bluuebunny/crossref_metadata_2025 huggingface dataset:
Digital Health Technologies for Alzheimer’s Disease and Related Dementias: Initial Results from a Landscape Analysis and Community Collaborative Effort
Authors: Lott Sarah Averill , Streel Emmanuel , Bachman Shelby L. , Bode Kai , Dyer John , Fitzer-Attas Cheryl , Goldsack Jennifer C. , Hake Ann , Jannati Ali , Fuertes Ricardo Sainz , Fromy Piper
Published: March 2024

Digital health technologies offer valuable advantages to dementia researchers and clinicians as screening tools, diagnostic aids, and monitoring instruments. To support the use and advancement of these resources, a comprehensive overview of the current technological landscape is essential.

A multi-stakeholder working group, convened by the Digital Medicine Society (DiMe), conducted a landscape review to identify digital health technologies for Alzheimer’s disease and related dementia populations. We searched studies indexed in PubMed, Embase, and APA PsycInfo to identify manuscripts published between May 2003 to May 2023 reporting analytical validation, clinical validation, or usability/feasibility results for relevant digital health technologies. Additional technologies were identified through community outreach. We collated peer-reviewed manuscripts, poster presentations, or regulatory documents for 106 different technologies for Alzheimer’s disease and related dementia assessment covering diverse populations such as Lewy Body, vascular dementias, frontotemporal dementias, and all severities of Alzheimer’s disease. Wearable sensors represent 32% of included technologies, non-wearables 61%, and technologies with components of both account for the remaining 7%. Neurocognition is the most prevalent concept of interest, followed by physical activity and sleep. Clinical validation is reported in 69% of evidence, analytical validation in 34%, and usability/feasibility in 20% (not mutually exclusive).

These findings provide clinicians and researchers a landscape overview describing the range of technologies for assessing Alzheimer’s disease and related dementias. A living library of technologies is presented for the clinical and research communities which will keep findings up-to-date as the field develops.
Quantitative transport mapping of multi-delay arterial spin labeling MRI detects early blood perfusion alteration in Alzheimer’s disease
Authors: Guo Yihao , Zhou Liangdong , Li Yi , Chiang Gloria C. , Liu Tao , Chen Huijuan , Huang Weiyuan , de Leon Mony J. , Wang Yi , Chen Feng
Published: March 2024

Background

Quantitative transport mapping (QTM) of blood velocity, based on the transport equation has been demonstrated higher accuracy and sensitivity of perfusion quantification than the traditional Kety’s method-based blood flow (Kety flow). This study aimed to investigate the associations between QTM velocity and cognitive function in Alzheimer’s disease (AD) using multiple post-labeling delay arterial spin labeling (ASL) MRI.

Methods

A total of 128 subjects (21 normal controls (NC), 80 patients with mild cognitive impairment (MCI), and 27 AD) were recruited prospectively. All participants underwent MRI examination and neuropsychological evaluation. QTM velocity and traditional Kety flow maps were computed from multiple delay ASL. Regional quantitative perfusion measurements were performed and compared to study group differences. We tested the hypothesis that cognition declines with reduced cerebral blood flow with consideration of age and gender effects.

Results

In cortical gray matter (GM) and the hippocampus, QTM velocity and Kety flow showed decreased values in AD group compared to NC and MCI groups; QTM velocity, but not Kety flow, showed a significant difference between MCI and NC groups. QTM velocity and Kety flow showed values decreasing with age; QTM velocity, but not Kety flow, showed a significant gender difference between male and female. QTM velocity and Kety flow in the hippocampus were positively correlated with cognition, including global cognition, memory, executive function, and language function.

Conclusion

This study demonstrated an increased sensitivity of QTM velocity as compared with the traditional Kety flow. Specifically, we observed only in QTM velocity, reduced perfusion velocity in GM and the hippocampus in MCI compared with NC. Both QTM velocity and Kety flow demonstrated reduction in AD vs controls. Decreased QTM velocity and Kety flow in the hippocampus were correlated with cognitive measures. These findings suggest QTM velocity as an improved biomarker for early AD blood flow alterations.
Time analysis of dengue deaths that occurred in two regions of Peru during the climatic-atmospheric phenomena El Niño Costero and Cyclone Yaku
Authors: Ramos Willy , Oyola-García Alfredo Enrique , Aguirre Aida , De la Cruz-Vargas Jhony A. , Luna Miguel , Alarcón Tania , Meléndez Mónica , Huaccho-Rojas Juan , Cóndor-Rojas Yudy Cley
Published: March 2024

OBJECTIVE

To perform a dengue-related death time analysis that occurred in Piura and Ica (Peru) during the atmospheric phenomena of El Niño Costero and Cyclone Yaku in 2023.

MATERIAL AND METHODS

A case-series study was performed. We included the deaths between January 1 and June 3, 2023. We reviewed the research data base of the deaths as well as the clinical epidemiology records, death certificates and laboratory test results. A time analysis was performed from the date of onset of symptoms, date of first visit at a health establishment, date that dengue diagnosis was first registered and date of death.

RESULTS

We included 40 deaths by dengue in the study. 70% were females, the median age of death was 51 years of age, and 70% came from Piura. 51.2% presented some comorbidity and 14% had self-medicated with metamizole, other NSAIDS or corticoids before the initial medical consultation. 37.5% presented an unconventional clinical pattern at admission and dengue was not suspected in 40% during the initial assessment. The median time until the initial assessment, the diagnosis time, and the time from diagnosis until death were 3 days, 0 days, and 1 day, respectively. Adults presented a time until the initial assessment significantly greater than the other age groups (p=0.048), the diagnosis time was significantly less than those seen at the Health Department establishments and regional government establishments (MINSA/GORE) than in private establishments (p=0.014) and greater in pediatrics (p=0.018). The time from diagnosis until death was significantly less in those that self-medicated before the initial assessment (p=0.041).

CONCLUSION

The adults presented a significantly greater time until the initial assessment; the diagnosis time was less than those seen in MINSA/GORE establishments and greater in pediatrics, furthermore, the time from diagnosis until death was significantly less in those who self-medicated before the initial assessment. An important fraction of deaths presented comorbidities and an unconventional clinical pattern at admission, with dengue frequently not suspected during the initial assessment.
Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations
Authors: Nishijima Suguru , Stankevic Evelina , Aasmets Oliver , Schmidt Thomas S. B. , Nagata Naoyoshi , Keller Marisa Isabell , Ferretti Pamela , Juel Helene Bæk , Fullam Anthony , Robbani Shahriyar Mahdi , Schudoma Christian , Hansen Johanne Kragh , Holm Louise Aas , Israelsen Mads , Schierwagen Robert , Torp Nikolaj , Arumugam Manimozhiyan , Bendtsen Flemming , Brøns Charlotte , Fonvig Cilius Esmann , Holm Jens-Christian , Nielsen Trine , Pedersen Julie Steen , Thiele Maja Sofie , Trebicka Jonel , Org Elin , Krag Aleksander , Hansen Torben , Kuhn Michael , Bork Peer ,   MicrobLiver Consortia
Published: March 2024

The microbiota in individual habitats differ both in relative composition and absolute abundance. While sequencing approaches determine only the relative abundances of taxa and genes, experimental techniques for absolute abundance determination are rarely applied to large-scale microbiome studies. Here, we developed a machine learning approach to predict fecal microbial loads (microbial cells per gram) solely from relative abundance data. Applied to large-scale datasets (n = 34,539), we demonstrate that microbial load is the major determinant of gut microbiome variation and associated with numerous host factors. We found that for several diseases, the altered microbial load, not the disease itself, was the main driver of the gut microbiome changes. Adjusting for this effect substantially reduced the significance of more than half of the disease-associated species. Our analysis reveals that the fecal microbial load is a major confounder in microbiome studies, highlighting its importance for understanding microbiome variation in health and disease.
Structural basis for surface activation of the classical complement cascade by the short pentraxin C-reactive protein
Authors: Noone Dylan P. , Isendoorn Marjolein M. E. , Hamers Sebastiaan M. W. R. , Keizer Mariska E. , Wulffelé Jip , van der Velden Tijn T. , Dijkstra Douwe J. , Trouw Leendert A. , Filippov Dmitri V. , Sharp Thomas H.
Published: March 2024

Human C-reactive protein (CRP) is a pentameric complex involved in defence against pathogens and regulation of autoimmunity. CRP is also a therapeutic target, with both administration and depletion of serum CRP being pursued as a possible treatment for autoimmune and cardiovascular diseases, among others. CRP binds to phosphocholine (PC) moieties on membranes in order to activate the complement system via the C1 complex, but it is unknown how CRP, or any pentraxin, binds to C1. Here, we present a cryo-electron tomography (cryoET)-derived structure of CRP bound to PC ligands and the C1 complex. To gain control of CRP binding, a synthetic mimotope of PC was synthesised and used to decorate cell-mimetic liposome surfaces. Structure-guided mutagenesis of CRP yielded a fully-active complex able to bind PC-coated liposomes that was ideal for cryoET and subtomogram averaging. In contrast to antibodies, which form Fc-mediated hexameric platforms to bind and activate the C1 complex, CRP formed rectangular platforms assembled from four laterally-associated CRP pentamers that bind only four of the six available globular C1 head groups. Potential residues mediating lateral association of CRP were identified from interactions between unit cells in existing crystal structures, which rationalised previously unexplained mutagenesis data regarding CRP-mediated complement activation. The structure also enabled interpretation of existing biochemical data regarding interactions mediating C1 binding, and identified additional residues for further mutagenesis studies. These structural data therefore provide a possible mechanism for regulation of complement by CRP, which limits complement progression and has consequences for how the innate immune system influences autoimmunity.

Significance statement

Human C-reactive protein (CRP) activates the complement system to protect us from infections, but can also contribute towards progression of cardiovascular and autoimmune diseases when erroneously activated. To understand these processes, the authors used cryo-electron tomography to solve thein situstructure of surface-bound CRP interacting with the complement C1 complex. The structure revealed new interfaces that explain previous, sometimes contradictory, biochemical data. Comparisons with existing structures of antibody-mediated C1 activation revealed distinct structural differences that may explain how CRP modulates complement activity. Together, these structural data identify residues for mutagenesis to gain control over CRP functions, and provide new routes for future therapeutic developments.
Classification and analysis of retinal interneurons by computational structure under natural scenes
Authors: Lee Dongsoo , Kim Juyoung , Baccus Stephen A.
Published: March 2024

Inhibitory neurons are diverse across the brain, but for the visual system we lack the ability to functionally classify these neurons under complex natural stimuli. Here we take the approach of classifying retinal amacrine cell responses to natural scenes using optical recording and an interpretable neural network model. We fit mouse amacrine cell responses to a two-layer convolutional neural network model of a class shown previously to accurately capture salamander ganglion cell responses to natural scenes. Using an approach from interpretable machine learning, we determined for each stimulus the model interneurons that generated each amacrine response, analogous to the set of bipolar cells that target the amacrine population. From this analysis we clustered amacrine cells not by their natural scene responses, but by the model presynaptic neurons that constructed those responses, conservatively finding approximately seven groups by this approach. By analyzing the set of model presynaptic input neurons for each amacrine cluster, we find that distributed rather than dedicated inputs generate natural scene responses for different amacrine cell types. Additional analyses revealed distinct transient and sustained modes exhibited by the network during the response to simple flashes. These results give insight into the computational structure of how the diverse amacrine cell population responds to natural scenes, and generate multiple quantitative hypotheses for how synaptic inputs generate those responses.
Mutating the arginine residue within the FRNK motif of HC-Pro yield highly attenuated strains that confer complete cross protection against telosma mosaic virus (TelMV) in passion fruit (Passiflora edulis)
Authors: Wang Linxi , Shi Wei , Aziz Asma , Wang Xiaoqing , Liu Haobin , Shen Wentao , Wang Aiming , Cui Hongguang , Dai Zhaoji
Published: March 2024

Telosma mosaic virus (TelMV,Potyvirus, Potyviridae) is an emerging viral pathogen causing a major global threat to passion fruit plantations. However, an efficient strategy for controlling such viruses is not yet available. Cross protection is a phenomenon in which pre-infection of a plant with one virus prevents or delays superinfection with the same or closely related virus. HC-Pro is the potyviral encoded multifunctional protein involved in several steps of viral infection, including multiplication, movement, transmission and RNA silencing suppression. The main hypothesis we tested in this study was whether it is possible to generate attenuated viral strains capable of conferring protection against severe TelMV infection by manipulating theHC-Progene. By introducing point mutation into the potyviral conserved motif FRNK of HC-Pro, we have successfully obtained three highly attenuated mutants of TelMV (R181K, R181D and R181E, respectively) that can systemically infect passion fruit plants without any noticeable symptoms. Importantly, these mutants confer complete protection against subsequent infection of severe recombinant virus TelMV-GFP, evidenced by no detection of viral RNA or protein of the superinfection virus in the systemic leaves of passion fruit plants in both early and late stages. Lastly, we demonstrated that the HC-Pros harbored by the highly attenuated mutants exhibited reduced RNA silencing suppression activity inNicotiana benthamianaleaves. Altogether, this study provides the first demonstration of the generation of highly attenuated strains for TelMV and highlights key amino acid residue involved in complete cross protection against TelMV, opening a new avenue to fight TelMV in the field.
Variational inference for microbiome survey data with application to global ocean data
Authors: Mishra Aditya , McNichol Jesse , Fuhrman Jed , Blei David , Müller Christian L.
Published: March 2024

Linking sequence-derived microbial taxa abundances to host (patho-)physiology or habitat characteristics in a reproducible and interpretable manner has remained a formidable challenge for the analysis of microbiome survey data. Here, we introduce a flexible probabilistic modeling framework, VI-MIDAS (VariationalInference forMIcrobiome surveyDAta analysiS), that enablesjointestimation of context-dependent drivers and broad patterns of associations of microbial taxon abundances from microbiome survey data. VI-MIDAS comprises mechanisms for direct coupling of taxon abundances with covariates and taxa-specific latent coupling which can incorporate spatio-temporal informationandtaxon-taxon interactions. We leverage mean-field variational inference for posterior VI-MIDAS model parameter estimation and illustrate model building and analysis using Tara Ocean Expedition survey data. Using VI-MIDAS’ latent embedding model and tools from network analysis, we show that marine microbial communities can be broadly categorized into five modules, including SAR11-, Nitrosopumilus-, and Alteromondales-dominated communities, each associated with specific environmental and spatiotemporal signatures. VI-MIDAS also finds evidence for largely positive taxon-taxon associations in SAR11 or Rhodospirillales clades, and negative associations with Alteromonadales and Flavobacteriales classes. Our results indicate that VI-MIDAS provides a powerful integrative statistical analysis framework for discovering broad patterns of associations between microbial taxa and context-specific covariate data from microbiome survey data.
Low effective population size but high heterozygosity revealed by SNP analyses in adult and juvenileThuja plicatain UK Woodlands
Authors: Guillardín Laura , Glover Ella , Kerr Gary , MacKay John J.
Published: March 2024

Thuja plicatais a conifer tree that is appreciated for its cultural, ecological and wood quality features in its natural range in western North America. It is also used in Europe and the UK for timber production. SomeT. Plicataplantations in the UK are converted to Continuous Cover Forestry (CCF) management which uses natural regeneration and concerns have been raised about the genetic diversity in both the adult trees and the offspring. We studied species diversity, stand structure, and genetic diversity in four UK woodlands planted withT. plicatawhich contained both adults and naturally regenerated individuals. We discovered 61,104 Single Nucleotide Polymorphisms (SNPs) using Genotyping-by-Sequencing (GBS) and retained 504 SNPs for analysis. We selected 67 SNPs for PCR-based genotyping of 163 adults and 176 juveniles. We found a large number of monomorphic sites (40.3%) most of which were restricted to adults in a single woodland, indicative of a high genetic differentiation among woodlands. The effective population size (Ne) was very low across all sites (Ne< 100), varied between adults and juveniles, and was lowest in the most diverse woodland in terms of species and structure. In contrast, heterozygosity was high overall (Ho= 0.38), except in the divergent woodland (Ho= 0.26), and did not vary between adults and juveniles. Our findings and genotyping methods provide insights into the ability of CCF-managed woodlands, including instances of low genetic diversity inT. plicata, to face environmental shifts and disease threats.
Transcriptional profiling of human brain cortex identifies novel lncRNA-mediated networks dysregulated in amyotrophic lateral sclerosis
Authors: Palma Alessandro , Ballarino Monica
Published: March 2024

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease for which a comprehensive knowledge about the pathological mechanisms is still lacking. A multitude of dysregulated cellular processes and pathways have been linked to ALS so far, including the recent focus directed toward the implication of several classes of non-coding (nc)RNAs. Within this context, the class of long ncRNAs (lncRNAs), may provide an important contribution to the onset and the severity of ALS pathogenesis, due to their high tissue specificity and their function as gene expression regulators. Nevertheless, their identification in humans often relies on differential expression analyses from bulk RNA-seq, which limits their targeting in the cellular contexts where they may be primarily involved.

Here we apply dedicated pipelines to single-nucleus nuclei datasets to study lncRNA from non-pathological and pre-frontal ALS human cortex. We found that in brain, distinct cell subtypes express very different pattern of lncRNAs to suggest possible roles in cellular processes found dysregulated in ALS patients. Moreover, we show the lncRNA involvement in important gene regulatory networks that result differentially regulated in pathological conditions and dissect the genomic organization of differentially expressed lncRNAs.
Presynaptic Rac1 in the hippocampus selectively regulates working memory
Authors: Kim Jaebin , Bustamante Edwin , Sotonyi Peter , Maxwell Nicholas D. , Parameswaran Pooja , Kent Julie K. , Wetsel William C. , Soderblom Erik J. , Rácz Bence , Soderling Scott H.
Published: March 2024

One of the most extensively studied members of the Ras superfamily of small GTPases, Rac1 is an intracellular signal transducer that remodels actin and phosphorylation signaling networks. Previous studies have shown that Rac1-mediated signaling is associated with hippocampal-dependent working memory and longer-term forms of learning and memory and that Rac1 can modulate forms of both pre- and postsynaptic plasticity. How these different cognitive functions and forms of plasticity mediated by Rac1 are linked, however, is unclear. Here, we show that spatial working memory is selectively impaired following the expression of a genetically encoded Rac1-inhibitor at presynaptic terminals, while longer-term cognitive processes are affected by Rac1 inhibition at postsynaptic sites. To investigate the regulatory mechanisms of this presynaptic process, we leveraged new advances in mass spectrometry to identify the proteomic and post-translational landscape of presynaptic Rac1 signaling. We identified serine/threonine kinases and phosphorylated cytoskeletal signaling and synaptic vesicle proteins enriched with active Rac1. The phosphorylated sites in these proteins are at positions likely to have regulatory effects on synaptic vesicles. Consistent with this, we also report changes in the distribution and morphology of synaptic vesicles and in postsynaptic ultrastructure following presynaptic Rac1 inhibition. Overall, this study reveals a previously unrecognized presynaptic role of Rac1 signaling in cognitive processes and provides insights into its potential regulatory mechanisms.
Establishing synthetic ribbon-type active zones in a heterologous expression system
Authors: Kapoor Rohan , Schwenzer Niko , Dresbach Thomas , Lehnart Stephan E. , Moser Tobias
Published: March 2024

Encoding of several sensory modalities into neural signals is mediated by ribbon synapses. The synaptic ribbon tethers synaptic vesicles at the presynaptic active zone (AZ) and might act as a super-scaffold organizing AZ topography. Here we employed a synthetic biology approach to reconstitute ribbon-type AZs in HEK293 cells for probing their minimal molecular requirements and studying presynaptic Ca2+channel clustering. Co-expressing a membrane-targeted version of the AZ-protein Bassoon and the ribbon core protein RIBEYE, we observed structures recapitulating basic aspects of ribbon-type AZs, which we callsyntheticribbons orSyRibbons.SyRibbonswith Ca2+channel clusters formed upon additional expression of CaV1.3 Ca2+channels and RIM-binding protein 2 (RBP2), known to promote presynaptic Ca2+channel clustering. Confocal and super-resolution microscopy along with functional analysis by patch-clamp and Ca2+-imaging revealed striking similarities and interesting differences ofSyRibbonsin comparison to native IHC ribbon-type AZs. In summary, we identify Ca2+channels, RBP, membrane-anchored Bassoon, and RIBEYE as minimal components for reconstituting a basic ribbon-type AZ.SyRibbonsmight complement animal studies on molecular interactions of AZ proteins.

Significance Statement

Encoding of sensory information in our eyes and ears builds on specialized ribbon synapses of sensory cells. Elucidating the molecular underpinning of their fascinating structure and function is an ongoing effort to which we add a bottom-up reconstitution approach in cultured cells. Aiming to recapitulate basic properties of ribbon-type presynaptic active zones of cochlear inner hair cells, we identified a minimal set of proteins that assemble in cellular nanodomains, structurally and functionally alike active zones. While not yet reconstituting synaptic vesicle exocytosis, we consider the established synthetic ribbon-type active zones a valuable platform for studying molecular interactions of active zone proteins. We expect the approach to complement, refine, and reduce experiments on native ribbon synapses asserted from animals.
GPCR surface creates a favorable pathway for membrane permeation of drug molecules
Authors: Herrero Cristina Gil , Thallmair Sebastian
Published: March 2024

G protein-coupled receptors (GPCRs) play a crucial role in modulating physiological responses and serve as the main drug target. Specifically, salmeterol and salbutamol which are used for the treatment of pulmonary diseases, exert their effects by activating the GPCR β2-adrenergic receptor (β2AR). In our study, we employed coarse-grained molecular dynamics simulations with the Martini 3 force field to investigate the dynamics of drug molecules in membranes in presence and absence of β2AR. Our simulations reveal that in more than 50% of theflip-flopevents the drug molecules use the β2AR surface to permeate the membrane. The pathway along the GPCR surface is significantly more energetically favorable for the drug molecules, which was revealed by umbrella sampling simulations along spontaneousflip-floppathways. Furthermore, we assessed the behavior of drugs with intracellular targets, such as kinase inhibitors, whose therapeutic efficacy could benefit from this observation. In summary, our results show that β2AR surface interactions can significantly enhance membrane permeation of drugs, emphasizing their potential for consideration in future drug development strategies.
miR-146a-5p mediates inflammation-induced β cell mitochondrial dysfunction and apoptosis
Authors: Krishnan Preethi , Branco Renato Chaves Souto , Weaver Staci A. , Chang Garrick , Lee Chih-Chun , Syed Farooq , Evans-Molina Carmella
Published: March 2024

We previously showed that miR-146a-5p is upregulated in pancreatic islets treated with pro-inflammatory cytokines. Others have reported that miR-146a-5p overexpression is associated with β cell apoptosis and impaired insulin secretion. However, the molecular mechanisms mediating these effects remain elusive. To investigate the role of miR-146a-5p in β cell function, we developed stable MIN6 cell lines to either overexpress or inhibit the expression of miR-146a-5p. Monoclonal cell populations were treated with pro-inflammatory cytokines (IL-1β, IFNγ, and TNFα) to model type 1 diabetes (T1D)in vitro. We found that overexpression of miR-146a-5p increased cell death under conditions of inflammatory stress and led to mitochondrial membrane depolarization, whereas inhibition of miR-146a-5p reversed these effects. Additionally, inhibition of miR-146a-5p increased insulin secretion, mitochondrial DNA copy number, respiration rate, and ATP production Further, RNA sequencing data showed enrichment of pathways related to insulin secretion, apoptosis, and mitochondrial function when the expression levels of miR-146a-5p were altered. Finally, a temporal increase in miR-146a-5p expression levels and a decrease in mitochondria function markers was observed in islets derived from NOD mice. Collectively, these data suggest that miR-146a-5p may promote β cell dysfunction and death during inflammatory stress by suppressing mitochondrial function.
Malaria-derived hemozoin alters chromatin remodelling and skews dendritic cell responses to subsequent bacterial infections
Authors: Lasaviciute Gintare , Tariq Kanwal , Sugathan Anaswara , Quin Jaclyn , Bujila Ioana , Skorokhod Oleksii , Troye-Blomberg Marita , Sverremark-Ekström Eva , Farrants Ann-Kristin Östlund
Published: March 2024

Hemozoin (HZ), the malaria pigment, is released together with the with the parasite merozoites during the blood stage of the disease, which is connected with the pro-inflammatory response to induce T-cells and B-cells. Co-infections with bacteria lead to a more severe disease progression and the underlying mechanisms are poorly understood. Here, we investigated the impact of HZ on the early response of monocyte-derived dendritic cells (moDC) to a common bacterial component, LPS. A short-term HZ exposure for two hours did not induce an inflammatory response, but it did alter the transcriptional response to LPS. In moDC co-exposed to HZ and LPS, the induction of HLA-DR and PD-L1 gene expression was reduced and associated with decreased binding of RELA compared to LPS-stimulated cells. These gene promoters recruited the silencing chromatin remodelling complex NuRD upon co-exposure, instead of the PBAF complex at the promoter in LPS-stimulated cells. Further, HZ maintained transcription of C-type lectin receptors associated to an immature DC phenotype, DC-SIGN (CD209) and macrophage mannose receptor (MMR/CD206). Here, activated RELA and IRF3 were recruited in a PBAF and ncBAF dependent manner. Upon LPS co-exposure, NuRD was replacing these complexes to allow for a reduced transcriptional level of these immature markers. The association of chromatin remodelling complexes did not alter the chromatin state at the promoters, which was changed during differentiation to DCs or even at an earlier point. In conclusion, HZ exposure primes specific gene promoters at an early time point, which results in a different transcriptional response and may also lead to a changed immune reaction to bacterial co-infections.

Graphical abstract
Transformation of the drug ibuprofen byPriestia megaterium: Reversible glycosylation and generation of hydroxylated metabolites
Authors: Hinzke Tjorven , Schlüter Rabea , Mikolasch Annett , Zühlke Daniela , Müller Patrick , Riedel Katharina , Lalk Michael , Becher Dörte , Sheikhany Halah , Schauer Frieder
Published: March 2024

As one of the most-consumed drugs worldwide, ibuprofen (IBU) reaches the environment in considerable amounts as environmental pollutant, necessitating studies of its further biotransformation as potential removal mechanism. Therefore, we screened bacteria with known capabilities to degrade aromatic environmental pollutants, belonging to the generaBacillus,Priestia(formerly alsoBacillus)Paenibacillus,Mycobacterium, andCupriavidus, for their ability to transform ibuprofen. We identified five transformation products, namely 2-hydroxyibuprofen, carboxyibuprofen, ibuprofen pyranoside, 2-hydroxyibuprofen pyranoside, and 4-carboxy-α-methylbenzene-acetic acid. Based on our screening results, we focused on ibuprofen biotransformation byPriestia megateriumSBUG 518 with regard to structure of transformation products and bacterial physiology. Biotransformation reactions by P. megaterium involved (A) the hydroxylation of the isobutyl side chain at two positions, and (B) conjugate formation via esterification with a sugar molecule of the carboxylic group of ibuprofen and an ibuprofen hydroxylation product. Glycosylation seems to be a detoxification process, since the ibuprofen conjugate (ibuprofen pyranoside) was considerably less toxic than the parent compound toP. megateriumSBUG 518. Based on proteome profile changes and inhibition assays, cytochrome P450 systems are likely crucial for ibuprofen transformation inP. megateriumSBUG 518. The toxic effect of ibuprofen appears to be caused by interference of the drug with different physiological pathways, including especially sporulation, as well as amino acid and fatty acid metabolism.

Importance

Ibuprofen is a highly consumed drug, and, as it reaches the environment in high quantities, also an environmental pollutant. It is therefore of great interest how microorganisms transform this drug and react to it. Here, we screened several bacteria for their ability to transform ibuprofen.Priestia megateriumSBUG 518 emerged as highly capable and was therefore studied in greater detail. We show thatP. megateriumtransforms ibuprofen via two main pathways, hydrolyzation and reversible conjugation. These pathways bear resemblance to those in humans. Ibuprofen likely impacts the physiology ofP. megateriumon several levels, including spore formation. Taken together,P. megateriumSBUG 518 is well suited as a model organism to study bacterial ibuprofen metabolism.
Novel carbon nanoparticles (CNPs) fromCatharanthus roseuspetals for metal ion sensing and root growth modulation
Authors: Omprabha Satya , Kaushal Charli , Gawande Nilesh D. , Barot Raviraj , Bhatia Dhiraj , Sankaranarayanan Subramanian
Published: March 2024

Nanoparticles are of major interest nowadays due to their distinctive properties. In this study, we present a microwave-assisted green synthesis of carbon nanoparticles from theCatharanthus roseuspetals. The nanoparticles exhibited a fluorescence emission in the 300 to 400 nm wavelength region and emitted a characteristic blue fluorescence. The extensive characterization using Bio-AFM showed that the size of nanoparticles was 25.38 nm. M-XRD and Zeta potential analysis confirmed that the nanoparticles were amorphous and exhibited a negative surface charge. The surface functional groups on the nanoparticles were highlighted by FTIR analysis. Metal sensing affinity of the synthesized CNPs and their effect on the plant growth was tested. These CNPs demonstrated the effective sequestration of metallic ions such as copper (Cu2+), iron (Fe2+), and nickel (Ni2+), indicating their potential to be used as biosensors in metal detection. It was found that the effect was proportionate to theCatharanthus roseuspetal nanoparticles (CRPNP) concentration, where it exhibits a great affinity for Fe2+.The effect of the nanoparticles analyzed on the root growth ofArabidopsis thalianashowed that CRPNP suppresses the primary root and lateral root numbers. These results demonstrate the use ofC. roseussynthesized CNPs in sustainable agriculture by targeting nutrient delivery.
Transcription factors ERα and Sox2 have differing multiphasic DNA and RNA binding mechanisms
Authors: Hemphill Wayne O. , Steiner Halley R. , Kominsky Jackson R. , Wuttke Deborah S. , Cech Thomas R.
Published: March 2024

Many transcription factors (TFs) have been shown to bind RNA, leading to open questions regarding the mechanism(s) of this RNA binding and its role in regulating TF activities. Here we use biophysical assays to interrogate the kon, koff, and Kdfor DNA and RNA binding of two model human transcription factors, ERα and Sox2. Unexpectedly, we found that both proteins exhibited multiphasic nucleic acid binding kinetics. We propose that Sox2 RNA and DNA multiphasic binding kinetics could be explained by a conventional model for sequential Sox2 monomer association and dissociation. In contrast, ERα nucleic acid binding exhibited biphasic dissociation paired with novel triphasic association behavior, where two apparent binding transitions are separated by a 10-20 min “lag” phase depending on protein concentration. We considered several conventional models for the observed kinetic behavior, none of which adequately explained all the ERα nucleic acid binding data. Instead, simulations with a model incorporating sequential ERα monomer association, ERα nucleic acid complex isomerization, and product “feedback” on isomerization rate recapitulated the general kinetic trends for both ERα DNA and RNA binding. Collectively, our findings reveal that Sox2 and ERα bind RNA and DNA with previously unappreciated multiphasic binding kinetics, and that their reaction mechanisms differ with ERα binding nucleic acids via a novel reaction mechanism.
Movement quality moderates the effect of spatially congruent cues on the stability of symmetric and asymmetric rhythmic bimanual finger movements
Authors: Denyer Ronan , Boyd Lara A.
Published: March 2024

Spatially congruent cues increase the speed of bimanual reach decisions compared to abstract symbolic cues, particularly for asymmetric reaches. Asymmetric rhythmic bimanual movements are less stable than symmetric rhythmic movements, but it is not well understood if spatially congruent cues similarly increase the stability of asymmetric rhythmic bimanual movements. To address this question, inExperiment 1, participants performed symmetric and asymmetric bimanual rhythmic finger tapping movements at different movement frequencies in time with flickering spatially congruent and abstract symbolic stimuli. As expected, symmetric movements were more stable. Spatially congruent cues similarly increased the stability of symmetric and asymmetric movements compared to abstract symbolic cues. The benefits of spatial congruence and movement symmetry were restricted to high movement frequencies (>2 hertz). To better understand if the emergence of these effects at high movement frequencies was driven by a change in movement strategy, inExperiment 2, video of the hands was concurrently recorded during task performance. Markerless motion tracking software revealed that participants switched from discontinuous to continuous movement strategies with increasing movement frequency. Since discontinuous and continuous movements are thought to be controlled by distinct neuro-cogntive systems, this might explain why the beneficial effects of spatial congruence and response symmetry emerged only at high movement frequencies. Overall, results from the current study indicate that the perceptual quality of the stimulus use to cue movement frequency can have powerful effects on the stability of rhythmic bimanual movements, but that these effects may depend on whether discontinuous or continuous movement strategies are selected.
Structural diversity and clustering of bacterial flagellar outer domains
Authors: Fields Jessie Lynda , Zhang Hua , Bellis Nathan F. , Petersen Holly A. , Halder Sajal K. , Rich-New Shane T. , Wu Hui , Wang Fengbin
Published: March 2024

Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a conserved inner D0/D1 core domain across different bacterial species. In contrast, approximately half of the flagellins possess additional, highly divergent outer domain(s), suggesting varied functional potential. In this study, we elucidate atomic structures of flagellar filaments from three distinct bacterial species:Cupriavidus gilardii,Stenotrophomonas maltophilia, andGeovibrio thiophilus. Our findings reveal that the flagella from the facultative anaerobicG. thiophiluspossesses a significantly more negatively charged surface, potentially enabling adhesion to positively charged minerals. Furthermore, we analyzed all AlphaFold predicted structures for annotated bacterial flagellins, categorizing the flagellin outer domains into 682 structural clusters. This classification provides insights into the prevalence and experimental verification of these outer domains. Remarkably, two of the flagellar structures reported herein belong to a previously unexplored cluster, indicating new opportunities on the study of the functional diversity of flagellar outer domains. Our findings underscore the complexity of bacterial flagellins and open up possibilities for future studies into their varied roles beyond motility.
Human spermatogonial stem cells retain states with a foetal-like signature
Authors: Bush Stephen J. , Nikola Rafail , Han Seungmin , Suzuki Shinnosuke , Yoshida Shosei , Simons Benjamin D. , Goriely Anne
Published: March 2024

Spermatogenesis involves a complex process of cellular differentiation maintained by spermatogonial stem cells (SSCs). Being critical to male reproduction, it is generally assumed that spermatogenesis starts and ends in equivalent transcriptional states in related species. Based on single-cell gene expression profiling it has been proposed that undifferentiated human spermatogonia can be sub-classified into four heterogenous subtypes, termed states 0, 0A, 0B, and 1. To increase the resolution of the undifferentiated compartment and trace the origin of the spermatogenic trajectory, we re-analysed the single-cell (sc)RNA-seq libraries of 34 post-pubescent human testes to generate an integrated atlas of germ cell differentiation. We then used this atlas to perform comparative analyses of the putative SSC transcriptome both across human development (using 28 foetal and pre-pubertal scRNA-seq libraries) and across species (including data from sheep, pig, buffalo, rhesus and cynomolgus macaque, rat and mouse).

Alongside its detailed characterisation, we show that the transcriptional heterogeneity of the undifferentiated spermatogonial cell compartment varies not only between species but across development. Our findings associate ‘state 0B’ with a suppressive transcriptomic program that, in adult humans, acts to functionally oppose proliferation and maintain cells in a ready-to-react state. Consistent with this conclusion, we show that human foetal germ cells – which are mitotically arrested – can be characterised solely as state 0B. While germ cells with a state 0B signature are also present in foetal mouse (and are likely conserved at this stage throughout mammals), they are not maintained into adulthood. We conjecture that in rodents, the foetal-like state 0B differentiates at birth into the renewing SSC population, whereas in humans it is maintained as a reserve population, supporting testicular homeostasis over a longer reproductive life while reducing mutagenic load. Together, these results suggest that SSCs adopt differing evolutionary strategies across species to ensure fertility and genome integrity over vastly differing life histories and reproductive timeframes.
Multiplexed DNA-PAINT Imaging of the Heterogeneity of Late Endosome/Lysosome Protein Composition
Authors: Bond Charles , Hugelier Siewert , Xing Jiazheng , Sorokina Elena M. , Lakadamyali Melike
Published: March 2024

Late endosomes/lysosomes (LELs) are crucial for numerous physiological processes and their dysfunction is linked to many diseases. Proteomic analyses have identified hundreds of LEL proteins, however, whether these proteins are uniformly present on each LEL, or if there are cell-type dependent LEL sub-populations with unique protein compositions is unclear. We employed a quantitative, multiplexed DNA-PAINT super-resolution approach to examine the distribution of six key LEL proteins (LAMP1, LAMP2, CD63, TMEM192, NPC1 and LAMTOR4) on individual LELs. While LAMP1 and LAMP2 were abundant across LELs, marking a common population, most analyzed proteins were associated with specific LEL subpopulations. Our multiplexed imaging approach identified up to eight different LEL subpopulations based on their unique membrane protein composition. Additionally, our analysis of the spatial relationships between these subpopulations and mitochondria revealed a cell-type specific tendency for NPC1-positive LELs to be closely positioned to mitochondria. Our approach will be broadly applicable to determining organelle heterogeneity with single organelle resolution in many biological contexts.

This study develops a multiplexed and quantitative DNA-PAINT super-resolution imaging pipeline to investigate the distribution of late endosomal/lysosomal (LEL) proteins across individual LELs, revealing cell-type specific LEL sub-populations with unique protein compositions, offering insights into organelle heterogeneity at single-organelle resolution.
All-atom protein sequence design based on geometric deep learning
Authors: Liu Jiale , Guo Zheng , Zhang Changsheng , Lai Luhua
Published: March 2024

The development of advanced deep learning methods has revolutionized computational protein design. Although the success rate of design has been significantly increased, the overall accuracy ofde novodesign remains low. Many computational sequence design approaches are devoted to recover the original sequences for given protein structures by encoding the environment of the central residue without considering atomic details of side chains. This may limit the exploration of new sequences that can fold into the same structure and restrain function design that depends on interaction details. In this study, we proposed a novel deep learning frame-work, GeoSeqBuilder, to learn the relationship between protein structure and sequence based on rotational and translational invariance by extracting the information from relative locations. We utilized geometric deep learning to fetch the spatial local geometric features from protein backbones and explicitly incorporated three-body interactions to learn the inter-residue coupling information, and then determined the central residue type. Our model recovers over 50% native residue types and simultaneously gives highly accurate prediction of side-chain conformations which gives the atomic interaction details and circumvents the dependence of protein structure prediction tools. We used the likelihood confidence logPas scoring function for sequence and structure consistence evaluation which exhibits strong correlation with TM-score, and can be applied to recognize near-native structures from protein decoys pool in protein structure prediction. We have used GeoSeqBuilder to design sequences for two proteins, including thiore-doxin and ade novohallucinated protein. All of the 15 sequences experimentally tested can be expressed as soluble monomeric proteins with high thermal stability and correct secondary structures. We further solved one crystal structure for thioredoxin and two for the hallucinated structure and all the experimentally solved structures are in good agreement with the designed models. The two designed sequences for the hallucination structure are novel without any homologous sequences within the latest released database clust30. The ability of GeoSeqBuilder to design new sequences for given protein structures with atomic details makes it applicable, not only forde novosequence design, but also for protein-protein interaction and functional protein design.
Multi-omics analysis of aggregative multicellularity
Authors: Edelbroek Bart , Orzechowski Westholm Jakub , Bergquist Jonas , Söderbom Fredrik
Published: March 2024

The extent to which mRNA and protein levels or their regulation correlate remains obscure, especially during development. In particular, this is true for organisms that exhibit aggregative multicellularity, such as the social amoebaDictyostelium discoideum. The transcriptome ofD. discoideumhas been thoroughly studied during multicellular development, however the proteome and the correlation to the transcriptome during transition from uni- to multicellular life have not been analyzed in detail. Here, we present the first paired transcriptomics and proteomics developmental time series during aggregative multicellularity. The dataset reveals that mRNA and protein levels correlate highly during growth, but decrease when multicellular development is initiated. This accentuates that transcripts alone cannot accurately describe gene expression. This dataset can therefore be an important resource to study gene expression during aggregative multicellular development, in particular inD. discoideum.