bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic context modulates aging and degeneration in the murine retina
Authors: Marola Olivia J. , MacLean Michael , Cossette Travis L. , Diemler Cory A. , Hewes Amanda A. , Reagan Alaina M. , Skelly Daniel A. , Howell Gareth R.
Published: April 2024

Background

Age is the principal risk factor for neurodegeneration in both the retina and brain. The retina and brain share many biological properties; thus, insights into retinal aging and degeneration may shed light onto similar processes in the brain. Genetic makeup strongly influences susceptibility to age-related retinal disease. However, studies investigating retinal aging have not sufficiently accounted for genetic diversity. Therefore, examining molecular aging in the retina across different genetic backgrounds will enhance our understanding of human-relevant aging and degeneration in both the retina and brain—potentially improving therapeutic approaches to these debilitating conditions.

Methods

Transcriptomics and proteomics were employed to elucidate retinal aging signatures in nine genetically diverse mouse strains (C57BL/6J, 129S1/SvlmJ, NZO/HlLtJ, WSB/EiJ, CAST/EiJ, PWK/PhK, NOD/ShiLtJ, A/J, and BALB/cJ) across lifespan. These data predicted human disease-relevant changes in WSB and NZO strains. Accordingly, B6, WSB and NZO mice were subjected to human-relevantin vivoexaminations at 4, 8, 12, and/or 18M, including: slit lamp, fundus imaging, optical coherence tomography, fluorescein angiography, and pattern/full-field electroretinography. Retinal morphology, vascular structure, and cell counts were assessedex vivo.

Results

We identified common molecular aging signatures across the nine mouse strains, which included genes associated with photoreceptor function and immune activation. Genetic background strongly modulated these aging signatures. Analysis of cell type-specific marker genes predicted age-related loss of photoreceptors and retinal ganglion cells (RGCs) in WSB and NZO, respectively. Fundus exams revealed retinitis pigmentosa-relevant pigmentary abnormalities in WSB retinas and diabetic retinopathy (DR)-relevant cotton wool spots and exudates in NZO retinas. Profound photoreceptor dysfunction and loss were confirmed in WSB. Molecular analyses indicated changes in photoreceptor-specific proteins prior to loss, suggesting photoreceptor-intrinsic dysfunction in WSB. In addition, age-associated RGC dysfunction, loss, and concomitant microvascular dysfunction was observed in NZO mice. Proteomic analyses revealed an early reduction in protective antioxidant processes, which may underlie increased susceptibility to DR-relevant pathology in NZO.

Conclusions

Genetic context is a strong determinant of retinal aging, and our multi-omics resource can aid in understanding age-related diseases of the eye and brain. Our investigations identified and validated WSB and NZO mice as improved preclinical models relevant to common retinal neurodegenerative diseases.
Balancing selection and the functional effects of shared polymorphism in crypticDaphniaspecies
Authors: Murray Connor S. , Karram Madison , Bass David J. , Doceti Madison , Becker Dörthe , Nunez Joaquin C. B. , Ratan Aakrosh , Bergland Alan O.
Published: April 2024

The patterns of genetic variation within and between related taxa represent the genetic history of a species. Shared polymorphisms, loci with identical alleles across species, are of unique interest as they may represent cases of ancient selection maintaining functional variation post-speciation. In this study, we investigate the abundance of shared polymorphism in theDaphnia pulexspecies complex. We test whether shared mutations are consistent with the action of balancing selection or alternative hypotheses such as hybridization, incomplete lineage sorting, or convergent evolution. We analyzed over 2,000 genomes from North American and EuropeanD. pulexand several outgroup species to examine the prevalence and distribution of shared alleles between the focal species pair, North American and EuropeanD. pulex. We show that while North American and EuropeanD. pulexdiverged over ten million years ago, they retained tens of thousands of shared alleles. We found that the number of shared polymorphisms between North American and EuropeanD. pulexcannot be explained by hybridization or incomplete lineage sorting alone. Instead, we show that most shared polymorphisms could be the product of convergent evolution, that a limited number appear to be old trans-specific polymorphisms, and that balancing selection is affecting young and ancient mutations alike. Finally, we provide evidence that a blue wavelength opsin gene with trans-specific polymorphisms has functional effects on behavior and fitness in the wild. Ultimately, our findings provide insights into the genetic basis of adaptation and the maintenance of genetic diversity between species.
Global patterns in the evolutionary relations between seed mass and germination traits
Authors: Maleki Keyvan , Vandelook Filip , Saatkamp Arne , Maleki Kourosh , Heshmati Siavash , Soltani Elias
Published: April 2024

During stressful climatic periods, plant populations face significant challenges, especially during germination and seedling establishment. Theoretical studies present conflicting findings regarding the relationship between seed size and germination rate. Some analyses suggest that species with larger seeds should exhibit rapid germination, while others point to faster germination in smaller seeds. This discrepancy can, for example, be attributed to the higher vulnerability of larger seeds to post-dispersal seed predation. To assess the correlation between seed mass and seed germination characteristics at a global scale, we performed a rigorous meta-analysis of published data sources, covering a wide range of germination traits across 1877 species with diverse dormancy types and global distribution. Additionally, we investigated the potential relationship between seed mass and dormancy level. Our findings revealed contrasting responses of germination traits to seed mass, suggesting complex eco-evolutionary correlations among these traits. Trade-offs and corelated evolution likely played an important role in the evolutionary history of seed mass, with seed mass displaying notable trait conservation across the phylogeny. Interestingly, our study demonstrated that seed dormancy exhibited trade-offs with post-germination traits and seed mass. The meta-analysis demonstrated that any changes in the relationship between seed mass and dormancy is dependent on dormancy types with physiological dormancy showing lower seed mass while other dormancy types were has a higher seed mass. These results underscore the critical role of seed mass in shaping plant performance and provide valuable insights into plant trait evolution. Our findings clearly indicate that the hypothesis of larger seeds conferring advantages in both pre- and post-germination traits might not be empirically true in all cases as theoretical studies suggest and that this relationship is complex and varies among species and growth forms. We interpret these results within the context of germination strategies and correlated evolution between seed dormancy and seed mass. Considering these traits in future analyses of plant germination strategies and species distributions is crucial. Factors such as lifespan, seed mass, and germination-related traits should be carefully considered to gain a comprehensive understanding of plant adaptation to challenging environmental conditions.
Colonization ofAnopheles coustani, a neglected malaria vector in Madagascar
Authors: Andrianinarivomanana Tsarasoa M. , Randrianaivo Fenomiaranjara T. , Andriamiarimanana Mandaniaina R. , Razafimamonjy Mihary R. , Velonirina Haja J.S , Puchot Nicolas , Girod Romain , Bourgouin Catherine
Published: April 2024

Anopheles coustanihas long be recognized as a secondary malaria vector in Africa. It has recently been involved in the transmission of bothPlasmodium falciparumandPlasmodium vivaxin Madagascar. As most secondary malaria vector,An. coustaniis mainly biting outdoor, which renders the control of this mosquito species difficult by the classical malaria control measures as the use of bed nets or indoor residual spraying of insecticides. The absence of a colony hinders a better understanding of its biology and vector competence towards the development of adapted mosquito control strategies. Here, we report the first successful establishment of anAn. coustanicolony from mosquito collected in Madagascar. We used a forced copulation procedure as this mosquito species will not mate in cages. We describe our mosquito colonization procedure with detailed biological features as larval to adult development and survival, recorded over the first six critical generations. The procedure should be easily applicable toAn. coustanifrom different African countries, facilitating local investigation onAn. coustanivector competence and insecticide resistance using the colony as a reference.
Classifying cell cycle states and a quiescent-like G0 state using single-cell transcriptomics
Authors: O‘Connor Samantha A. , Garcia Leonor , Hoover Rori , Patel Anoop P. , Bartelle Benjamin B. , Hugnot Jean-Philippe , Paddison Patrick J. , Plaisier Christopher L.
Published: April 2024

Single-cell transcriptomics has unveiled a vast landscape of cellular heterogeneity in which the cell cycle is a significant component. We trained a high-resolution cell cycle classifier (ccAFv2) using single cell RNA-seq (scRNA-seq) characterized human neural stem cells. The ccAFv2 classifies six cell cycle states (G1, Late G1, S, S/G2, G2/M, and M/Early G1) and a quiescent-like G0 state (Neural G0), and it incorporates a tunable parameter to filter out less certain classifications. The ccAFv2 classifier performed better than or equivalent to other state-of-the-art methods even while classifying more cell cycle states, including G0. We demonstrate that the ccAFv2 classifier effectively generalizes the S, S/G2, G2/M, and M/Early G1 states across cell types derived from all three germ layers. While the G0, G1, and Late G1 states perform well in neuroepithelial cell types, their accuracy is lower in other cell types. However, misclassifications are confined to the G0, G1, and Late G1 states. We showcased the versatility of ccAFv2 by successfully applying it to classify cells, nuclei, and spatial transcriptomics data in humans and mice, using various normalization methods and gene identifiers. We provide methods to regress the cell cycle expression patterns out of single cell or nuclei data to uncover underlying biological signals. The classifier can be used either as an R package integrated with Seurat or a PyPI package integrated with SCANPY. We proved that ccAFv2 has enhanced accuracy, flexibility, and adaptability across various experimental conditions, establishing ccAFv2 as a powerful tool for dissecting complex biological systems, unraveling cellular heterogeneity, and deciphering the molecular mechanisms by which proliferation and quiescence affect cellular processes.
Integrative machine learning approaches for predicting disease risk using multi-omics data from the UK Biobank
Authors: Aguilar Oscar , Chang Cheng , Bismuth Elsa , Rivas Manuel A.
Published: April 2024

We train prediction and survival models using multi-omics data for disease risk identification and stratification. Existing work on disease prediction focuses on risk analysis using datasets of individual data types (metabolomic, genomics, demographic), while our study creates an integrated model for disease risk assessment. We compare machine learning models such as Lasso Regression, Multi-Layer Perceptron, XG Boost, and ADA Boost to analyze multi-omics data, incorporating ROC-AUC score comparisons for various diseases and feature combinations. Additionally, we train Cox proportional hazard models for each disease to perform survival analysis. Although the integration of multi-omics data significantly improves risk prediction for 8 diseases, we find that the contribution of metabolomic data is marginal when compared to standard demographic, genetic, and biomarker features. Nonetheless, we see that metabolomics is a useful replacement for the standard biomarker panel when it is not readily available.
Functional diversities within neurons and astrocytes in the adult rat auditory cortex revealed by single-nucleus RNA sequencing
Authors: Aydin Aysegul Gungor , Lemenze Alexander , Bieszczad Kasia M
Published: April 2024

The mammalian cerebral cortex is composed of a rich diversity of cell types. Cortical cells are organized into networks that rely on their functional diversity to ultimately carry out a variety of sophisticated cognitive functions. To investigate the breadth of transcriptional diverse cell types in the sensory cortex, we have used single-nucleus RNA sequencing (snRNA-seq) in the auditory cortex of the adult rat. A variety of unique excitatory and inhibitory neuron types were identified. In addition, we report for the first time a diversity of astrocytes in the auditory cortex that may represent functionally unique subtypes. Together, these results pave the way for building models of how neurons in the sensory cortex work in concert with astrocytes at synapses to fulfill high-cognitive functions like learning and memory.
Sequence, Structural and Functional Diversity of the Ubiquitous DNA/RNA-Binding Alba Domain
Authors: Jaiganesh Jagadeesh , Vembar Shruthi Sridhar
Published: April 2024

The DNA/RNA-binding Alba domain is prevalent across all kingdoms of life. Discovered in archaea more than 40 years ago, this protein domain appears to have evolved from RNA- to DNA- binding, with a concomitant expansion in the range of cellular processes that it regulates. Indeed, Alba domain-containing proteins continue to exhibit functional ingenuity, with their most recent association being R-loop regulation in plants: they accomplish this by binding to DNA:RNA hybrid structures as heterodimers. To further explore Alba diversity and evolutionary relatedness, which could in turn lead to new functional revelations, we employed iterative searches in PSI-BLAST to identify 15161 true Alba domain-containing proteins from the NCBI non-redundant protein database. Next, by building sequence similarity networks (SSNs), we identified 13 distinct clusters representing various Alba subgroups. These included the classic eukaryotic Rpp20/Pop7 and Rpp25/Pop6 proteins as well as novel fungal Alba proteins andPlasmodium-specific Albas. Conservation analysis indicated that, despite overall low primary sequence similarity between the SSN clusters, the homo- or hetero-dimer interface is highly conserved. Furthermore, the presence of the classic Alba fold was confirmed in representative sequences from each cluster by comparison of their Hidden Markov Model (HMM) profiles andab initiothree-dimensional structures. Notably, Alba domains from lower, unicellular eukaryotes and fungal Albas exhibit structural deviations towards their C-terminal end. Finally, phylogenetic analysis, while supporting SSN clustering, revealed the evolutionary branchpoint at which the eukaryotic Rpp20- and Rpp25-like clades emerged from archaeal Albas, and the subsequent taxonomic lineage-based divergence within each clade. Taken together, this comprehensive analysis enhances our understanding of the evolutionary history of Alba domain-containing proteins across diverse organisms, their sequence and structural conservation, and functional implications for genome and RNA biology.
Autonomic Modulation with Mindfulness-Based Stress Reduction in Chronic Kidney Disease: A Randomized Controlled Trial
Authors: Jeong Jinhee , Hu Yingtian , Zanuzzi Matias , DaCosta Dana , Li Sabrina , Park Jeanie
Published: April 2024

Background

Chronic kidney disease (CKD) is characterized by overactivation of the sympathetic nervous system (SNS) that leads to increased cardiovascular disease risk. Despite the deleterious consequences of SNS overactivity, there are very few therapeutic options available to combat sympathetic overactivity.

Aim

To evaluate the effects of Mindfulness-Based Stress Reduction (MBSR) on SNS activity in CKD patients.

Method

Participants with CKD stages III-IV were randomized to an 8-week MBSR program or Health Education Program (HEP; a structurally parallel, active control group). Primary outcomes were direct intraneural measures of SNS activity directed to muscle (MSNA) via microneurography at rest and during stress maneuvers.

Results

28 participants (63 ±9 years; 86% males) completed the intervention with 16 in MBSR and 12 in HEP. There was a significant Group (MBSR vs. HEP) by Time (baseline vs. post-intervention) interaction in the change in MSNA reactivity to mental stress (p=0.026), with a significant reduction in the mean change in MSNA over 3 minutes of mental arithmetic at post-intervention (10.6 ± 7.1 to 5.0 ± 5.7 bursts/min, p<0.001), while no change was observed within the HEP group (p=0.773).

Conclusions

In this randomized controlled trial, patients with CKD had an amelioration of sympathetic reactivity during mental stress following 8-weeks of MBSR but not after HEP. Our findings demonstrate that mindfulness training is feasible and may have clinically beneficial effects on autonomic function in CKD.
Stochastic modelling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones
Authors: Hirsch M.G. , Pal Soumitra , Mehrabadi Farid Rashidi , Malikic Salem , Gruen Charli , Sassano Antonella , Pérez-Guijarro Eva , Merlino Glenn , Sahinalp Cenk , Molloy Erin K. , Day Chi-Ping , Przytycka Teresa M.
Published: April 2024

Cancer progression is an evolutionary process driven by the selection of cells adapted to gain growth advantage. We present the first formal study on the adaptation of gene expression in subclonal evolution. We model evolutionary changes in gene expression as stochastic Ornstein–Uhlenbeck processes, jointly leveraging the evolutionary history of subclones and single-cell expression data. Applying our model to sublines derived from single cells of a mouse melanoma revealed that sublines with distinct phenotypes are underlined by different patterns of gene expression adaptation, indicating non-genetic mechanisms of cancer evolution. Interestingly, sublines previously observed to be resistant to anti-CTLA-4 treatment showed adaptive expression of genes related to invasion and non-canonical Wnt signaling, whereas sublines that responded to treatment showed adaptive expression of genes related to proliferation and canonical Wnt signaling. Our results suggest that clonal phenotypes emerge as the result of specific adaptivity patterns of gene expression.
Single-embryo metabolomics reveals developmental metabolism in the earlyDrosophila embryo
Authors: Pérez-Mojica J. Eduardo , Madaj Zachary B. , Isaguirre Christine N. , Roy Joe , Lau Kin H. , Sheldon Ryan D. , Lempradl Adelheid
Published: April 2024

Early embryonic development is characterized by the transition from maternal factor reliance to zygotic control. These processes set the stage for the embryo’s basic structure and cellular differentiation. While relatively detailed knowledge exists of the transcriptional events during early development, little is known about the concurrent metabolic processes. Understanding these processes, however, is important since they are linked to cell fate determination and organ and tissue formation. The primary reasons for the limited progress in the field are technical limitations due to the small amount of material available during early embryonic time windows. Here, we introduce a novel single-embryo methodology that places us in an exciting position to analyze the early embryo’s metabolome and transcriptome in an integrated manner and at high temporal resolution. The resulting data allow us to map concomitant metabolic and transcriptional programs in earlyDrosophilaembryonic development. Our results reveal that a substantial number of metabolites exhibit dynamic patterns with some changing even before the onset of zygotic transcription. dNTPs for example show a temporal pattern that correlates with cell division patterns in the early embryo. In summary, here we present an operationally simple single-embryo metabolomics methodology and provide a detailed picture of early developmental metabolic processes at unprecedented temporal resolution.
Cholesterol Dependence of the Conformational Changes in Metabotropic Glutamate Receptor 1
Authors: Isu Ugochi H. , Badiee Shadi A. , Polasa Adithya , Tabari Seyed H. , Derakhshani-Molayousefi Mortaza , Moradi Mahmoud
Published: April 2024

Metabotropic glutamate receptors (mGluRs) are class C G protein-coupled receptors that function as obligate dimers in regulating neurotransmission and synaptic plasticity in the central nervous system. The mGluR1 subtype has been shown to be modulated by the membrane lipid environment, particularly cholesterol, though the molecular mechanisms remain elusive. In this study, we employed all-atom molecular dynamics simulations to investigate the effects of cholesterol on the conformational dynamics of the mGluR1 seven-transmembrane (7TM) domain in an inactive state model. Simulations were performed with three different cholesterol concentrations (0%, 10%, and 25%) in a palmitoyl-oleoyl phosphatidylcholine (POPC) lipid bilayer system. Our results demonstrate that cholesterol induces conformational changes in the mGluR1 dimer more significantly than in the individual protomers. Notably, cholesterol modulates the dynamics and conformations of the TM1 and TM2 helices at the dimer interface. Interestingly, an intermediate cholesterol concentration of 10% elicits more pronounced conformational changes compared to both cholesterol-depleted (0%) and cholesterol-enriched (25%) systems. Specific electrostatic interaction unique to the 10% cholesterol system further corroborate these conformational differences. Given the high sequence conservation of the 7TM domains across mGluR subtypes, the cholesterol-dependent effects observed in mGluR1 are likely applicable to other members of this receptor family. Our findings provide atomistic insights into how cholesterol modulates the conformational landscape of mGluRs, which could impact their function and signaling mechanisms.
Warm temperature inhibits cytoplasmic incompatibility induced by endosymbiotic Rickettsiella in a spider host
Authors: Proctor Jordyn D. , Mackevicius-Dubickaja Virginija , Gottlieb Yuval , White Jen
Published: April 2024

Bacterial endosymbionts manipulate reproduction in arthropods to increase prevalence in the host population. One such manipulation is cytoplasmic incompatibility (CI), wherein the bacteria sabotage sperm in infected males to reduce hatch rate when mated with uninfected females, but zygotes are "rescued" when that male mates with an infected female. In the spider Mermessus fradeorum (Linyphiidae), Rickettsiella symbionts cause variable levels of CI. We hypothesized that temperature affects CI strength and rescue in M. fradeorum, potentially mediated by bacterial titer. We reared Rickettsiella-infected spiders in two temperature conditions (26C vs 20C) and tested CI induction in males and CI rescue in females. In incompatible crosses between infected males and uninfected females, hatch rate from warm males was doubled (Mean +/- S.E. = 0.687 +/- 0.052) relative to cool males (0.348 +/- 0.046), indicating that CI induction is weaker in warm males. In rescue crosses between infected females and infected males, female rearing temperature had a marginal effect on CI rescue, but hatch rate remained high for both warm (0.960 +/- 0.023) and cool females (0.994 +/- 0.004). Bacterial titer as measured by qPCR was lower in warm than cool spiders, particularly in females, suggesting that bacterial titer may play a role in causing the temperature-mediated changes in CI.
A miniaturised semi-dynamicin-vitromodel of human digestion
Authors: Calero Victor , Rodrigues Patrícia M. , Dias Tiago , Ainla Alar , Vilaça Adriana , Pastrana Lorenzo , Xavier Miguel , Gonçalves Catarina
Published: April 2024

Reliablein-vitrodigestion models that are able to successfully replicate the conditions found in the human gastrointestinal tract (GIT) are key to assess the fate and efficiency of new formulations aimed for oral consumption. However, currentin-vitromodels either lack the capability to replicate crucial dynamics of digestion or require large volumes of sample/reagents, which can be scarce when working with nanomaterials under development. Here, we propose a miniaturised digestion system, a digestion-chip, based on incubation chambers integrated on a polymethylmethacrylate (PMMA) device. The digestion-chip incorporates key dynamic features of human digestion, such as gradual acidification and gradual addition of enzymes and simulated fluids in the gastric phase, and controlled gastric emptying, while maintaining low complexity and using small volumes of sample and reagents. In addition, the new approach integrates real-time automated closed-loop control of two key parameters, pH and temperature, during the two main phases of digestion (gastric and intestinal) with an accuracy down to ±0.1°C and ±0.2 pH points. The experimental results demonstrate that the digestion-chip successfully replicates the gold standard static digestion INFOGEST protocol and that the semi-dynamic digestion kinetics can be reliably fitted to a first kinetic order model. These devices can be easily adapted to dynamic features in an automated, sensorised, and inexpensive platform and will enable reliable, low-cost and efficient assessment of the bioaccessibility of new and expensive drugs, bioactive ingredients or nano-engineered materials aimed for oral consumption, thereby avoiding unnecessary animal testing.
Zebrafish arterial valve development occurs through direct differentiation of second heart field progenitors
Authors: Derrick Christopher J. , Eley Lorraine , Alqahtani Ahlam , Henderson Deborah J. , Chaudhry Bill
Published: April 2024

Aims

Bicuspid Aortic Valve (BAV) is the most common congenital heart defect, affecting at least 2% of the population. The embryonic origins of BAV remain poorly understood, limiting the identification of assays for validating patient variants and ultimately causative genes for BAV. In both human and mouse, the left and right leaflets of the arterial valves arise from the outflow tract cushions, with interstitial cells originating from neural crest cells and endocardial-to-mesenchymal transition (EndoMT). In contrast, an EndoMT-independent mechanism of direct differentiation by cardiac progenitors from the second heart field (SHF) is responsible for the formation of the anterior and posterior leaflets. Defects in either of these developmental mechanisms can result in BAV. Although zebrafish have been suggested as a model for human variant testing, their naturally bicuspid arterial valve has not been considered suitable for understanding human arterial valve development. Here, we have set out to investigate to what extent the processes involved in arterial valve development are conserved in zebrafish and ultimately, whether functional testing of BAV variants could be carried out in zebrafish.

Methods and Results

Using a combination of live imaging, immunohistochemistry and Cre-mediated lineage tracing, we show that the zebrafish arterial valve primordia develop directly from undifferentiated SHF progenitors with no contribution from EndoMT or neural crest, in keeping with the human and mouse anterior and posterior leaflets. Moreover, once formed, these primordia share common subsequent developmental events with all three mammalian arterial valve leaflets.

Conclusions

Our work highlights a conserved ancestral mechanism of arterial leaflet formation from the SHF and identifies that development of the zebrafish arterial valve is distinct from that of the atrioventricular valve. Crucially, this confirms the utility of zebrafish for understanding the development of specific BAV subtypes and arterial valve dysplasia, offering potential for high-throughput variant testing.

Translational Perspective

Large genomic studies of patients with Bicuspid Aortic Valve (BAV) have identified numerous variants predicted to be causative, yet due to a lack of suitable,in vivofunctional assays, advancement of genetic testing, discussion of risk to family members and accurate prognosis is not yet widely possible. Here, we show that zebrafish demonstrate a high level of conservation in arterial valve development with the intercalated leaflets in human, establishing zebrafish as a suitablein vivomodel that can begin to overcome the disconnect between clinical genetics and developmental biology.
Treatment options for Chagas Disease: a systematic review and meta-analysis applied to the preclinical studies using animal models
Authors: Machaca-Luque Laura Yesenia , Candia-Puma Mayron Antonio , Roque-Pumahuanca Brychs Milagros , Barazorda-Ccahuana Haruna Luz , Goyzueta-Mamani Luis Daniel , Galdino Alexsandro Sobreira , Machado-de-Ávila Ricardo Andrez , Giunchetti Rodolfo Cordeiro , Ferraz Coelho Eduardo Antonio , Chávez-Fumagalli Miguel Angel
Published: April 2024

Chagas disease (CD) is a neglected tropical disease endemic to Latin America and has emerged as a global health concern due to the migration of infected individuals. With its epidemiological complexity, difficulty in obtaining appropriate diagnoses, and poor treatment, the search for novel therapeutic options remains. In this context, we conducted a systematic review and meta-analysis of preclinical studies employing animal models to verify the progress in CD treatment. We searched the PubMed database for CD treatment studies published between 1990 and 2023, adhering to the PRISMA guidelines. Twelve papers met the inclusion criteria. The findings indicate that the fifteen treatment alternatives examined, mainly between 2010 and 2014, demonstrated efficacy in experimental CD models, evidenced by significant parasitemia reduction. Bis-triazole DO870 and VNI were effective in the acute and chronic phases, respectively. However, of these emerging therapies, only posaconazole and fexinidazole have progressed to clinical trials, yielding unsatisfactory outcomes as CD monotherapies. This meta-analysis highlights the existence of promising new drug candidates for CD treatment, but most remain in the preclinical stages. Those that reached clinical trials did not demonstrate optimal results, underscoring the ongoing challenges in CD therapy. Collaborative efforts among the academic community, pharmaceutical industries, funding agencies, and government agencies are urgently needed to accelerate the development of more effective medications against CD.
Green Synthesis of Silver and Gold Nanoparticles by Aqueous Artemisia Pallens Extract
Authors: Verma Ashutosh Kumar
Published: April 2024

We successfully harnessed the potential of Artemisia pallens extracts for the eco-friendly biosynthesis of silver, gold, and silver-gold bimetallic nanoparticles, employing aqueous silver nitrate and chloroauric acid solutions. This innovative approach departs from traditional methods, often involving toxic chemical agents like hydrazine hydrate and sodium borohydride. In the quest for greener protocols, the biological route emerges as a non-toxic, straight-forward, and environmentally sound alternative, opening new avenues for translational research. This article discusses the production of silver, gold, and silver-gold nanoparticles using different species of Artemisia plants. Nanoparticle characterization was carried out using UV-visible spectrophotometry, TEM, XRD, and FTIR techniques. Microwave-assisted synthesis resulted in well-dispersed nanoparticles. In the case of silver nanoparticles, a spherical shape with a size of 6 nm was achieved using the microwave radiation-assisted method, while a size of 20 nm was obtained with UV-assisted synthesis. Gold nanoparticles exhibited diverse shapes, including spherical, triangular, prisms, trapezoids, and hexagonal, with a predominant size of 10 nm. The size range for gold nanoparticles varied from 10 nm to 400 nm.
Comprehensive Whole Genome Sequencing Reveals Origins of Mutational Signatures Associated with Aging and Temozolomide Chemotherapy
Authors: Hwang Taejoo , Sitko Lukasz Karol , Khoirunnisa Ratih , Aguad Fernanda Navarro , Samuel David M , Park Hajoong , Cheon Banyoon , Mutsnaini Luthfiyyah , Lee Jaewoong , Takeda Shunichi , Lee Semin , Ivanov Dmitri , Gartner Anton
Published: April 2024

In a comprehensive study to decipher the multi-layered response to the chemotherapeutic agent temozolomide (TMZ), we analyzed 427 genomes and determined mutational patterns in a collection of ∼40 isogenic DNA repair-deficient human TK6 lymphoblast cell lines. We demonstrate that the spontaneous mutational background is very similar to the aging-associated mutational signature SBS40 and mainly caused by polymerase zeta-mediated translesion synthesis (TLS).MSH2-/-mismatch repair knockout in conjunction with additional repair deficiencies uncovers cryptic mutational patterns. We report how distinct mutational signatures are induced by TMZ upon sequential inactivation of DNA repair pathways, mirroring the acquisition of chemotherapy resistance by glioblastomas. The most toxic adduct induced by TMZ,O6-meG, is directly repaired by theO6-methylguanine-DNA methyltransferase (MGMT). InMGMT-/-cells, mismatch repair (MMR) leads to cell death and limits mutagenesis. MMR deficiency results in TMZ resistance, allowing the accumulation of ∼105C>T substitutions corresponding to signature SBS11. Under these conditions, N-alkylated bases, processed by base excision repair (BER), limit cell survival. Without BER, 3-meA is read through via error-prone TLS, causing T>A substitutions but not affecting survival. Blocking BER after abasic site formation results in large deletions and TMZ hypersensitization. Our findings reveal potential vulnerabilities of TMZ-resistant tumors.
How to deal with internal fragment ions?
Authors: Grimaud Arthur , Babović Maša , Haugaard Holck Frederik , Jensen Ole N. , Schwämmle Veit
Published: April 2024

1

Tandem mass spectrometry of peptides and proteins generates mass spectra of their gas-phase fragmentation product ions, including N-terminal, C-terminal, and internal fragment ions. Whereas N- and C-terminal ions are routinely assigned and identified using computational methods, internal fragment ions are often difficult to annotate correctly. They become particularly relevant for long peptides and full proteoforms where the peptide backbone is more likely to be fragmented multiple times. Internal fragment ions potentially offer tremendous information regarding amino acid sequences and positions of post-translational modifications of peptides and intact proteins. However, their practical application is challenged by the vast number of theoretical internal fragments that exist for long amino acid sequences, leading to a high risk of false-positive annotations. We analyze the mass spectral contributions of internal fragment ions in spectra from middle-down and top-down experiments and introduce a novel graph-based annotation approach designed to manage the complexity of internal fragments. Our graph-based representation allows us to compare multiple candidate proteoforms in a single graph, and to assess different candidate annotations in a fragment ion spectrum. We demonstrate cases from middle-down and top-down data where internal ions enhance amino acid sequence coverage of polypeptides and proteins and accurate localization of post-translational modifications. We conclude that our graph-based method provides a general approach to process complex tandem mass spectra, enhance annotation of internal fragment ions, and improve proteoform sequencing and characterization by mass spectrometry.
Iron transport pathways in the human malaria parasitePlasmodium falciparumrevealed by RNA-sequencing
Authors: Wunderlich Juliane , Kotov Vadim , Votborg-Novél Lasse , Ntalla Christina , Geffken Maria , Peine Sven , Portugal Silvia , Strauss Jan
Published: April 2024

Host iron deficiency is protective against severe malaria as the human malaria parasitePlasmodium falciparumdepends on bioavailable iron from its host to proliferate. The essential pathways of iron acquisition, storage, export, and detoxification in the parasite differ from those in humans, as orthologs of the mammalian transferrin receptor, ferritin, or ferroportin, and a functional heme oxygenase are absent inP. falciparum. Thus, the proteins involved in these processes may be excellent targets for therapeutic development, yet remain largely unknown. Here, we show that parasites cultured in erythrocytes from an iron-deficient donor displayed significantly reduced growth rates compared to those grown in red blood cells from healthy controls. Sequencing of parasite RNA revealed diminished expression of genes involved in overall metabolism, hemoglobin digestion, and metabolite transport under low-iron versus control conditions. Supplementation with hepcidin, a specific ferroportin inhibitor, resulted in increased labile iron levels in erythrocytes, enhanced parasite replication, and transcriptional upregulation of genes responsible for merozoite motility and host cell invasion. Through endogenous GFP tagging of differentially expressed putative transporter genes followed by confocal live-cell imaging, proliferation assays with knockout and knockdown lines, and protein structure predictions, we identified six proteins that are likely required for ferrous iron transport inP. falciparum. Of these, we localizedPfVIT andPfZIPCO to cytoplasmic vesicles,PfMRS3 to the mitochondrion, and the novel putative iron transporterPfE140 to the plasma membrane for the first time inP. falciparum.PfNRAMP/PfDMT1 andPfCRT were previously reported to efflux Fe2+from the digestive vacuole. Our data support a new model for parasite iron homeostasis, in whichPfE140 is involved in iron uptake across the plasma membrane,PfMRS3 ensures non-redundant Fe2+supply to the mitochondrion as the main site of iron utilization,PfVIT transports excess iron into cytoplasmic vesicles, andPfZIPCO exports Fe2+from these organelles in case of iron scarcity. These results provide new insights into the parasite’s response to differential iron availability in its environment and into the mechanisms of iron transport inP. falciparumas promising candidate targets for future antimalarial drugs.
SON-dependent nuclear speckle rejuvenation alleviates proteinopathies
Authors: Dion William , Tao Yuren , Chambers Maci , Zhao Shanshan , Arbuckle Riley K. , Sun Michelle , Kubra Syeda , Jamal Imran , Nie Yuhang , Ye Megan , Larsen Mads B. , Camarco Daniel , Ickes Eleanor , DuPont Claire , Wang Haokun , Wang Bingjie , Liu Silvia , Pi Shaohua , Chen Bill B , Chen Yuanyuan , Chen Xu , Zhu Bokai
Published: April 2024

Current treatments targeting individual protein quality control have limited efficacy in alleviating proteinopathies, highlighting the prerequisite for a common upstream druggable target capable of global proteostasis modulation. Building on our prior research establishing nuclear speckles as a pivotal membrane-less organelle responsible for global proteostasis transcriptional control, we aim to alleviate proteinopathies through nuclear speckle rejuvenation. We identified pyrvinium pamoate as a small-molecule nuclear speckle rejuvenator that enhances protein quality control while suppressing YAP1 signaling via decreasing the surface/interfacial tension of nuclear speckle condensates through interaction with the intrinsically disordered region of nuclear speckle scaffold protein SON. In pre-clinical models, nanomolar pyrvinium pamoate alleviated retina degeneration and reduced tauopathy by promoting autophagy and ubiquitin-proteasome system in a SON-dependent manner without causing cellular stress. Aberrant nuclear speckle morphology, reduced protein quality control and increased YAP1 activity were also observed in human tauopathies. Our study uncovers novel therapeutic targets for tackling protein misfolding disorders within an expanded proteostasis framework encompassing nuclear speckles and YAP1.
Characterization of a novel zebrafish model ofMTMR5-associated CMT4B3
Authors: Lindzon Jordan , List Maia , Geissah Salma , Zhao Mo , Dowling James J.
Published: April 2024

Biallelic loss of expression/function variants inMTMR5cause the inherited peripheral neuropathy Charcot-Marie-Tooth (CMT) Type 4B3. There is an incomplete understanding of the disease pathomechanism(s) underlying CMT4B3, and despite its severe clinical presentation, currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre-clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier, we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion ofmtmr5.Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However, starting by 14 day-post-fertilization, mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination, changes reminiscent of the nerve pathology in human CMT4B3. Overall, ourmtmr5zebrafish mirror genetic, clinical, and pathologic features of human CMT4B3. As such, it represents a first pre-clinical model to phenocopy the disease, and an ideal tool for future studies on disease pathomechanism(s) and therapy development.

Summary Statement

We created a novel zebrafishmtmr5/sbf1mutant model of Charcot-Marie-Tooth Type 4B3 that recapitulates key features of the human disorder and provides the firstin vivomodel for therapy development.
Intracortical microstimulation of human somatosensory cortex is sufficient to induce perceptual biases
Authors: Greenspon Charles M. , Shelchkova Natalya D. , Hobbs Taylor G. , Bensmaia Sliman J. , Gaunt Robert A.
Published: April 2024

Abstract

Time-order error, a psychophysical phenomenon in which the duration in between successive stimuli alters perception, has been studied for decades by neuroscientists and psychologists. To date, however, the locus of these effects is unknown. We use intracortical microstimulation of somatosensory cortex in humans as a tool to bypass initial stages of processing and restrict the possible locations that signals could be modified. We find that, using both amplitude discrimination and magnitude estimation paradigms, intracortical microstimulation reliably evoked time-order errors across all participants. Points of subjective equality were symmetrically shifted during amplitude discrimination experiments and the intensity of a successive stimulus was perceived as being more intense when compared to single stimulus trials in magnitude estimation experiments. The error was reduced for both paradigms at longer inter-stimulus intervals. These results show that direct activation of primary somatosensory cortex is sufficient to induce time-order errors.
A 10-Year Longitudinal Study of Brain Cortical Thickness in People with First-Episode Psychosis using Normative Models
Authors: Berthet Pierre , Haatveit Beathe C. , Kjelkenes Rikka , Worker Amanda , Kia Seyed Mostafa , Wolfers Thomas , Rutherford Saige , Alnaes Dag , Dinga Richard , Pedersen Mads L. , Dahl Andreas , Fernandez-Cabello Sara , Dazzan Paola , Agartz Ingrid , Nesvåg Ragnar , Ueland Torill , Andreassen Ole A. , Simonsen Carmen , Westlye Lars T. , Melle Ingrid , Marquand Andre
Published: April 2024

Background

Clinical forecasting models have potential to optimize treatment and improve outcomes in psychosis, but predicting long-term outcomes is challenging and long-term follow up data are scarce. In this 10-year longitudinal study we aimed to characterize the temporal evolution of cortical correlates of psychosis and their associations with symptoms.

Design

Structural MRI from people with first-episode psychosis and controls (n=79 and 218) were obtained at enrollment, after 12 months (n=67 and 197), and 10 years (n=23 and 77), within the Thematically Organized Psychosis (TOP) study. Normative models for cortical thickness estimated on public MRI datasets (n=42983) were applied to TOP data to obtain deviation scores for each region and timepoint. Positive And Negative Syndrome Scale (PANSS) scores were acquired at each timepoint along with registry data. Linear mixed effects (LME) models assessed effects of diagnosis, time and their interactions on cortical deviations plus associations with symptoms.

Results

LMEs revealed conditional main effects of diagnosis and time x diagnosis interactions in a distributed cortical network, where negative deviations in patients attenuate over time. In patients, symptoms also attenuate over time. LMEs revealed effects of anterior cingulate on PANSS total, and insular and orbitofrontal regions on PANSS negative scores.

Conclusions

This long-term longitudinal study revealed a distributed pattern of cortical differences which attenuated over time together with a reduction in symptoms. These findings are not in line with a simple neurodegenerative account of schizophrenia, and deviations from normative models offer a promising avenue to develop biomarkers to track clinical trajectories over time.
Postoperative Karnofsky performance status prediction in patients withIDHwild-type glioblastoma: a multimodal approach integrating clinical and deep imaging features
Authors: Sasagasako Tomoki , Ueda Akihiko , Mineharu Yohei , Mochizuki Yusuke , Doi Souichiro , Park Silsu , Terada Yukinori , Sano Noritaka , Tanji Masahiro , Arakawa Yoshiki , Okuno Yasushi
Published: April 2024

Background and Purpose

Glioblastoma is a highly aggressive brain tumor with limited survival that poses challenges in predicting patient outcomes. The Karnofsky Performance Status (KPS) score is a valuable tool for assessing patient functionality and contributes to the stratification of patients with poor prognoses. This study aimed to develop a 6-month postoperative KPS prediction model by combining clinical data with deep learning-based image features from pre- and postoperative MRI scans, offering enhanced personalized care for glioblastoma patients.

Materials and Methods

Using 1,476 MRI datasets from the Brain Tumor Segmentation Challenge 2020 public database, we pretrained two variational autoencoders (VAEs). Imaging features from the latent spaces of the VAEs were used for KPS prediction. Neural network-based KPS prediction models were developed to predict scores below 70 at 6 months postoperatively. In this retrospective single-center analysis, we incorporated clinical parameters and pre- and postoperative MRI images from 150 newly diagnosed IDH wild-type glioblastoma, divided into training (100 patients) and test (50 patients) sets. In training set, the performance of these models was evaluated using the area under the curve (AUC), calculated through fivefold cross-validation repeated 10 times. The final evaluation of the developed models assessed in the test set.

Results

Among the 150 patients, 61 had 6-month postoperative KPS scores below 70 and 89 scored 70 or higher. We developed three models: a clinical-based model, an MRI-based model, and a multimodal model that incorporated both clinical parameters and MRI features. In the training set, the mean AUC was 0.785±0.051 for the multimodal model, which was significantly higher than the clinical-based model (0.716±0.059, P=0.038) using only clinical parameters and MRI-based model (0.651±0.028, P<0.001) using only MRI features. In the test set, the multimodal model achieved an AUC of 0.810, outperforming the clinical-based (0.670) and MRI-based (0.650) models.

Conclusion

The integration of MRI features extracted from VAEs with clinical parameters in the multimodal model substantially enhanced KPS prediction performance. This approach has the potential to improve prognostic prediction, paving the way for more personalized and effective treatments for patients with glioblastoma.