bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of SARS-CoV-2 Persistent Intestinal Epithelial Syndrome (SPIES) as a Novel Disease Entity using Clinical, Histologic, and RNA Programmatic Data
Authors: Wallach Thomas , Soliman Ahmed , Agboola John , Sharma Shagun , Araujo-Coelho Lais , Pittman Meredith , Chatzinakos Christos , Kolokotronis Sergios-Orestis
Published: July 2024

“Long COVID” (LC) remains an ongoing issue and one which has created a substantial burden of disease. Gastrointestinal LC is relatively poorly understood. In this study we characterize a syndrome of persistent SARS-CoV2 viral material via clinical and histologic data, and RNA sequencing

Methods

We reviewed patients aged 5-22 years with an esophagogastroduodenoscopy (EGD) for gastrointestinal (GI) symptoms from 6/2020-6/2023, excluding patients with known histologic disease. Biopsies were sent for immunohistochemical staining. Clinical data was collected. Duodenal, ileal, cecal, and sigmoid colon samples were stained for SARS-CoV-2 using a SARS-CoV-2 nucleocapsid antibody. Slides were reviewed by a blinded pathologist. 8 patients with known duodenal SARS-CoV-2 nucleocapsid antigen (SC-NA) positivity and 8 demographically matched IBS matched patients from prior to 2020 were identified for RNA sequencing comparison. Results were compared with public data from the Gene Expression Omnibus (GEO) data repository for intestinal tissue with IBS and epithelial tissues with active SARS-CoV2 infection.

Results

Of 30 patients, fifteen (50%) were identified to have positive SC-NA. 3 (20%) had received at least a single SARS-CoV2 vaccine in the + cohort, and 8 (53.3%) in the - (P=0.05). Primary symptoms were pain (86%, nausea (66.6%), and weight loss (60%). 37.5% of patients with colonic SC-NA displayed hematochezia. 33% of + patients showed elevated ESR/CRP. Mean + calprotectin was 317.3 vs. 156.4 (p=0.2). 11/15 (73.3%) +SC-NA had large lymphoid aggregates (LLA) (p = 0.00338). RNA expression was consistent with known acute SARS-CoV2 infection. Hub network analysis showed a tight shift in RNA expression centered around HSPE-1p26, with involvement of known SARS-CoV2 immune mediators like NEAT1. DGE comparative analysis with IBS and acute SARS-CoV2 infection showed higher overlap with acute infection vs. IBS. FGSEA analysis with the same source data demonstrated the same.

Conclusions

Our findings establish a syndrome mediated by persistent viral infection (SARS-CoV2 Persistent Intestinal Epithelial Syndrome (SPIES)). We hypothesize that persistent sparse infection drives ongoing immune signaling altering movement and function, creating epithelial and movement effects overlapping with DGBI and IBD
Integration of multi-omics data and deep phenotyping of potato enables novel insights into single- and combined abiotic stress responses
Authors: Zagorščak Maja , Abdelhakim Lamis , Rodriguez-Granados Natalia Yaneth , Široká Jitka , Ghatak Arindam , Bleker Carissa , Blejec Andrej , Zrimec Jan , Novák Ondřej , Pěnčík Aleš , Baebler Špela , Borroto Lucia Perez , Schuy Christian , Županič Anže , Afjehi-Sadat Leila , Wurzinger Bernhard , Weckwerth Wolfram , Novak Maruša Pompe , Knight Marc R. , Strnad Miroslav , Bachem Christian , Chaturvedi Palak , Sonnewald Sophia , Sasidharan Rashmi , Panzarová Klára , Gruden Kristina , Teige Markus
Published: July 2024

Potato is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, or flooding, which are severely exacerbated by climate change. Understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Desirée) under heat, drought and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress-responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising transcriptomics, proteomics, metabolomics and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analysed at the end of the stress period. Integrative analysis of multi-omics data was performed using a bioinformatic pipeline, which was established here, based on machine learning and knowledge networks. Overall, waterlogging had the most immediate and dramatic effects on potato plants, interestingly activating ABA-responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids and diverse stress induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies towards climate-adapted potato varieties.

One Sentence Summary

Integrated multi-omics analysis of high-throughput phenotyping in potato reveals distinct molecular signatures of acclimation to single and combined abiotic stresses related to climate change.
Early and Delayed STAT1-Dependent Responses Drive Local Trained Immunity of Macrophages in the Spleen
Authors: Solomon Aryeh , Ben-Moshe Noa Bossel , Hoffman Dotan , Trzebanski Sebastien , Yehezkel Dror , Vainman Leia , Netea Mihai , Avraham Roi
Published: July 2024

Trained immunity (TI) is the process wherein innate immune cells gain functional memory upon exposure to specific ligands or pathogens, leading to augmented inflammatory responses and pathogen clearance upon secondary exposure. While the differentiation of hematopoietic stem cells (HSCs) and reprogramming of bone marrow (BM) progenitors are well-established mechanisms underpinning durable TI protection, remodeling of the cellular architecture within the tissue during TI remains underexplored. Here, we study the effects of peritoneal Bacillus Calmette–Guérin (BCG) administration to find TI-mediated protection in the spleen against a subsequent heterologous infection by the Gram-negative pathogenSalmonellaTyphimurium (S.Tm). Utilizing single cell RNA-sequencing and flow cytometry, we discerned STAT1-regulated genes in TI-associated resident and recruited splenic myeloid populations. The temporal dynamics of TI were further elucidated, revealing both early and delayed myeloid subsets with time-dependent, cell type-specific STAT1 signatures. Using lineage tracing, we find that tissue-resident red pulp macrophages (RPM), initially depleted by BCG exposure, are restored from both tissue-trained, self-renewing macrophages and from bone marrow-derived progenitors, fostering long lasting local defense. Early inhibition of STAT1 activation, using specific JAK-STAT inhibitors, reduces both RPM loss and recruitment of trained monocytes. Our study suggests a temporal window soon after BCG vaccination, in which STAT1-dependent activation of long-lived resident cells in the tissue mediates localized protection.
Arabidopsis root apical meristem adaptation to an osmotic gradient condition: an integrated approach from cell expansion to gene expression
Authors: Pezzutto Selene Píriz , Martínez-Moré Mauro , Sainz María Martha , Borsani Omar , Silveira Mariana Sotelo
Published: July 2024

Climate change triggers abiotic stress, such as drought and high salinity, that can cause osmotic stress. Water availability can limit plant growth, and the root tip tissues initially sense it. Most experiments destined to understand root growth adaptation to osmotic stress apply homogeneous high osmotic potentials (osmotic shock) to shoots and roots. However, this treatment does not represent natural field conditions where a root may encounter increasing osmotic potentials while exploring the soil. Osmotic shock severely reduces root growth rate, decreasing cell division in the proximal meristem and reducing mature cell length. In this work, we developed anin vitroosmotic gradient experimental system with increasing osmotic potentials. The system generates a controlled osmotic gradient in the root growth zone while exposing the aerial tissues to control conditions. The osmotic gradient system allowed Arabidopsis seedlings of Col-0 andttl1mutant to sustain proper root growth for 25 days, reaching osmotic potentials of −1.2 MPa. We demonstrated that roots of seedlings grown in the osmotic gradient sustain a higher root growth rate than those that were grown under a homogeneous high osmotic potential. Furthermore, we found out that the expression of some genes is modified in the roots grown in the osmotic gradient compared to those grown in osmotic shock. Our data indicate that using an osmotic gradient can improve our understanding of how plants respond to osmotic stress and help find new genes to improve plant field performance.
White matter tract crossing and bottleneck regions in the fetal brain
Authors: Calixto Camilo , Soldatelli Matheus D. , Li Bo , Pierotich Lana , Gholipour Ali , Warfield Simon K. , Karimi Davood
Published: July 2024

There is a growing interest in using diffusion MRI to study the white matter tracts and structural connectivity of the fetal brain. Recent progress in data acquisition and processing suggests that this imaging modality has a unique role in elucidating the normal and abnormal patterns of neurodevelopment in utero. However, there have been no efforts to quantify the prevalence of crossing tracts and bottleneck regions, important issues that have been extensively researched for adult brains. In this work, we determined the brain regions with crossing tracts and bottlenecks between 23 and 36 gestational weeks. We performed probabilistic tractography on 59 fetal brain scans and extracted a set of 51 distinct white tracts, which we grouped into 10 major tract bundle groups. We analyzed the results to determine the patterns of tract crossings and bottlenecks. Our results showed that 20-25% of the white matter voxels included two or three crossing tracts. Bottlenecks were more prevalent. Between 75-80% of the voxels were characterized as bottlenecks, with more than 40% of the voxels involving four or more tracts. The results of this study highlight the challenge of fetal brain tractography and structural connectivity assessment and call for innovative image acquisition and analysis methods to mitigate these problems.
Consequences of decoy site repair and feedback regulation on neurotransmission dynamics
Authors: Gambrell Oliver , Singh Abhyudai
Published: July 2024

Neurons form the fundamental unit of the central nervous system with the human brain containing close to 100 billion neurons. We present a systems-level model of a chemical synapse by which signals from a presynaptic neuron are transmitted to a postsynaptic neuron. In this model, neurotransmitter-filled synaptic vesicles (SVs) dock with a given rate at a fixed number of docking sites in the axon terminal of the presynaptic neuron. Upon the arrival of an action potential (AP), each docked SV has a certain probability to fuse with the presynaptic membrane and release neurotransmitters into the synaptic cleft. After the SV fusion event, the corresponding docking site undergoes repair before becoming available to be reoccupied by an SV. We develop a stochastic model of these coupled processes and derive exact analytical results quantifying the mean and the degree of random fluctuations (i.e., noise) in the levels of docked SVs and released neurotransmitters in response to a train of APs. Our results show that the repair of docking sites exacerbates synaptic depression, i.e., reduces the ability of the chemical synapse to release neurotransmitters in response to an AP. Moreover, repair amplifies statistical fluctuations in neurotransmission for fixed mean neurotransmitter levels. We next consider feedback regulation where the released neurotransmitters affect the rate of SV docking. Counterintuitively, our analysis reveals that for certain physiological parameter spaces, positive feedback loops can reduce noise levels in both the number of docked SVs and neurotransmitters in the cleft.
Modulation Of SUDEP By Central Serotonergic Cooperating with Noradrenergic Circuits: A Synergistic-Dependent Manner
Authors: Xu Qing , Xu XiaoXia , Wu YaXuan , Yang Yue , Gu LeYuan , Zhang ZhuoYue , Zhang ZiWen , Di XuanYi , Wang YuLing , Yu Qian , Lian XiTing , Ma HaiXiang , Zhang HongHai
Published: July 2024

Sudden unexpected death in epilepsy (SUDEP) is the leading cause of death in refractory epilepsy patients. Despite previous accumulating evidence has shown that seizure-induced respiratory arrest (S-IRA) may play the main contributor to SUDEP as an initiating event preeminent cause of mortality, the specific underlying mechanism of action remains unclear. Based on our previous work, serotonin (5-HT) signaling in the dorsal raphe nucleus (DRN) is strongly implicated in S-IRA in animal models, including the DBA/1 mice, on the meanwhile, norepinephrine (NE) neurons of the locus coeruleus (LC) also plays a vital role in regulating respiratory function on its own. Superficially, monoaminergic neuron, as important neurotransmitters in the central nervous system, have similar modes of action in the maintenance of nervous system balance, and each of them has a regulatory effect on SUDEP. However, it remains to be investigated whether monoaminergic neuron family (NE and 5-HT) are related in the mechanism of regulating SUDEP, what is even more curious is whether the two are intrinsically linked. Thus, we hypothesize neural mechanism of central noradrenergic and serotonergic circuits in modulating SUDEP in a synergistic-dependent manner, this endeavor will culminate in a significant breakthrough in elucidating the precise mechanism of action underlying SUDEP. In our study, we will use chemogenetics, optogenetics, calcium signal recording, and bidirectional tracing to explore the internal mechanism of DR-LC regulating the occurrence of SUDEP, and by specifically injecting 5-HT2AR antagonist Ketanserin (KET) and/or NEα-1R antagonist Prazosin into the pre-Bötzinger complex (PBC), it was finally elucidate that the DR-LC-PBC network can effectively reduce the incidence of SIRA. We firstly proposed a powerful target for exploring the reduction of the incidence of SUDEP, which has great clinical translation potential.
Quantifying hope: An EU perspective of rare disease therapeutic space and market dynamics
Authors: Cacoub Emmanuelle , Lefebvre Nathalie Barreto , Milunov Dimitrije , Sarkar Manish , Saha Soham
Published: July 2024

Rare diseases, affecting millions globally, pose a significant healthcare burden despite impacting a small population. While approximately 70% of all rare diseases are are genetic and often begin in childhood, diagnosis remains slow and only 5% have approved treatments. The UN emphasizes improved access to primary care for these patients and their families. Whole-genome sequencing (WGS) and next-generation sequencing (NGS) offer hope for earlier and more accurate diagnoses, potentially leading to preventative measures and targeted therapies. This study explores the therapeutic landscape for rare diseases, analyzing drugs in development and those already approved by the European Medicines Agency (EMA). We differentiate between orphan drugs with market exclusivity and repurposed existing drugs, both crucial for patients. By analyzing market size, segmentation, and publicly available data, this comprehensive study aims to pave the way for improved treatments and a brighter future for rare disease patients.

Funding:

This work received no external funding. External agencies or companies had no role in the idea and study design, model execution and evaluation, and drafting of figures and manuscript.
TDSTDP
Authors: Liu Bingkun
Published: July 2024

This is a preliminary thesis on Temporal Difference Spike-Timing Dependent Plasticity (TDSTDP), a variation of STDP that considers dendritic potential. TDSTDP is capable of performing temporal difference (TD) learning without dopamine modulation. Major characteristics of TD learning, including value estimation, value propagation, and temporal shifting of dopamine, are demonstrated in simulations. Additionally, a synaptic calcium model demonstrates its biological plausibility.
Stiffness-tunable neurotentacles for minimally invasive implantation and long-term neural activity recordings
Authors: Wang Yang , Xu Xing , Yang Xiaowei , Tang Rongyu , Chen Ying , Wang Yijun , Liang Jing , Pei Weihua
Published: July 2024

Flexible implantable microelectrodes have been demonstrated to exhibit excellent biocompatibility for chronic neural activity recordings. However, the low bending strength of the commonly employed flexible materials presents a significant challenge for probe insertion into the brain. Traditional implantation methods for flexible electrodes generally require additional auxiliary materials or tools, which tend to have a much larger footprint than the probes themselves, greatly increasing the damage to neurons during insertion. Here we have proposed a stiffness-tunable polyimide probe for deep brain implantation, referred to as Neurotentacle, enabled by embedded microchannels in which the liquid pressure is controllable (from 0.1MPa to more than 2.0MPa). During the insertion phase into the brain, the neurotentacle can pose a high stiffness under elevated internal pressure to penetrate the brain tissues without the use of any additional materials or tools. Once the device has been successfully inserted, it can regain its flexibility by reducing the internal pressure. Importantly, the novel multilayer microfabrication process keeps the structural dimensions of the neurotentacle similar to those of a regular flexible probe. Therefore, the neurotentacle can produce an extremely low level of damage to brain tissue during its insertion phase, while extending its long-term biocompatibility and stability, which has been experimentally verified in histological evaluations conducted on both acute and chronic animal specimens. In addition, the chronically implanted neurotentacles enabled stable neural activity recordings in mice with an average spike yield of 96% and an average signal-to-noise ratio of 15.2. The proposed neurotentacle does not necessitate the use of complex devices and its insertion process is straightforward and highly controllable, thus rendering it an appealing technique for minimally invasive implantation and long-term neural recording of flexible electrodes.
A Molecular Image-based Explainable Artificial intelligence Framework Identifies Novel Candidate Antibiotics
Authors: Lin Kingsten , Yang Yuxin , Cheng Feixiong
Published: July 2024

The continued growth of antibiotic resistance and the slowing of antibiotic discovery poses a large challenge in fighting infectious diseases. Recent advances in Artificial intelligence (AI) technologies offer a time- and cost-effective solution for the rapid development of effective antibiotics. In this study, we presented an explainable AI framework from a pre-trained model using 10 million drug-like molecular images. Specifically, we created a fine-tuned ImageMol from experimentalStaphylococcus aureusinhibition assays which contained 24,521 molecules consisting of 516 active compounds and 24,005 non-active compounds. Our optimized AI model achieved a strong AUROC of 0.926. The model was then used to predict the antibiotic activities from 10,247 FDA-approved, clinically investigational, or experimental molecules from the DrugBank database. After further filtering, 340 molecules were identified to have antibacterial behavior while simultaneously being dissimilar to known antibiotics. Finally, 76 candidates were identified as FDA-approved drugs for other applications. Thus, those candidates can be repurposed into needed novel antibiotics. We further illustrated explainable molecular images for top predicted candidate drugs via Gradient-weighted Class Activation Mapping (Grad-CAM) heatmap analysis. In summary, the presented molecular image-based AI model in drug discovery could be highly favorable due to its high performance, speed, and biological interpretation.
The multifaceted process of human coronary atherosclerotic cap destabilisation
Authors: Bruijn L.E. , Neves N. Fonseca , van Rhijn C.M. , Hamming J.F. , van den Bogaerdt AJ , Lindeman J.H.N.
Published: July 2024

Introduction

Plaque rupture is the primary trigger of the acute clinical manifestations of atherosclerotic disease. So far, factual insight in the processes leading up to cap destabilization is largely missing. In order to overcome this knowledge gap, a pseudo-timeline of atherosclerosis progression was established in order to systematically map the qualitative changes in cap characteristics during lesion progression and destabilization.

Material and Methods

A pseudo-timeline was created by randomly selecting preclassified (revised AHA classification, at least 10 per stage) left coronary artery FFPE specimens obtained during tissue donation (aortic valve procurement). Qualitative changes were visualized by (immuno)histochemistry, immunofluorescence and confocal microscopy. Scoring was performed by two observers using semiquantitative scoring estimates.

Results

The median age of the donors was 56 years (IQR 51.5-59), and 67% of the patients was male. Movat staining indicated a consistent pattern of cap formation, maturation and destabilization. A distinctive cap emerged in the early fibroatheroma stage of progressive atherosclerosis. Disease progression was accompanied by profound fibrotic changes in the gap, and a progressive presence of inanotic (nutritional deprivation leading to dissolution) mesenchymal cells. Plaque rupture was preceded by thinning of the collagen fibers and accumulation of foam cells in the central portion of the thin cap. No evidence was found for a direct involvement of neovascularization in the destabilization process.

Conclusion

The pseudo-time line of atherosclerotic lesion development characterizes the development of an unstable cap as a degenerative and fibrotic process with progressive exhaustion of the mesenchymal cell population. This study provides a rationale for the limited efficacy of medical strategies aimed at plaque stabilization.
Molecular basis of enhanced GLP-1 signaling mediated by GLP-1(9-36) in conjunction with LSN3318839
Authors: Li Jie , Li Guanyi , Mai Yiting , Liu Xiao , Yang Dehua , Zhou Qingtong , Wang Ming-Wei
Published: July 2024

Glucagon-like peptide-1 (GLP-1) receptor (GLP-1R) is essential for glucose metabolism and energy balance. It is primarily activated by the endogenous hormone GLP-1(7-36) and its weaker metabolite GLP-1(9-36). Although GLP-1(9-36) was previously considered biologically inactive, emerging evidence indicate that it exerts cardioprotective and insulinotropic actions. Here, we present cryo-electron microscopy structures showing that GLP-1(9-36) binds to an atypical site composed of the upper halves of transmembrane helices 1 (TM1) and 2 (TM2), extracellular loop 1, and the extracellular domain, distinct from the binding site of GLP-1(7-36). Meanwhile, LSN3318839, an orally effective positive allosteric modulator selective for GLP-1(9-36), anchors in the TM1-TM2 cleft and repositions GLP-1(9-36) to adopt a binding pose like GLP-1(7-36), thereby enhancing GLP-1R-mediated signal transduction. Mutagenesis and molecular dynamics simulations confirmed the crucial interactions and structural adjustments involved in this modulation. Our study uncovers a novel binding mode of GLP-1 metabolite and allosteric modulation that augments GLP-1R signaling, both are potentially insightful to unveil the physiological role of GLP-1(9-36) and design better small molecule therapeutics targeting GLP-1R.
Standards for Health Promoting Hospitals and Health Services: Development and tools for implementation and measurement
Authors: Groene Oliver , Katsaros Keriin , Chiarenza Antonio , Fawkes Sally , Kristenson Margareta
Published: July 2024

The need to reorient health services towards health promotion is greater than ever. Health systems are overburdened by treating an ever-growing number of chronic patients, many of which seek care for problems that could partly be avoided or postponed through better health promotion implementation. Since its establishment, the International Network of Health Promoting Hospitals and Health Services has explicitly addressed this issue by developing specific standards on evidence-based health promotion approaches and interventions that should be implemented in health services organizations. These approaches and interventions not only address the health of patients, but also of staff and the wider community. Since the development of the standards in 2006, health systems and legitimate patient demands have evolved considerably. At the same time, topics emerged that are strongly associated with health promotion strategies, such as the climate impact of health services. An update of the 2006 standards was therefore overdue.

The purpose of this paper is, firstly, to describe the methodology used to develop and outline the 2020 Standards for Health Promoting Hospitals and Health Services. Secondly, we present a self-assessment tool, which was developed to operationalize and provide concrete measurable elements for each standard against which performance and progress towards implementation can be measured and tracked. The 2020 standards are health-oriented, continue to uphold the strategies defined in the Ottawa Charter for Health Promotion, and respond to recent international declarations and charters.
Autistic voice: Sharing autistic children’s experiences and insights
Authors: Mullally Sinéad L. , Wood Alice E. , Edwards Cherice C. , Connolly Sophie E. , Constable Hannah , Watson Stuart , Rodgers Jacqui , Rose Kieran , King Nic
Published: July 2024

Autism research rarely amplifies the voices of autistic children. Here, we aim to counter this by collating and sharing the first-hand experiences and insights of autistic children. A total of 136 children (8-14 years of age) self-reported their experiences of being autistic via a semi-structured online questionnaire/video call. Both qualitative and quantitative data was gathered, and inductive thematic analysis used to analyse qualitative responses. Four core themes were identified: ‘Safety and Security’, ‘Conformity, Fitting in and Masking’, ‘Identity’, and ‘Sensory Sensitivity. The initial theme of safety and security permeated the children’s narratives and overwhelmingly, the children spoke of the need for them to be alert to who in their lives is a safe person and who is not. They were also highly attuned to whether specific places are safe for them, as past experiences appear to have taught them that their safety in everyday places cannot be assumed. Teachers, health and social care professionals, and neurotypical peers were frequently singled out as unsafe people and school as an unsafe place, whilst parents, home, and autistic peers were often referred to as safe. This distinction was also evident in the statistical analysis of the quantitative data, whereby autistic children were significantly more likely to report that it is okay for them to be autistic at home, relative to when they are at school or with their friends/peers. Judging a person as safe was closely linked to that persons’ understanding of the child and of their autistic experiences, and understanding was important in establishing trust. When trust was established, it appeared possible for trusted people to facilitate a sense of safety for the children even within otherwise unsafe places. A sense of belonging within autistic/neurodivergent communities was positively linked to the core theme of safety and security and to having a positive autistic identity, whilst masking and sensory distress were linked to feeling unsafe and insecure. These first-hand accounts provide valuable insights into autistic children’s lives and demand that we urgently explore how places outside of the family home (including places of education) can be transformed into safe spaces for autistic children.
Enhanced Discrimination ofClostridioides difficileTransmission Using Whole Genome Sequencing andIn-SilicoMulti-locus Variable Number Tandem Repeat Analysis
Authors: Sundermann Alexander J. , Mills Emma G. , Srinivasa Vatsala Rangachar , Griffith Marissa P. , Ereifej Deena , Waggle Kady D. , Snyder Graham M. , Van Tyne Daria , Pless Lora Lee , Harrison Lee H.
Published: July 2024

Whole genome sequencing (WGS) is used to establish genetic relatedness of bacteria and track outbreaks in healthcare settings. While WGS provides sufficient discriminatory power to make inferences about genetic relatedness and transmission for most bacterial species, WGS forClostridioides difficileoften fails to provide discriminatory power, even at low single nucleotide polymorphism (SNP) differences. Multi-locus variable number tandem repeat analysis (MLVA), which analyzes rapidly mutating tandem repeat loci has previously been shown to be useful for this purpose forC. difficile. We investigated whetherin silicoMLVA can further elucidate genetic relatedness ofC. difficileclusters identified by short-read WGS but lacking epidemiological links. Potential healthcare-associated toxin-positiveC. difficileisolates were collected at our hospital from November 2016 to November 2019. Short-read WGS was performed on the Illumina platform to cluster isolates with ≤2 SNPs, and Nanopore long-read sequencing was used to resolve MLVA loci within these clustered isolates. Among 666 isolates, 62 unique patient isolates met the ≤2 SNP criterion and underwent MinION sequencing. Of the 105 pairs with 0-2 SNP differences, 79.0% had a summed tandem-repeat difference (STRD) of 0-5, 10.5% had an STRD of 6-10, and 10.5% had an STRD of 11-20. A significant correlation was found between a lower STRD value and the presence of a unit/procedure epidemiological link within low SNP clusters (OR: 0.45; 95% CI: 0.29, 0.70). Our findings demonstrate that MLVA provides additional genomic discrimination for closely relatedC. difficileisolates identified by WGS, enhancing outbreak investigation precision.
Early morphogenetic patterns of protonemata and gametophores ofPhyscomitrium patens(Hedw.) Mitt
Authors: Raju M.V.S. , Ashton N.W.
Published: July 2024

In axenic culture, protonemata ofPhyscomitrium(formerlyPhyscomitrella)patens(Hedw.) Mitt. are comprised of chloronemata and caulonemata that can be distinguished morpho-structurally. On solid nutrient agar medium, a protonemal inoculum proliferates, initially generating primary chloronemata, and expands radially across the surface of the substratum forming approximately round colonies. The expansion of the colonies derives mainly from centrifugal elongation of newly formed caulonemata, which arise by differentiation of primary chloronemal apical cells in the central region. Most commonly, oblique cross walls separate cells of the uniseriate caulonemal filaments. Each oblique wall organises a smaller and a larger angle with the outer wall of a tubular caulonemal cell. The smaller angle may lie in four different positions, vertically upward or downward, and laterally, to the right or left, parallel to the surface of the solid medium. Chloronemal filaments, which contain cells separated by transverse cross walls, develop from side branch initials (SBIs) at or near the smaller angle at the distal end of caulonemal cells. Like the smaller angle of the oblique cross walls in caulonemata, these secondary chloronemata also show four different orientations, vertically, upward or downward, and laterally, right or left. A strong inverse correlation exists between the placement of SBIs and secondary chloronemata and the direction of caulonemal tip growth. If the caulonemal tips curve downward into the medium, chloronemata are situated vertically on the upper side of caulonemata; similarly, if they turn upward, chloronemata are situated on the lower side. A similar correlation exists when caulonemal tips curve to the right or left on the surface of solid medium, in which case laterally directed chloronemata grow in the opposite direction, i.e. on the outside of the curve. The procumbent caulonemata with their associated protruding secondary chloronemal branches are reminiscent of the heterotrichous branching habit of filaments of some green algae. Gametophore buds develop from a minority of caulonemal SBIs and also occasionally from chloronemata; a stalk cell, which resembles a chloronemal cell, supports each bud. Buds develop into leafy gametophores that are arranged in a fairy ring. We discuss the relative merits of several models that might explain the temporally and spatially regulated clustering of buds resulting in the formation of a fairy ring.
The Orphan G Protein-Coupled Receptor GPR52 is a Novel Regulator of Breast Cancer Multicellular Organization
Authors: Hanif Sarah Z. , Au CheukMan Cherie , Torregroza Ingrid , Jannath Syeda Y. , Fabiha Tabassum , Bhinder Bhavneet , Washburn Michael , Devost Dominic , Liu Shuchen , Bhardwaj Priya , Evans Todd , Anand Pradeep Kumar , Tarran Robert , Palikhe Sailesh , Elemento Olivier , Dow Lukas , Blenis John , Hébert Terence E. , Brown Kristy A.
Published: July 2024

G protein-coupled receptors (GPCRs) are the largest class of membrane-bound receptors and transmit critical signals from the extracellular to the intracellular spaces. Transcriptomic data of resected breast tumors shows that low mRNA expression of the orphan GPCR GPR52 correlates with reduced overall survival in breast cancer patients, leading to the hypothesis that loss of GPR52 supports breast cancer progression. CRISPR-Cas9 was used to knockout GPR52 in human triple-negative breast cancer (TNBC) cell lines MDA-MB-468 and MDA-MB-231, and in the non-cancerous breast epithelial cell line, MCF10A. Loss of GPR52 was found to be associated with increased cell-cell interaction in 2D cultures, altered 3D spheroid morphology, and increased propensity to organize and invade collectively in Matrigel. Furthermore, GPR52 loss was associated with features of EMT in MDA-MB-468 cells. To determine thein vivoimpact of GPR52 loss, MDA-MB-468 cells were injected into zebrafish and loss of GPR52 was associated with a greater total cancer area compared to control cells. RNA-sequencing and proteomic analyses of GPR52-null breast cancer cells reveal an increased cAMP signaling signature. Consistently, we found that treatment of wild-type (WT) cells with forskolin, which stimulates production of cAMP, induces some phenotypic changes associated with GPR52 loss, and inhibition of cAMP production rescued some of the GPR52 KO phenotypes. Overall, our results reveal GPR52 loss as a potential mechanism by which breast cancer progression may occur and support the investigation of GPR52 agonism as a therapeutic option in breast cancer.

Statement of Significance

We show that loss of the orphan G protein-coupled receptor GPR52 in human breast cell lines leads to increased cell clustering, hybrid/partial EMT, and increased tumor burden in zebrafish.
Bacterial Wastewater-Based Epidemiology Using Surface-Enhanced Raman Spectroscopy and Machine Learning
Authors: Herndon Liam K. , Zhang Yirui , Safir Fareeha , Ogunlade Babatunde , Balch Halleh B. , Boehm Alexandria B. , Dionne Jennifer A.
Published: July 2024

Wastewater-based epidemiology (WBE) is a powerful tool for monitoring community disease occurrence, but current methods for bacterial detection suffer from limited scalability, the need fora prioriknowledge of the target organism, and the high degree of genetic similarity between different strains of the same species. Here, we show that surface-enhanced Raman spectroscopy (SERS) can be a scalable, label-free method for detection of bacteria in wastewater. We preferentially enhance Raman signal from bacteria in wastewater using positively-charged plasmonic gold nanorods (AuNRs) that electrostatically bind to the bacterial surface. Transmission cryoelectron microscopy (cryoEM) confirms that AuNRs bind selectively to bacteria in this wastewater matrix. We spike the bacterial speciesStaphylococcus epidermidis, Staphylococcus aureus, Serratia marcescens, andEscerichia coliand AuNRs into filter-sterilized wastewater, varying the AuNR concentration to achieve maximum signal across all pathogens. We then collect 540 spectra from each species, and train a machine learning (ML) model to identify bacterial species in wastewater. For bacterial concentrations of 109cells/mL, we achieve an accuracy exceeding 85%. We also demonstrate that this system is effective at environmentally-realistic bacterial concentrations, with a limit of bacterial detection of 104cells/mL. These results are a key first step toward a label-free, high-throughput platform for bacterial WBE.
Pheno-morphological screening and acoustic sorting of 3D multicellular aggregates using drop millifluidics
Authors: Rembotte Leon , Beneyton Thomas , Buisson Lionel , Badon Amaury , Boyreau Adeline , Douillet Camille , Hermant Loic , Jana Anirban , Nassoy Pierre , Baret Jean-Christophe
Published: July 2024

Three-dimensional multicellular aggregates like organoids and spheroids have become essential tools to study the biological mechanisms involved in the progression of diseases. In cancer research, they are now widely used as in vitro models for drug testing. However, their analysis still relies on tedious manual procedures, which hinders their routine use in large-scale biological assays. Here, we introduce a novel drop millifluidic approach to screen and sort large populations containing over one thousand multicellular aggregates. Our system utilizes real-time image processing to detect pheno-morphological traits in cellular aggregates. They are then encapsulated in millimetric drops, actuated on-demand using the acoustic radiation force. We demonstrate the performance of our system by sorting spheroids with uniform sizes from a heterogeneous population, and by isolating organoids from spheroids with different phenotypes. We anticipate that this work offers the potential to standardize drug testing on multicellular aggregates, which promises accelerated progress in biomedical research.
Protein restriction associated with high fat induces metabolic dysregulation without obesity in juvenile mice
Authors: Joly Amélie , Thoumas Jean-Louis , Lambert Anne , Caillon Estelle , Leulier François , De Vadder Filipe
Published: July 2024

Dysregulation of energy metabolism, including hyperglycemia, insulin resistance and fatty liver have been reported in a substantial proportion of lean children. However, non-obese murine models recapitulating these features are lacking to study the mechanisms underlying the development of metabolic dysregulations in lean children. Here, we develop a model of diet-induced metabolic dysfunction without obesity in juvenile mice by feeding male and female mice a diet reflecting Western nutritional intake combined with protein restriction (mWD) during 5 weeks after weaning. mWD-fed mice (33% fat, 8% protein) do not exhibit significant weight gain and have moderate increase in adiposity compared to control mice (16% fat, 20% protein). After 3 weeks of mWD, juvenile mice have impaired glucose metabolism including hyperglycemia, insulin resistance and glucose intolerance. mWD also triggers hepatic metabolism alterations, as shown by the development of simple liver steatosis. Both male and female mice fed with mWD displayed metabolic dysregulation, which a probiotic treatment withLactiplantibacillus plantarumWJL failed to improve. Overall, mWD-fed mice appear to be a good preclinical model to study the development of diet-induced metabolic dysfunction without obesity in juveniles.
Dynamic B0field shimming for improving pseudo-continuous arterial spin labeling at 7 Tesla
Authors: Ji Yang , Woods Joseph G. , Li Hongwei , Okell Thomas W.
Published: July 2024

Purpose

B0inhomogeneity within the brain-feeding arteries is a major issue for pseudo-continuous arterial spin labeling (PCASL) at 7T because it reduces labeling efficiency and leads to a loss of perfusion signal. This study aimed to develop a vessel-specific dynamic B0field shimming method for 7T PCASL to enhance labeling efficiency by correcting off-resonance in the arteries within the labeling region.

Methods

We implemented a PCASL sequence with dynamic B₀ shimming at 7T that compensates for B0field offsets at the brain-feeding arteries by updating linear shimming terms and adding a phase increment to the PCASL RF pulses. Rapidly acquired vessel-specific B₀ field maps were used to calculate dynamic shimming parameters. We evaluated both 2D and 3D variants of our method, comparing their performance against established global frequency offset and optimal-encoding-scheme (OES)-based corrections. Cerebral blood flow (CBF) maps were quantified before and after corrections. CBF values from different methods in the whole brain, white matter, and grey matter regions were compared.

Results

All off-resonance correction methods significantly enhanced perfusion signals across the brain. The proposed vessel-specific dynamic B₀ shimming method improved labeling efficiency while maintaining optimal static shimming in the imaging region. Perfusion-weighted images demonstrated the superiority of 3D dynamic B₀ shimming method compared to global or 2D-based correction approaches. CBF analysis revealed that 3D dynamic B₀ shimming significantly increased CBF values relative to the other methods.

Conclusion

Our proposed dynamic B0shimming method offers a significant advancement in PCASL robustness and effectiveness, enabling full utilization of 7T ASL’s high sensitivity and spatial resolution.
Hexokinase-I directly binds to a charged membrane-buried glutamate of mitochondrial VDAC1 and VDAC2
Authors: Bieker Sebastian , Timme Michael , Woge Nils , Hassan Dina G. , Brown Chelsea M. , Marrink Siewert J. , Melo Manuel N. , Holthuis Joost C. M.
Published: July 2024

Binding of hexokinase HKI to mitochondrial voltage-dependent anion channels (VDACs) has far-reaching physiological implications. However, the structural basis of this interaction is unclear. Combining computer simulations with experiments in cells, we here show that complex assembly relies on intimate contacts between theN-terminal α-helix of HKI and a charged membrane-buried glutamate on the outer wall of VDAC1 and VDAC2. Protonation of this residue blocks complex formation in silico while acidification of the cytosol causes a reversable release of HKI from mitochondria. Membrane insertion of HKI occurs adjacent to the bilayer-facing glutamate where a pair of polar channel residues mediates a marked thinning of the cytoplasmic leaflet. Disrupting the membrane thinning capacity of VDAC1 dramatically impairs its ability to bind HKI in silico and in cells. Our data reveal key topological and mechanistic insights into HKI-VDAC complex assembly that may benefit the development of therapeutics to counter pathogenic imbalances in this process.
Impact of vertebrate host parasitaemia onPlasmodiumdevelopment within mosquitoes
Authors: Isaïa Julie , Baur Molly , Wassef Jérôme , Monod Sarah , Glaizot Olivier , Christe Philippe , Pigeault Romain
Published: July 2024

Background

In vector-borne diseases, invertebrate hosts are exposed to highly variable quantities of parasites during their blood meal. This heterogeneity may partly explain the overdispersed distribution of parasites within the vector population, as well as the variability in the extrinsic incubation period (EIP) of the parasite. Indeed, the quantity of parasites ingested is often considered as a good predictor of the quantity of parasites that will develop within the vectors, as well as the speed at which they will develop (EIP). However, density-dependent processes can strongly influence the relationship between parasite burden in the vertebrate host and in vectors, making this relationship not always clear.

Methods

Here, we used the avian malaria system to investigate whether the proportion of red blood cells infected by sexual and/or asexual stages of malaria parasite influences the intensity of malaria infection and the EIP ofPlasmodiumwithin the invertebrate vectors. For this purpose, we have experimentally infected twelve vertebrate hosts in order to generate a range of intensity of infection. More than a thousand mosquitoes took a blood meal on these hosts and the development ofPlasmodiumwithin the vectors was followed for more than 20 days.

Results

The main finding presented in this study reveals a negative relationship between the intensity of infection in the vertebrate host and the EIP. Four days were sufficient for 10% of infected mosquitoes fed on the most infected hosts to become infectious. However, the number of transmissible stages did not significantly vary according to the vertebrate host intensity of infection.

Conclusion

While the quantity of ingested parasites had no impact on the density of transmissible stages in infectious mosquitoes, the EIP was affected. Studies have demonstrated that small changes in the EIP can have a significant effect on the number of mosquitoes living long enough to transmit parasites. Here, we observed a difference of 4-6 days in the detection of the first transmissible stages, depending on the intensity of infection of the bitten vertebrate host. Considering that a gonotrophic cycle lasts 3-4 days, the shortened EIP observed here may have significant effects onPlasmodiumtransmission.
Prediction of plant resistance proteins using alignment-based and alignment-free approaches
Authors: Gahlot Pushpendra Singh , Choudhury Shubham , Bajiya Nisha , Kumar Nishant , Raghava Gajendra P. S.
Published: July 2024

Plant Disease Resistance (PDR) proteins are critical in identifying and killing plant pathogens. Predicting PDR protein is essential for understanding plant-pathogen interactions and developing strategies for crop protection. This study proposes a hybrid model for predicting and designing PDR proteins against plant-invading pathogens. Initially, we tried alignment-based approaches, such as BLAST for similarity search and MERCI for motif search. These alignment-based approaches exhibit very poor coverage or sensitivity. To overcome these limitations, we developed alignment-free or machine learning-based methods using compositional features of proteins. Our machine learning-based model, developed using compositional features of proteins, achieved a maximum performance AUROC of 0.92. The performance of our model improved significantly from AUROC of 0.92 to 0.95 when we used evolutionary information instead of protein sequence. Finally, we developed a hybrid or ensemble model that combined our best machine learning model with BLAST and obtained the highest AUROC of 0.98 on the validation dataset. We trained and tested our models on a training dataset and evaluated them on a validation dataset. None of the proteins in our validation dataset are more than 40% similar to proteins in the training dataset. One of the objectives of this study is to facilitate the scientific community working in plant biology. Thus, we developed an online platform for predicting and designing plant resistance proteins, “PlantDRPpred” (https://webs.iiitd.edu.in/raghava/plantdrppred).

Highlights

Development of a Machine-learning model for resistance protein prediction.

Used alignment-based and alignment-free ensemble methods.

Web server development and standalone package.

Prediction and design of PDR proteins.