bluuebunny/crossref_metadata_2025 huggingface dataset:
Discovering Signature Disease Trajectories in Pancreatic Cancer and Soft-tissue Sarcoma from Longitudinal Patient Records
Authors: Wang Liwei , Li Rui , Wen Andrew , Lu Qiuhao , Wang Jinlian , Ruan Xiaoyang , Gamboa Adriana , Malik Neha , Roland Christina L. , Katz Matthew H.G. , Lyu Heather , Liu Hongfang
Published: February 2025

Understanding the disease trajectories of specific diseases can provide important clinical insights. In this paper, we aimed to discover signature disease trajectories of 3 rare cancer types: pancreatic cancer, soft tissue sarcoma (STS) of the trunk and extremity (STS-TE), and STS of the abdomen and retroperitoneum (STS-AR), leveraging IQVIA Oncology Electronic Medical Record. We identified significant diagnosis pairs in patients with these cancers through matched cohort sampling, statistical computation, right-tailed binomial hypothesis test, and visualized trajectories up to 3 progressions. Results included 266 significant diagnosis pairs for pancreatic cancer, 130 for STS-TE, and 118 for STS-AR. We further found 44 2-hop (i.e., 2- progression) and 136 3-hop trajectories before pancreatic cancer, 36 2-hop and 37 3-hop trajectories before STS-TE, and 17 2-hop and 5 3-hop trajectories before STS-AR. Meanwhile, we found 54 2-hop and 129 3-hop trajectories following pancreatic cancer, 11 2-hop and 17 3- hop trajectories following STS-TE, 5 2-hop and 0 3-hop trajectories following STS-AR. Systematic validation of discovered trajectories with the UTHealth Electronic Health Records confirmed the feasibility and reliability of our method. Our result suggested that some key clinical features can potentially serve as early markers of rare cancers. This approach is generalizable to other disease types and real-world longitudinal patient records.
Exploring Causal Association between Neuroticism Subclusters and Risk of Coronary Atherosclerosis: A Mendelian Randomization Analysis based on Genome-Wide Association Studies
Authors: Ming Jie , Li Rui-lin , Gao Yi-li , Huang Shu-ting , Yao Xiao-yan , Tan Qi , Zong Ming , Fan Lie-ying
Published: February 2025

Background

Understanding the risk factors associated with coronary atherosclerosis (CA)—an evident cardiovascular disease—is vital. This study aimed to explore the causal relationship between neuroticism subclusters and CA, focusing on lipids as mediators, using genome-wide association studies and Mendelian randomization (MR).

Methods and Results

Instrumental variables were selected based on their genetic associations with neuroticism subclusters and CA. Causal effects were primarily assessed using inverse variance-weighted (IVW) methods. Sensitivity analyses and colocalization analyses were conducted, and possible confounders were determined using multivariable MR analysis. IVW modeling revealed that neuroticism subclusters significantly affect CA risk (ebi-a-GCST006475odds ratio [OR]: 1.02, 95% confidence interval [95%CI]: 1.01–1.03,P= 1.52E-05;ebi-a-GCST006478OR: 1.01, 95%CI: 1.00–1.02,P= 0.026;ebi-a-GCST006950OR: 1.01, 95%CI: 1.00–1.02,P= 0.036). Cochran’s Q test demonstrated moderate heterogeneity (ebi-a-GCST006475,P< 0.05,I²= 28%). The Steiger test confirmed the correct causal direction (P< 0.05). Multivariable MR remained significant after adjusting for confounders (P< 0.05). Mediation analyses suggested that lipids partially mediated the neuroticism–CA effect.

Conclusions

Overall, our findings indicated a causal link between neuroticism subclusters and CA, with lipids partially mediating this relationship, emphasizing the role of psychosocial factors in cardiovascular risk assessment and intervention strategies.
Neuronal development shapes activity-dependent gene expression in a stimulus-specific manner
Authors: Lukin Jeronimo , Beckel Maximiliano S , Pedroncini Olivia , Giusti Sebastian A , Linenberg Ivana Marcela , Patop Ines Lucia , Chernomoretz Ariel , Marin-Burgin Antonia , Kadener Sebastian , Refojo Damian
Published: February 2025

Neuronal activity-dependent gene expression is fundamental to a wide variety of brain functions. However, how development progress and stimulation modalities specifically affect neuron transcription is not fully understood. In this work, we first investigate the influence of development on neuronal firing and activity-driven transcription. We used an RNA sequencing approach over 7 daysin vitro(DIV) or mature 21 DIV neurons, comparing neuronal depolarization with potassium chloride (KCl) versus Biccuculine application, a synaptic modality to induce neuronal activity. To further investigate how different activity patterns influence gene transcription in mature neurons, we compared global gene expression in neurons treated with three different and extensively used activation protocols: KCl, Bicuculine (Bic), and TTX withdrawal (TTXw). Our results demonstrate a strong influence of development on activity-dependent gene expression, and showed that different patterns of neuronal activity induce different transcriptional profiles and exhibit distinct temporal dynamics for the same genes. These findings offer novel insights into the complex relationship between neuronal activity and gene expression, shedding light on the context-dependent nature of activity-dependent transcriptional responses.
Ciliated cell domains with locally coordinated ciliary motion generate a mosaic of microflows in the brain’s lateral ventricles
Authors: Mellanson Kennelia , Zhou Lei , Michurina Tatiana , Mikhailik Anatoly , Benveniste Helene , Samaras Dimitris , Enikolopov Grigori , Peunova Natalia
Published: February 2025

Circulation of cerebrospinal fluid (CSF) through the brain’s ventricles is essential for maintaining brain homeostasis and supporting neurogenesis. CSF flow is supported by the structural polarization of multiciliated cells, which align with the flow direction. However, it remains unclear how the organization of tissue-wide polarity across the ciliary epithelium comprised of thousands of cells, determines the trajectory of the flow and efficient distribution of the CSF.

Here, we used new approaches to analyze the organization of translational polarity across extensive areas of the lateral ventricular wall. We also used live imaging to examine cilia motion, flow trajectories, and ciliary beat frequency (CBF) in live preparations of ventricles. In addition to the primary flow running across the ventricular wall from the posterior area to the anterior (P-A), we found multiple local microflows with both direct and curved trajectories that deviate from the mainstream P-A direction.

Our results suggest that the ciliated epithelium in the lateral ventricles varies in the alignment of ciliated cell translational polarity: whereas in the narrow dorsal area translational polarity is aligned with the direction of the mainstream flow, in the periphery of the mainstream it is organized into distinct cell clusters with locally aligned polarity vectors. We posit that the cluster organization of the multiciliated ependymal cells underpins the generation of a complex mosaic of flows, with the local microflows facilitating the wide spreading of the CSF across the ependyma. We demonstrate that nNOS is involved in the control of translational polarity, cluster organization, microflows, and CBF in the ependyma.

Significance

The flow of cerebrospinal fluid (CSF) is crucial for brain homeostasis. This flow is driven by the coordinated beating of cilia on thousands of ciliated cells. Planar polarity vector of the ciliated cells is aligned with the flow direction in the areas of the ependyma underlying the mainstream flow (1). However, the overall alignment of planar cell polarity and flow across the whole tissue is unclear. Here we report a discovery of complex flow patterns over the ependyma, consisting of numerous microflows in the periphery of the mainstream flow. Using new approaches, we found that planar polarity of the ependymal ciliated cells on the periphery of the mainstream flow aligns only locally, indicating a clustered organization of the ependyma that supports various flow directions.
Characterization of neurite and soma organization in the brain and spinal cord with diffusion MRI
Authors: Schilling Kurt G , Palombo Marco , Witt Atlee A. , O’Grady Kristin P. , Pizzolato Marco , Landman Bennett A , Smith Seth A.
Published: February 2025

The central nervous system (CNS), comprised of both the brain and spinal cord, and is a complex network of white and gray matter responsible for sensory, motor, and cognitive functions. Advanced diffusion MRI (dMRI) techniques offer a promising mechanism to non-invasively characterize CNS architecture, however, most studies focus on the brain or spinal cord in isolation. Here, we implemented a clinically feasible dMRI protocol on a 3T scanner to simultaneously characterize neurite and soma microstructure of both the brain and spinal cord. The protocol enabled the use of Diffusion Tensor Imaging (DTI), Standard Model Imaging (SMI), and Soma and Neurite Density Imaging (SANDI), representing the first time SMI and SANDI have been evaluated in the cord, and in the cord and brain simultaneously. Our results demonstrate high image quality even at high diffusion weightings, reproducibility of SMI and SANDI derived metrics similar to those of DTI with few exceptions, and biologically feasible contrasts between and within white and gray matter regions. Reproducibility and contrasts were decreased in the cord compared to that of the brain, revealing challenges due to partial volume effects and image preprocessing. This study establishes a harmonized approach for brain and cord microstructural imaging, and the opportunity to study CNS pathologies and biomarkers of structural integrity across the neuroaxis.
Learning molecular traits of human pain disease via voltage-gated sodium channel structure renormalization
Authors: Xenakis Markos N. , Lampert Angelika
Published: February 2025

Mammalian neurophysiology vitally depends on the stable functioning of transmembrane, pore-forming voltage-sensing proteins known as voltage-gated sodium channels (NaVChs). Deciphering the principles of NaVCh spatial organization can illuminate fundamental structure-function aspects of pore-forming proteins and offer new opportunities for pharmacological treatment of associated diseases such as chronic pain. Here, we introduce a renormalization group flow paradigm permitting a formal investigation of NaVCh thermostability properties. Our procedures are solidified by deriving aq-deformed statistical mechanical entropy and validated over 121 experimentally resolved NaVCh structures of prokaryotic and eukaryotic origin. We uncover the universality of a critical inflection point regulating the thermostability of the pore domain relative to the voltage sensors, summarized in terms of a generalized Widom scaling law. A machine learning algorithm, rationalized in terms of the ‘loosening’ of inertia and conductivity channel constraints, identifies pain-disease-associated mutation hotspots in the human NaV1.7 channel. Our work illustrates how first-principles-based machine learning approaches can deliver accurate insights for human pain medicine and clinicians at a reduced computational cost, while clarifying the self-organized critical nature of NaVChs.
A Myosin Nanomotor Essential for Stereocilia Maintenance Expands the Etiology of Hereditary Hearing Loss DFNB3
Authors: Behnammanesh Ghazaleh , Dragich Abigail K. , Liao Xiayi , Hadi Shadan , Kim Mi-Jung , Perrin Benjamin , Someya Shinichi , Frolenkov Gregory I. , Bird Jonathan E.
Published: February 2025

Cochlear hair cells transduce sound using stereocilia, and disruption to these delicate mechanosensors is a significant cause of hearing loss. Stereocilia architecture is dependent upon the nanomotor myosin 15. A short isoform (MYO15A-2) drives stereocilia development by delivering an elongation-promoting complex (EC) to stereocilia tips, and an alternatively spliced long isoform (MYO15A-1) tunes postnatal size in shorter stereocilia, which possess mechanosensitive ion channels. Disruption of these functions causes two distinct stereocilia pathologies, which underly human autosomal recessive non-syndromic hearing loss DFNB3. Here, we characterize a new isoform, MYO15A-3, that increases expression in postnatal hair cells as the developmental MYO15A-2 isoform wanes reciprocally. We show the critical EC complex is initially delivered by MYO15A-2, followed by a postnatal handover to MYO15A-3, which continues to deliver the EC. In aMyo15a-3mutant mouse, stereocilia develop normally with correct EC targeting, but lack the EC postnatally and do not maintain their adult architecture, leading to progressive hearing loss. We conclude MYO15A-3 delivers the EC in postnatal hair cells and that the EC and MYO15A-3 are both required to maintain stereocilia integrity. Our results add to the spectrum of stereocilia pathology underlying DFNB3 hearing loss and reveal new molecular mechanisms necessary for resilient hearing during adult life.
Reduced amino acid substitution matrices find traces of ancient coding alphabets in modern day proteins
Authors: Douglas Jordan , Bouckaert Remco , Carter Charles W. , Wills Peter R.
Published: February 2025

All known living systems make proteins from the same twenty canonically-coded amino acids, but this was not always the case. Early genetic coding systems likely operated with a restricted pool of amino acid types and limited means to distinguish between them. Despite this, amino acid substitution models like LG and WAG all assume a constant coding alphabet over time. That makes them especially inappropriate for the aminoacyl-tRNA synthetases (aaRS) - the enzymes that govern translation. To address this limitation, we created a class of substitution models that accounts for evolutionary changes in the coding alphabet size by defining the transition from nineteen states in a past epoch to twenty now. We use a Bayesian phylogenetic framework to improve phylogeny estimation and testing of this two-alphabet hypothesis. The hypothesis was strongly rejected by datasets composed exclusively of “young” eukaryotic proteins. It was generally supported by “old” (aaRS and non-aaRS) proteins whose origins date from before the last universal common ancestor. Standard methods overestimate the divergence ages of proteins that originated under reduced coding alphabets in both simulated and aaRS alignments. The new model reduces this bias substantially. Our findings support the late incorporation of tryptophan into the genetic code (relative to tyrosine) and suggest that isoleucine and valine were once coded interchangeably, forming protein quasispecies. This work provides a robust, seamless framework for reconstructing phylogenies from ancient protein datasets and offers further insights into the dawn of molecular biology.
The Adhesion GPCR ADGRL2 engages Gα13 to Enable Epidermal Differentiation
Authors: Yang Xue , He Feng , Porter Douglas F , Garbett Krassimira , Meyers Robin M , Reynolds David L , Duy Lan Hung Bui , Hong Audrey , Ducoli Luca , Siprashvili Zurab , Lopez-Pajares Vanessa , Mondal Smarajit , Ko Lisa , Jing Yuqing , Tao Shiying , Singal Bharti , Sando Richard , Skiniotis Georgios , Khavari Paul A
Published: February 2025

Homeostasis relies on signaling networks controlled by cell membrane receptors. Although G-protein-coupled receptors (GPCRs) are the largest family of transmembrane receptors, their specific roles in the epidermis are not fully understood. Dual CRISPR-Flow and single cell Perturb-seq knockout screens of all epidermal GPCRs were thus performed, uncovering an essential requirement for adhesion GPCR ADGRL2 (latrophilin 2) in epidermal differentiation. Among potential downstream guanine nucleotide-binding G proteins, ADGRL2 selectively activated Gα13. Perturb-seq of epidermal G proteins and follow-up tissue knockouts verified that Gα13 is also required for epidermal differentiation. A cryo-electron microscopy (cryo-EM) structure in lipid nanodiscs showed that ADGRL2 engages with Gα13 at multiple interfaces, including via a novel interaction between ADGRL2 intracellular loop 3 (ICL3) and a Gα13-specific QQQ glutamine triplet sequence in its GTPase domain. In situ gene mutation of this interface sequence impaired epidermal differentiation, highlighting an essential new role for an ADGRL2-Gα13 axis in epidermal differentiation.
De novo annotation of centromere with centroAnno
Authors: Qi Junhai , Ma Junchi , Han Renmin , Han Zheng , Yu Ting , Li Guojun
Published: February 2025

Accurate centromere annotation is essential for elucidating chromosomal stability, gene regulation, and the complexities of genome architecture. However, existing methods are often constrained by their dependence on prior knowledge and their limited applicability across diverse genomic contexts. In this study, we present Centromere Annotator (centroAnno), a novel de novo algorithm tailored for the precise annotation of centromeres and tandem repeats directly within complex genomes, assemblies, centromeric sequences, or raw sequencing data. Through extensive evaluations on both simulated and real-world datasets, centroAnno consistently outperforms existing tools in annotation accuracy. Additionally, centroAnno significantly enhances efficiency, achieving annotation speeds 12 to 44 times faster than other methods when applied to human centromeric regions.
Fusion of magnet resonance imaging and electronic health records promotes the multimodal prediction of postoperative delirium
Authors: Giesa Niklas , Dell’Orco Andrea , Scheel Michael , Finke Carsten , Balzer Felix , Spies Claudia Doris , Sekutowicz Maria
Published: February 2025

The role of individual brain morphometry, derived from clinical imaging, for the analysis as well as the early prediction of postoperative delirium (POD), as a severe complication after a surgery, is currently under-explored. We extensively analyzed patient trajectories of magnet resonance imaging (MRI) and electronic health records (EHRs) for two POD definitions covering 557 and 201 patients. Age-adjusted correlations with linear mixed-effect models identified middle temporal and superior temporal cortical thickness as well as thalamus and brain stem volumes. We trained highly non-linear multi-layer perceptrons (MLPs) on EHRs, MRI measures, and the combination of both as multimodal fusions. MLP models achieved high performance metrics, as are under receiver operating characteristics (AUROC) values up to 86%, outperforming baselines. Multimodal fusion was especially beneficial for 645 less critically ill patients. MLP model weights for this cohort focused on cerebral atrophy measures of higher order cortical areas, such as the temporalpole -, superiofrontal gyrus-, and the insula. Our results pave the way for the far unrecognized potential of clinical MRI features for early multimodal predictions of POD.
Women’s Sociocultural Representations of HIV Pre-Exposure Prophylaxis and Intimate Partner Violence in Heterosexual Relationships: A Qualitative Story Method
Authors: Willie Tiara C. , Sharpless Laurel , Knight Deja , Shah Aashna , Antar Amina , Watts Z. Thomasina , Alexander Kamila A. , Kershaw Trace
Published: February 2025

Objective

The current study sought to assess women’s understanding of pre-exposure prophylaxis interest and initiation in heterosexually-active relationships with and without histories of intimate partner violence.

Design

2017-18 prospective cohort study with an embedded, story completion exercise in the 90-day follow-up such that participants were randomized to receive one of two versions of a story stem based on whether they experienced intimate partner violence.

Setting

Connecticut.

Participants

132 heterosexually-active, cisgender adult women residing in the state of Connecticut.

Primary outcomes measures

Our primary outcome included identifying principal narratives that describes women’s conceptualizations of pre-exposure prophylaxis interest and initiation in heterosexually-active relationships.

Results

Using both story mapping and thematic analysis techniques, four principal narratives were identified across the stories: 1) theInformed and Empowered PrEP User, 2) theClandestine PrEP User, 3) theHesitant PrEP Contemplator, and 4) theDisenfranchised PrEP Non-User. These novel narratives provide insights on how social, clinical, and interpersonal factors are underpinning heterosexually-active, cisgender adult women’s ability to display interest and initiate pre-exposure prophylaxis in their relationships.

Conclusions

If our findings are replicated in studies in different settings, it will provide substantial support for future prevention interventions adopting empowerment-centered approaches to refocus women’s needs in the context of PrEP initiation and healthy relationships.
Bayesian multistate modelling of prefrailty and frailty: a microsimulation study with weight management interventions for prevention in Asian settings
Authors: Zhang Xinyu , Jin Shihui , Song Haolong , Yeo Johnathan , Dickens Borame L
Published: February 2025

Background

Pre-frailty and frailty prevalence is increasing in the Western Pacific, resulting in substantial morbidity and mortality in older populations. Modelling frameworks are required to estimate the prevalence of frailty and potential impacts of ongoing population level nutritional interventions.

Methods

Using a microsimulation sociodemographic model of 3,353,032 individuals from 1990 to 2050, and data from the Singapore Longitudinal Ageing Study 2 of 3,270 participants, we developed a Bayesian multistate model of robust, pre-frailty and frailty stages with estimated transition probabilities by age, race, and gender for each body-mass index (BMI) category. We then explored four scenarios where nutritional and physical activity interventions are applied that modify the annual distribution of underweight, normal weight, overweight, obese I and obese II individuals.

Findings

Between 2011 and 2050, the overall prevalence of pre-frailty and frailty increased from 44.2% to 50.5%, and from 3.2% to 11.8% respectively. Reductions of 9,529 pre-frail (95% CI: 7,303-11,673) and 6,960 frail individuals (6,094-7,886) were estimated when underweights shifted to normal weights, 11,598 (8,270-15,184) and 57,131 (39,258-82,696) when obese II moved to obese I, and 21,091 (16,179-25,846) and 63,891 (45,372-90,072) when both groups shifted respectively. Total healthcare utilization decreases by 6.9% (5.5%-8.3%) with the latter intervention.

Interpretation

Frailty prevalence is projected to substantially increase by 2050 where large-scale weight management interventions could be utilised to avert cases of both pre-frailty and frailty in older individuals.
Exploring Microbiota-Associated Metabolites in Twins Discordant for Type 1 Diabetes
Authors: Flammer Elizabeth R. , Christopher Michael W. , Powers Esabella R. , Broncucia Hali , Steck Andrea K. , Gitelman Stephen E. , Garrett Timothy J. , Ismail Heba M.
Published: February 2025

Objective

Identify microbial and microbiota-associated metabolites in monozygotic (MZ) and dizygotic (DZ) twins discordant for type 1 diabetes (T1D) to gain insight into potential environmental factors that may influence T1D.

Research Design and Methods

Serum samples from 39 twins discordant for T1D were analyzed using a semi-targeted metabolomics approach via liquid chromatography-high-resolution tandem mass spectrometry (LC-HRMS/MS). Statistical analyses identified significant metabolites (p < 0.1) within three groups: All twins (combined group), MZ twins, and DZ twins.

Results

Thirteen metabolites were identified as significant. 3-indoxyl sulfate and 5-hydroxyindole were significantly reduced in T1D individuals across all groups. Carnitine was reduced, and threonine, muramic acid, and 2-oxobutyric acid were significantly elevated in both All and MZ groups. Allantoin was significantly reduced and 3-methylhistidine was significantly elevated in All and DZ groups.

Conclusions

Metabolite dysregulation associated with gut dysbiosis was observed. However, further validation of our findings in a larger cohort is needed.

Article Highlights

Why did we undertake this study? We believed this cohort of twins discordant for type 1 diabetes (T1D) would allow for control over genetic variability to examine environmental factors.

What is the specific question(s) we wanted to answer? We aimed to identify differences in microbial and microbiota-associated metabolites in twins discordant for T1D to examine the effect of the gut microbiome on T1D.

What did we find? Thirteen metabolites were identified as significantly different.

What are the implications of our findings? Our results show the dysregulation of several microbial metabolites in twin pairs, suggesting that the gut microbiome plays a role in the pathogenesis of T1D.
Evaluating risks and benefits of Newer Diabetes medications when Used in Routine care (ENDURe)
Authors: Colacci Michael , Hurst Mack , Fritz Jamie Lee , Olar Patricia , Ray Prachi , Verma Amol , Razak Fahad , Mamdani Muhammad , Quinn Kieran L. , Rosella Laura , Fralick Michael
Published: February 2025

Introduction

Sodium glucose co-transporter 2 inhibitors (SGLT2i) and glucagon-like peptide 1 analogues (GLP1a) improve clinical outcomes (e.g., myocardial infarction, stroke, death from CV causes) for adults with type 2 diabetes mellitus. The majority of available data from clinical trials and observational studies are from outpatients. Data on their effectiveness among hospitalized patients, however, are lacking.

Methods

We conducted a multicentre, retrospective, cohort study of adults aged 65 years and older with type 2 diabetes mellitus hospitalized between 2017 and 2023 in Ontario. We compared adults newly prescribed an SGLT2i or GLP1a in hospital to adults newly prescribed a DPP4i in hospital. In a sensitivity analysis, new use of sulfonylurea was the comparator. Our primary outcome was the 1-year risk of a composite of all-cause mortality, hospitalization with myocardial infarction, stroke, heart failure, or renal failure. Secondary outcomes included components of the composite, short-term (i.e., 30 day) risk of hypoglycemia, and the 1-year risk of DKA.

Results

We identified 6,713 older adults with diabetes who were newly prescribed one of the following medications during an inpatient hospitalization: SGLT2i (N=1520), GLP1 (N=90), DPP4i (N=3726), sulfonylurea (N=1377). Because new use of GLP1 was rare in hospital, we updated our exposure group to SGLT2i alone. Adults who received an SGLT2i were typically younger, and more likely to have heart failure or coronary artery disease compared to adults who received a DPP4i or sulfonylurea. Among adults who received an SGLT2i, at 1-year the primary outcome occurred in 26% compared to 31% who newly received a DPP4i (adjusted hazard ratio [HR] 0.82 95% Confidence Interval [CI] 0.69,0.97). In our sensitivity analysis using sulfonylurea as the comparator group, the hazard ratio for the primary outcome was 0.97 (95% CI 0.80, 1.18). We did not identify an increased risk of DKA or hypoglycemia for SGLT2i compared to DPP4i, though patients receiving an SGLT2i did have a lower rate of 30-day readmission (HR 0.73, 95%CI 0.58-0.92).

Conclusion

Among older adults with type 2 diabetes mellitus, newly prescribing an SGLT2i or GLP1 during a hospitalization was uncommon. New use of an SGLT2i was associated with improved outcomes compared to DPP4i but this finding was not robust when new use of a sulfonylurea was the comparator. Future larger studies are needed to provide more definitive results.
Arginine metabolism has a pivotal function for the encystation ofGiardia duodenalis
Authors: Klotz Christian , Leisering Ricarda , Hagen Kari D , Starcevich Hannah N , Ewald Christoph , Türken Samuel , Marquardt Malte , Schramm Saskia , Ehret Kasemo Totta , Marek Stefanie , Seeber Frank , Ignatius Ralf , Dawson Scott , Aebischer Toni
Published: February 2025

Arginine metabolism plays a key role in the energy metabolism of the intestinal parasiteGiardia duodenalis, an amitochondrial protozoan that infects humans and animals and causes significant morbidity. An arginine deiminase (ADI) has been implicated in virulence, but it is currently unknown if ADI allele variants from the different geneticG. duodenalissubgroups (assemblages) differ in function. Here, the hypothesis was tested that sequence variation detected betweenG. duodenalisADI alleles from the twoG. duodenalisassemblage types found in humans affects functional parameters of the enzyme with potential consequences in life cycle progression.

The ADI enzyme affinity for arginine was drastically reduced in sub-assemblage AII isolates, a human specific assemblage, in comparison to zoonotic sub-assemblage AI and B isolates. We identified the two amino acid residues responsible for the lower substrate affinity of ADIAIIvariant. Using genetic approaches to generate ADI knockout mutants, biochemical approaches to unravel substrate affinity as well as cellular approaches to determine efficiency of life cycle progression, we show that ADI is essential for efficient encystation of the parasite and that the lower substrate affinity in ADIAIIcorrelates with lower encystation efficiency. We further demonstrate that arginine is essential for efficient encystation, and by generating ADI knock-out parasites we present evidence that ADI is the functional correlate for this arginine dependence.

Thus, our data describe ADI as a quantitative trait that affects life cycle progression ofG. duodenaliswith putative clinical and epidemiological relevance.

Author summary

In the human pathogenic parasiteGiardia duodenalis, arginine deiminase (ADI) mediates the first step in the arginine dehydrolase pathway (ADH), metabolizing arginine to provide chemical energy in form of ATP. The bacterial-derived ADH pathway had been inherited by horizontal gene transfer, and ADI has been proposed as a virulence factor. We show here by biochemical and genetic approaches with ADI knock-out mutants that arginine and its metabolizing enzyme ADI are essential for efficient life cycle progression (encystation) to form infectious cysts. Furthermore, we show a drastically impaired arginine substrate affinity for the human-specificG. duodenalisgenotype AII in comparison to the zoonotic genotypes AI and B and identified the molecular entities responsible for this altered substrate affinity. This lower substrate affinity also correlated with lower cyst formation in the AII genotype.
Emergence of cooperation promoted by higher-order strategy updates
Authors: Wang Dini , Yi Peng , Hong Yiguang , Chen Jie , Yan Gang
Published: February 2025

Cooperation is fundamental to human societies, and the interaction structure among individuals profoundly shapes its emergence and evolution. In real-world scenarios, cooperation prevails in multi-group (higher-order) populations, beyond just dyadic behaviors. Despite recent studies on group dilemmas in higher-order networks, the exploration of cooperation driven by higher-order strategy updates remains limited due to the intricacy and indivisibility of group-wise interactions. Here we investigate four categories of higher-order mechanisms for strategy updates in public goods games and establish their mathematical conditions for the emergence of cooperation. Such conditions uncover the impact of both higher-order strategy updates and network properties on evolutionary outcomes, notably highlighting the enhancement of cooperation by overlaps between groups. Interestingly, we discover that the group-mutual comparison update – selecting a high-fitness group and then imitating a random individual within this group – can prominently promote cooperation. Our analyses further unveil that, compared to pairwise interactions, higher-order strategy updates generally improve cooperation in most higher-order networks. These findings underscore the pivotal role of higher-order strategy updates in fostering collective cooperation in complex social systems.

Author summary

Human societies often organize and cooperate within social groups, where relatives, friends, neighbors, and colleagues influence behavior at both group and individual levels. Individuals may exhibit biased or neutral attitudes when selecting a neighboring group and a peer within it for imitation or comparison, a process termed as higher-order strategy update. These selection preferences originate from four personality types: aggressive, open-minded, myopic, and passive. This work demonstrates that the open-minded type – indiscriminately imitating a peer within a well-functioning group – significantly promotes cooperation. The mathematical framework proposed in this study deepens the understanding of how decision-making within higher-order structures affects the emergence and spread of cooperative behaviors.
The impact of testosterone on paraventricular nucleus gene expression in male and female spontaneously hypertensive rats
Authors: Paterson Alex , Loh Su-Yi , Gholami Shadi Kadijeh , Rogers Mark F , Murugan Dharmani Devi , Sau-Kuen Lam , Mustafa Mohammad Rais , Ott Benjamin P , Balaratnam Prusha , Mecawi Andre S , Murphy David , Hindmarch Charles C. T.
Published: February 2025

Background

Hypertension is a polygenic, complex disease that impacts men and women differently; whilst the incidence of high blood pressure (BP) is roughly equal over a lifetime, men typically are at higher risk of developing the disease earlier in life, before 50 years of age. There is adequate evidence that the brain is critical for the BP setpoint. The paraventricular nucleus (PVN) of the hypothalamus is an integrative structure that can influence not only neurohumoral responses to blood pressure changes, but also sympathetic drive. Here we manipulate the androgenic status of both male and female spontaneously hypertensive rats (SHRs) to determine how this changes gene expression within the PVN of these animals.

Methods

SHR (8-weeks old) were either sham-operated or orchiectomized, whereas all females were oophorectomized, half of which received 10mg testosterone propionate subcutaneously. Mean arterial pressure (MAP) and testosterone (T) were measured by carotid cannulation and ELISA respectively. Sequencing was performed on hand-punched PVN sections and subjected to robust bioinformatic analysis.

Results

In total, 6,571 differentially regulated genes (DRGs) are regulated in the PVN of male and female rats. High T (endogenous or replaced) correlates with higher MAP in both sexes. Orchidectomy-induced T depletion resulted in the significant regulation of 5,104 genes, involved in thousands of biological roles, including ones related to hormone and sex-hormone signalling. In the female SHR, testosterone replacement in oophorectomized animals induced the regulation of 1,727 genes, sharing many biological functions with those in the high T males. We validated key genes by qPCR to determine false discovery rate.

Conclusions

T status in hypertensive rats correlates with MAP, and consistent changes in PVN transcriptome
Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss
Authors: Tabatabaee Yasamin , Zhang Chao , Arasti Shayesteh , Mirarab Siavash
Published: February 2025

Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT) can complicate the estimation of species tree branch lengths. While several tools exist for estimating the topology of a species tree addressing various causes of gene tree discordance, much less attention has been paid to branch length estimation on multi-locus datasets. For single-copy gene trees, some methods are available that summarize gene tree branch lengths onto a species tree, including coalescent-based methods that account for heterogeneity due to ILS. However, no such branch length estimation method exists for multi-copy gene family trees that have evolved with gene duplication and loss. To address this gap, we introduce the CASTLES-Pro algorithm for estimating species tree branch lengths while accounting for both GDL and ILS. CASTLES-Pro improves on the existing coalescent-based branch length estimation method CASTLES by increasing its accuracy for single-copy gene trees and extends it to handle multi-copy ones. Our simulation studies show that CASTLES-Pro is generally more accurate than alternatives, eliminating the systematic bias toward overestimating terminal branch lengths often observed when using concatenation. Moreover, while not theoretically designed for HGT, we show that CASTLES-Pro maintains relatively high accuracy under high rates of random HGT.

Code availability

CASTLES-Pro is implemented inside the software package ASTER, available athttps://github.com/chaoszhang/ASTER.

Data availability

The datasets and scripts used in this study are available athttps://github.com/ytabatabaee/CASTLES-Pro-paper.
Epigenetic and Transcriptomic Alterations Precede Amyloidosis in the Hippocampus of the Alzheimer’s DiseaseAppNL-G-FKnock in Mouse Model
Authors: Okhovat Mariam , Layman Cora , Davis Brett A. , Pederson Alexandra , O’Niel Abigail , Holden Sarah , Kessler Kat , Acharya Sonia , Wheeler Kandace J. , Nevonen Kimberly A. , Herrera Jarod , Ward Samantha , Vigh-Conrad Katinka , Adey Andrew , Raber Jacob , Carbone Lucia
Published: February 2025

Detecting and understanding the early stages of Alzheimer’s disease (AD) is essential for uncovering initial mechanisms of neuropathology and devising effective interventions. In this study, we leveraged the humanizedAppNL-G-Fmouse which exhibits early-onset amyloid pathology with a predictable timeline, to investigate molecular changes in the hippocampus and blood before the onset of severe neuropathology and independent of aging. Employing a multi-omics approach, we identified alterations in chromatin accessibility, gene expression, and DNA methylation associated with early amyloidosis. Chromatin accessibility changes were prominent in excitatory neurons during early pathology, with a later shift to inhibitory neurons, potentially reflecting compensatory mechanisms to mitigate excitatory neuron dysregulation. Despite broadly comparable hippocampal cell composition, transcriptomic comparisons between wild-type andAppNL-G-Fmice revealed major gene expression differences, particularly in pathways related to mitochondrial function and protein biosynthesis, preceding severe amyloid plaque deposition. In later stages, upregulation of immune and neuroinflammatory pathways was observed, aligning with established neuroinflammatory processes in AD. Additionally, we identified extensive DNA methylation differences in both the blood and hippocampus ofAppNL-G-Fmice during early and late stages of pathology. Many differentially methylated regions in the blood, even at early pathology stages, were associated with cis-regulatory elements in the brain and were located near differentially expressed genes in the hippocampus. These regions were enriched in pathways associated with brain function, including neuron development and synaptic processes, highlighting a connection between blood methylation patterns and brain activity. This finding suggests the potential use of blood DNA methylation as a biomarker for the early detection of amyloidosis. Notably, we identified five candidate biomarker genes, includingRbfox1andCamta1, with epigenetic dysregulation detectable in both the brain and blood prior to severe amyloid accumulation. Our study, leveraging a unique AD mouse model and a multi-omics approach, highlights epigenetic signatures of AD before the onset of clinical symptoms, providing a foundation for future research into early diagnosis and therapeutic strategies, as well as potential blood biomarkers.
RAB23 Modulates Signaling Protein Ciliary Homeostasis through Promoting RAB18-mediated Inward BBSome Transition Zone Passage
Authors: Sun Sheng-Nan , Sun Wen-Jian , Wei Yan , Fan Zhen-Chuan
Published: February 2025

As an intraflagellar transport (IFT) cargo adaptor, the BBSome targets the basal body region located just below the transition zone (TZ) before proceeding to cross the TZ for ciliary entry. This process of TZ crossing crucially governs BBSome presence and quantity available for signaling protein coupling within cilia, influencing the dynamic behavior of signaling proteins in cilia by controlling their ciliary removal. Our previous study revealed that the GTPase RAB18 binds to its BBSome effector in the basal bodies right below the TZ and recruits the BBSome to cross the TZ for ciliary entry by lateral transport between the plasma and ciliary membranes. However, the mechanism by which RAB18 is activated to accomplish this function has remained elusive. This study uncovers that, under physiological conditions,ChlamydomonasRAB23 in its GDP-bound state (RAB23-GDP) predominantly localizes to the same basal body region as RAB18-GDP and activates RAB18-GDP as a RAB18-specific guanine nucleotide exchange factor. RAB18-GDP attaches to the membrane and binds to the BBSome. This interaction occurs independently of anterograde IFT association, allowing the BBSome to diffuse through the TZ and enter cilia. Subsequently, RAB23-GDP facilitates its own ciliary entry by binding to the RAB18-GTP/BBSome entity as a BBSome cargo. Our findings establish a model where the BBSome enters cilia through the RAB23-RAB18 module-mediated inward BBSome TZ diffusion pathway. According to this model, hedgehog signaling defects caused byrab23mutations could induce Carpenter syndrome in humans, providing a mechanistic understanding behind the inward BBSome TZ passage required for proper ciliary signaling.

Significance statement

Certain ciliary signaling proteins are removed from cilia through the outward BBSome transition zone (TZ) diffusion pathway. The inward BBSome TZ crossing is orchestrated by RAB18. The current study unveils that RAB23 in its GDP-bound state (RAB23-GDP) and RAB18-GDP predominantly localize to the same basal body region located just below the TZ. RAB23-GDP activates RAB18-GDP as a RAB18-specific guanine nucleotide exchange factor. RAB18-GTP subsequently recruits the BBSome as its effector to cross the TZ for ciliary entry. Following this, RAB23-GDP enters cilia as a BBSome cargo. The regulatory interplay between RAB23 and RAB18, with RAB23 promoting inward BBSome TZ crossing via RAB18, establishes a molecular mechanism for the BBSome-dependent retrieval of signaling proteins from cilia.
A novel method for detection of Cas9 gRNAs using a fluorophore-labeled DNA oligo
Authors: Bandara Ranmal Avinash , Zhou Zhichang Peter , Chen Ziyan Rachel , Duan Rongqi , Davidson Alan Richard , Wong Amy P , Hu Jim
Published: February 2025

Clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 (Cas9) has become one of the most important gene editing tools. CRISPR guide RNA (gRNA) serves as an important component in guiding Cas proteins to a target site in gene editing processes. For effective gene editing or site specific gene integration, levels of gRNA present in a target cell are critical. Especially, for prime editing, even the ratio of different gRNAs present in target cells has a major effect on gene editing efficiency. Therefore, having a convenient, highly sensitive method for direct detection of gRNAs can improve editing design and optimize targeting efficiency. Here, we have developed a convenient, highly sensitive method for direct detection of gRNAs, which may be used to improve editing design and optimize targeting efficiency.
Reward-based prosocial choices in mice
Authors: Esteve-Agraz Joan , Rodríguez-Milan Víctor Javier , Márquez Cristina
Published: February 2025

Prosocial behaviors, actions that benefit others, are an essential part of the social life of humans and other animals, by promoting bonding and cohesion among individuals and groups. Here we present a new behavioural paradigm to assess prosociality in food foraging contexts in laboratory mice, based in our paradigm previously developed for rats. In this task, the decision-maker can choose between two options, one that will only provide rewards to itself (selfish choice) or one that will reward both itself and its cagemate (prosocial choice). Our work reveals that prosocial choices in male mice are not widespread and are only observed in a small proportion of animals. Using detailed analysis of behavior, we describe that recipients of help express different social cues in prosocial and selfish trials, but decision makers do not take them into account to guide their choices. Furthermore, we assess how the level of individual training and the physical layout of the paradigm might affect the performance in this social task. Only those mice with increased social attention (16% of the animals) display prosocial preferences, suggesting these to be rooted in similar behavioural factors and social interactions that we previously described in other work with rats.
Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
Authors: Shen Jiawei , Cheng Siyuan , Purushotham Deepak , Zhuo Xiaoyu , Du Alan Y , Zhang Wenjin , Li Daofeng , Wang Ting
Published: February 2025

Repetitive elements, mostly derived from transposable elements (TEs), account for half the DNA in human and other mammalian genomes. Although epigenetic mechanisms, including DNA methylation and repressive histone modifications, have evolved to suppress TE activities, TEs have substantially shaped the regulatory landscape of the host genome by contributing regulatory sequences to it. TE-derived sequences are often highly repetitive and thus have low mappability, making it difficult to profile the genomics of TEs using short-read sequencing technology. Many specialized bioinformatics tools have been developed for TE-related analysis, but meaningfully visualizing, navigating, and interpreting such data remains challenging. Here, we describe the WashU Repeat Browser to host genomics profiles of human and mouse TEs using data produced by the ENCODE Project and to support the navigation, interactive visualization, integration, comparison, and analysis in the context of TEs. WashU Repeat Browser is a web-based platform allowing users to browse genomic and statistical signals over repetitive elements derived from ENCODE, Roadmap, and FANTOM datasets. The Browser provides a TE-centric view including TE subfamily enrichments, TE subfamily profiling, as well as overviews of genomic signals on individual TE loci where we extend the WashU Epigenome Browser to display user-selected datasets and TE loci. These features could help to close the gaps in our understanding of the repetitive sequences and their putative regulatory functions and aid investigators in formulating new hypotheses by integrating their data with public data.
Gravitational wave production during reheating: From the inflaton to primordial black holes
Authors: Gross Mathieu , Mambrini Yann , Kpatcha Essodjolo , Olea-Romacho Maria Olalla , Roshan Rishav
Published: February 2025

We calculate the gravitational waves (GWs) produced by primordial black holes (PBHs) in the presence of the inflaton condensate in the early Universe. Combining the GW production from the evaporation process, the gravitational scattering of the inflaton itself, and the density fluctuations due to the inhomogeneous distribution of PBHs, we propose for the first time a complete coherent analysis of the spectrum, revealing three peaks, one for each source. Three frequency ranges (∼kHz, GHz, and PHz, respectively) are expected, each giving rise to a similar GW peak amplitude ΩGW. We also compare our predictions with current and future GWs detection experiments.

Published by the American Physical Society
2025