ability to measure calcium dynamics in mature-hearing, noise-exposed mice. We used a genetically encoded calcium indicator mouse model in which GcAMP is expressed specifically in hair cells or supporting cells under control of Myo15Cre or Sox2Cre, respectively. We performed live calcium imaging and UPR gene expression analysis in 8-week-old mice exposed to levels of noise that cause cochlear synaptopathy (98 db SPL) or permanent hearing loss (106 dB SPL). UPR activation occurred immediately after noise exposure and was noise dose-dependent, with the pro-apoptotic pathway upregulated only after 106 dB noise exposure. Spontaneous calcium transients in hair cells and intercellular calcium waves in supporting cells, which are present in neonatal cochleae, were quiescent in mature-hearing cochleae, but re-activated upon noise exposure. 106 dB noise exposure was associated with more persistent and expansive ICS wave activity. These findings demonstrate a strong and dose-dependent association between noise exposure, UPR activation, and changes in calcium homeostasis in hair cells and supporting cells, suggesting that targeting these pathways may be effective to develop treatments for noise-induced hearing loss.
Amygdala Self-Neuromodulation Capacity as a Window for Process-Related Network Recruitment
Authors: Gurevitch Guy , Lubianiker Nitzan , Markovits Taly , Or-Borichev Ayelet , Fine Naomi B. , Fruchtman-Steinbok Tom , Keynan Jacob N. , Friedman Alon , Singer Neomi , Hendler Talma
Published: June 2024

Neurofeedback (NF) has emerged as a promising avenue for demonstrating process-related neuroplasticity, enabling self-regulation of brain function. NF targeting the amygdala has drawn attention for therapeutic potential in psychiatry, by potentially harnessing emotion-regulation processes. However, not all individuals respond equally to NF training, possibly due to varying self-regulation abilities. This underscores the importance of understanding the mechanisms behind successful neuromodulation (i.e. capacity). This study aimed to investigate the establishment and neural correlates of neuromodulation capacity by using data from repeated sessions of Amygdala Electrical Finger Print (EFP)-NF and post-training fMRI-NF session.

Results from 97 psychiatric patients and healthy participants revealed increased amygdala-EFP neuromodulation capacity over training, associated with post-training amygdala fMRI modulation-capacity and improvements in alexithymia. Individual differences in this capacity were associated with pre-training amygdala reactivity and initial neuromodulation success. Additionally, amygdala down-regulation during fMRI-NF co-modulated with other regions such as the posterior-insula and parahippocampal gyrus. This combined modulation better explained EFP-modulation capacity and improvement in alexithymia than the amygdala modulation alone, suggesting the relevance of this broader network to the gained capacity. These findings support a network-based approach for NF and highlight the need to consider individual differences in brain function and modulation capacity to optimize NF interventions.
LRRK2 mediates haloperidol-induced changes in indirect pathway striatal projection neurons
Authors: Chen Chuyu , Masotti Meghan , Shepard Nathaniel , Promes Vanessa , Tombesi Giulia , Arango Daniel , Manzoni Claudia , Greggio Elisa , Hilfiker Sabine , Kozorovitskiy Yevgenia , Parisiadou Loukia
Published: June 2024

Haloperidol is used to manage psychotic symptoms in several neurological disorders through mechanisms that involve antagonism of dopamine D2 receptors that are highly expressed in the striatum. Significant side effects of haloperidol, known as extrapyramidal symptoms, lead to motor deficits similar to those seen in Parkinson’s disease and present a major challenge in clinical settings. The underlying molecular mechanisms responsible for these side effects remain poorly understood. Parkinson’s disease-associated LRRK2 kinase has an important role in striatal physiology and a known link to dopamine D2 receptor signaling. Here, we systematically explore convergent signaling of haloperidol and LRRK2 through pharmacological or genetic inhibition of LRRK2 kinase, as well as knock-in mouse models expressing pathogenic mutant LRRK2 with increased kinase activity. Behavioral assays show that LRRK2 kinase inhibition ameliorates haloperidol-induced motor changes in mice. A combination of electrophysiological and anatomical approaches reveals that LRRK2 kinase inhibition interferes with haloperidol-induced changes, specifically in striatal neurons of the indirect pathway. Proteomic studies and targeted intracellular pathway analyses demonstrate that haloperidol induces a similar pattern of intracellular signaling as increased LRRK2 kinase activity. Our study suggests that LRRK2 kinase plays a key role in striatal dopamine D2 receptor signaling underlying the undesirable motor side effects of haloperidol. This work opens up new therapeutic avenues for dopamine-related disorders, such as psychosis, also furthering our understanding of Parkinson’s disease pathophysiology.

Chen et al. demonstrate that haloperidol mediated changes in the striatal indirect pathway neurons and circuits are linked to Parkinson’s disease associated LRRK2. Inhibiting LRRK2 kinase activity ameliorates the motoric side effects of haloperidol, suggesting a potential approach to alleviating the unwanted side effects of antipsychotics.
A Nanobody Interaction with SARS-CoV-2 Spike Allows the Versatile Targeting of Lentivirus Vectors
Authors: Alfadhli Ayna , Bates Timothy A. , Barklis Robin Lid , Romanaggi CeAnn , Tafesse Fikadu G. , Barklis Eric
Published: June 2024

While investigating methods to target gene delivery vectors to specific cell types, we examined the potential of using a nanobody against the SARS-CoV-2 Spike protein receptor binding domain to direct lentivirus infection of Spike-expressing cells. Using three different approaches, we found that lentiviruses with surface-exposed nanobody domains selectively infect Spike-expressing cells. The targeting is dependent on the fusion function of Spike, and conforms to a model in which nanobody binding to the Spike protein triggers the Spike fusion machinery. The nanobody-Spike interaction also is capable of directing cell-cell fusion, and the selective infection of nanobody-expressing cells by Spike-pseudotyped lentivirus vectors. Significantly, cells infected with SARS-CoV-2 are efficiently and selectively infected by lentivirus vectors pseudotyped with a chimeric nanobody protein. Our results suggest that cells infected by any virus that forms syncytia may be targeted for gene delivery using an appropriate nanobody or virus receptor mimic. Vectors modified in this fashion may prove useful in the delivery of immunomodulators to infected foci to mitigate the effects of viral infections.

IMPORTANCE

We have discovered that lentiviruses decorated on their surfaces with a nanobody against the SARS-CoV-2 Spike protein selectively infect Spike-expressing cells. Infection is dependent on the specificity of the nanobody and the fusion function of the Spike protein, and conforms to a reverse fusion model, in which nanobody binding to Spike triggers the Spike fusion machinery. The nanobody-Spike interaction also can drive cell-cell fusion, and infection of nanobody-expressing cells with viruses carrying the Spike protein. Importantly, cells infected with SARS-CoV-2 are selectively infected with nanobody-decorated lentiviruses. These results suggest that cells infected by any virus that expresses an active receptor-binding fusion protein may be targeted by vectors for delivery of cargoes to mitigate infections.
Molecular and spatial transcriptomic classification of midbrain dopamine neurons and their alterations in a LRRK2G2019Smodel of Parkinson’s disease
Authors: Gaertner Zachary , Oram Cameron , Schneeweis Amanda , Schonfeld Elan , Bolduc Cyril , Chen Chuyu , Dombeck Daniel , Parisiadou Loukia , Poulin Jean-Francois , Awatramani Rajeshwar
Published: June 2024

Several studies have revealed that midbrain dopamine (DA) neurons, even within a single neuroanatomical area, display heterogeneous properties. In parallel, studies using single cell profiling techniques have begun to cluster DA neurons into subtypes based on their molecular signatures. Recent work has shown that molecularly defined DA subtypes within the substantia nigra (SNc) display distinctive anatomic and functional properties, and differential vulnerability in Parkinson’s disease (PD). Based on these provocative results, a granular understanding of these putative subtypes and their alterations in PD models, is imperative. We developed an optimized pipeline for single-nuclear RNA sequencing (snRNA-seq) and generated a high-resolution hierarchically organized map revealing 20 molecularly distinct DA neuron subtypes belonging to three main families. We integrated this data with spatial MERFISH technology to map, with high definition, the location of these subtypes in the mouse midbrain, revealing heterogeneity even within neuroanatomical sub-structures. Finally, we demonstrate that in the preclinical LRRK2G2019Sknock-in mouse model of PD, subtype organization and proportions are preserved. Transcriptional alterations occur in many subtypes including those localized to the ventral tier SNc, where differential expression is observed in synaptic pathways, which might account for previously described DA release deficits in this model. Our work provides an advancement of current taxonomic schemes of the mouse midbrain DA neuron subtypes, a high-resolution view of their spatial locations, and their alterations in a prodromal mouse model of PD.

Teaser: Using snRNASeq and MERFISH we identified midbrain DA subtypes, mapped their spatial location, and identified alterations in a LRRK2 model
Optimizing in vitro spherulation cues in the fungal pathogenCoccidioides
Authors: Homer Christina , Ochoa Elena , Voorhies Mark , Sil Anita
Published: June 2024

Coccidioides spp. are part of a group of thermally dimorphic fungal pathogens, which grow as filamentous cells (hyphae) in the soil and transform to a different morphology upon inhalation into the host. TheCoccidioideshost form, the spherule, is unique and highly under characterized due to both technical and biocontainment challenges. Each spherule arises from an environmental spore (arthroconidium), matures, and develops hundreds of internal endospores, which are released from the spherule upon rupture. Each endospore can then go on to form another spherule in a cycle called spherulation. One of the foremost technical challenges has been reliably growing spherules in culture without the formation of contaminating hyphae, and consistently inducing endospore release from spherules. Here, we present optimization of in vitro spherule growth and endospore release, by closely controlling starting cell density in the culture, using freshly-harvested arthroconidia, and decreasing the concentration of multiple salts in spherulation media. We developed a minimal media to test spherule growth on various carbon and nitrogen sources. We defined a critical role for the dispersant Tamol in both early spherule formation and prevention of the accumulation of a visible film around spherules. Finally, we examined how the conditions under which arthroconidia are generated influence their transcriptome and subsequent development into spherules, demonstrating that this is an important variable to control when designing spherulation experiments. Together, our data reveal multiple strategies to optimize in vitro spherulation growth, enabling characterization of this virulence-relevant morphology.
Antibody response against SARS-CoV-2 spike protein in people with HIV after COVID-19 vaccination
Authors: Munoz-Gomez Maria Jose , Ryan Pablo , Quero-Delgado Marta , Martin-Vicente Maria , Cuevas Guillermo , Valencia Jorge , Jimenez-Gonzalez Eva , Blanca Natalia , Martinez de Gandara Amalia , Redondo Gerardo , Mas Vicente , Vazquez Monica , Torres-Macho Juan , Martinez Isidoro , Resino Salvador
Published: June 2024

Background: People with HIV (PWH) often have a suboptimal response to vaccines, raising concerns about the efficacy of coronavirus disease 2019 (COVID-19) vaccines in this population. We aimed to evaluate the humoral immune response to the B.1 lineage and Omicron variant in PWH following COVID-19 vaccination. Methods: We conducted a prospective study on 19 PWH who received a two-dose series of the COVID-19 mRNA vaccine and a booster six months later. Participants without HIV infection were included as a healthy control (HC) group. The humoral response to the COVID-19 vaccine (anti-SARS-CoV-2 S IgG levels and ability to block ACE2-S interaction) against both the original B.1 lineage and the Omicron variant was measured by immunoassays. Results: The humoral response in PWH was very strong (GMFR >8) after the second dose and strong (GMFR >4) after the booster dose for both the B.1 lineage and the Omicron variant. We found similar humoral responses to the B.1 lineage and Omicron variant between PWH and HC groups after the second and booster doses (q-value >0.05). The COVID-19 vaccine generated a significantly weaker humoral response against the Omicron variant compared to the B.1 lineage in both groups (q-value <0.05). However, this response improved after the booster dose, although the inhibition of ACE2-S interaction remained weaker in PWH. Conclusions: PWH generated a strong humoral response to the COVID-19 vaccine against both the B.1 lineage and the Omicron variant, similar to individuals without HIV infection. However, our data suggest the need for booster doses to improve immunogenicity and update COVID-19 vaccines for new variants like Omicron.
Proteome-wide autoantibody screening and holistic autoantigenomic analysis unveil COVID-19 signature of autoantibody landscape
Authors: Matsuda Kazuki M , Kawase Yoshiaki , Iwadoh Kazuhiro , Kurano Makoto , Yatomi Yutaka , Okamoto Koh , Moriya Kyoji , Kotani Hirohito , Hisamoto Teruyoshi , Kuzumi Ai , Fukasawa Takemichi , Yoshizaki-Ogawa Asako , Kono Masanori , Okamura Tomohisa , Shoda Hirofumi , Fujio Keishi , Yamaguchi Kei , Okumura Taishi , Ono Chihiro , Kobayashi Yuki , Sato Ayaka , Miya Ayako , Goshima Naoki , Uchino Rikako , Murakami Yumi , Matsunaka Hiroshi , Imai Hiroshi , Sato Shinichi , Raymond Rudy , Yoshizaki Ayumi
Published: June 2024

This study presents "aUToAntiBody Comprehensive Database (UT-ABCD)", a proteome-wide catalog of autoantibody profiles in 284 human individuals. The subjects included patients diagnosed with Coronavirus disease 2019 (COVID-19), systemic sclerosis (SSc), systemic lupus erythematosus (SLE), anti-neutrophil cytoplasmic antibody-associated vasculitis (AAV), atopic dermatitis (AD), as well as healthy controls (HC). Our investigation employed proteome-wide autoantibody screening (PWAS) that utilizes 13,350 autoantigens displayed on wet protein arrays, covering approximately 90% of the human transcriptome. Our findings demonstrated significant elevation of autoantibody levels in COVID-19, SSc, and SLE patients. Unique sets of disease-specific autoantibodies were identified, highlighting the role of autoantibodies against proteins associated with cytokine signaling in immune systems and viral infection pathways. Employing machine learning, we distinguished COVID-19 cases with high accuracy based on autoantibody profiles, notably identifying antibodies against proteins encoded by BCORP1 and KAT2A as highly specific to COVID-19. Longitudinal analysis revealed dynamic changes in autoantibody levels throughout the course of COVID-19, independent of disease severity. Our research highlights the effectiveness of integrating PWAS and autoantigenomics in exploring immune responses in COVID-19 and other diseases. It provides a deeper understanding of the autoimmunity landscape in human disorders and introduces a new bioresource for further investigation.
Uncovering social states in healthy and clinical populations using digital phenotyping and Hidden Markov Models
Authors: Leaning Imogen E. , Costanzo Andrea , Jagesar Raj , Reus Lianne M. , Visser Pieter Jelle , Kas Martien J.H. , Beckmann Christian , Ruhé Henricus G. , Marquand Andre F.
Published: June 2024

Brain related disorders are characterised by observable behavioural symptoms. Smartphones can passively collect objective behavioural data, avoiding recall bias. Despite promising clinical utility, analysing smartphone data is challenging as datasets often include a range of missingness-prone temporal features. Hidden Markov Models (HMMs) provide interpretable, lower-dimensional temporal representations of data, allowing missingness. We applied an HMM to an aggregate dataset of smartphone measures designed to assess social functioning in healthy controls (HCs) (n=247), participants with schizophrenia (n=18), Alzheimer’s disease (AD) (n=26) and memory complaints (n=57). We selected a model with socially “active” and “inactive” states, generated hidden state sequences per participant and calculated their “dwell time”, i.e. the percentage of time spent in the socially active state. We identified lower dwell times in AD versus HCs and higher dwell times related to increased social functioning questionnaire scores in HCs, finding the HMM to be a practical method for digital phenotyping analysis.
Assessing the impact of a mandatory calorie labelling policy in out-of-home food outlets in England on consumer behaviour: a natural experimental study
Authors: Essman Michael , Burgoine Thomas , Jones Andrew , Polden Megan , Robinson Eric , Sacks Gary , Sharp Stephen J. , Smith Richard , Vanderlee Lana , White Christine M. , White Martin , Hammond David , Adams Jean
Published: June 2024

Background

Out-of-home (OOH) food tends to be energy-dense and nutrient-poor. In response, England implemented a mandatory calorie labelling policy in the OOH sector. We evaluated changes in consumer behaviours after the policy was implemented in April 2022.

Methods

We employed a natural experimental design to assess pre-post changes in noticing and using nutrition information, and behaviours associated with menu labelling. We compared changes in England to comparator jurisdictions without similar policies. Data included four consecutive years (2019-2022) from the International Food Policy Study; participants were adults aged 18 years or older. Mixed effects logistic regression models assessed pre-post changes in binary outcomes, and mixed effects negative binomial regression assessed changes in frequency of OOH eating.

Results

In England, noticing nutrition information increased from 16.0% (15.6 to 16.4) in 2020 to 19.7% (19.1 to 20.2) in 2021 and to 25.8% (25.5 to 26.1) in 2022. This increase was 4.8 percentage points (95% CI 2.5 to 7.1) higher in England versus the comparator group. Using nutrition information increased in England from 8.0% (7.5% to 8.4%) in 2020 to 11.8% (10.9% to 12.6%) in 2021 and to 13.5% (13.1% to 13.9%) in 2022. There was a 2.7 percentage point (95% CI 2.0 to 3.4) greater increase in England versus the comparator group from 2020 to 2021. Ordering something different was the only behaviour associated with menu labelling that increased after the policy in England: from 12.6% (12.4 to 12.7) in 2020 to 15.2% (14.7 to 15.6) in 2021 and to 17.7% (17.6 to 17.8) in 2022. There was a 2.8 percentage points (95% CI 1.8 to 3.9) greater increase in England versus the comparator group from 2021 to 2022. Frequency of OOH eating did not change after policy implementation.

Conclusions

The introduction of mandatory calorie labelling in England led to increases in self-reported noticing and using, with the key behavioural impact on ordering something different. This suggests that while calorie labelling can enhance awareness, translating this into behaviour change remains limited to shifting orders. Additional strategies may be required to maximize the public health benefits of calorie labelling.
AI-Enhanced Subtyping of Thymic Tumors: Attention-based MIL with Pathology-Specific Feature Extraction
Authors: Kussaibi Haitham
Published: June 2024

Purpose

The precise classification of thymic tumors using whole slide images (WSIs) is essential for accurate diagnosis and treatment. While traditional Convolutional Neural Networks (CNNs) are commonly used for this purpose, emerging models tailored to pathology, such as Phikon and HistoEncoder, present promising alternatives as feature extractors. Additionally, the limited availability of annotated WSIs has driven the development of weakly-supervised classifiers like multiple-instance learning (MIL) models. In this study, we evaluate nine different combinations of extractor-classifier pairs for thymic tumor subtyping, including a novel, self-developed attention-based MIL classifier, AttenMIL.

Methods

The process began with curating a dataset of thymic tumor Whole Slide Images (WSIs) from the TCGA platform. Using the Yottixel method, patches were derived from these WSIs, and features were extracted from the patches using three different pathology-specific models: Phikon, HistoEncoder, and a pathology-fine-tuned ResNet50. The extracted features were then organized into small bags of instances through a chunking technique. Subsequently, three MIL classifiers AttenMIL, TransMIL, and Chowder were trained. Finally, the efficacy and generalizability of nine different combinations of extractor-classifier pairs were evaluated on unseen test images. Confusion matrices for each pair were utilized to provide insights into misclassification patterns and potential error sources.

Results

The Phikon feature extractor consistently delivered the highest classification accuracies, particularly when paired with the AttenMIL and Chowder classifiers, achieving up to 99% accuracy. This combination significantly outperformed other feature extractor-classifier pairs. Confusion matrices revealed that the AB and B3 subtypes were the most commonly confused classes across the different models.

Conclusions

The study demonstrates the potential of domain-specific feature extractors like Phikon, when coupled with robust MIL classifiers such as the novel AttenMIL and Chowder, in enhancing the accuracy and reliability of thymic tumor classification. The chunking-based augmentation method proved effective for thymic tumors, which are relatively homogeneous, but its applicability to heterogeneous tumors remains to be explored. Future research should address class imbalances and improve generalizability to different datasets.

Statements and Declarations

Competing Interests

The author has declared no competing interest.

No funding was received for conducting this study.

Declaration of generative AI and AI-assisted technologies in the writing process

While preparing this work, the author used ChatGPT to improve language and readability. After using this tool/service, the author reviewed and edited the content as needed and took full responsibility for the publication’s content.
Pathogenic diversification of the gut commensalProvidencia alcalifaciensvia acquisition of a second type III secretion system
Authors: Klein Jessica A. , Predeus Alexander V. , Greissl Aimee R. , Clark-Herrera Mattie M. , Cruz Eddy , Cundiff Jennifer A. , Haeberle Amanda L. , Howell Maya , Lele Aaditi , Robinson Donna J. , Westerman Trina L. , Wrande Marie , Wright Sarah J. , Green Nicole M. , Vallance Bruce A. , McClelland Michael , Mejia Andres , Goodman Alan G. , Elfenbein Johanna R. , Knodler Leigh A.
Published: June 2024

Providencia alcalifaciensis a Gram-negative bacterium found in a wide variety of water and land environments and organisms. It has been isolated as part of the gut microbiome of animals and insects, as well as from stool samples of patients with diarrhea. SpecificP. alcalifaciensstrains encode gene homologs of virulence factors found in other pathogenic members of the same Enterobacterales order, such asSalmonella entericaserovar Typhimurium andShigella flexneri.Whether these genes are also pathogenic determinants inP. alcalifaciensis not known. Here we have usedP. alcalifaciens205/92, a clinical isolate, within vitroandin vivoinfection models to investigateP. alcalifaciens-host interactions at the cellular level. Our particular focus was the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS1bis widespread inProvidenciaspp. and encoded on the chromosome. T3SS1ais encoded on a large plasmid that is present in a subset ofP. alcalifaciensstrains, which are primarily isolates from diarrheal patients. Using a combination of electron and fluorescence microscopy and gentamicin protection assays we show thatP. alcalifaciens205/92 is internalized into eukaryotic cells, rapidly lyses its internalization vacuole and proliferates in the cytosol. This triggers caspase-4 dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS1ain entry, vacuole lysis and cytosolic proliferation is host-cell type specific, playing a more prominent role in human intestinal epithelial cells as compared to macrophages. In a bovine ligated intestinal loop model,P. alcalifacienscolonizes the intestinal mucosa, inducing mild epithelial damage with negligible fluid accumulation. No overt role for T3SS1aor T3SS1bwas seen in the calf infection model. However, T3SS1bwas required for the rapid killing ofDrosophila melanogaster. We propose that the acquisition of two T3SS by horizontal gene transfer has allowedP. alcalifaciensto diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.
CLCC1 Governs Bilayer Equilibration at the Endoplasmic Reticulum to Maintain Cellular and Systemic Lipid Homeostasis
Authors: Wu Lingzhi , Wang Jianqin , Wang Yawei , Yang Junhan , Yao Yuanhang , Huang Dong , Hu Yating , Xu Xinxuan , Wang Renqian , Du Wenjing , Shi Yiting , Li Quan , Liu Lu , Zhu Yuangang , Wang Xiao , Guo Qiang , Xu Li , Li Peng , Chen Xiao-Wei
Published: June 2024

The intricate orchestration of lipid production, storage, and mobilization is vital for cellular and systemic homeostasis1,2. Dysfunctional plasma lipid control represents the major risk factor for cardio-metabolic diseases, the leading cause of human mortality3,4. Within the cellular landscape, the endoplasmic reticulum (ER) is the central hub of lipid synthesis and secretion, particularly in metabolically active hepatocytes in the liver or enterocytes in the gut5,6. Initially assembled in the ER lumen, lipid-ferrying lipoproteins necessitate the cross-membrane transfer of both neutral and phospho-lipids onto the lumenal apolipoprotein B (APOB), in a poorly-defined process7–10. Here we show that trans-bilayer equilibration of phospholipids, regulated by the ER protein CLCC1, determines lipid partition across the ER membrane and consequently systemic lipid homeostasis. CLCC1 partners with the phospholipid scramblase TMEM41B11,12to recognize imbalanced bilayers and promote lipid scrambling, thereby licensing lipoprotein biogenesis and the subsequent bulk lipid transport. Strikingly, loss of CLCC1 or TMEM41B leads to the emergence of giant lumenal lipid droplets enclosed by extensively imbalanced ER bilayers, and consequently drastically accelerated pathogenesis of metabolic-dysfunction-associated liver steatohepatitis (MASH). The above results establish phospholipid scrambling at the ER as the lynchpin to maintain a dynamic equilibrium. Considering the requirement of trans-bilayer phospholipid equilibration in numerous biological processes, ranging from catabolic autophagy to viral infection13–16, our study may enable further elucidation of a previously under-appreciated homeostatic control mechanism intrinsic to the ER function in lipid biogenesis and distribution.
Lower motor performance is linked with poor sleep quality, depressive symptoms, and grey matter volume alterations
Authors: Küppers Vincent , Bi Hanwen , Nicolaisen-Sobesky Eliana , Hoffstaedter Felix , Yeo B.T. Thomas , Drzezga Alexander , Eickhoff Simon B. , Tahmasian Masoud
Published: June 2024

Motor performance (MP) is essential for functional independence and well-being, particularly in later life. However, the relationship between behavioural aspects such as sleep quality and depressive symptoms, which contribute to MP, and the underlying structural brain substrates of their interplay remains unclear. This study used three population-based cohorts of younger and older adults (n=1,950) from the Human Connectome Project-Young Adult (HCP-YA), HCP-Aging (HCP-A), and enhanced Nathan Kline Institute-Rockland sample (eNKI-RS). Several canonical correlation analyses were computed within a machine learning framework to assess the associations between each of the three domains (sleep quality, depressive symptoms, grey matter volume (GMV)) and MP. The HCP-YA analyses showed progressively stronger associations between MP and each domain: depressive symptoms (unexpectedly positive, r=0.13, SD=0.06), sleep quality (r=0.17, SD=0.05), and GMV (r=0.19, SD=0.06). Combining sleep and depressive symptoms significantly improved the canonical correlations (r=0.25, SD=0.05), while the addition of GMV exhibited no further increase (r=0.23, SD=0.06). In young adults, better sleep quality, mild depressive symptoms, and GMV of several brain regions were associated with better MP. This was conceptually replicated in young adults from the eNKI-RS cohort. In HCP-Aging, better sleep quality, fewer depressive symptoms, and increased GMV were associated with MP. Robust multivariate associations were observed between sleep quality, depressive symptoms and GMV with MP, as well as age-related variations in these factors. Future studies should further explore these associations and consider interventions targeting sleep and mental health to test the potential effects on MP across the lifespan.
A Laboratory-Adapted and a Clinical Isolate of Dengue Virus Serotype 4 Differently Impact Aedes aegypti Life-History Traits Relevant to Vectorial Capacity
Authors: Maraschin Mariana , Novak Diego , Klein Junior Valdorion Jose , Granella Lucilene W , Hubner Luiza J , Medeiros Athina R , Graf Tiago , Toledo-Silva Guilherme , Mansur Daniel S , Oliveira Jose Henrique M
Published: June 2024

Dengue virus cases are on the rise globally, and strategies to reduce new infections by controlling its primary vector, the mosquito Aedes aegypti, represent a promising biotechnological approach. However, the interaction between virus serotypes and genotypes with Aedes aegypti is poorly characterized at the molecular level, as well as in terms of life-history traits related to vector capacity and mosquito disease tolerance. Here, we infected Aedes aegypti with two philogenetically distant strains of Dengue virus serotype 4 genotype II: a laboratory-adapted strain, DENV4 - TVP/360, and a recent clinical strain isolated from southern Brazil, DENV4 - LRV 13/422. These strains, which exhibit 26 amino acid differences in their sequences, have been shown in to produce distinct immune phenotypes in vertebrate cells. Here, we assessed various life-history traits of Aedes aegypti, including mortality, fecundity, fertility, and induced flight capacity, as well as vector competence-related parameters such as infection intensity and prevalence, following exposure to different viral concentrations. We found that each viral strain differentially affected mosquito traits. While neither strain significantly reduced mosquito lifespan, Aedes aegypti infection prevalence was influenced by the initial dose of DENV4 - TVP/360. This laboratory-adapted strain also enhanced mosquito induced-flight capacity at early (24 hours post-infection - DPI) and late (21 DPI) time points. On the other hand, the recent clinical isolate, DENV4 - LRV 13/422, specifically reduced Aedes aegypti fertility. A better understanding of how different arbovirus strains influence mosquito life-history traits connected to disease spread will be critical in public health efforts to mitigate arbovirus outbreaks that are focused on the mosquito vector.
Extreme diversity of phage amplification rates and phage-antibiotic interactions revealed by PHORCE
Authors: Mulla Yuval , Müller Janina , Trimcev Denny , Bollenbach Tobias
Published: June 2024

Growth rate plays a fundamental role in microbiology and serves as an important proxy for fitness in evolution. While high-throughput measurements of bacterial growth rates are easily performed in any microbiology lab, similar methods are lacking for bacteriophages. This gap hinders systematic comparisons of important phage phenotypes, such as their amplification rate in bacterial populations and their bactericidal effect, across different phages and environmental conditions. Here, we show that the amplification rate of lytic phages can be quantified by analyzing bacterial population growth and collapse dynamics under phage predation using a parsimonious mathematical model – an approach termed PHORCE (Phage-Host Observation for Rate estimation from Collapse Events). We found that the resulting phage amplification rate captures the bactericidal effect independent of initial phage and bacterial population sizes and across different growth conditions. Using high-throughput PHORCE, we found that the amplification rates ofEscherichia coliphages vary widely by more than three orders of magnitude. Furthermore, our approach suggests that phage–antibiotic interactions are predominantly determined by the antibiotic, and not by the phage. In particular, the ribosome-inhibiting antibiotic doxycycline generally showed antagonism with phage amplification, whereas the DNA-damaging antibiotic nitrofurantoin was synergistic. This framework provides a means to quantitatively characterize phage phenotypes and may facilitate future high-throughput phage screens for antibacterial applications.
Astrocyte-induced firing in primary afferent axons
Authors: Gaudel Fanny , Giraud Julia , Morquette Philippe , Couillard-Larocque Marc , Verdier Dorly , Kolta Arlette
Published: June 2024

The mesencephalic trigeminal nucleus is unique in that it contains the cell bodies of large-caliber primary afferents that are usually located in the periphery in the dorsal root ganglia or trigeminal ganglia. The activity of these afferents is typically associated with proprioception of the jaw-closing muscles or mechanoreception on the teeth and periodontal ligament. However, like other large-caliber afferents from the body which display ectopic firing in neuropathic pain models, these afferents exhibit increased excitability and ectopic discharges even in a relatively mild muscle pain model. These discharges normally emerge from subthreshold membrane oscillations (SMOs) supported by a persistent sodium current (INaP) which is exquisitely sensitive to extracellular Ca2+-decreases. We have shown in the trigeminal main sensory nucleus that the release of a Ca2+-binding astrocytic protein, S100β, is sufficient to modulate this sodium current. Here, we explore if this astrocyte-dependent mechanism contributes to emergence of this hyperexcitability and aim to localize the cellular site where ectopic discharge may arise using whole-cell patch-clamp recordings, confocal imaging, and immunohistochemistry methods on mice brain slices. We found that astrocytes, by lowering [Ca2+]eat focal points along the axons of NVmes neurons through S100β, enhance the amplitude of the NaV1.6-dependent SMOs leading to ectopic firing. These findings suggest a crucial role for astrocytes in excitability regulation and raise questions about this neuron-astrocyte interaction as a key contributor to hyperexcitability in several pathologies.
Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria
Authors: Zhang Pengfan , Roque Breanna , Romero Pedro , Shapiro Nicole , Eloe-Fadrosh Emiley , Kebreab Ermias , Diamond Spencer , Hess Matthias
Published: June 2024

Macroalgae belonging to the genus Asparagopsis have been shown to reduce the production of methane (CH4) during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the microbial community in the rumen responds to Asparagopsis supplementation, and how changes in the rumen microbiome may contribute to shifts in rumen function and ultimately the hosts phenotype. In this study, we generated and analyzed metagenomic and metatranscriptomic data from the microbiome associated with rumen fluid collected from two cohorts of lactating dairy cows, one fed a diet supplemented with Asparagopsis armata (treatment) and another fed the same diet without A. armata supplementation (control). The reduction of CH4 emission from animals that received A. armata was coupled to a qualitative decrease in relative archaeal abundance and a significant reduction in the transcription of methanogenesis pathways. Additionally, a significant decrease in the transcription of genes for complex carbon catabolism and a re-organization of the expression profile of carbon catabolic genes at the species level was observed in treated animals. Increased H2 production, a consequence of methanogenesis suppression, was coupled to a significant increase in the transcription of hydrogenases that mediate hydrogenotrophic metabolism in the treatment group. Analysis of metatranscriptome data identified a single uncultured hydrogenotrophic bacterial species (a Duodenibacillus sp.) as the dominant driver of this transcriptional change. Comparative genomic analysis between the Duodenibacillus sp. and other hydrogenotrophic rumen organisms revealed metabolic traits in the Duodenibacillus that may provide a competitive advantage in H2 scavenging. These findings provide an initial understanding of how rumen microbiota respond to a promising CH4 reducing feed additive, and may serve as a model to understand alternative stable rumen microbiome states that produce less methane and increase animal productivity.
The Histidine Kinase NahK Regulates Denitrification and Nitric Oxide Accumulation through RsmA inPseudomonas aeruginosa
Authors: Guercio Danielle , Boon Elizabeth
Published: June 2024

Pseudomonas aeruginosahave a versatile metabolism; they can adapt to many stressors, including limited oxygen and nutrient availability. This versatility is especially important within a biofilm where multiple microenvironments are present. As a facultative anaerobe,P. aeruginosacan survive under anaerobic conditions utilizing denitrification. This process produces nitric oxide (NO) which has been shown to result in cell elongation. However, the molecular mechanism underlying this phenotype is poorly understood. Our laboratory has previously shown that NosP is a NO-sensitive hemoprotein that works with the histidine kinase NahK to regulate biofilm inP. aeruginosa. In this study, we identify NahK as a novel regulator of denitrification under anaerobic conditions. Under anaerobic conditions, deletion ofnahKleads to a reduction of growth coupled with reduced transcriptional expression and activity of the denitrification reductases. Further, during stationary phase under anaerobic conditions, ΔnahKdoes not exhibit cell elongation, which is characteristic ofP. aeruginosa. We determine the loss of cell elongation is due to changes in NO accumulation inΔnahK. We further provide evidence that NahK may regulate denitrification through modification of RsmA activity.

Importance

P. aeruginosais an opportunistic multi-drug resistance pathogen that is associated with hospital acquired infections.P. aeruginosais highly virulent, in part due to its versatile metabolism and ability to form biofilms. Therefore, better understanding of the molecular mechanisms that regulate these processes should lead to new therapeutics to treatP. aeruginosainfections. The histidine kinase NahK has been previously shown to be involved in both NO signaling and quorum sensing through RsmA. The data presented here demonstrate that NahK is responsive to NO produced during denitrification to regulate cell morphology. Understanding NahK’s role in metabolism under anaerobic conditions has larger implications in determining Nahk’s role in a heterogeneous metabolic environment such as a biofilm.
Systematic analysis of protein stability associated with species-specific developmental tempo
Authors: Matsuda Mitsuhiro , Hammarén Henrik M. , Lázaro Jorge , Savitski Mikhail M. , Ebisuya Miki
Published: June 2024

Human embryonic development is generally slower compared with mouse, and one of the model systems for such inter-species differences in developmental tempo is the segmentation clock. The oscillation period of the human segmentation clock, as measured in induced presomitic mesoderm (iPSM) cells, is two times longer than that of mouse. While the core clock gene HES7 is known to show slower protein degradation in human iPSM compared with mouse iPSM, it remains unclear whether the concept of species-specific protein stability is generalizable to other genes. Here we systematically compared the protein degradation rates of approximately 5000 genes between human and mouse iPSM by using dynamic SILAC-based proteomics, demonstrating a pervasive trend of slower protein degradation in human cells. The inter-species difference was observed not only for proteasome-mediated but also for lysosome-mediated degradation. We further investigated the effect of metabolism on the protein stability profile. Treating mouse iPSM cells with a glycolysis inhibitor extended the segmentation clock period, aligning the protein stability profile more closely with that of human cells, though with less effect on lysosome-mediated degradation. These results highlight the universality of slower protein degradation in human development compared with mouse, and suggest metabolism as one of the modulators.
Coral larvae employ nitrogen sequestration mechanisms to stabilize carbon provisioning from algal symbionts under increased temperature
Authors: Huffmyer Ariana S. , Ashey Jill , Strand Emma , Chiles Eric , Su Xiaoyang , Putnam Hollie M.
Published: June 2024

Rising sea surface temperatures are increasingly causing breakdown in the nutritional relationship between corals and algal endosymbionts (Symbiodiniaceae), threatening the basis of coral reef ecosystems and highlighting the critical role of coral reproduction in reef maintenance. The effects of thermal stress on metabolic exchange (i.e., transfer of fixed carbon photosynthates from symbiont to host) during sensitive early life stages, however, remains understudied. We exposed symbioticMontipora capitatacoral larvae in Hawaiʻi to high temperature (+2.5°C for 3 days), assessed rates of photosynthesis and respiration, and used stable isotope tracing (4mM13C sodium bicarbonate; 4.5 h) to quantify metabolite exchange. While larvae did not show any signs of bleaching and did not experience declines in survival and settlement, metabolic depression was significant under high temperature, indicated by a 19% reduction in respiration rates, but with no change in photosynthesis. Larvae exposed to high temperature showed evidence for maintained translocation of a major photosynthate, glucose, from the symbiont, but there was reduced metabolism of glucose through central carbon metabolism (i.e., glycolysis). The larval host invested in nitrogen cycling by increasing ammonium assimilation, urea metabolism, and sequestration of nitrogen into dipeptides, a mechanism that may support the maintenance of glucose translocation under thermal stress. Host nitrogen assimilation via dipeptide synthesis appears to be used for nitrogen limitation to the Symbiodiniaceae, with the outcome of reduced symbiont population growth and retention of fixed carbon, effectively simulating photosynthate translocation to the host. Collectively, our findings indicate that although these larvae are susceptible to metabolic stress under high temperature, they can combat bleaching by diverting energy to nitrogen assimilation to maintain symbiont population density, photosynthesis, and carbon translocation.
Ultracold
LiCr
: A New Pathway to Quantum Gases of Paramagnetic Polar Molecules
Authors: Finelli S. , Ciamei A. , Restivo B. , Schemmer M. , Cosco A. , Inguscio M. , Trenkwalder A. , Zaremba-Kopczyk K. , Gronowski M. , Tomza M. , Zaccanti M.
Published: June 2024

Quantum gases of doubly polar molecules represent appealing frameworks for a variety of cross-disciplinary applications, encompassing quantum simulation and computation, controlled quantum chemistry, and precision measurements. Through a joint experimental and theoretical study, here we explore a novel class of ultracold paramagnetic polar molecules combining lithium alkali and chromium transition metal elements. Focusing on the specific bosonic isotopologue 6Li53Cr, leveraging on the Fermi statistics of the parent atomic mixture and on suitable Feshbach resonances recently discovered, we produce up to 50×103 ultracold LiCr molecules at peak phase-space densities exceeding 0.1, prepared within the least bound rotationless level of the LiCr electronic ground state X6Σ+. By also developing new probing methods, we thoroughly characterize the molecular gas, demonstrating the paramagnetic nature of LiCr dimers and the precise control of their quantum state. We investigate their stability against inelastic processes and identify a parameter region where pure LiCr samples exhibit lifetimes exceeding 0.2 s. Parallel to this, we employ state-of-the-art quantum chemical calculations to accurately predict the properties of LiCr ground and excited electronic states. This model, able to reproduce the experimental Li-Cr high-spin, scattering length, allows us to identify both efficient paths to coherently transfer weakly bound LiCr dimers to their absolute ground state, and suitable transitions for their subsequent optical manipulation. Our studies establish Li-Cr as a prime candidate to realize ultracold gases of doubly polar molecules with significant electric (3.3 D) and magnetic (5μB) dipole moments.

Published by the American Physical Society
2024