bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Antibiotic and Steroid Treatment on Leptospirosis Outcomes: A Single-Center Retrospective Cohort Study in the Transcarpathian Region of Ukraine
Authors: Petakh Pavlo , Oksenych Valentyn , Poliak Mykhailo , Poliak Ivan , Kohutych Anton , Kamyshnyi Oleksandr
Published: June 2024

Leptospirosis presents a significant health challenge in the Transcarpathian region of Ukraine, with higher incidence rates and mortality compared to national averages. We conducted a retrospective cohort study to investigate the effects of antibiotic and steroid treatments on outcomes in leptospirosis patients. Our analysis of clinical and laboratory data from a single center revealed that dexamethasone showed significant effects on various clinical variables, as did investigated antibiotics. Particularly, direct bilirubin levels emerged as a strong predictor of death. These findings provide valuable insights for clinicians in managing leptospirosis, aiding in outcome prediction and treatment decision-making not only in the Transcarpathian region but globally.
Contracted anterior-posterior systematic covariance of cortical thickness in early-onset schizophrenia
Authors: Fan Yun-Shuang , Xu Yong , Wan Bin , Sheng Wei , Wang Chong , Valk Sofie Louise , Chen Huafu
Published: June 2024

Background and Hypothesis: Schizophrenia is a neurodevelopmental condition with alterations in both sensory and association cortical areas. These alterations have been reported to follow structural connectivity patterning, and to occur in a system-level fashion. Here, we investigated whether pathological alterations of schizophrenia originated from an early disruption of cortical organization by using 7−17-years-old individuals with early-onset schizophrenia (EOS). Study Design: We estimated cortical thickness using T1-weighted structural MRI data from 95 patients with antipsychotic-naive first-episode EOS and 99 typically developing (TD) controls. We then computed structural covariance of cortical thickness and estimated system-level organizational axes by performing nonlinear dimensionality reduction techniques on covariance matrices for the EOS and TD groups. Finally, we tested for group differences between EOS and TD individuals in terms of both structural covariance and covariance distances along the systematic axis. Study Results: The first covariance gradient differentiated motor regions from other cortical areas. Similar to the macrostructural axis in adults, the second gradient axis in young TD discriminated anterior from posterior regions and was compressed in EOS patients relative to TD controls. In addition, patients showed increased structural covariance between two ends of the systematic axis, with increased geodesic distance of covarying regions between two ends. Conclusion: Our findings revealed a contracted organizational axis of cortical thickness in EOS patients, which was attributed to excessive distally coordinated changes between anterior and posterior regions of the cortex. Taken together, our study suggests a possible early disruption of system-level neurodevelopment in schizophrenia.
Evolutionary Insights into Muscle Fiber Distribution in the Twin Tails of Ornamental Goldfish
Authors: Ota Kinya G , Abe Gembu , Wang Chen-Yi , Li Ing-Jia , Sanchez Paul Gerald Layague , Chi Tzu-Chin
Published: June 2024

Twin-tail ornamental goldfish have a bifurcated caudal fin with a morphology that is extremely diverged from the conventional body plan of the vertebrates. Here, we investigate the muscu-loskeletal histology of this bifurcated caudal fin. From some of the investigated twin-tail goldfish, we found a twin-tail goldfish specific muscle (hereafter referred to as the “medial caudal muscle”) between left and right bifurcated caudal fin skeletons. Our immunohistochemical analyses revealed that the medial caudal muscle showed laterally biased distribution patterns of the slow and fast muscle fibers. Similar distribution patterns were also commonly observed in several deep muscles of wild-type goldfish as well as zebrafish, suggesting that these muscle fiber distribution patterns are formed by the same molecular developmental mechanisms even though their morphologies are highly diverged. These findings provide empirical evidence to consider how the histological features of a newly emerged morphology are influenced by selective pressures and pre-existing developmental mechanisms.
Hybrid xyloglucan utilisation loci are prevalent among plant-associated Bacteroidota
Authors: Martin Hannah , Rogers Lucy A. , Moushtaq Laila , Brindley Amanda A. , Forbes Polly , Quintion Amy R. , Murphy Andrew R.J. , Daniell Tim J. , Ndeh Didier , Amsbury Sam , Hitchcock Andrew , Lidbury Ian D.E.A.
Published: June 2024

The plant hemicellulose xyloglucan (XyG) is secreted from the roots of numerous plant species, including cereals, and contributes towards soil aggregate formation in terrestrial systems. Whether XyG represents a key nutrient for plant-associated bacteria is unclear. The phylum Bacteroidota are abundant in the plant microbiome and provide several beneficial functions for their host. However, the metabolic and genomic traits underpinning their success remain poorly understood. Here, using proteomics, bacterial genetics, and genomics, we revealed that plant-associatedFlavobacterium, a genus within the Bacteroidota, can efficiently utilise XyG through the occurrence of a distinct and conserved gene cluster, referred to as the Xyloglucan Utilisation Loci (XyGUL).FlavobacteriumXyGUL is a hybrid of the molecular machinery found in gutBacteroidesspp.,Cellvibrio japonicus, and the plant pathogenXanthomonas. Combining protein biochemistry, computational modelling and phylogenetics, we identified a mutation in the enzyme required for initiating hydrolysis of the XyG polysaccharide, an outer membrane endoxyloglucanase glycoside hydrolase family 5 subfamily 4 (GH5_4), which enhances activity towards XyG. A subclade of GH5_4 homologs carrying this mutation were the dominant form found in soil and plant metagenomes due to their occurrence in Bacteroidota and Proteobacteria. However, only in members of the Bacteroidota spp., particularlyFlavobacteriumspp. was such a remarkable degree of XyGUL conservation detected. We propose this mechanism enables plant-associatedFlavobacteriumto specialise in competitive acquisition of XyG exudates and that this hemicellulose may represent an important nutrient source, enabling them to thrive in the plant microbiome, which is typified by intense competition for low molecular weight carbon exudates.
Degradation and Stable Maintenance of AAV Inverted Terminal Repeats inE. coli
Authors: Radukic Marco T. , Le Dinh To , Krassuski Timo , Borchert Philipp , Leach David R. F. , Müller Kristian M.
Published: June 2024

Current plasmid propagation compromises large inverted repeats, like inverted terminal repeats (ITRs) of adeno-associated virus (AAV). Direct long-read sequencing analyses upon varying culture conditions and strains revealed ITR instability mechanisms, which diminished in absence of SbcC or at elevated growth temperatures (e.g. 42 °C), with a combination being optimal. Resulting full ITRs improved rAAV yield and purity. The findings advance plasmid biology, cloneable sequences, and therapeutic AAV manufacturing.
Accounting for fast vs slow exchange in single molecule FRET experiments reveals hidden conformational states
Authors: Miller Justin J. , Mallimadugula Upasana L. , Zimmerman Maxwell I. , Stuchell-Brereton Melissa D. , Soranno Andrea , Bowman Gregory R.
Published: June 2024

Proteins are dynamic systems whose structural preferences determine their function. Unfortunately, building atomically detailed models of protein structural ensembles remains challenging, limiting our understanding of the relationships between sequence, structure, and function. Combining single molecule Förster resonance energy transfer (smFRET) experiments with molecular dynamics simulations could provide experimentally grounded, all-atom models of a protein’s structural ensemble. However, agreement between the two techniques is often insufficient to achieve this goal. Here, we explore whether accounting for important experimental details like averaging across structures sampled during a given smFRET measurement is responsible for this apparent discrepancy. We present an approach to account for this time-averaging by leveraging the kinetic information available from Markov state models of a protein’s dynamics. This allows us to accurately assess which timescales are averaged during an experiment. We find this approach significantly improves agreement between simulations and experiments in proteins with varying degrees of dynamics, including the well-ordered protein T4 lysozyme, the partially disordered protein apolipoprotein E (ApoE), and a disordered amyloid protein (Aβ40). We find evidence for hidden states that are not apparent in smFRET experiments because of time averaging with other structures, akin to states in fast exchange in NMR, and evaluate different force fields. Finally, we show how remaining discrepancies between computations and experiments can be used to guide additional simulations and build structural models for states that were previously unaccounted for. We expect our approach will enable combining simulations and experiments to understand the link between sequence, structure, and function in many settings.
The conformational landscape of fold-switcher KaiB is tuned to the circadian rhythm timescale
Authors: Wayment-Steele Hannah K. , Otten Renee , Pitsawong Warintra , Ojoawo Adedolapo M. , Glaser Andrew , Calderone Logan A. , Kern Dorothee
Published: June 2024

How can a single protein domain encode a conformational landscape with multiple stably-folded states, and how do those states interconvert? Here, we use real-time and relaxation-dispersion NMR to characterize the conformational landscape of the circadian rhythm protein KaiB fromRhodobacter sphaeroides. Unique among known natural metamorphic proteins, this KaiB variant spontaneously interconverts between two monomeric states: the “Ground” and “Fold-switched” (FS) state. KaiB in its FS state interacts with multiple binding partners, including the central KaiC protein, to regulate circadian rhythms. We find that KaiB itself takes hours to interconvert between the Ground and FS state, underscoring the ability of a single sequence to encode the slow process needed for function. We reveal the rate-limiting step between the Ground and FS state is thecis-transisomerization of three prolines in the fold-switching region by demonstrating interconversion acceleration by the prolyl isomerase CypA. The interconversion proceeds through a “partially disordered” (PD) state, where the C-terminal half becomes disordered while the N-terminal half remains stably folded. We discovered two additional properties of KaiB’s landscape. Firstly, the Ground state experiences cold denaturation: at 4°C, the PD state becomes the majorly populated state. Secondly, the Ground state exchanges with a fourth state, the “Enigma” state, on the millisecond timescale. We combine AlphaFold2-based predictions and NMR chemical shift predictions to predict this “Enigma” state is a beta-strand register shift that eases buried charged residues, and support this structure experimentally. These results provide mechanistic insight in how evolution can design a single sequence that achieves specific timing needed for its function.

Significance Statement

One can conceptualize KaiB as an on-off switch to regulate circadian rhythms in bacteria, where the “On state” is the Fold-switched state that binds KaiC and other proteins, and the “Off state” is the Ground state. Our work exemplifies how evolution tuned the kinetics of interconversion to align with the hour-long timescale of its biological function. The Ground state is dramatically destabilized at cold temperatures, and the system contains an alternate “off” conformation that exchanges with the primary “off” conformation at faster timescales than the rate-limiting step. Our findings demonstrate a simple principle for evolving a protein switch: one part of a protein domain remains stably folded to serve as a scaffold for the rest of the protein to re-fold.
Reduced Non-Specific Binding of Super-Resolution DNA-PAINT Markers by Shielded DNA-PAINT Labeling Protocols
Authors: Lučinskaitė Evelina , Bokhobza Alexandre F. E. , Stannard Andrew , Meletiou Anna , Estell Chris , West Steven , Di Michele Lorenzo , Soeller Christian , Clowsley Alexander H.
Published: June 2024

The DNA-based single molecule super-resolution imaging approach, DNA-PAINT, can achieve nanometer resolution of single targets. However, the approach can suffer from significant non-specific background signals originating from non-specifically bound DNA-conjugated DNA-PAINT secondary antibodies as shown here. Using dye-modified oligonucleotides the location of DNA-PAINT secondary antibody probes can easily be observed with widefield imaging prior to beginning a super-resolution measurement. This reveals that a substantial proportion of DNA probes can accumulate, non-specifically, within the nucleus, as well as across the cytoplasm, of cells. Here, Shielded DNA-PAINT labeling is introduced, a method using partially or fully double-stranded docking strand sequences, prior to labeling, in buffers with increased ionic strength to greatly reduce non-specific interactions in the nucleus as well as the cytoplasm. This new labeling approach is evaluated against various conditions and it is shown that applying Shielded DNA-PAINT can reduce non-specific events ∼5 fold within the nucleus. This marked reduction in non-specific binding of probes during the labeling procedure is comparable to results obtained with unnatural left-handed DNA albeit at a fraction of the cost. Shielded DNA-PAINT is a straightforward adaption of current DNA-PAINT protocols and enables nanometer precision imaging of nuclear targets with low non-specific background.
Artificial intelligence as a ploy to delve into the intricate relationship between genetics and mitochondria in MASLD patients
Authors: Longo Miriam , Paolini Erika , Meroni Marica , Ripolone Michela , Napoli Laura , Gentile Francesco , Cespiati Annalisa , Maggioni Marco , Alisi Anna , Miele Luca , Soardo Giorgio , Moggio Maurizio , Fracanzani Anna Ludovica , Dongiovanni Paola
Published: June 2024

Background and Aims

Mitochondrial (mt-) dysfunction is a hallmark of progressive MASLD. MtDNA copy number (mtDNA-CN) and cell-free circulating mtDNA (ccf-mtDNA), which reflect mt-mass and mt-dysfunction, respectively, are gaining attention as non-invasive disease biomarkers. We previously demonstrated thatPNPLA3/MBOAT7/TM6SF2deficiency in HepG2 cells increased mt-mass, mtDNA-CN and ccf-mtDNA. This study furtherly explored mt-biogenesis, function and mt-biomarkers in biopsied MASLD patients from a Discovery (n=28) and a Validation (n=824) cohort, stratified by the number of risk variants (NRV=3). We took advantage of artificial intelligence (AI) to develop new risk scores, predicting MASLD evolution by integrating anthropometric and genetic data (Age, BMI, NRV) with mt-biomarkers.

Methods

Hepatic mt-morphology and dynamics were assessed by TEM, IHC and gene expression. mtDNA-CN and ccf-mtDNA were measured in PBMCs and serum samples. GPT-4 was employed as AI tool to support the construction of novel risk scores for MASLD progressive forms (MASH, fibrosis and HCC).

Results

In the Discovery cohort, NRV=3 patients showed the highest mt-mass and significant mt-morphological changes (i.e. membranes rupture). An elevated PGC-1α, OPA1, DRP1 and PINK1, markers of mt-biogenesis, fusion and fission were found in these patients, supporting an enhanced mt-dynamics. However, PRKN protein levels were reduced, suggesting a premature block of mitophagy. In the Validation cohort,PGC-1αmRNA levels and mtDNA-CN were significantly higher in NRV=3 compared to patients with 1,2 or no variants. Circulating mtDNA-CN and ccf-mtDNA were augmented in NRV=3 patients and correlated with genetics and MASLD severity at multivariate analysis, supporting that both may independently modulate mt-dynamics and activity. By exploiting rsGPT-4 we then optimized the combination of non-invasive variables to get prediction models named Mitochondrial, Anthropometric, and Genetic Integration with Computational intelligence (“MAGIC-“) for assessing MASH, fibrosis, and HCC, respectively. The MAGIC-MASH and MAGIC-Fib models showed AUCs of 73% and 76% in detecting MASH and fibrosis >1. Of note, MAGIC-HCC achieved an AUC of 86% (95% CI: 0.823-0.885), with 78.6% sensitivity and 81.5% specificity thus resulting the best score for the desired outcome.

Conclusions

mtDNA-CN and ccf-mtDNA may have pathological and prognostic significance in MASLD patients, especially in those genetically-predisposed.
Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome
Authors: Yuan Yifeng , DeMott Michael S. , Byrne Shane R. , Flores Katia , Poyet Mathilde , Groussin Mathieu ,   Global Microbiome Conservancy, Berdy Brittany , Comstock Laurie , Alm Eric J. , Dedon Peter C.
Published: June 2024

Among dozens of microbial DNA modifications regulating gene expression and host defense, phosphorothioation (PT) is the only known backbone modification, with sulfur inserted at a non-bridging oxygen bydndandsspgene families. Here we explored the distribution of PT genes in 13,663 human gut microbiome genomes, finding that 6.3% possesseddndorsspgenes predominantly in Bacillota, Bacteroidota, and Pseudomonadota. This analysis uncovered several putative new PT synthesis systems, including Type 4 Bacteriophage Exclusion (BREX)brxgenes, which were genetically validated inBacteroides salyersiae.Mass spectrometric analysis of DNA from 226 gut microbiome isolates possessingdnd,ssp, andbrxgenes revealed 8 PT dinucleotide settings confirmed in 6 consensus sequences by PT-specific DNA sequencing. Genomic analysis showed PT enrichment in rRNA genes and depletion at gene boundaries. These results illustrate the power of the microbiome for discovering prokaryotic epigenetics and the widespread distribution of oxidation-sensitive PTs in gut microbes.

One-sentence Summary

Application of informatic, mass spectrometric, and sequencing-based mapping tools to human gut bacteria revealed new phosphorothioate epigenetic systems widespread in the gut microbiome.
Single-nucleus transcriptomic analysis reveals the regulatory circuitry of myofiber XBP1 during regenerative myogenesis
Authors: Joshi Aniket S. , Castillo Micah B. , Tomaz da Silva Meiricris , Vuong Anh Tuan , Gunaratne Preethi H. , Darabi Radbod , Liu Yu , Kumar Ashok
Published: June 2024

Endoplasmic reticulum (ER) stress-induced unfolded protein response (UPR) are activated in skeletal muscle in multiple conditions. However, the role of the UPR in the regulation of muscle regeneration remains less understood. We demonstrate that gene expression of various markers of the UPR is induced in both myogenic and non-myogenic cells in regenerating muscle. Genetic ablation of XBP1, a downstream target of the IRE1α arm of the UPR, in myofibers attenuates muscle regeneration in adult mice. Single nucleus RNA sequencing (snRNA-seq) analysis showed that deletion of XBP1 in myofibers perturbs proteolytic systems and mitochondrial function in myogenic cells. Trajectory analysis of snRNA-seq dataset showed that XBP1 regulates the abundance of satellite cells and the formation of new myofibers in regenerating muscle. In addition, ablation of XBP1 disrupts the composition of non-myogenic cells in injured muscle microenvironment. Collectively, our study suggests that myofiber XBP1 regulates muscle regeneration through both cell-autonomous and -non-autonomous mechanisms.

HIGHLIGHTS

The UPR is activated in different cell types during muscle regeneration.

Targeted deletion of XBP1 impairs muscle regeneration in adult mice

Myofiber XBP1 regulates satellite cell dynamics during regenerative myogenesis

Myofiber XBP1 regulates abundance of non-myogenic cells in regenerating muscle
Insights into the Contribution of Type VI Secretion Towards AHPND Pathogenesis
Authors: Cavanagh Damian , Martinez Karina , Froelich Brett
Published: June 2024

The Type VI Secretion System (T6SS) is a bacterial organelle resembling a poison-tipped spear that can be deployed by a wide range of gram-negative bacteria to intoxicate prokaryotic and eukaryotic prey. In this capacity, Type VI Secretion Systems (T6SSs) play various roles in facilitating interbacterial competition and augmenting virulence towards animal and plant hosts. Prior reports have elucidated that many strains ofVibrio parahaemolyticusthat cause Acute Hepatopancreatic Necrosis Disease (AHPND) in shrimp harbor two functional T6SSs (T6SS1 and T6SS2), leading to speculations about the contribution of these systems to disease progression. In the present study, we demonstrate the antibacterial functionality of T6SS1 and T6SS2 in a representative VPAHPNDstrain, and provide direct evidence that T6SS1 augments the lethality of this isolate against whiteleg shrimp (Litopenaeus vannamei) postlarvae under conditions relevant to commercial aquaculture. Our findings provide early evidence that Type VI Secretion (T6S) plays a role in facilitating AHPND pathogenesis, and invites additional lines of inquiry aimed at uncovering the mechanisms responsible for this contribution.

Author Summary

Type VI Secretion Systems (T6SSs) have drawn interest as important determinants of virulence and fitness in the bacterial taxa that utilize them. Included among these species are members of the genusVibrio, many of which have clinical and commercial relevance as pathogens or aquaculture pests.Vibrio parahaemolyticusisolates that harbor thepirA/Btoxin genes encoded on pVA1-like plasmids have been identified as a causative agent of Acute Hepatopancreatic Necrosis Disease (AHPND), an illness which results in mass mortality events in shrimp aquaculture systems. It has previously been noted that, aside from the PirA/B binary toxin, many VPAHPNDstrains harbor two T6SSs (T6SS1 and T6SS2), which they may rely on to outcompete and displace the native shrimp microbiome during colonization. In this study, we have directly assessed the effects of inactivating T6SS1 and T6SS2 on the lethality of a representative VPAHPNDisolate againstL. vannameipostlarvae (PL) using a simple infection assay. Our findings indicate that T6SS1 putatively contributes to the pathogenicity of VPAHPNDagainstL. vannameiPL under warm, marine-like conditions. These initial results help to provide insight into the factors which enable AHPND pathogenesis, and may inform future efforts to develop countermeasures against this disease.
Bhlhe40 limits proliferation and prevents excessive angiogenesis in mouse embryoid bodies under hypoxia
Authors: Acosta-Iborra Barbara , Gil-Acero Ana Isabel , Sanz-Gómez Marta , Berrouayel Yosra , Puente-Santamaría Laura , Alieva Maria , del Peso Luis , Jiménez Benilde
Published: June 2024

Knowledge of the molecular mechanisms that underlie the regulation of the major adaptive responses to an unbalanced oxygen tension is central to understanding tissue homeostasis and disease. Hypoxia-inducible transcription factors (HIFs) coordinate changes in the transcriptome that control these adaptive responses. Here, we focused on the functional role of the transcriptional repressor basic-helix-loop-helix family member e40 (Bhlhe40), which we previously identified in a meta-analysis as one of the most consistently up-regulated genes in response to hypoxia across various cell types. We investigated the role of Bhlhe40 in controlling proliferation and angiogenesis using a gene editing strategy in mouse embryonic stem cells (mESCs) that we differentiated in embryoid bodies (EBs). We observed that hypoxia-induced Bhlhe40 expression was compatible with the rapid proliferation of pluripotent mESCs under low oxygen tension. However, in EBs, hypoxia triggered a Bhlhe40-dependent cell cycle arrest in most progenitor cells and endothelial cells within vascular structures. Furthermore, Bhlhe40 knockout increased the basal vascularization of the EBs in normoxia and exacerbated the hypoxia-induced vascularization, supporting a novel role for Bhlhe40 as a negative regulator of blood vessel formation. Our findings implicate Bhlhe40 in mediating key functional adaptive responses to hypoxia, such as proliferation arrest and angiogenesis.
Exploring memory-related network via dorsal hippocampus suppression
Authors: Han Xu , Cramer Samuel R. , Chan Dennis C.Y. , Zhang Nanyin
Published: June 2024

Memory is a complex brain process that requires coordinated activities in a large-scale brain network. However, the relationship between coordinated brain network activities and memory-related behavior is not well understood. In this study, we investigated this issue by suppressing the activity in the dorsal hippocampus (dHP) using chemogenetics and measuring the corresponding changes in brain-wide resting-state functional connectivity (RSFC) and memory behavior in awake rats. We identified an extended brain network contributing to the performance in a spatial-memory related task. Our results were cross-validated using two different chemogenetic actuators, clozapine (CLZ) and clozapine-N-oxide (CNO). This study provides a brain network interpretation of memory performance, indicating that memory is associated with coordinated brain-wide neural activities.

Significance Statement

Successful memory processes require coordinated activity in a large-scale brain network, extending beyond a few key, well-known brain regions like the hippocampus. However, the specific brain regions involved and how they orchestrate their activity that is pertinent to memory processing remain unclear. Our study, using a chemogenetics-rsfMRI- behavior approach in awake rats, elucidates a comprehensive framework of the extended memory-associated network. This knowledge offers a broader interpretation of memory processes, enhancing our understanding of the neural mechanisms behind memory function, particularly from a network perspective.
APOE Christchurch enhances a disease-associated microglial response to plaque but suppresses response to tau pathology
Authors: Tran Kristine M. , Kwang Nellie , Gomez-Arboledas Angela , Kawauchi Shimako , Mar Cassandra , Chao Donna , Da Cunha Celia , Wang Shuling , Collins Sherilyn , Walker Amber , Shi Kai-Xuan , Alcantara Joshua A. , Neumann Jonathan , Tenner Andrea J. , LaFerla Frank M. , Hohsfield Lindsay A. , Swarup Vivek , MacGregor Grant R. , Green Kim N.
Published: June 2024

Background

Apolipoprotein E ε4 (APOE4) is the strongest genetic risk factor for late-onset Alzheimer’s disease (LOAD). A recent case report identified a rare variant in APOE, APOE3-R136S (Christchurch), proposed to confer resistance to autosomal dominant Alzheimer’s Disease (AD). However, it remains unclear whether and how this variant exerts its protective effects.

Methods

We introduced the R136S variant into mouseApoe(ApoeCh) and investigated its effect on the development of AD-related pathology using the 5xFAD model of amyloidosis and the PS19 model of tauopathy. We used immunohistochemical and biochemical analysis along with single-cell spatial transcriptomics and proteomics to explore the impact of theApoeChvariant on AD pathological development and the brain’s response to plaques and tau.

Results

In 5xFAD mice,ApoeChenhances a Disease-Associated Microglia (DAM) phenotype in microglia surrounding plaques, and reduces plaque load, dystrophic neurites, and plasma neurofilament light chain. By contrast, in PS19 mice,ApoeChsuppresses the microglial and astrocytic responses to tau-laden neurons and does not reduce tau accumulation or phosphorylation, but partially rescues tau-induced synaptic and myelin loss. We compared how microglia responses differ between the two mouse models to elucidate the distinct DAM signatures induced byApoeCh. We identified upregulation of antigen presentation-related genes in the DAM response in a PS19 compared to a 5xFAD background, suggesting a differential response to amyloid versus tau pathology that is modulated by the presence ofApoeCh.

Conclusions

These findings highlight the ability of theApoeChvariant to modulate microglial responses based on the type of pathology, enhancing DAM reactivity in amyloid models and dampening neuroinflammation to promote protection in tau models. This suggests that the Christchurch variant’s protective effects likely involve multiple mechanisms, including changes in receptor binding and microglial programming.
Machine learning elucidates electrophysiological properties predictive of multi- and single-firing human and mouse dorsal root ganglia neurons
Authors: Zurek Nesia A. , Thiyagarajan Sherwin , Ehsanian Reza , Goins Aleyah E. , Goyal Sachin , Shilling Mark , Lambert Christophe G. , Westlund Karin N. , Alles Sascha R.A.
Published: June 2024

Human and mouse dorsal root ganglia (hDRG and mDRG) neurons are important tools in understanding the molecular and electrophysiological mechanisms that underlie nociception and drive pain behaviors. One of the simplest differences in firing phenotypes is that neurons are single-firing (exhibit only one action potential) or multi-firing (exhibit 2 or more action potentials). To determine if single- and multi-firing hDRG exhibit differences in intrinsic properties, firing phenotypes, and AP waveform properties, and if these properties could be used to predict multi-firing, we measured 22 electrophysiological properties by whole-cell patch-clamp electrophysiology of 94 hDRG neurons from 6 male and 4 female donors. We then analyzed the data using several machine learning models to determine if these properties could be used to predict multi-firing. We used 1000 iterations of Monte Carlo Cross Validation to split the data into different train and test sets and tested the Logistic Regression, k-Nearest Neighbors, Random Forest, Supported Vector Classification, and XGBoost machine learning models. All models tested had a greater than 80% accuracy on average, with Supported Vector Classification and XGBoost performing the best. We found that several properties correlated with multi-firing hDRG neurons and together could be used to predict multi-firing neurons in hDRG including a long decay time, a low rheobase, and long first spike latency. We also found that the hDRG models were able to predict multi-firing with 90% accuracy in mDRG. Targeting the neuronal properties that lead to multi-firing could elucidate better targets for treatment of chronic pain.
LONP1 regulation of mitochondrial protein folding provides insight into beta cell failure in type 2 diabetes
Authors: Li Jin , Zhu Jie , Deng Yamei , Reck Emma C. , Walker Emily M. , Sidarala Vaibhav , Hubers Dre L. , Pasmooij Mabelle B. , Shin Chun-Shik , Bandesh Khushdeep , Motakis Eftyhmios , Nargund Siddhi , Kursawe Romy , Basrur Venkatesha , Nesvizhskii Alexey I. , Stitzel Michael L. , Chan David C. , Soleimanpour Scott A.
Published: June 2024

Proteotoxicity is a contributor to the development of type 2 diabetes (T2D), but it is unknown whether protein misfolding in T2D is generalized or has special features. Here, we report a robust accumulation of misfolded proteins within the mitochondria of human pancreatic islets in T2D and elucidate its impact on β cell viability. Surprisingly, quantitative proteomics studies of protein aggregates reveal that human islets from donors with T2D have a signature more closely resembling mitochondrial rather than ER protein misfolding. The matrix protease LonP1 and its chaperone partner mtHSP70 were among the proteins enriched in protein aggregates. Deletion of LONP1 in mice yields mitochondrial protein misfolding and reduced respiratory function, ultimately leading to β cell apoptosis and hyperglycemia. Intriguingly, LONP1 gain of function ameliorates mitochondrial protein misfolding and restores human β cell survival following glucolipotoxicity via a protease-independent effect requiring LONP1-mtHSP70 chaperone activity. Thus, LONP1 promotes β cell survival and prevents hyperglycemia by facilitating mitochondrial protein folding. These observations may open novel insights into the nature of impaired proteostasis on β cell loss in the pathogenesis of T2D that could be considered as future therapeutic targets.
Do Deep Learning Models for Co-Folding Learn the Physics of Protein-Ligand Interactions?
Authors: Masters Matthew R. , Mahmoud Amr H. , Lill Markus A.
Published: June 2024

Co-folding models are the newest innovation in deep-learning-based protein-ligand structure prediction. The recent publications of RoseTTAFold All-Atom and AlphaFold 3 have shown high-quality results on predicting the structures of proteins interacting with small-molecules, other proteins and nucleic-acids. Despite these advanced capabilities and broad potential, the current study presents critical findings that question these models’ adherence to fundamental physical principles and its susceptibility to overfitting specific protein families. Through adversarial examples based on established physical, chemical, and biological principles, we demonstrate notable discrepancies in protein-ligand structural predictions when subjected to biologically plausible perturbations. These discrepancies reveal a significant divergence from expected physical behaviors, indicating potential overfitting to particular data subsets within its training corpus. Our findings underscore the models’ limitations in generalizing effectively across diverse biological structures and highlight the necessity of integrating robust physical and chemical priors in the development of such predictive tools. The results advocate a measured reliance on deep-learning-based models for critical applications in drug discovery and protein engineering, where a deep understanding of the underlying physical and chemical properties is crucial.
Group identification drives brain integration for collective performance
Authors: Xie Enhui , Zha Shuyi , Xu Yiyang , Li Xianchun
Published: June 2024

Group identification may influence collective behaviors and result in variations in collective performance. However, the evidence for this hypothesis and the neural mechanisms involved remain elusive. To this end, we conducted a study using both single-brain activation and multi-brain synchronization analyses to investigate how group identification influences collective problem-solving in a murder mystery case. Our results showed that groups with high levels of identification performed better individually compared to those with low identification, as supported by single-brain activation in the dorsolateral prefrontal cortex (DLPFC). Furthermore, high-identification groups also showed enhanced collective performance, supported by within-group neural synchronization (GNS) in the orbitofrontal cortex (OFC). The DLPFC-OFC connectivity played a crucial role in linking individual and collective performance. Overall, our study provides a two-in-one neural model to explain how group identification affects collective decision-making processes, offering valuable insights into the dynamics of group interactions.
Prominin-1 null Xenopus laevis develop subretinal drusenoid-like deposits, cone-rod dystrophy, and RPE atrophy
Authors: Carr Brittany J. , Skitsko Dominic , Song Jun , Li Zixuan , Ju Myeong Jin , Moritz Orson L.
Published: June 2024

Mutations in thePROMININ-1(PROM1)gene are associated with inherited, non-syndromic vision loss. Here, we used CRISPR/Cas9 to induce truncatingprom1-null mutations inXenopus laevisto create a disease model. We then tracked progression of retinal degeneration in these animals from the ages of 6 weeks to 3 years old. We found that retinal degeneration caused byprom1-null is age-dependent and likely involves death or damage to the retinal pigment epithelium (RPE) that precedes photoreceptor degeneration. Asprom1-null frogs age, they develop large cellular debris deposits in the subretinal space and outer segment layer which resemble subretinal drusenoid deposits (SDD) in their location, histology, and representation in color fundus photography and optical coherence tomography (OCT). In older frogs, these SDD-like deposits accumulate in size and number, and they are present before retinal degeneration occurs. Evidence for an RPE origin of these deposits includes infiltration of pigment granules into the deposits, thinning of RPE as measured by OCT, and RPE disorganization as measured by histology and OCT. The appearance and accumulation of SDD-like deposits and RPE thinning and disorganization in our animal model suggests an underlying disease mechanism forprom1-null mediated blindness of death and dysfunction of the RPE preceding photoreceptor degeneration, instead of direct effects upon photoreceptor outer segment morphogenesis, as was previously hypothesized.
Transcriptomic Analysis of the Spatiotemporal Axis of Oogenesis and Fertilization inC. elegans
Authors: Su Yangqi , Shea Jonathan , DeStephanis Darla , Su Zhengchang
Published: June 2024

The oocyte germline of theC. eleganshermaphrodite presents a unique model to study the formation of oocytes. However, the size of the model animal and difficulties in retrieval of specific stages of the germline have obviated closer systematic studies of this process throughout the years. Here, we present a transcriptomic level analysis into the oogenesis ofC. eleganshermaphrodites. We dissected a hermaphrodite gonad into seven sections corresponding to the mitotic distal region, the pachytene, the diplotene, the early diakinesis region and the 3 most proximal oocytes, and deeply sequenced the transcriptome of each of them along with that of the fertilized egg using a single-cell RNA-seq protocol. We identified specific gene expression events as well as gene splicing events in finer detail along the oocyte germline and provided novel insights into underlying mechanisms of the oogenesis process. Furthermore, through careful review of relevant research literature coupled with patterns observed in our analysis, we attempt to delineate transcripts that may serve functions in the interaction between the germline and cells of the somatic gonad. These results expand our knowledge of the transcriptomic space of theC. elegansgermline and lay a foundation on which future studies of the germline can be based upon.
Comparative Analysis of Human-Chimpanzee Divergence in Brain Connectivity and its Genetic Correlates
Authors: Wang Yufan , Cheng Luqi , Li Deying , Lu Yuheng , Wang Changshuo , Wang Yaping , Gao Chaohong , Wang Haiyan , Vanduffel Wim , Hopkins William D. , Sherwood Chet C. , Jiang Tianzi , Chu Congying , Fan Lingzhong
Published: June 2024

Chimpanzees (Pan troglodytes) are humans’ closest living relatives, making them the most directly relevant comparison point for understanding human brain evolution. Zeroing in on the differences in brain connectivity between humans and chimpanzees can provide key insights into the specific evolutionary changes that might have occured along the human lineage. However, conducting comparisons of brain connectivity between humans and chimpanzees remains challenging, as cross-species brain atlases established within the same framework are currently lacking. Without the availability of cross-species brain atlases, the region-wise connectivity patterns between humans and chimpanzees cannot be directly compared. To address this gap, we built the first Chimpanzee Brainnetome Atlas (ChimpBNA) by following a well-established connectivity-based parcellation framework. Leveraging this new resource, we found substantial divergence in connectivity patterns across most association cortices, notably in the lateral temporal and dorsolateral prefrontal cortex between the two species. Intriguingly, these patterns significantly deviate from the patterns of cortical expansion observed in humans compared to chimpanzees. Additionally, we identified regions displaying connectional asymmetries that differed between species, likely resulting from evolutionary divergence. Genes associated with these divergent connectivities were found to be enriched in cell types crucial for cortical projection circuits and synapse formation. These genes exhibited more pronounced differences in expression patterns in regions with higher connectivity divergence, suggesting a potential foundation for brain connectivity evolution. Therefore, our study not only provides a fine-scale brain atlas of chimpanzees but also highlights the connectivity divergence between humans and chimpanzees in a more rigorous and comparative manner and suggests potential genetic correlates for the observed divergence in brain connectivity patterns between the two species. This can help us better understand the origins and development of uniquely human cognitive capabilities.
GCRTcall: a Transformer based basecaller for nanopore RNA sequencing enhanced by gated convolution and relative position embedding via joint loss training
Authors: Li Qingwen , Sun Chen , Wang Daqian , Lou Jizhong
Published: June 2024

Nanopore sequencing, renowned for its ability to sequence DNA and RNA directly with read lengths extending to several hundred kilobases or even megabases, holds significant promise in fields like transcriptomics and other omics studies. Despite its potential, the technology’s limited accuracy in base identification has restricted its widespread application. Although many algorithms have been developed to improve DNA decoding, advancements in RNA sequencing remain limited. Addressing this challenge, we introduce GCRTcall, a novel approach integrating Transformer architecture with gated convolutional networks and relative positional encoding for RNA sequencing signal decoding. Our evaluation demonstrates that GCRTcall achieves state-of-the-art performance in RNA basecalling.
Constraining the chameleon-photon coupling with atomic spectroscopy
Authors: Elder Benjamin , Sakstein Jeremy
Published: June 2024

We compute bounds from atomic spectroscopy on chameleon fields that couple to the photon. Chameleons are a wide class of scalar field models that generically lead to screened fifth forces and a host of novel phenomenologies, particularly when the photon coupling is included. We account for perturbations to the atomic energy levels from both the scalar field ‘fifth force’ and the scalar field’s correction to the electric field. We also account for the electromagnetic interaction’s contribution to the scalar charge of the proton, which enables a considerably wider class of models to be tested than without this effect. We find bounds that cover different areas of chameleon parameter space. A range of models spanning approximately one order of magnitude in chameleon coupling parameters (around M,Mγ≈10−16MPl) are excluded for the first time. We also show that improvements to the theoretical uncertainty of hydrogen’s spectrum within the Standard Model would immediately rule out additional chameleon theory space by this analysis.

Published by the American Physical Society
2024
Development and validation of a food safety survey for older adults
Authors: Kavanaugh Melissa , Shewokis Patricia A. , Quinlan Jennifer J.
Published: June 2024

Purpose

The purpose of this study was to create and validate a food safety survey for older adults.

Design/methodology/approach

The survey was designed to measure food handling and consumption behaviors related to high-risk foods. Survey questions were also designed to capture behavioral constructs from the health belief model (HBM). The first administration of the survey was completed by 349 participants, 55 years of age and older. Exploratory factor analysis was used to assess construct validity, and Cronbach’s alpha was used to assess the internal consistency of the subscales generated through factor analysis. Two weeks after the first administration, the survey was completed a second time by 149 participants from the original sample. The intraclass correlation coefficient was used to evaluate test-retest reliability.

Findings

Exploratory factor analysis yielded four factors related to the HBM (perceived susceptibility, perceived severity, perceived barriers and cues to action) and three factors related to food handling practices (handling of processed meats, food thermometer use with poultry and washing or rinsing poultry). Inclusion in a factor meant that the related questions measured the same underlying construct. Cronbach’s alpha for these factors ranged from 0.63 to 0.77. Modification of the survey following validation resulted in the development of a 44-question instrument that can be used with older adults.

Practical implications

This survey will next be administered to a representative sample of older adults to assess relationships between HBM constructs and food handling behaviors and is available for use by other researchers.

Originality/value

There are few validated tools that can be used with older adults to evaluate food safety risks.
Influence of welding-induced mechanical stress on the electromagnetic properties of magnetic lamination
Authors: Ukwungwu David , Emadmostoufi Sobhan , Reisgen Uwe , Hameyer Kay
Published: June 2024

Purpose

This paper aims to analyze the influence of welding-induced mechanical stress of a magnetic core material on the performance behavior of a permanent magnet excited synchronous machine (PMSM). Welding, interlocking, clinching and the use of adhesives are state-of-the-art packaging technologies used in the manufacturing of electrical machines. However, the packaging processes degrade the electromagnetic properties of the electric steel sheets, thereby decreasing the performance and achievable range of the electric vehicle.

Design/methodology/approach

In this paper, an approach that maps the local changes in magnetic properties due to welding induced stress with the stress values is developed. The welding process induces internal stress inside the steel sheet due to the diffusion of thermal energy into the sheets. Other effects are the changes in the micro structures of the steel sheets (grain sizes). These induced mechanical stresses lead to significant deterioration of the electromagnetic properties. They also lead to an increase in iron loss attributed to steel lamination.

Findings

A low speed (city), a high-speed (highway) and WLTC-c3 driving cycle will be used to analyze the effects of the induced stresses on the machine efficiency at the different operating conditions. A high-speed PMSM with a maximum speed of 26,000 min−1 and maximum torque of 130 Nm is designed for this study.

Originality/value

The value of this study is in the development of a local varying modeling approach that analyses the influence of weld-induced stress on the performance of electrical machines. Its originality is evident in the mapping methodology. This will enable an application dependent improvement possibilities due to the understanding of the impact of weld-induced stress on the electromagnetic properties of weld-packaged core.