bluuebunny/crossref_metadata_2025 huggingface dataset:
4D Single-Particle Tracking with Asynchronous Read-Out SPAD-Array Detector
Authors: Bucci Andrea , Tortarolo Giorgio , Held Marcus Oliver , Bega Luca , Perego Eleonora , Castagnetti Francesco , Bozzoni Irene , Slenders Eli , Vicidomini Giuseppe
Published: August 2023

Single-particle tracking (SPT) techniques are essential for investigating the com-plex functions and interactions of individual, specifically labelled particles in biological environments. Many SPT techniques exist, each optimised towards a different balance between spatiotemporal resolution and range, technical com-plexity, and information content. This bargain is exemplified by the contrast between wide-field camera-based and real-time SPT approaches, with the latter being generally more advanced but at the cost of high complexity. Further-more, the fluorescence lifetime, a powerful tool for investigating the particle’s interactions and nano-environment, has yet to be measured consistently.

To overcome these limitations, we propose a novel real-time three-dimensional SPT technique based on a hybrid approach. In our implementation, we equip a confocal laser-scanning microscope with an asynchronous read-out single-photon avalanche diode (SPAD) array detector and few other optics. Each sensitive detector element acts as a confocal pinhole, and the recorded intensity distribu-tion reflects the particle’s position in three dimensions relative to the excitation volume. This localization is used in a real-time feedback system to keep the par-ticle in the centre of the excitation volume. Importantly, as each pixel is an independent single-photon detector, SPT is combined with fluorescence lifetime measurement.

Our system achieves a localization precision of up to 30 nm with 100 photons and microsecond time resolution, while also performing fluorescence lifetime mea-surements. First, we validated the technique by tracking fluorescent particles in artificial environments. Secondly, as further validation, we investigated the move-ment of lysosomes in living SK-N-BE cells and measured the fluorescence lifetime of the GFP marker expressed on a membrane protein. We observed an unprece-dented correlation between the changes in fluorescence lifetime and the motion state of the lysosomes.

Thanks to its simplicity and the great momentum of confocal microscopy based on SPAD array detector, we expect that this implementation will open to many information-rich correlative imaging and tracking studies.
SNAP-25, but not SNAP-23, is essential for photoreceptor function and survival in mice
Authors: Huang Mengjia , Chow Chun Hin , Gurdita Akshay , Harada Hidekiyo , Pham Truong Victor Q. B. , Eide Sarah , Sun Hong-Shuo , Feng Zhong-Ping , Monnier Philippe P. , Wallace Valerie A. , Sugita Shuzo
Published: August 2023

Vesicular transport plays critical roles in photopigment delivery at photoreceptor outer segments and glutamate exocytosis at photoreceptor synapses. Previous studies into the role of photoreceptor SNAP proteins are limited in their characterizations into only gene/protein expression and do not delve further into their functional role. Here, we examine the expression and localization of SNAP-23 and SNAP-25 mRNA and protein. Using SNAP-23 and SNAP-25 conditional knockout mice, we further evaluated the morphological and functional consequences that the absence of these proteins has on vision. Although we found that the ubiquitously expressed SNAP-23 showed weak mRNA expression in photoreceptors, removal of SNAP-23 did not result in any observable phenotype. We found that neuronal SNAP-25 is developmentally regulated and SNAP-25 mRNA undergoes mRNA trafficking to the photoreceptor inner segments coinciding with the development of photoreceptor outer segments. Removal of SNAP-25 in photoreceptor cells led to changes in both outer segment protein trafficking and synaptic integrity, resulting in a complete loss of vision in SNAP-25 cKO mice. Our results conclude that SNAP-25, but not SNAP-23, is the essential isoform for photoreceptor survival and function.
Differential cross-reactivity to the influenza B virus haemagglutinin underpins lineage-specific susceptibility between birth cohorts
Authors: Edler Peta , Schwab Lara S.U. , Aban Malet , Wille Michelle , Spirason Natalie , Deng Yi-Mo , Carlock Michael A. , Ross Ted M. , Juno Jennifer A. , Rockman Steve , Wheatley Adam K. , Kent Stephen J. , Barr Ian G. , Price David J. , Koutsakos Marios
Published: August 2023

Influenza exposures early in life are believed to shape future susceptibility to influenza infections by imprinting immunological biases that engender differential cross-reactivity to future influenza viruses, but direct serological evidence linked to susceptibility is limited. We analysed hemagglutination-inhibition titres in 1451 cross-sectional samples collected between 1992-2020, from individuals born between 1917-2008, against influenza B virus (IBV) isolates from 1940-2021, including ‘future’ isolates that circulated after sample collection. We demonstrate that immunological biases are conferred by early life IBV infection and result in lineage-specific cross-reactivity of a birth cohort towards future IBV isolates. This translates into differential estimates of susceptibility between birth cohorts towards the two IBV antigenic lineages, explaining lineage-specific age distributions of observed medically attended IBV infections. Our data bridge a critical gap between early life exposure, cross-reactivity, and influenza epidemiology and identify a plausible model to further dissect the interplay between host immunity, viral evolution and epidemiology.
Towards a more accurate quasi-static approximation of the electric potential for neurostimulation with kilohertz-frequency sources
Authors: Caussade Thomas , Paduro Esteban , Courdurier Matias , Cerpa Eduardo , Grill Warren M , Medina Leonel E
Published: August 2023

Objective: Our goal was to determine the conditions for which a more precise calculation of the electric potential than the quasi-static approximation may be needed in models of electrical neurostimulation, particularly for signals with kilohertz-frequency components. Approach: We conducted a comprehensive quantitative study of the differences in nerve fiber activation and conduction block when using the quasi-static and Helmholtz approximations for the electric potential in a model of electrical neurostimulation. Main results: We first show that the potentials generated by sources of unbalanced pulses exhibit different transients as compared to those of energy-balanced pulses, and this is disregarded by the quasi-static assumption. Secondly, the relative errors for current-distance curves were below 3%, while for strength-duration curves the variations ranged between 1-17%, but could be improved to less than 3% across the range of pulse duration by providing a corrected quasi-static conductivity. Third, we extended our analysis to trains of pulses and reported a "congruence area" below 700 Hz, where the fidelity of fiber responses is maximal for supra-threshold stimulation. Further examination of waveforms and polarities revealed similar fidelities in the congruence area, but significant differences were observed beyond this area. However, the spike-train distance revealed differences in activation patterns when comparing the response generated by each model. Finally, in simulations of conduction-block, we found that block thresholds exhibited errors above 20% for repetition rates above 10 kHz. Yet, employing a corrected value of the conductivity improved the agreement between models, with errors no greater than 8%. Significance: Our results emphasize that the quasi-static approximation cannot be naively extended to electrical stimulation with high-frequency components, and notable differences can be observed in activation patterns. As well, we introduce a methodology to obtain more precise model responses using the quasi-static approach, which can be a valuable resource in computational neuroengineering.
Von Willebrand Factor Synergizes with Tumor-Derived Extracellular Vesicles to Promote Gastric Cancer Metastasis
Authors: Wang Chen-yu , Wang Min , Cai Wei , Zhao Chan-yuan , Zhou Quan , Zhang Xiao-yu , Wang Feng-xia , Zhang Chen-li , Dang Yun , Yang Ai-jun , Dong Jing-fei , Li Min
Published: August 2023

Cells of gastric cancer invade local tissue extensively and also metastasize through the circulation to remote organs. Patients with metastasized gastric cancer have poor outcomes. Cancer cells are known to release extracellular vesicles (EVs) that contribute to cancer progression, but how cancer cell-derived EVs promote cancer growth and metastasis remains poorly understood. We have recently reported that levels of circulating gastric cancer cell-derived EVs (gcEVs) and the adhesive ligand von Willebrand factor (VWF) are associated with cancer metastasis and poor prognosis of patients, but the underlying mechanism of this gcEV-VWF interaction was not known. Here we report results from a study designed to investigate the synergistic action of VWF and gcEVs in vitro and in mouse models. We showed that VWF in cancer-bearing mice was hyperadhesive and became microvesicle-bound. EV-bound VWF mediated the adhesion of gcEVs to the endothelium to disrupt endothelial integrity and facilitate the transendothelial migration of cancer cells and pulmonary metastasis. Reducing VWF adhesive activity by the metalloprotease ADAMTS-13 or promoting gcEV clearance by the scavenging factor lactadherin prevented pulmonary metastasis in mice. These results highlight the synergistic action of gcEVs and VWF in promoting gastric cancer metastasis and identifying new targets for its prevention.

Key point: Author contributions

Hyperadhesive VWF becomes microvesicle-bound to induce endothelial leakage and promote the pulmonary metastasis of gastric cancer in mice.

Reducing VWF activity by ADAMTS-13 and accelerating microvesicle clearance by lactadherin reduces pulmonary metastasis of gastric cancer.
Identification of a subpopulation of highly adherent endothelial cells for seeding synthetic vascular grafts
Authors: Wolfe Jayne T. , Chen Vaya , Chen Yiliang , Tefft Brandon J.
Published: August 2023

Objective

There is an unmet clinical need for a bypass graft that can be used as an alternative to an autologous vessel graft for the treatment of severe coronary artery disease. Small-diameter (<6mm) synthetic vascular grafts are not suitable because of unacceptable patency rates. This mainly occurs without an endothelial cell (EC) monolayer to prevent platelet activation, thrombosis, and intimal hyperplasia. While numerous studies have explored methods to improve EC adhesion to biomaterials, there are still no reliable methods to endothelialize small-diameter grafts, as most seeded ECs are lost due to exposure to fluid shear stress (SS) after implantation. The goal of this work is to determine if EC loss is a random process or if it is possible to predict which cells are more likely to remain adherent.

Approach and Results

In initial studies, we sorted ECs using fluid SS and identified a subpopulation of ECs that are more likely to resist detachment. We use RNA-sequencing (RNA-seq) to examine gene expression of adherent ECs compared to the whole population to identify targets for improving adhesion. Fibronectin leucine rich transmembrane protein 2 (FLRT2), which encodes protein FLRT2, emerged as a candidate due to its downregulation in the adherent ECs and known role in cell adhesion. Using fluorescence activated cell sorting (FACS), we sorted ECs based on FLRT2 expression levels and demonstrated that ECs expressing low levels of FLRT2 exhibit greater retention under fluid SS in vitro.

Conclusion

For the first time, we show EC detachment is not an entirely random process and we predicted which ECs were more likely to remain adherent on a vascular graft upon exposure to fluid SS. This provides validation for the concept that we can seed a small-diameter vascular graft only with highly adherent ECs to maintain a stable endothelium and improve graft patency rates.

Non-standard Abbreviations and Acronyms

endothelial cell (EC), shear stress (SS), fibronectin leucine rich transmembrane protein 2 (FLRT2), tissue engineered vascular graft (TEVG), fluorescence activated cell sorting (FACS)
Timing of methamphetamine exposure during adolescence differentially influences parvalbumin and perineuronal net immunoreactivity in the medial prefrontal cortex of female, but not male, rats
Authors: Brinks Amara S. , Carrica Lauren K. , Tagler Dominic J. , Gulley Joshua M. , Juraska Janice M.
Published: August 2023

Adolescence involves significant reorganization within the medial prefrontal cortex (mPFC), including modifications to inhibitory neurotransmission mediated through parvalbumin (PV) interneurons and their surrounding perineuronal nets (PNNs). These developmental changes, which result in increased PV neuron activity in adulthood, may be disrupted by drug use resulting in lasting changes in mPFC function and behavior. Methamphetamine (METH), which is a readily available drug used by some adolescents, increases PV neuron activity and could influence the activity-dependent maturational process of these neurons. In the present study, we used male and female Sprague Dawley rats to test the hypothesis that METH exposure influences PV and PNN expression in a sex- and age-specific manner. Rats were injected daily with saline or 3.0 mg/kg METH from early adolescence (EA; 30-38 days old), late adolescence (LA; 40-48 days old), or young adulthood (60-68 days old). One day following exposure, effects of METH on PV cell and PNN expression were assessed using immunofluorescent labeling within the mPFC. METH exposure did not alter male PV neurons or PNNs. Females exposed in early adolescence or adulthood had more PV expressing neurons while those exposed in later adolescence had fewer, suggesting distinct windows of vulnerability to changes induced by METH exposure. In addition, females exposed to METH had more PNNs and more intense PV neuron staining, further suggesting that METH exposure in adolescence uniquely influences development of inhibitory circuits in the female mPFC. This study indicates that the timing of METH exposure, even within adolescence, influences its neural effects in females.
Neuropsychiatric Disturbances in Mild Cognitive Impairment: A Scientometric Analysis
Authors: Amrapala Arisara , Sabé Michel , Solmi Marco , Maes Michael
Published: August 2023

Behavioral and psychological symptoms of dementia (BPSD) have been extensively studied in dementia than its prodromal stage, known as mild cognitive impairment (MCI). A scientometric study on BPSD in MCI would be valuable in synthesizing the existing body of research and provide insights into the trends, networks, and influencers within this area. We searched for related literature in the Web of Science database and extracted complete text and citation records of each publication. The primary objective was to map the research evolution of BPSD in MCI and highlight dominant research themes. The secondary objective was to identify research network characteristics (authors, journals, countries, and institutions) and abundances. A total of 12,369 studies published between 1980 to 2022 were included in the analysis. We found 51 distinct clusters from the co-cited reference network that were highly credible with significant modularity (Q = 0.856) and silhouette scores (S = 0.932). Five major research domains were identified: symptoms, diagnosis, brain substrates, biochemical pathways, and interventions. Within recent years, the research focus in this area is on gut microbiota, e-health, COVID-19, cognition, and delirium. Collectively, findings from this scientometric analysis can help clarify the scope and direction of future research and clinical practices.
Dietary Practice and its Association with Glycemic Control among Individuals with Type 2 Diabetes Mellitus in Ethiopia: A Multi-Center Cross-Sectional Study
Authors: Kitaw Firegenet Asnake , Megiso Muluken Zeleke , Yesuf Indris Ahmed , Tewodros Bersabel Hilawi , Shaweno Yohannes Shiferaw , Teklu Blen Solomon , Berhanu Mefthe Fikru , Weldesenbet Edengenet Solomon , Leulseged Tigist Workneh
Published: August 2023

Background

Type 2 Diabetes Mellitus (T2DM) is a chronic metabolic disorder that needs a comprehensive management plan. The integral role of nutrition therapy in diabetes management is getting special attention in guidelines though the practice is in a primitive stage, especially in resource limited settings where lifestyle modifications have a large role in the overburdened healthcare system. Understanding the current dietary practice and its effect on disease control in settings where a tertiary level care is provided is a critical step in providing targeted intervention. Therefore, the aim of the study was to assess dietary practice and its association with level of glycemic control among individuals with T2DM who were on follow-up at two large tertiary hospitals in Ethiopia.

Methods

A hospital based cross-sectional study was conducted from January to March 2023 among 314 systematically selected individuals with T2DM who were on follow-up at diabetes clinics of St. Paul’s Hospital Millennium Medical College and Tikur Anbessa Specialized Hospital. Data was collected using a pre-tested structured questionnaire and summarized using frequency and median (interquartile range). To examine the association of dietary practice with level of glycemic control, a binary logistic regression model was run at 5% level of significance where Adjusted Odds Ratio (AOR) and 95% CI for AOR were used to interpret the results.

Results

From the 314 participants, 146 (46.5%) patients had adequate knowledge regarding the recommended dietary practices and only 42 (13.4%) of the individuals practiced a healthy diet. A total of 107 (34.1%, 95% CI=29.0%-39.2%) had optimal glycemic control. Poor dietary practice (AOR=7.93, 95% CI=2.63-23.89, p<0.001), obesity (AOR=2.74, 95% CI=1.05-7.18%, p=0.04), and taking combination oral anti-diabetic drugs (AOR=6.22, 95% CI=3.05-12.69, p<0.001) were significantly associated with suboptimal glycemic control.

Conclusions

Dietary knowledge and practice among individuals with T2DM were very low, as is the level of glycemic control, which are similar to studies conducted years back, indicating a lack of improvement in the desired behavior over time. Poor dietary practice in turn was associated with suboptimal glycemic control. It is important to target interventions that enhance the understanding and application of dietary practice in these individuals.
Immune Response of Transplanted Kidney Tissues Assembled from Organoid Building Blocks
Authors: Borges Thiago J. , Ganchiku Yoshikazu , Aceves Jeffrey O. , van Gaal Ronald , Uzel Sebastien G. M. , Rubins Jonathan E. , Kobayashi Kenichi , Hiratsuka Ken , Tekguc Murat , Rosales Ivy A. , Ribas Guilherme T. , Lima Karina , Gassen Rodrigo B. , Morizane Ryuji , Lewis Jennifer A. , Riella Leonardo V.
Published: August 2023

The increasing scarcity of organs and the significant morbidity linked to dialysis requires the development of engineered kidney tissues from human-induced pluripotent stem cells. To accomplish this, integrative approaches that synergize scalable kidney organoid differentiation, tissue biomanufacturing, and comprehensive assessment of their immune response and host integration are essential. Here, we create engineered human kidney tissues composed of kidney organoid building blocks (OBBs) and transplant them into mice reconstituted with allogeneic human immune cells. We assess their host vascular integration,in vivomaturation, and their ability to trigger human immune responses. Tissue-infiltrating human immune cells are composed of effector T cells and innate cells. This immune infiltration leads to kidney tissue injury characterized by reduced microvasculature, enhanced kidney cell apoptosis, and a unique inflammatory gene signature comparable to kidney organ transplant rejection in humans. Upon treatment with the immunosuppressive agent Rapamycin, the induced immune response is greatly suppressed. Our model serves as a translational platform to study engineered kidney tissue immunogenicity and develop novel therapeutic targets for kidney rejection.
Human TUBA1B short open reading frame product regulates cancer cell growth via importin β
Authors: Tao Yaling , Bai Xuefeng , Zhou Yinjie , Zhao Yue , Yang Liangwei , Zhang Shun , Liu Huina , Huang Xiaochun , Schneider Edoardo , Zampetaki Anna , Margariti Andriana , Giacca Mauro , Arnold James N. , Zeng Lingfang , Cai Ting
Published: August 2023

Understanding cancer biology is crucial for improving treatment strategies. This study identified TUBA1B-sORF1, a short open reading frame product alternatively translated from the human α-tubulin gene (TUBA1B), which has a completely different amino acid sequence from the α-tubulin 1B chain. TUBA1B-sORF1 is highly expressed in cancer cell lines and gastric carcinoma. Both methionine-initiated canonical and leucine-initiated noncanonical translations of TUBA1B-sORF1 coexist in cancer cells, and there is a transition between sORF1 and α-tubulin translations, evidenced by the TUBA1B-sORF1⁺/α-tubulinlow/-subpopulation. Knocking down TUBA1B-sORF1 reduces cancer cell proliferation and tumorigenicity. TUBA1B-sORF1 facilitates protein nuclear translocation, leading to the upregulation of proliferation-promoting genes and downregulation of proliferation-inhibiting genes. Specifically, it forms a complex with importin β and β-catenin, promoting β-catenin nuclear translocation and target gene transcription. These findings reveal that TUBA1B is a polycistronic gene translating at least two entirely different proteins: α-tubulin and TUBA1B-sORF1. The variable translation between them may regulate tumorigenesis, making TUBA1B-sORF1 a promising therapeutic target and diagnostic biomarker for cancer treatment.
Uncovering the Infection Strategy ofPhyllachora maydisduring Maize Colonization: A Comprehensive Analysis
Authors: Caldwell Denise L. , Da Silva Camila R. , McCoy Austin G. , Avila Harryson , Bonkowski John C. , Chilvers Martin I. , Helm Matthew , Telenko Darcy E. , Iyer-Pascuzzi Anjali S.
Published: August 2023

Tar spot, a disease caused by the ascomycete fungal pathogenPhyllachora maydis, is considered one of the most significant yield-limiting diseases of maize (Zea maysL.) within the United States.P. maydismay also be found in association with other fungi, forming a disease complex with characteristic fish eye lesions. Understanding howP. maydiscolonizes maize leaf cells is essential for developing effective disease control strategies. Here, we used histological approaches to elucidate howP. maydisinfects and multiplies within susceptible maize leaves. We collected tar spot-infected maize leaf samples from four different fields in northern Indiana at three different time points during the growing season. Samples were chemically fixed and paraffin-embedded for high-resolution light and scanning electron microscopy. We observed a consistent pattern of disease progression in independent leaf samples collected across different geographical regions. Each stromata contained a central pycnidium that produced asexual spores. Perithecia with sexual spores developed in the stomatal chambers adjacent to the pycnidia, and a cap of spores formed over the stromata.P. maydisreproductive structures formed around but not within the vasculature. In our samples containing fish eye lesions,P. maydisis associated with two additional fungi, one of which is likely a member of theParaphaeospheriagenus; the other is an unknown fungi. Our data provide fundamental insights into how this pathogen colonizes and spreads within maize leaves. This knowledge can inform new approaches to managing tar spot, which could help mitigate the significant economic losses caused by this disease.
Adult sex ratio variation and its sex-specific predictors in shorebirds
Authors: Valdebenito José O. , Torres-Paris Tamara , Navedo Juan G.
Published: August 2023

The proportion of adult males to females in the adult population, the adult sex ratio (ASR), is an important demographic parameter that has implications in sexual selection, ecology and conservation. ASR variation can be multifactorial but specific variables including sex roles – sex differences in courtship, mate competition, social pair-bonds and parental care– and sex-specific mortality have been suggested as important ASR determinants in birds. However, these relationships have not yet been comprehensively tested in specific avian groups. Here, we used phylogenetic comparative methods to study drivers of ASR variation across shorebirds (Charadrii and Scolopaci; n = 205 species), a charismatic bird group characterised by displaying extreme variations in ecology, sex roles and sexual selection traits. We found that ASR variation is associated with most sex role components but not with their sex-specific mortality. Although sex role and life history variables showed no significant sex bias, we found a trend towards reversed size dimorphism and sex role reversal across shorebirds. Sex roles components also showed correlations among each other that were surprisingly strong and in unexpected directions. Our results confirm that sex roles are important drivers of ASR variation and suggest that shorebirds may have alternative means of sex-specific mortality, possibly linked to their ecology.
Inhibitory feedback enables predictive learning of multiple sequences in neural networks
Authors: Saponati Matteo , Vinck Martin
Published: August 2023

Anticipating future events is a key computational task for neuronal networks. Experimental evidence suggests that reliable temporal sequences in neural activity play a functional role in the association and anticipation of events in time. However, how neurons can differentiate and anticipate multiple spike sequences remains largely unknown. We implement a learning rule based on predictive processing, where neurons exclusively fire for the initial, unpredictable inputs in a spiking sequence, leading to an efficient representation with reduced post-synaptic firing. Combining this mechanism with inhibitory feedback leads to sparse firing in the network, enabling neurons to selectively anticipate different sequences in the input. We demonstrate that intermediate levels of inhibition are optimal to decorrelate neuronal activity and to enable the prediction of future inputs. Notably, each sequence is independently encoded in the sparse, anticipatory firing of the network. Overall, our results demonstrate that the interplay of self-supervised predictive learning rules and inhibitory feedback enables fast and efficient classification of different input sequences.
Antibacterial activity ofXenopsylla cheopisattacins againstYersinia pestis
Authors: Mathew Basil , Aoyagi Kari L , Fisher Mark A.
Published: August 2023

Antimicrobial peptide resistance has been proposed to play a major role in the flea-borne transmission ofYersinia pestis. However, the antimicrobial peptide response in fleas and their interaction withY. pestisis largely unknown. Attacins are one of the most abundantly expressed antimicrobial peptides within the first hours afterY. pestisinfection ofXenopsylla cheopis, a major vector of plague. In this study, we report the cloning, expression, and purification of twoX. cheopisattacin peptides and describe their interactions with and antimicrobial activities againstY. pestis. These flea attacins were shown to bind lipopolysaccharides and have potent activity againstY. pestis, however the mechanism of killing does not involve extensive membrane damage. Treatment with attacins rapidly inhibitsY. pestiscolony formation and results in oxidative stress, yet live-cell imaging revealed that bacteria continue to grow and divide for several hours in the presence of attacins before undergoing morphological changes and subsequent lysis. This data provides insights into an early battle between vector and pathogen that may impact transmission of one of the most virulent diseases known to man.
Structural dynamics at cytosolic inter-protomer interfaces control gating of a mammalian TRPM5 channel
Authors: Karuppan Sebastian , Schrag Lynn Goss , Jara-Oseguera Andrés , Zubcevic Lejla
Published: August 2023

The Transient Receptor Potential Melastatin (TRPM) family of tetrameric cation channels is involved in a wide range of biological functions, from sensory perception to cardiac function. The structurally conserved TRPM cytoplasmic domains make up > 70 % of the total protein. To investigate the mechanism by which the TRPM cytoplasmic domains contribute to gating, we employed electrophysiology and cryo-EM to study TRPM5 – a channel that primarily relies on activation via intracellular Ca2+. Here we show that activation of mammalian TRPM5 channels is strongly altered by desensitization. Structures of rat TRPM5 identify a series of conformational transitions triggered by Ca2+binding. These transitions involve formation and dissolution of cytoplasmic inter-protomer interfaces, where the MHR1/2 domain and the rib helix play important roles. This study shows the importance of the cytoplasmic assembly in TRPM5 channel function and sets the stage for future investigations of other members of the TRPM family.
A conserved ion channel function of STING mediates non-canonical autophagy and cell death
Authors: Xun Jinrui , Zhang Zhichao , Lyu Bo , Lu Defen , Yang Haoxiang , Shang Guijun , Tan Jay Xiaojun
Published: August 2023

The cGAS/STING pathway triggers inflammation in response to diverse cellular stresses such as infection, cellular damage, senescence, normal aging, and age-related disease. Besides inflammation, STING also triggers non-canonical autophagy and cell death, the former of which requires the proton pump V-ATPase- mediated LC3 lipidation to single membrane STING vesicles. V-ATPase is known to sense organelle de- acidification in other contexts and recruits the ATG16L1 complex for direct conjugation of LC3/ATG8 to single membranes (CASM). However, it is unclear how STING activates V-ATPase for non-canonical autophagy. Here we report that upon STING activation, the transmembrane domain (TMD) of STING significantly reorganizes and forms an electron-sparse pore in the center. Cellular imaging and in vitro ion flux assays revealed that STING is critical for proton efflux and pH neutralization of Golgi-derived STING vesicles. A chemical ligand of STING, C53, which binds to and blocks the channel of STING strongly inhibited STING-mediated proton flux in vitro and vesicular de-acidification in cells. C53 also abolished STING-dependent LC3 lipidation and cell death. Thus, the ion channel function of STING activates non-canonical autophagy and cell death through vesicle de-acidification.
Evaluating the role of amino acids in type 2 diabetes risk: a Mendelian randomization study
Authors: Mo Jacky Man Yuen , He Baoting , Wong Tommy Hon Ting , Liang Ying , Luo Shan , Lo Kenneth , Louie Jimmy Chun Yu , Au Yeung Shiu Lun
Published: August 2023

Background

Previous observational and Mendelian randomization studies suggested different amino acids associated with type 2 diabetes (T2D). However, these studies may suffer from confounding or the use of invalid instruments, respectively.

Methods

We extracted strong (p< 5×10-8), independent (r2< 0.001) genetic variants associated with nine amino acids (alanine, glutamine, glycine, histidine, phenylalanine, tyrosine, isoleucine, leucine, and valine) from summary statistics of UK Biobank (N ≤ 115,075), with exclusion of potentially pleiotropic variants. We then applied them to T2D summary statistics from DIAMANTE Consortium (without UK Biobank participants) (N = 455,313) and FinnGen study (N = 365,950), and glycemic traits (MAGIC consortium, N ≤ 209,605). Inverse variance weighed (IVW) method was the main analysis, with multiple sensitivity analyses to assess robustness of findings.

Results

Alanine was associated with higher T2D risk, correcting for multiple testing (Odds Ratio (OR) 1.50 per SD; 95% CI 1.16 to 1.95). At nominal significance, isoleucine was associated with higher T2D risk (OR 1.13; 95% CI 1.00 to 1.27) and tyrosine was associated with lower T2D risk (OR 0.89; 95% CI 0.80 to 0.99). Alanine was also associated with lower insulin, higher glycated hemoglobin and glucose whereas isoleucine and leucine were associated with lower insulin. These associations were consistent in most sensitivity analyses.

Conclusion

Alaine likely contributed to higher T2D risk whilst the associations for isoleucine and tyrosine requires further verification. Whether these findings explain health effects of sources of amino acids, such as diet, should be further explored.
Improvement of immune dysregulation and health-related quality of life in individuals with long COVID at 24-months following SARS-CoV-2 infection
Authors: Phetsouphanh Chansavath , Jacka Brendan , Ballouz Sara , Jackson Katherine JL , Wilson Daniel B , Manandhar Bikash , Klemm Vera , Tan Hyon-Xhi , Wheatley Adam , Aggarwal Anupriya , Akerman Anouschka , Milogiannakis Vanessa , Starr Mitchell , Cunningham Phillip , Turville Stuart G , Kent Stephen J , Byrne Anthony , Brew Bruce J , Darley David R , Dore Gregory J , Kelleher Anthony D , Matthews Gail V
Published: August 2023

This study investigated the humoral and cellular immune responses in individuals with long COVID (LC) compared to age and gender matched recovered COVID-19 controls (MC) over 24-months. LC participants showed elevated spike and nucleocapsid IgG levels, higher neutralizing capacity, and increased spike- and nucleocapsid-specific CD4+ T cells, PD-1, and TIM-3 expression on CD4+ and CD8+ T cells at 3- and 8-months, but these differences did not persist at 24-months. Some LC participants had detectable IFN-γ and IFN-β, that was attributed to reinfection and antigen re-exposure. Single-cell RNA sequencing at 24-month timepoint revealed similar immune cell proportions and reconstitution of naïve T and B cell subsets in LC. No significant differences in exhaustion scores or antigen-specific T cell clones were observed. These findings suggest resolution of immune activation in LC and return to comparable immune responses between LC and MC over time. Improvement in self-reported health-related quality of life at 24-months was also evident in the majority of LC (62%). PTX3, CRP levels and platelet count were associated with improvements in health-related quality of life.
Spatiotemporal development of growth and death zones in expanding bacterial colonies driven by emergent nutrient dynamics
Authors: Kannan Harish , Sun Paul , Çağlar Tolga , Yao Pantong , Taylor Brian R. , Sahu Kinshuk , Ge Daotong , Mori Matteo , Warren Mya , Kleinfeld David , Dong JiaJia , Li Bo , Hwa Terence
Published: August 2023

Bacterial colony growth on hard agar is commonplace in microbiology; yet, what occurs inside a growing colony is complex even in the simplest cases. Robust colony expansion kinetics featuring a linear radial growth and a saturating vertical growth indicates a common developmental program which is elucidated here forEscherichia colicells using a combination of modeling and experiments. Radial colony expansion is found to be limited by mechanical factors rather than nutrients as commonly assumed. In contrast, vertical expansion is limited by glucose depletion inside the colony, an effect compounded by reduced growth yield due to anaerobiosis. Carbon starvation in the colony interior results in substantial cell death within 1-2 days, with a distinct death zone that expands with the growing colony. Overall, the development of simple colonies lacking EPS production and differentiation is dictated by an interplay of mechanical constraints and emergent nutrient gradients arising from obligatory metabolic processes.
Chloride intracellular channel (CLIC) proteins function as fusogens
Authors: Manori Bar , Vaknin Alisa , Vaňková Pavla , Nitzan Anat , Zaidel-Bar Ronen , Man Petr , Giladi Moshe , Haitin Yoni
Published: August 2023

Chloride Intracellular Channel (CLIC) family members uniquely transition between soluble and membrane-associated conformations. Despite decades of extensive functional and structural studies, CLICs’ function as ion channels remains debated, rendering our understanding of their physiological role incomplete. Here, we expose a novel function of CLIC5 as a fusogen. We demonstrate that purified CLIC5 directly interacts with the membrane and induces fusion, as reflected by increased liposomal diameter and lipid and content mixing between liposomes. Moreover, we show that this activity is facilitated by acidic pH, a known trigger for CLICs’ transition to a membrane-associated conformation, and that increased exposure of the hydrophobic inter-domain interface is crucial for this process. Finally, mutation of a conserved hydrophobic interfacial residue diminishes the fusogenic activity of CLIC5in vitroand impairs excretory canal extension inC. elegans in vivo. Together, our results unravel the long-sought physiological role of these enigmatic proteins.
Water fluxes contribute to growth patterning in shoot meristems
Authors: Alonso-Serra Juan , Cheddadi Ibrahim , Kiss Annamaria , Cerutti Guillaume , Lionnet Claire , Godin Christophe , Hamant Olivier
Published: August 2023

In multicellular organisms, localized tissue outgrowth creates a new water sink thereby modifying hydraulic patterns at the organ level. These fluxes are often considered passive by-products of development and their patterning and potential contribution to morphogenesis remains largely unexplored. Here, we generated a complete map of cell volumetric growth and deformation across the shoot apex inArabidopsis thaliana. Within the organ-meristem boundary, we found that a subpopulation of cells next to fast-growing cells experiences volumetric shrinkage. To understand this process, we used a vertex-based model integrating mechanics and hydraulics, informed by the measured growth rates. Organ outgrowth simulations revealed the emerging water fluxes and predicted water deficit with volume loss for a few cells at the boundary. Consistently,in planta,a water-soluble dye is preferentially allocated to fast-growing tissues and fails to enter the boundary domain. Analysis of intact meristems further validated our model by revealing cell shrinkage next to fast-growing cells in different contexts of tissue surface curvature and cell deformation. A molecular signature of water deficit at the boundary further confirmed our conclusion. Taken together, we propose a model where the differential sink strength of emerging organs prescribes the hydraulic patterns that define the boundary domain at the shoot apex.
Kinase inhibitor-induced cell-type specific vacuole formation in the absence of canonical ATG5-dependent autophagy
Authors: Jose Susan , Sharma Himanshi , Insan Janki , Sharma Khushboo , Arora Varun , Dhamija Sonam , Eid Nabil , Menon Manoj B.
Published: August 2023

Pyridinyl imidazole class p38 MAPKα/β (MAPK14/MAPK11) inhibitors including SB202190 have been shown to induce a cell-type specific defective autophagy response resulting in micron-scale vacuole formation, autophagy-dependent death, and tumor growth suppressionin vivo.We had earlier shown that this is an off-target effect of SB202190. Here we provide evidence that the cell-type specific vacuole formation is independent of canonical autophagy pathway. While SB202190 seems to interfere with autophagic flux in many cell lines in parallel to vacuolation, autophagy-deficient DU-145 cells and CRISPR/Cas9 gene-edited ATG5 knockout A549 cells also undergo vacuolation upon SB202190 treatment. Late-endosomal GTPase RAB7 colocalizes with these compartments and RAB7 GTP-binding seems to be essential for SB202190-induced vacuolation. RAB7 is a driver of tumor progression and interfering with RAB7-positive endo/lysosomal compartments may enhance cytotoxicity. A screen for modulators of SB202190-induced vacuolation revealed molecules including multi-kinase inhibitor Sorafenib as inhibitor of vacuolation and sorafenib co-treatment enhanced the cytotoxicity of SB202190. Moreover VE-821, an ATR kinase inhibitor was found to phenocopy the cell-type specific vacuolation response of SB202190. To identify the factors determining the cell-type specificity of the vacuolation response induced by SB-compounds and VE-821, we compared the transcriptomics data from vacuole forming and non-vacuole forming cancer cell lines and identified a gene expression signature which may define sensitivity of cancer cells to these small-molecule kinase inhibitors. Further analyses using the small molecule tools and the gene signature discovered here, could reveal novel mechanisms regulating this interesting phenotype relevant to anti-cancer therapy.
ZFP57 is a regulator of postnatal growth and life-long health
Authors: Hanin Geula , Alsulaiti Boshra , Costello Kevin R , Tavares Hugo , Takahashi Nozomi , Mikheeva Liudmila A , Freeman Anjuli Karmi , Patel Shrina , Jenkins Benjamin , Koulman Albert , Ferguson-Smith Anne C
Published: August 2023

Early-life factors, including nutrition, shape long-term health outcomes. Despite the essential role of lactation in maternal nutritional support, the influence of epigenetic factors on lactation and postnatal growth remains poorly understood. Zinc-finger protein 57 (ZFP57), is an epigenetic regulator of genomic imprinting, a process that directs gene expression based on parental origin, playing a vital role in mammalian prenatal growth.

Here, we identify a novel function of ZFP57 in regulating the mammary gland, where it serves as a key modulator of postnatal resource control, independently of imprinted genes. ZFP57 influences multiple aspects of mammary gland function, including ductal branching and cellular homeostasis. Its absence leads to significant differential gene expression, related to alveologenesis, lactogenesis and milk synthesis, associated with delayed lactation and altered milk composition. This results in life-long impacts on offspring including the development of metabolic syndrome.

Cross-fostering reveals intricate dynamics between mother and offspring during lactation. Pups raised by a dam of a different genotype than their birth mother exhibit exacerbated metabolic features in adulthood, providing additional insight into the programming of offspring long-term health by maternal context. This study deepens our understanding of the interplay between epigenetic factors, lactation, and postnatal resource control and identifies ZFP57 as a major regulator of both pre and postnatal resource control in mammals.
Mesoscale functional architecture in medial posterior parietal cortex
Authors: Hira Riichiro , Townsend Leah B. , Smith Ikuko T. , Yu Che-Hang , Stirman Jeffrey N. , Yu Yiyi , Smith Spencer LaVere
Published: August 2023

The posterior parietal cortex (PPC) in mice has various functions including multisensory integration, vision-guided behaviors, working memory, and posture control. However, an integrated understanding of these functions and their cortical localizations in and around the PPC and higher visual areas (HVAs), has not been completely elucidated. Here we simultaneously imaged the activity of thousands of neurons within a 3 mm x 3 mm field-of-view, including eight cortical areas around the PPC, during behavior. Mice performed both a vision-guided task and a choice history-dependent task, and the imaging results revealed distinct, localized, behavior-related functions of two medial PPC areas. Neurons in the anteromedial (AM) HVA responded to both vision and choice information, and thus AM is a locus of association between these channels. By contrast, the anterior (A) HVA stores choice history with rotational dynamics and represents posture. Mesoscale correlation analysis on the intertrial variability of neuronal activity demonstrated that neurons in area A shared fluctuations with S1t (trunk primary somatosensory area), while neurons in AM exhibited diverse, area-dependent interactions. Pairwise interarea interactions among neurons were precisely predicted by the anatomical input correlations, with the exception of some global interactions. Thus, the medial PPC has two distinct modules, areas A and AM, which each have distinctive modes of cortical communication. These medial PPC modules can serve separate higher-order functions: area A for transmission of information including posture, movement, and working memory; and area AM for multisensory and cognitive integration with locally processed signals.
Energy flux couples sulfur isotope fractionation to proteomic and metabolite profiles inDesulfovibrio vulgaris
Authors: Leavitt William D , Waldbauer Jacob , Venceslau Sofia S , Sim Min Sub , Zhang Lichun , Boidi Flavia Jaquelina , Plummer Sydney , Diaz Julia M. , Pereira Ines A.C. , Bradley Alexander S
Published: August 2023

Microbial sulfate reduction is central to the global carbon cycle and the redox evolution of Earths surface. Tracking the activity of sulfate reducing microorganisms over space and time relies on a nuanced understanding of stable sulfur isotope fractionation in the context of the biochemical machinery of the metabolism. Here we link the magnitude of stable sulfur isotopic fractionation to proteomic and metabolite profiles under different cellular energetic regimes. When energy availability is limited, cell specific sulfate respiration rates and net sulfur isotope fractionation inversely co-vary. Beyond net S isotope fractionation values, we also quantified shifts in protein expression, abundances and isotopic composition of intracellular S metabolites, and lipid structures and lipid/water H isotope fractionation values. These coupled approaches reveal which protein abundances shift directly as a function of energy flux, those that vary minimally, and those that may vary independent of energy flux and likely do not contribute to shifts in S-isotope fractionation. By coupling the bulk S-isotope observations with quantitative proteomics, we provide novel constraints for metabolic isotope models. Together, these results lay the foundation for more predictive metabolic fractionation models, alongside interpretations of environmental sulfur and sulfate reducer lipid-H isotope data.
One-year subthalamic recordings in a patient with Parkinson’s disease under adaptive deep brain stimulation
Authors: Caffi Laura , Romito Luigi Michele , Palmisano Chiara , Aloia Vanessa , Arlotti Mattia , Rossi Lorenzo , Marceglia Sara , Priori Alberto , Eleopra Roberto , Levi Vincenzo , Mazzoni Alberto , Isaias Ioannis Ugo
Published: August 2023

We present the clinical data and subthalamic recordings of a patient with Parkinson’s disease treated for one year with adaptive deep brain stimulation (aDBS). This novel stimulation mode, which adjusts the current amplitude linearly with respect to subthalamic beta power, produced a clinical benefit that was superior to the previous conventional stimulation that used constant, predefined parameters (cDBS). Compared with cDBS, the subthalamic beta amplitude was higher with aDBS and displayed larger daily fluctuations. Furthermore, subthalamic beta amplitude decreased during sleeping with respect to waking hours under aDBS. These data suggest a robust neuromodulatory mechanism of aDBS, with a clinical effect that was superior in this patient compared to cDBS. Our results open new perspectives for a restorative brain network effect of aDBS as a more physiologic, bidirectional, brain–computer interface.