bluuebunny/crossref_metadata_2025 huggingface dataset:
High-throughputin vivosynaptic connectivity mapping of neuronal micro-circuits using two-photon holographic optogenetics and compressive sensing
Authors: Chen I-Wen , Chan Chung Yuen , Navarro Phillip , de Sars Vincent , Ronzitti Emiliano , Oweiss Karim , Tanese Dimitrii , Emiliani Valentina
Published: September 2023

Understanding the intricate synaptic connectivity in living neural circuits is crucial for unraveling the relationship between network structure and function, as well as its evolution during development, learning, and recovery from injury. However, current methodologies for identifying connected neuronsin vivosuffer from limitations, particularly with regards to their throughput. In this study, we introduce a groundbreaking framework forin vivoconnectivity mapping that combines two-photon holographic optogenetics for activating single or multiple potential presynaptic neurons, whole-cell recording of postsynaptic responses, and a compressive sensing strategy for efficiently retrieving individual postsynaptic neurons’ responses when multiple potential presynaptic neurons are simultaneously activated. The approach was validated in the layer 2/3 of the visual cortex in anesthetized mice, enabling rapid probing of up to 100 cells in approximately 5 minutes. By identifying tens of synaptic pairs, including their connection strength, kinetics, and spatial distribution, this method showcases its potential to significantly advance circuit reconstruction in large neuronal networks with minimal invasiveness. Moreover, through simultaneous multi-cell stimulation and compressive sensing, we demonstrate up to a three-fold reduction in the number of required measurements to infer connectivity with limited loss in accuracy, thereby enabling high-throughput connectivity mappingin vivo. These results pave the way for a more efficient and rapid investigation of neuronal circuits, leading to deeper insights into brain function and plasticity.
Invariant natural killer T-cell and CD4+T-cell derived IL22 is a regulator of epithelial-to-mesenchymal transition and extracellular matrix remodelling in perianal fistulas
Authors: Constable Laura E , Iqbal Nusrat , Cozzetto Domenico , Csabai Luca , Anandabaskaran Sulak , Korcsmaros Tamas , Hart Ailsa , Tozer Phillip J , Powell Nick
Published: September 2023

Background and aims

Perianal fistulization is a challenging phenotype of Crohn’s disease (CD). Unravelling the cytokine networks and cellular mediators driving tissue injury in perianal CD (pCD) will help inform much needed novel treatment strategies.

Methods

The phenotype of different T-cell subsets, including unconventional lineages, such as γδ T-cells, MAIT and iNKT-cells in fistula tract tissue and blood samples of patients with pCD or cryptoglandular perianal fistulas was determined using multiparameter flow cytometry. Transcriptomic profiling of fistula tract tissue was performed by RNA-sequencing.

Results

CD161+CD4+T-cells and CD161+CD4-CD8-iNKT-cells significantly accumulated in fistula tissue and produced interleukin-(IL)22 and IL13. Transcripts associated with epithelial-to-mesenchymal transition (EMT), extracellular matrix (ECM) remodelling, interferon-gamma, JAK-STAT and lymphocyte signalling were enriched in pCD, as well as inhibition of pathways associated with wound closure. IL22-responsive transcripts were significantly enriched in fistulas and network analysis identified IL22-mediated regulation of EMT, ECM and other inflammatory pathways.

Conclusion

This study provides novel molecular and cellular insights into fistula pathogenesis, identifying IL22 producing lymphocytes as novel immune regulators of EMT and ECM dysregulation in perianal fistulas. Targeting the regulatory networks controlling IL22 producing lymphocytes may offer novel therapeutic strategies in pCD.
Beta bursts question the ruling power for brain-computer interfaces
Authors: Papadopoulos Sotirios , Szul Maciej J , Congedo Marco , Bonaiuto James J , Mattout Jérémie
Published: September 2023

Current efforts to build reliable brain-computer interfaces (BCI) span multiple axes from hardware, to software, to more sophisticated experimental protocols, and personalized approaches. However, despite these abundant efforts, there is still room for significant improvement. We argue that a rather overlooked direction lies in linking BCI protocols with recent advances in fundamental neuroscience. In light of these advances, and particularly the characterization of the burst-like nature of beta frequency band activity and the diversity of beta bursts, we revisit the role of beta activity in “left vs. right hand” motor imagery tasks. Current decoding approaches for such tasks take advantage of the fact that motor imagery generates time-locked changes in induced power in the sensorimotor cortex, and rely on band-pass filtered power changes or covariance matrices which also describe co-varying power changes in signals recorded from different channels. Although little is known about the dynamics of beta burst activity during motor imagery, we hypothesized that beta bursts should be modulated in a way analogous to their activity during performance of real upper limb movements. We show that classification features based on patterns of beta burst modulations yield decoding results that are equivalent to or better than typically used beta power across multiple open electroencephalography datasets, thus providing insights into the specificity of these bio-markers.
Sub-second Dopamine Signals during Risky Decision-Making in Patients with Impulse Control Disorder
Authors: Liebenow Brittany , Wilson Thomas , Maas Benjamin , Aladnani Emily , Moran Rosalyn J. , White Jason , Lohrenz Terry , Haq Ihtsham ul , Siddiqui Mustafa S. , Laxton Adrian W. , Tatter Stephen B. , Montague P. Read , Kishida Kenneth T.
Published: September 2023

Background

Impulse Control Disorder (ICD) in Parkinson’s disease is a behavioral addiction arising secondary to dopaminergic therapies, most often dopamine receptor agonists. Prior research implicates changes in striatal function and heightened dopaminergic activity in the dorsal striatum of patients with ICD. However, this prior work does not possess the temporal resolution required to investigate dopaminergic signaling during real-time progression through various stages of decision-making involving anticipation and feedback.

Methods

We recorded high-frequency (10Hz) measurements of extracellular dopamine in the striatum of patients with (N=3) and without (N=3) a history of ICD secondary to dopamine receptor agonist therapy for Parkinson’s disease symptoms. These measurements were made using carbon fiber microelectrodes during awake DBS neurosurgery and while participants performed a sequential decision-making task involving risky investment decisions and real monetary gains and losses. Per clinical standard-of-care, participants withheld all dopaminergic medications prior to the procedure.

Results

Patients with ICD invested significantly more money than patients without ICD. On each trial, patients with ICD made smaller adjustments to their investment levels compared to patients without ICD. In patients with ICD, dopamine levels rose or fell on sub-second timescales in anticipation of investment outcomes consistent with increased or decreased confidence in a positive outcome, respectively; dopamine levels in patients without ICD were significantly more stable during this phase. After outcome revelation, dopamine levels in patients with ICD rose significantly more than in inpatients without ICD for better-than-expected gains. For worse-than-expected losses, dopamine levels in patients with ICD remained level whereas dopamine levels in patients without ICD fell.

Conclusion

We report significantly increased risky behavior and exacerbated phasic dopamine signaling, on sub-second timescales, anticipating and following the revelation of the outcomes of risky decisions in patients with ICD. Notably, these results were obtained when patients who had demonstrated ICD in the past but were, at the time of surgery, in an off-medication state. Thus, it is unclear whether observed signals reflect an inherent predisposition for ICD that was revealed when dopamine receptor agonists were introduced or whether these observations were caused by the introduction of dopamine receptor agonists and the patients having experienced ICD symptoms in the past. Regardless, future work investigating dopamine’s role in human cognition, behavior, and disease should consider the signals this system generates on sub-second timescales.
Learning to operate an imagined speech Brain-Computer Interface involves the spatial and frequency tuning of neural activity
Authors: Bhadra Kinkini , Giraud Anne Lise , Marchesotti Silvia
Published: September 2023

Brain-Computer Interfaces (BCI) will revolutionize the way people with impaired speech production can communicate. While recent studies confirm the possibility of decoding imagined speech based on pre-recorded intracranial neurophysiological signals, current efforts focus on collecting vast amounts of data to train classifiers, rather than exploring how the individual’s brain adapts to improve BCI control, an important aspect given the known problem of “BCI illiteracy”, the inability of some individuals to operate a BCI. This issue can be investigated by providing real-time feedback to allow users to identify the best control strategy. In this study, we trained 15 healthy participants to operate a simple binary BCI system based on electroencephalography (EEG) signals through syllable imagery for five consecutive days. We explored whether BCI-control improves with training and characterized the underlying neural dynamics, both in terms of EEG power changes and of the neural features contributing to real-time classification. Despite considerable interindividual variability in performance and learning, a significant improvement in BCI control was observed from day 1 to 5. Performance improvement was associated with a global EEG power increase in frontal theta and a focal increase in temporal low-gamma, showing that learning to operate an imagined-speech BCI involves global and local dynamical changes involving low- and high-frequency neural features, respectively. These findings indicate that both machine and human learning must be considered to reach optimal controllability of imagined-speech BCI, and that non-invasive BCI-learning can help predict the individual benefit from an invasive speech BCI and guide both the electrode implantation and decoding strategies.
A brain circuit and neuronal mechanism for decoding and adapting to change in daylength
Authors: Maddaloni G , Chang YJ , Senft RA , Dymecki SM
Published: September 2023

Changes in daylight amount (photoperiod) drive pronounced alterations in physiology and behaviour1,2. Adaptive responses to seasonal photoperiods are vital to all organisms – dysregulation is associated with disease, from affective disorders3to metabolic syndromes4. Circadian rhythm circuitry has been implicated5,6yet little is known about the precise neural and cellular substrates that underlie phase synchronization to photoperiod change. Here we present a previously unknown brain circuit and novel system of axon branch-specific and reversible neurotransmitter deployment that together prove critical for behavioural and sleep adaptation to photoperiod change. We found that the recently defined neuron type called mrEn1-Pet17located in the mouse brainstem Median Raphe Nucleus (MRN) segregates serotonin versus VGLUT3 (here proxy for the neurotransmitter glutamate) to different axonal branches innervating specific brain regions involved in circadian rhythm and sleep/wake timing8,9. We found that whether measured during the light or dark phase of the day this branch-specific neurotransmitter deployment in mrEn1-Pet1neurons was indistinguishable; however, it strikingly reorganizes on photoperiod change. Specifically, axonal boutons but not cell soma show a shift in neurochemical phenotype upon change away from equinox light/dark conditions that reverses upon return to equinox. When we genetically disabled the deployment of VGLUT3 in mrEn1-Pet1neurons, we found that sleep/wake periods and voluntary activity failed to synchronize to the new photoperiod or was significantly delayed. Combining intersectional rabies virus tracing and projection-specific neuronal silencingin vivo, we delineated a Preoptic Area-to-mrEn1Pet1connection responsible for decoding the photoperiodic inputs, driving the neurochemical shift and promoting behavioural synchronization. Our results reveal a previously unrecognized brain circuit along with a novel form of periodic, branch-specific neurotransmitter deployment that together regulate organismal adaptation to photoperiod changes.
Synaptic connectome of theDrosophilacircadian clock
Authors: Reinhard Nils , Fukuda Ayumi , Manoli Giulia , Derksen Emilia , Saito Aika , Möller Gabriel , Sekiguchi Manabu , Rieger Dirk , Helfrich-Förster Charlotte , Yoshii Taishi , Zandawala Meet
Published: September 2023

The circadian clock and its output pathways play a pivotal role in optimizing daily processes. To obtain novel insights into how diverse rhythmic physiology and behaviors are orchestrated, we have generated the first comprehensive connectivity map of an animal circadian clock using theDrosophilaFlyWire brain connectome. Intriguingly, we identified additional dorsal clock neurons, thus showing that theDrosophilacircadian network contains ∼240 instead of 150 neurons. We also revealed extensive contralateral synaptic connectivity within the network and discovered novel indirect light input pathways to the clock neurons. Interestingly, we observed sparse monosynaptic connectivity between clock neurons and down-stream higher-order brain centers and neurosecretory cells known to regulate behavior and physiology. Therefore, we integrated single-cell transcriptomics and receptor mapping to decipher putative paracrine peptidergic signaling by clock neurons. Our analyses identified additional novel neuropeptides expressed in clock neurons and suggest that peptidergic signaling significantly enriches interconnectivity within the clock network.
Dynamic categorization rules alter representations in human visual cortex
Authors: Henderson Margaret M. , Serences John T. , Rungratsameetaweemana Nuttida
Published: September 2023

Everyday perceptual tasks require sensory stimuli to be dynamically encoded and analyzed according to changing behavioral goals. For example, when searching for an apple at the supermarket, one might first find the Granny Smith apples by separating all visible apples into the categories “green” and “non-green”. However, suddenly remembering that your family actually likes Fuji apples would necessitate reconfiguring the boundary to separate “red” from “red-yellow” objects. This flexible processing enables identical sensory stimuli to elicit varied behaviors based on the current task context. While this phenomenon is ubiquitous in nature, little is known about the neural mechanisms that underlie such flexible computation. Traditionally, sensory regions have been viewed as mainly devoted to processing inputs, with limited involvement in adapting to varying task contexts. However, from the standpoint of efficient computation, it is plausible that sensory regions integrate inputs with current task goals, facilitating more effective information relay to higher-level cortical areas. Here we test this possibility by asking human participants to visually categorize novel shape stimuli based on different linear and non-linear boundaries. Using fMRI and multivariate analyses of retinotopically-defined visual areas, we found that shape representations in visual cortex became more distinct across relevant decision boundaries in a context-dependent manner, with the largest changes in discriminability observed for stimuli near the decision boundary. Importantly, these context-driven modulations were associated with improved categorization performance. Together, these findings demonstrate that codes in visual cortex are adaptively modulated to optimize object separability based on currently relevant decision boundaries.
Proteonano™: a novel deep proteomics platform with 1000-plex profiling capacity and picogram sensitivity and its application in diabetic kidney disease
Authors: Zhao Ban , Gao Xuechun , Ouyang Xiehua , Fang Jiakai , Deng Zihao , Wu Hao , Mao Yonghui
Published: September 2023

The development of blood-based multi-biomarker panels for screening diabetic patients, and as an easy-to-access tool for identifying individuals at greatest risk of developing diabetic kidney disease (DKD) and its progression, is essential. However, conventional blood biomarker-based methodologies (e.g. clinical tests and ELISA) are unable to predict DKD progression with high sensitivity and specificity. To overcome these challenges, we developed a deep, untargeted plasma proteome profiling technology (Proteonano™ platform) to identify potential multiple protein biomarkers involved in DKD progression. The Proteonano™ technology is an affinity selective mass spectrometric platform that comprises nanoparticle-based affinity binders (nanobinders) for low abundant protein enrichment, automated workflow for parallel sample preparation, and machine learning empowered bioinformatic software for data analysis.

Using the Proteonano™ platform, we performed untargeted proteomics on 75 subjects (DKD progressors, n = 30; DKD non-progressors, n = 45) and identified an average of 953 ± 80 (AVG ± SD) protein groups, with a wide dynamic range of 8 orders of magnitude (with the lowest concentration down to 3.00 pg/mL). Among these, 38 proteins were differentially expressed between DKD progressors relative to non-progressors, and the predictive power for these proteins were assessed. Further, we performed random forest and LASSO analyses for additional variable selection. Variables selected by these approaches were assessed by Akaike information criterion method followed by ROC analysis, which identified a combination of multiple proteins (including VWF, PTGDS, B2M, BT3A2, and LCAT) that showed excellent predictive power over current methods, with an area under the curve value up to 0.97. Some of these plasma proteins are not previously recognized in the context of DKD progression, suggesting they are novel biomarkers. Our studies pave the way to develop multi-biomarker panels for DKD progression management. This study suggests that the Proteonano™ technology platform reported here can be employed as an established workflow enabling untargeted deep proteomic analysis to identify highly discriminative biomarkers for precise medicine.
Inhibiting Stromal Class I HDACs Curbs Pancreatic Cancer Progression
Authors: Liang Gaoyang , Oh Tae Gyu , Hah Nasun , Tiriac Hervé , Shi Yu , Truitt Morgan L. , Antal Corina E. , Atkins Annette R. , Li Yuwenbin , Fraser Cory , Ng Serina , Pinto Antonio F. M. , Nelson Dylan C. , Estepa Gabriela , Bashi Senada , Banayo Ester , Dai Yang , Liddle Christopher , Yu Ruth T. , Hunter Tony , Engle Dannielle D. , Han Haiyong , Von Hoff Daniel D. , Downes Michael , Evans Ronald M.
Published: September 2023

Oncogenic lesions in pancreatic ductal adenocarcinoma (PDAC) hijack the epigenetic machinery in stromal components to establish a desmoplastic and therapeutic resistant tumor microenvironment (TME). Here we identify Class I histone deacetylases (HDACs) as key epigenetic factors facilitating the induction of pro-desmoplastic and pro-tumorigenic transcriptional programs in pancreatic stromal fibroblasts. Mechanistically, HDAC-mediated changes in chromatin architecture enable the activation of pro-desmoplastic programs directed by serum response factor (SRF) and forkhead box M1 (FOXM1). HDACs also coordinate fibroblast pro-inflammatory programs inducing leukemia inhibitory factor (LIF) expression, supporting paracrine pro-tumorigenic crosstalk. HDAC depletion in cancer-associated fibroblasts (CAFs) and treatment with the HDAC inhibitor entinostat (Ent) in PDAC mouse models reduce stromal activation and curb tumor progression. Notably, HDAC inhibition (HDACi) enriches a lipogenic fibroblast subpopulation, a potential precursor for myofibroblasts in the PDAC stroma. Overall, our study reveals the stromal targeting potential of HDACi, highlighting the utility of this epigenetic modulating approach in PDAC therapeutics.
Evolving alterations of structural organization and functional connectivity in feedforward neural networks after induced P301L tau mutation
Authors: Weir Janelle S. , Hanssen Katrine Sjaastad , Winter-Hjelm Nicolai , Sandvig Axel , Sandvig Ioanna
Published: September 2023

Reciprocal structure–function relationships underlie both healthy and pathological behaviors in complex neural networks. Thus, understanding neuropathology and network dysfunction requires a thorough investigation of the complex interactions between structural and functional network reconfigurations in response to perturbation. Such adaptations are often difficult to studyin vivo. For example, subtle, evolving changes in synaptic connectivity, transmission, and the electrophysiological shift from healthy to pathological states, as for example alterations that may be associated with evolving neurodegenerative disease, such as Alzheimeŕs, are difficult to study in the brain. Engineeredin vitroneural networks are powerful models that enable selective targeting, manipulation, and monitoring of dynamic neural network behavior at the micro- and mesoscale in physiological and pathological conditions. In this study, we engineered feedforward cortical neural networks using two-nodal microfluidic devices with controllable connectivity interfaced with microelectrode arrays (mMEAs). We induced P301L mutated tau protein to the presynaptic node of these networks and monitored network dynamics over three weeks. Induced perturbation resulted in altered structural organization and extensive axonal retraction starting in the perturbed node. Perturbed networks also exhibited functional changes in intranodal activity, which manifested as an overall decline in both firing rate and bursting activity, with a progressive increase in synchrony over time, and decrease in internodal signal propagation between pre- and postsynaptic nodes. These results provide insights into dynamic structural and functional reconfigurations at the micro- and mesoscale as a result of evolving pathology and illustrate the utility of engineered networks as models of network function and dysfunction.
High-resolution double vision of the archetypal protein tyrosine phosphatase
Authors: Sharma Shivani , Mehlman Tamar (Skaist) , Sagabala Reddy Sudheer , Boivin Benoit , Keedy Daniel A.
Published: September 2023

Protein tyrosine phosphatase 1B (PTP1B) plays important roles in cellular homeostasis and is a highly validated therapeutic target for multiple human ailments including diabetes, obesity, and breast cancer. However, much remains to be learned about how conformational changes may convey information through the structure of PTP1B to enable allosteric regulation by ligands or functional responses to mutations. High-resolution X-ray crystallography can offer unique windows into protein conformational ensembles, but comparison of even high-resolution structures is often complicated by differences between datasets including non-isomorphism. Here we present the highest-resolution crystal structure of apo wildtype (WT) PTP1B to date, out of ∼350 total PTP1B structures in the PDB. Our structure is in a crystal form that is rare for PTP1B, with two unique copies of the protein that exhibit distinct patterns of conformational heterogeneity, allowing a controlled comparison of local disorder across the two chains within the same asymmetric unit. We interrogate the conformational differences between these chains in our apo structure, and between several recently reported high-resolution ligand-bound structures. We also examine electron density maps in a high-resolution structure of a recently reported activating double mutant, and discover unmodeled alternate conformations in the mutant structure that coincide with regions of enhanced conformational heterogeneity in our new WT structure. Our results validate the notion that these mutations operate by enhancing local dynamics, and suggest a latent susceptibility to such changes in the WT enzyme. Together, our new data and analysis provide a freshly detailed view of the conformational ensemble of PTP1B, and highlight the utility of high-resolution crystallography for elucidating conformational heterogeneity with potential relevance for function.
Identification of a Druggable Site on GRP78 at the GRP78-SARS-CoV-2 Interface and Compounds to Disrupt that Interface
Authors: Lazou Maria , Hutton Jonathan R. , Chakravarty Arijit , Joseph-McCarthy Diane
Published: September 2023

SARS-CoV-2, the virus that causes COVID-19, led to a global health emergency that claimed the lives of millions. Despite the widespread availability of vaccines, the virus continues to exist in the population in an endemic state which allows for the continued emergence of new variants. Most of the current vaccines target the spike glycoprotein interface of SARS-CoV-2, creating a selection pressure favoring viral immune evasion. Antivirals targeting other molecular interactions of SARS-CoV-2 can help slow viral evolution by providing orthogonal selection pressures on the virus. GRP78 is a host auxiliary factor that mediates binding of the SARS-CoV-2 spike protein to human cellular ACE2, the primary pathway of cell infection. As GRP78 forms a ternary complex with SARS-CoV-2 spike protein and ACE2, disrupting the formation of this complex is expected to hinder viral entry into host cells. Here, we developed a model of the GRP78-spike protein-ACE2 complex. We then used that model together with hot spot mapping of the GRP78 structure to identify the putative binding site for spike protein on GRP78. Next, we performed structure-based virtual screening of known drug/candidate drug libraries to identify binders to GRP78 that are expected to disrupt spike protein binding to the GRP78, and thereby preventing viral entry to the host cell. A subset of these compounds have previously been shown to have some activity against SARS-CoV-2. The identified hits are starting points for the further development of novel SARS-CoV-2 therapeutics, potentially serving as proof-of-concept for GRP78 as a potential drug target for other viruses.
Chronic optogenetic activation of hippocampal pyramidal neurons replicates the proteome footprint of Alzheimer’s disease-like pathology
Authors: Keramidis Iason , Samiotaki Martina , Sansonetti Romain , Alonso Johanna , Papanikolopoulou Katerina , Koninck Yves De
Published: September 2023

Neuronal overexcitability can elicit synaptic changes, leading to neuronal hyperactivity and abnormal neural circuit processing. Such network disruption impairs neuronal function and survival, initiating neurodegeneration and Alzheimer’s disease (AD). Yet, the sequence of synaptic changes resulting from excessive neuronal activity remains elusive. We employed optogenetics to induce sustained neuronal hyperactivity in the hippocampi of wild-type and AD-like 5xFAD mice. Surprisingly, after a month of daily optogenetic stimulation, the proteomic profiles of photoactivated wild-type and 5xFAD mice exhibited remarkable similarity. Proteins involved in translation, protein transport, autophagy, and notably in the AD pathology were upregulated in wild-type mice. Conversely, both glutamatergic and GABAergic synaptic proteins were downregulated. These hippocampal proteomic and signaling alterations in wild-type mice resulted in spatial memory loss and augmented Αβ42 secretion. Collectively, these findings indicate that sustained neuronal hyperactivity alone replicates proteome changes seen in AD-linked mutant mice. Therefore, prolonged neuronal hyperactivity may contribute to synaptic transmission disruption, memory deficits and the neurodegenerative process associated with AD.
Systemic 4-1BB stimulation augments extrafollicular memory B cell formation and recall responses duringPlasmodiuminfection
Authors: Caloba Carolina , Sturtz Alexandria J. , Lyons Taylor A. , John Lijo , Ramachandran Akshaya , Minns Allen M. , Cannon Anthony M. , Whalley Justin P. , Watts Tania H. , Kaplan Mark H. , Lindner Scott E. , Vijay Rahul
Published: September 2023

T-dependent germinal center (GC) output, comprising plasma cells (PC) and memory B cells (MBC), is crucial for the clearance ofPlasmodiuminfection and protection against reinfection. In this study, we examined the effect of an agonistic antibody targeting 4-1BB (CD137), a member of the Tumor Necrosis Factor Receptor Superfamily (TNFRSF), during experimental malaria. Here we show that exogenous 4-1BB stimulation, despite delaying the effector GC response, surprisingly enhanced humoral memory recall and protection from reinfection. Single cell RNA and ATAC sequencing of MBCs from mice that received 4-1BB stimulation revealed distinct populations with transcriptional and epigenetic signatures indicative of superior recall and proliferative potential. Importantly, our results indicate that the effects of 4-1BB stimulation are dependent on IL-9R signaling in B cells but independent of parasite load during primary infection. Our study proposes an immunomodulatory approach to enhance the quality of the MBC pool, providing superior protection during infection and vaccination, particularly in the context of malaria.
Microbial metabolic potential of hydrothermal vent chimneys along the Submarine Ring of Fire
Authors: Murray Laura , Fullerton Heather , Moyer Craig L.
Published: September 2023

Hydrothermal vents host a diverse community of microorganisms that utilize chemical gradients from the venting fluid for their metabolisms. The venting fluid can solidify to form chimney structures that these microbes adhere to and colonize. These chimney structures are found throughout many different locations in the world’s oceans. In this study, comparative metagenomic analyses of microbial communities on five chimney structures from around the Pacific Ocean were elucidated focusing on the core taxa and genes that are characteristic for each of these hydrothermal vent chimneys, as well as highlighting differences among the taxa and genes found at each chimney due to parameters such as physical characteristics, chemistry, and activity of the vents. DNA from the chimneys was sequenced, assembled into contigs, annotated for gene function, and binned into metagenome-assembled genomes, or MAGs. Genes used for carbon, oxygen, sulfur, nitrogen, iron, and arsenic metabolism were found at varying abundances at each of the chimneys, largely from either Gammaproteobacteria or Campylobacteria. Many taxa had an overlap of these metabolic genes, indicating that functional redundancy is critical for life at these hydrothermal vents. A high relative abundance of oxygen metabolism genes coupled with low carbon fixation genes could be used as a unique identifier for inactive chimneys. Genes used for DNA repair, chemotaxis, and transposases were found to be at higher abundances at each of these hydrothermal chimneys allowing for enhanced adaptations to the ever-changing chemical and physical conditions encountered.

IMPORTANCE

The metabolic byproducts of microorganisms that form and reside in hydrothermal vent chimneys facilitate nutrient cycling in both the hydrothermal vent ecosystem and throughout the world’s oceans. Diverse communities of microbes utilize chemicals in the venting fluid to gain energy and biomass. Here, metagenomic and amplicon sequencing was used to identify metabolism genes to better understand the metabolic potential of chimneys. The combination of genes detected in this study sheds light on hydrothermal vent chimneys’ community structure and metabolic potential throughout the Pacific Ocean.
Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases
Authors: da Silva Joana Ferreira , Tou Connor J. , King Emily M. , Eller Madeline L. , Ma Linyuan , Rufino-Ramos David , Kleinstiver Benjamin P.
Published: September 2023

Genome editing technologies that install diverse edits can widely enable genetic studies and new therapeutics. Here we develop click editing, a genome writing platform that couples the advantageous properties of DNA-dependent DNA polymerases with RNA-programmable nickases (e.g. CRISPR-Cas) to permit the installation of a range of edits including substitutions, insertions, and deletions. Click editors (CEs) leverage the “click”-like bioconjugation ability of HUH endonucleases (HUHes) with single stranded DNA substrates to covalently tether “click DNA” (clkDNA) templates encoding user-specifiable edits at targeted genomic loci. Through iterative optimization of the modular components of CEs (DNA polymerase and HUHe orthologs, architectural modifications, etc.) and their clkDNAs (template configurations, repair evading substitutions, etc.), we demonstrate the ability to install precise genome edits with minimal indels and no unwanted byproduct insertions. Since clkDNAs can be ordered as simple DNA oligonucleotides for cents per base, it is possible to screen many different clkDNA parameters rapidly and inexpensively to maximize edit efficiency. Together, click editing is a precise and highly versatile platform for modifying genomes with a simple workflow and broad utility across diverse biological applications.
Notch3 deletion regulates HIV-1 gene expression and systemic inflammation to ameliorate chronic kidney disease
Authors: Thornton Mackenzie , Sommer Nicole , McGonigle Mercedes , Ram Anil Kumar , Yerrathota Sireesha , Ehirim Henrietta , Chaturvedi Aakriti , Phan Johnny Dinh , Chakraborty Anubhav , Chakravarthi Praveen V , Gunewardena Sumedha , Tyagi Mudit , Talreja Jaya , Wang Tao , Singhal Pravin , Tran Pamela V , Fields Timothy A , Ray Patricio E , Dhillon Navneet K , Sharma Madhulika
Published: September 2023

Antiretroviral therapy (ART) has decreased HIV-1 associated morbidity. However, despite ART, immune cells remain latently infected and slowly release viral proteins, leading to chronic inflammation and HIV-1 associated comorbidities. New strategies are needed to target viral proteins and inflammation. We found activation of Notch3 in several renal cells of the HIV-1 mouse model (HIV-Tg26) and in patients with HIV associated Nephropathy. We hypothesized that targeting Notch3 activation constitutes an effective therapy for HIV-related chronic kidney diseases (HIV-CKD). We generated HIV-Tg26 mice with Notch3 knocked out (Tg-N3KO). Compared to HIV-Tg26 mice at 3 months, HIV-Tg-N3KO mice showed a marked reduction in renal injury, skin lesions and mortality rate. Bulk RNA sequencing revealed that N3KO not only reduced renal infiltrating cells but significantly reduced the expression of HIV genes. Moreover, Notch3 activated the HIV-promoter and induction of HIV-1 resulted in increased Notch3 activation indicating a feedback mechanism. Further, bone marrow derived macrophages (BMDMs) from HIV-Tg26 mice showed activation of Notch3 indicating systemic effects. Consistent with that, systemic levels of TNF-α, MCP-1 and other inflammatory chemokines and cytokines were reduced in Tg-N3KO mice. Thus, Notch3 inhibition/deletion has a dual therapeutic effect in HIV-CKD and may extend to other HIV-related pathologies.
Leveraging long-term smartwatch data to inform Parkinson’s disease progression, subtypes, and risk
Authors: Schalkamp Ann-Kathrin , Peall Kathryn J , Harrison Neil A , Escott-Price Valentina , Sandor Cynthia
Published: September 2023

Use of digital sensors to passively collect long-term, longitudinal data offers a step change in our ability to monitor Parkinson’s disease (PD). However, to date the evaluation of long-term digital sensor data has been neglected in favour of evaluating short-term data collected in controlled settings. To address this, we combined longitudinal clinical and biological assessment data from the Parkinson’s Progression Marker Initiative (PPMI) cohort with long-term (mean: 485 days) at-home digital monitoring data collected with the Verily Study Watch. We then derived digital timeseries components leveraging the long-term monitoring of the PPMI. We found three key findings: Firstly, that these digital timeseries components correlated with the rate of progression of motor (r = 0.23, p-value = 8.5×10-3, r = 0.26, p-value = 2.2×10-3) and autonomic symptoms (r = −0.23, p-value = 8.2×10-3), impairments in daily living (r = 0.26, p-value = 2.5×10-3), increase in medication requirements and complications (r = −0.25, p-value = 4.2×10-3), and rate of increase in cerebrospinal fluid (CSF) tau (ptau: r = 0.28, p-value = 2.6×10-3; ttau: r = 0.34, p-value = 1.2×10-4). Second, we derived digitally informed subtypes of PD and found higher similarity with CSF (0.35) and DaTscan (0.35) subtypes than has been found for previously published subtypes (CSF: 0.31±0.01, DaTscan: 0.31±0.02). Finally, we showed that long-term digital monitoring can inform PD risk and sensitively detect individuals with probable prodromal PD. Our findings highlight the wealth of application areas for digital sensors in PD research.
Working Memory Gating in Obesity: Insights from a Case-Control fMRI Study
Authors: Herzog Nadine , Hartmann Hendrik , Janssen Lieneke K. , Waltmann Maria , Deserno Lorenz , Fallon Sean J. , Horstmann Annette
Published: September 2023

Computational models and neurophysiological data propose that a ‘gating mechanism’ coordinates distractor-resistant maintenance and flexible updating of working memory contents: While maintenance of information is mainly implemented in the prefrontal cortex, updating of information is signaled by phasic increases in dopamine in the striatum. Previous literature demonstrates structural and functional alterations in these brain areas, as well as differential dopamine transmission among individuals with obesity, suggesting potential impairments in these processes. To test this hypothesis, we conducted an observational case-control fMRI study, dividing participants into groups with and without obesity based on their BMI. We probed maintenance and updating of working memory contents using a modified delayed match to sample task and investigated the effects of SNPs related to the dopaminergic system. While the task elicited the anticipated brain responses, our findings revealed no evidence for group differences in these two processes, neither at the neural level nor behaviorally. However, depending on Taq1A genotype, which affects dopamine receptor density in the striatum, participants with obesity performed worse on the task. In conclusion, this study does not support the existence of overall obesity-related differences in working memory gating. Instead, we propose that potentially subtle alterations may manifest specifically in individuals with a ’vulnerable’ genotype.
Gastric coagulation and postprandial amino acid absorption of milk is affected by mineral composition: a randomized crossover trial
Authors: van Eijnatten Elise J.M. , Roelofs Julia J.M. , Camps Guido , Huppertz Thom , Lambers Tim T. , Smeets Paul A.M.
Published: September 2023

Background

In vitrostudies suggest that casein coagulation of milk is influenced by its mineral composition, and may therefore affect the dynamics of protein digestion, gastric emptying and appearance of amino acids (AA) in the blood, but this remains to be confirmedin vivo.

Objective

This study aimed to compare gastrointestinal digestion between two milks with the same total calcium content but different casein mineralization (CM).

Design

Fifteen males (age 30.9±13.8 y, BMI 22.5±2.2 kg/m2) participated in this randomized cross-over study with two treatments. Participants underwent gastric magnetic resonance imaging (MRI) scans at baseline and every 10 min up to 90 min after consumption of 600 ml milk with low or high CM. Blood samples were taken at baseline and up to 5 hours postprandially. Primary outcomes were postprandial plasma AA concentrations and gastric emptying rate. Secondary outcomes were postprandial glucose and insulin levels, gastric coagulation as estimated by image texture metrics, and appetite ratings.

Results

Gastric content volume over time was similar for both treatments. However, gastric content image analysis suggested that the liquid fraction emptied quicker in the high CM milk, while the coagulum emptied slower. Relative to high CM, low CM showed earlier appearance of AAs that are more dominant in casein, such as proline (MD 4.18 µmol/L, 95%CI [2.38-5.98], p<0.001), while there was no difference in appearance of AAs that are more dominant in whey protein, such as leucine. The image texture metrics homogeneity and busyness differed significantly between treatments (MD 0.007, 95%CI [0.001, 0.012], p=0.022; MD 0.005, 95%CI [0.001, 0.010], p=0.012) likely because of a reduced coagulation in the low CM milk.

Conclusions

Mineral composition of milk can influence postprandial serum AA kinetics, likely due to differences in coagulation dynamics.
What are the most effective interventions to support children and young people bereaved by suicide in the family: a rapid review
Authors: Mann Mala , Kiseleva Meg , Searchfield Lydia , Mazzaschi Francesca , Jones Rhiannon , Lifford Kate , Weightman Alison , John Ann , Lewis Ruth , Edwards Rhiannon Tudor , Davies Jacob , Cooper Alison , Edwards Adrian
Published: September 2023

Bereavement by suicide is different from other forms of bereavement and needs specialised support. Children and young people who lost loved ones to suicide are more likely to suffer a complicated bereavement process and have poorer mental health.

This review aims to assess the evidence for the effectiveness of interventions to support children and young people (up to the age of 24 years) bereaved by suicide. The review included evidence available up until 29 March 2023. Three studies were identified and all reported on group therapy interventions lasting between 10 and 14 weeks.

Key findings and certainty of the evidence

Reductions in anxiety and depressive symptoms were found in children who received the group interventions. However, due to the types of study designs used and limitations of the included studies, it is unclear if this is attributable to the interventions, so caution should be applied when generalising the results.

The strongest evidence came from a non-randomised controlled study, in which children in the intervention group had significantly greater reduction of anxiety and depressive symptoms compared with children in the control group. However, this study was limited due to numbers of participants lost to follow-up.

Research Implications and Evidence Gaps

Further research is needed to develop interventions to support children and young people bereaved through death by suicide of a family member. Additional research is needed to evaluate the effectiveness and cost-effectiveness of planned interventions.

Policy and Practice Implications

It is difficult to draw firm conclusions due to the limited evidence and low quality of included studies. However, there are indications that group interventions may help to reduce anxiety and depressive symptoms in children bereaved by suicide. It will be important to develop guidance and standards of practice for these services based on best available evidence. All such services must use validated outcome measures as part of an integral evaluation process set up from service initiation.

Funding statement

The Specialist Unit for Review Evidence was funded for this work by the Health and Care Research Wales Evidence Centre, itself funded by Health and Care Research Wales on behalf of Welsh Government
An Innovative Visual Approach to Monitor Simultaneously Two Dimensions of Progress in Longevity: An Application to French and German Regions
Authors: Bonnet Florian , Klüsener Sebastian , Meslé France , Mühlichen Michael , Grigoriev Pavel
Published: September 2023

Background

Both enhancing life expectancy as well as diminishing inequalities in lifespan among social groups represent significant goals for public policy. However, there is a lack of methodological tools to simultaneously monitor progress in both dimensions. Additionally, there is a consensus that absolute and relative inequalities in lifespan must be scrutinized together.

Methods

We introduce a novel graphical representation that combines national mortality rates with social inequalities, considering both absolute and relative measures. We use French and German data stratified by place of residence to illustrate this representation.

Results

For all-age mortality we detect for France a rather continuous pace of decline in both mortality levels and variation. In Germany, substantial progress was made in the 1990s, which was mostly driven by convergence between eastern and western Germany, followed by a period with less progress. Age-specific analyses reveal for Germany some worrying regional divergence trends at ages 35-74 in recent years. This is particularly pronounced among women.

Conclusion

Our novel visual approach allows evaluating easily the dynamics of societal progress in terms of longevity, and facilitates meaningful comparisons between populations, even when their current mortality rates differ. The methods we employ can be reproduced easily in any country with longitudinal mortality data stratified by relevant socio-economic information or regions. It is both useful for scientific analyses as well as policy advice.

Key messages

What is already known on this topic

Improving life expectancy as well as reducing social inequalities in longevity are major public policy objectives. However, there is a lack of proper methodological tools to evaluate progress on these objectives.

What this study adds

This study proposes an innovative graphical representation that combines national mortality and social inequalities in both absolute and relative terms in order to assess the dynamics of societal progress in longevity and make relevant comparisons between populations whose mortality rates are not at the same level nowadays.

How this study might affect research, practice or policy

Methods are freely and easily reproducible for all countries with longitudinal mortality data stratified by socio-economic information or geographic regions.
Adopting orphan receptors: group IX/X transition metals as potential ligands of zebrafish Tlr4 homologs
Authors: Fox Aaron P.D. , Lee Tracy S. , Mithaiwala Sakina N. , Pollock Niall M. , Bhavsar Amit P. , Allison W. Ted
Published: September 2023

TLR4 is the prototype immune receptor and central to infection defence via detecting lipopolysaccharide (LPS). Surprisingly, the impacts of LPS upon the TLR4 homologs in zebrafish, an important animal model, are equivocal and the function of TLR4 homologs across all fishes remains debatable. Recent work suggests zebrafish Tlr4 mediates ototoxic responses to a platinum-based chemotherapeutic. This prompts our hypothesis that Tlr4 detects group IX/X transition metals and thus has conserved roles with human TLR4 mediating allergic responses to nickel. Here, we use the larval zebrafish lateral line model to demonstrate (sub-)micromolar Ni, Co and Pt are ototoxic in a dose-dependent manner. TLR4 homologs are required for this toxicity because Tlr4 knockdown via CRISPR significantly reduced the metals’ impacts by ∼50%. Moreover, zebrafish Tlr4 was sufficient to mediate inflammatory responses to metals when expressed in a human cell line. These data are consistent with the notion that mediating responses to transition metals was a function of TLR4 homologs in the last common ancestor of fish and mammals, and begins to resolve the function(s) of TLR4 homologs in the zebrafish animal model of disease.