bluuebunny/crossref_metadata_2025 huggingface dataset:
Nuclear compression-mediated DNA damage drives ATR-dependent Lamin expression and mouse ESC differentiation
Authors: Roy Tanusri , Ghosh Swetlana , Piplani Niyati , Sthanam Lakshmi Kavitha , Tiwary Niharika , Dhar Sayak , Konyak W. Chingmei Wangsa , Panigrahi Santosh Surendra , Singh Priya , Sowpati Divya Tej , Nair Sreelaja , Kumar Sushil , Shekar P. Chandra , Sen Shamik
Published: March 2024

Embryonic stem cells (ESCs) which are susceptible to DNA damage depend on a robust and highly efficient DNA damage response (DDR) mechanism for their survival. However, the implications of physical force-mediated DNA damage on ESC fate remains unclear. We show that stiffness-dependent spreading of mouse ESCs (mESCs) induces DNA damage through nuclear compression, with DNA damage causing differentiation through early induction of Lamin A/C expression. Interestingly, differentiation is associated with rescue of DNA damage and activation of the DDR factor ATR. While ATR is typically known to play roles in DDR pathway, its role during stiffness-mediated nuclear compression and mESC differentiation is unknown. Nuclear enrichment of activated ATR on stiff substrates and reduction of Lamin A/C expression upon ATR inhibition suggests that mESC differentiation is driven by nuclear compression-mediated DNA damage and involves ATR-dependent modulation of Lamin A/C.
Putaminal dopamine modulates movement motivation in Parkinson’s disease
Authors: Banwinkler Magdalena , Dzialas Verena , Rigoux Lionel , Asendorf Adrian L. , Theis Hendrik , Giehl Kathrin , Tittgemeyer Marc , Hoenig Merle C. , van Eimeren Thilo
Published: March 2024

The relative inability to produce effortful movements (akinesia) is the most specific motor sign of Parkinson’s disease. The motor motivation hypothesis suggests that akinesia may not reflect a deficiency in motor controlper se, but a deficiency in cost-benefit considerations for motor effort. For the first time, we investigated the quantitative effect of dopamine depletion on the motivation of motor effort in Parkinson’s disease.

A total of 21 patients with Parkinson’s disease and 26 healthy controls were included. An incentivized force task was used to capture the amount of effort participants were willing to invest for different monetary incentive levels and dopamine transporter depletion in the bilateral putamen was assessed.

Our results demonstrate that patients with Parkinson’s disease applied significantly less grip force than healthy controls, especially for low incentive levels. Congruously, decrease of motor effort with greater loss of putaminal dopaminergic terminals was most pronounced for low incentive levels. This signifies that putaminal dopamine is most critical to motor effort when the trade-off with the benefit is poor.

Taken together, we provide direct evidence that the reduction of effortful movements in Parkinson’s disease depends on motivation and that this effect is associated with putaminal dopaminergic degeneration.
Low-grade systemic inflammation stimulates microglial turnover and accelerates the onset of Alzheimer’s-like pathology
Authors: Guerrero-Carrasco Monica , Targett Imogen , Olmos-Alonso Adrian , Vargas-Caballero Mariana , Gomez-Nicola Diego
Published: March 2024

Severalin vivostudies have shown that systemic inflammation, mimicked by LPS, triggers an inflammatory response in the CNS, driven by microglia, characterised by an increase in inflammatory cytokines and associated sickness behaviour. However, most studies induce relatively high systemic inflammation, not directly compared with the more common low grade inflammatory events experienced in humans during the life course. Using mice, we investigated the effects of low-grade systemic inflammation during an otherwise healthy early life, and how this may pre-condition the onset and severity of Alzheimer’s disease (AD)-like pathology. Our results indicate that low grade systemic inflammation induces sub-threshold brain inflammation and promotes microglial proliferation driven by the CSF1R pathway, contrary to the effects caused by high systemic inflammation. In addition, repeated systemic challenges with low grade LPS induce disease-associated microglia. Finally, using an inducible model of AD-like pathology (Line 102 mice), we observed that pre-conditioning with repeated doses of low-grade systemic inflammation, prior to APP induction, promotes a detrimental effect later in life, leading to an increase in Aβ accumulation and disease-associated microglia. These results support the notion that episodic low grade systemic inflammation has the potential to influence the onset and severity of age-related neurological disorders, such as Alzheimer’s disease.
Evaluation of Gene Set Enrichment Analysis (GSEA) tools highlights the value of single sample approaches over pairwise for robust biological discovery
Authors: Bull Courtney , Byrne Ryan M , Fisher Natalie C , Corry Shania M , Amirkhah Raheleh , Edwards Jessica , Hillson Lily , Lawler Mark , Ryan Aideen , Lamrock Felicity , Dunne Philip D , Malla Sudhir B
Published: March 2024

Background

Gene set enrichment analysis (GSEA) tools can be used to identify biological insights from transcriptional datasets and have become an integral analysis within gene expression-based cancer studies. Over the years, additional methods of GSEA-based tools have been developed, providing the field with an ever-expanding range of options to choose from. Although several studies have compared the statistical performance of these tools, the downstream biological implications that arise when choosing between the range of pairwise or single sample forms of GSEA methods remain understudied.

Methods

In this study, we compare the statistical and biological interpretation of results obtained when using a variety of pre-ranking methods and options for pairwise GSEA and fast GSEA (fGSEA), alongside single sample GSEA (ssGSEA) and gene set variation analysis (GSVA). These analyses are applied to a well-established cohort of n=215 colon tumour samples, using the clinical feature of cancer recurrence status, non-relapse (NR) and relapse (R), as an initial exemplar, in conjunction with the Molecular Signatures Database “Hallmark” gene sets.

Results

Despite minor fluctuations in statistical performance, pairwise analysis revealed remarkably similar results when deployed using a range of gene pre-ranking methods or across a range of choices of GSEA versus fGSEA, with the same well-established prognostic signatures being consistently returned as significantly associated with relapse status. In contrast, when the same statistically significant signatures, such as Interferon Gamma Response, were assessed using ssGSEA and GSVA approaches, there was a complete absence of biological distinction between these groups (NR and R).

Conclusions

Data presented here highlights how pairwise methods can overgeneralise biological enrichment within a group, assigning strong statistical significance to gene sets that may be inadvertently interpreted as equating to distinct biology. Importantly, single sample approaches allow users to clearly visualise and interpret statistical significance alongside biological distinction between samples within groups-of-interest; thus, providing a more robust and reliable basis for discovery research.
The dynamin-related protein Dyn2 is essential for both apicoplast and mitochondrial fission inPlasmodium falciparum
Authors: Morano Alexander A. , Xu Wei , Shadija Neeta , Dvorin Jeffrey D. , Ke Hangjun
Published: March 2024

Dynamins, or dynamin-related proteins (DRPs), are large mechano-sensitive GTPases mediating membrane dynamics or organellar fission/fusion events.Plasmodium falciparumencodes three dynamin-like proteins whose functions are poorly understood. Here, we demonstrate that PfDyn2 mediates both apicoplast and mitochondrial fission. Using super-resolution and ultrastructure expansion microscopy, we show that PfDyn2 is expressed in the schizont stage and localizes to both the apicoplast and mitochondria. Super-resolution long-term live cell microscopy shows that PfDyn2-deficient parasites cannot complete cytokinesis because the apicoplast and mitochondria do not undergo fission. Further, the basal complex or cytokinetic ring inPlasmodiumcannot fully contract upon PfDyn2 depletion, a phenotype secondary to physical blockage of undivided organelles in the middle of the ring. Our data suggest that organellar fission defects result in aberrant schizogony, generating unsuccessful merozoites. The unique biology of PfDyn2, mediating both apicoplast and mitochondrial fission, has not been observed in other organisms possessing two endosymbiotic organelles.

Highlights

PfDyn2 is essential for schizont-stage development.

PfDyn2 mediates both apicoplast and mitochondrial fission.

Deficiency of PfDyn2 leads to organellar fission failures and blockage of basal complex contraction.

Addition of apicoplast-derived metabolite IPP does not rescue the growth defects.
GGTyper: genotyping complex structural variants using short-read sequencing data
Authors: Mirus Tim , Lohmayer Robert , Halldorsson Bjarni V , Kehr Birte
Published: March 2024

Motivation: Complex structural variants are genomic rearrangements that involve multiple segments of DNA. They contribute to human diversity and have been shown to cause Mendelian disease. Nevertheless, our abilities to analyse complex structural variants are very limited. As opposed to deletions and other canonical types of structural variants (SVs), there are no established tools that have explicitly been designed for analysing complex SVs. Here, we describe a new computational approach that we specifically designed for genotyping complex SVs in short-read sequenced genomes. Given a variant description, our approach computes genotype-specific probability distributions for observing aligned read pairs with a wide range of properties. Subsequently, these distributions can be used to efficiently determine the most likely genotype for any set of aligned read pairs observed in a sequenced genome. In addition, we use these distributions to compute a genotyping difficulty for a given variant, which predicts the amount of data needed to achieve a reliable call. Careful evaluation confirms that our approach outperforms other genotypers by making reliable genotype predictions across both simulated and real data. On up to 7829 human genomes, we achieve high concordance with population-genetic assumptions and expected inheritance patterns. On simulated data, we show that precision correlates well with our prediction of genotyping difficulty. This together with low memory and time requirements makes our approach well-suited for application in biomedical studies involving small to very large numbers of short-read sequenced genomes.
A λ-dynamics investigation of insulinWakayamaand other A3 variant binding affinities to the insulin receptor
Authors: Barron Monica P. , Vilseck Jonah Z.
Published: March 2024

InsulinWakayamais a clinical insulin variant where a conserved valine at the third residue on insulin’s A chain (ValA3) is replaced with a leucine (LeuA3), impairing insulin receptor (IR) binding by 140-500 fold. This severe impact on binding from such a subtle modification has posed an intriguing problem for decades. Although experimental investigations of natural and unnatural A3 mutations have highlighted the sensitivity of insulin-IR binding to minor changes at this site, an atomistic explanation of these binding trends has remained elusive. We investigate this problem computationally using λ-dynamics free energy calculations to model structural changes in response to perturbations of the ValA3side chain and to calculate associated relative changes in binding free energy (ΔΔGbind). TheWakayamaLeuA3mutation and seven other A3 substitutions were studied in this work. The calculated ΔΔGbindresults showed high agreement compared to experimental binding potencies with a Pearson correlation of 0.88 and a mean unsigned error of 0.68 kcal/mol. Extensive structural analyses of λ-dynamics trajectories revealed that critical interactions were disrupted between insulin and the insulin receptor as a result of the A3 mutations. This investigation also quantifies the effect that adding an A3 Cδatom or losing an A3 Cγatom has on insulin’s binding affinity to the IR. Thus, λ-dynamics was able to successfully model the effects of subtle modifications to insulin’s A3 side chain on its protein-protein interactions with the IR and shed new light on a decades-old mystery: the exquisite sensitivity of hormone-receptor binding to a subtle modification of an invariant insulin residue.

SIGNIFICANCE STATEMENT

This work addresses a decades-old question of how subtle modifications to insulin’s A3 side chain affects its binding affinity to the insulin receptor. λ-Dynamics computed free energies of binding match experimental activity trends with high accuracy. Atomistic insights into hormone-receptor protein-protein interactions were obtained through a detailed investigation of λ-dynamic trajectories. This work quantifies the effects of adding and removing atoms to insulin’s conserved A3 residue and identifies clear conformational preferences for insulin A3 residues when bound to the insulin receptor.
Caskin2 is a novel talin and Abi1-binding protein that promotes cell motility
Authors: Wang Wei , Atherton Paul , Kreft Maaike , te Molder Lisa , van der Poel Sabine , Hoekman Liesbeth , Celie Patrick , Joosten Robbie P , Faessler Reinhard , Perrakis Anastassis , Sonnenberg Arnoud
Published: March 2024

Talin couples the actomyosin cytoskeleton to integrins and transmits tension to the extracellular matrix. Talin also interacts with numerous additional proteins capable of modulating the actin-integrin linkage and thus downstream mechanosignaling cascades. Here, we demonstrate that the scaffold protein Caskin2 interacts directly with the R8 domain of talin through its C-terminal LD motif. Caskin2 also associates with the WAVE Regulatory Complex to promote cell migration in an Abi1-dependent manner. Furthermore, we demonstrate that the Caskin2-Abi1 interaction is regulated by growth factor-induced phosphorylation of Caskin2 on serine 878. In MCF7 and UACC893 cells, which contain an amplification of CASKIN2, Caskin2 localizes in plasma membrane-associated plaques and around focal adhesions in CMSCs. Taken together, our results identify Caskin2 as a novel talin-binding protein that may not only connect integrin-mediated adhesion to actin polymerization, but could also play a role in crosstalk between integrins and microtubules.
Seasonal variation of behavioural thermoregulation in the Spotted Salamander (Ambystoma maculatum)
Authors: Giacometti Danilo , Tattersall Glenn J.
Published: March 2024

Mounting evidence suggests that temperature seasonality plays a pivotal role in shaping the thermal biology of ectotherms. However, we still have a limited understanding of how amphibians maintain thermal balance in the face of varying temperatures, especially in fossorial species. Due to thermal buffering underground, theory predicts relaxed selection pressure over thermoregulation in fossorial ectotherms. As a result, fossorial ectotherms typically show low thermoregulatory precision and low evidence of thermotactic behaviours when tested in laboratory thermal gradients. In this study, we evaluated how temperature selection (Tsel) and behavioural thermoregulation differed between seasons in the fossorial Spotted Salamander (Ambystoma maculatum). By comparing thermoregulatory parameters between the activity and overwintering seasons, we provide evidence thatA.maculatumengages in active behavioural thermoregulation despite its fossorial habit. In both seasons, we foundTselto be consistently offset higher than prevailing thermal conditions. Thermoregulation differed between seasons, with salamanders having higherTseland showing greater evidence of thermophilic behaviours in the active season compared to the overwintering season. Our study highlights that the combination of behavioural and thermal biology measurements is a necessary step to better understand the mechanisms that underlie body temperature control in amphibians. Ultimately, our study provides a broader understanding of thermoregulation in amphibians, particularly in the context of behavioural responses to seasonality in fossorial species.

Summary statement

By comparing thermoregulatory parameters between seasons, we demonstrate that the Spotted Salamander engages in active behavioural thermoregulation despite being fossorial.
Spatial contextual information modulates affordance processing and early electrophysiological markers of scene perception
Authors: Naveilhan Clément , Saulay-Carret Maud , Zory Raphaël , Ramanoël Stephen
Published: March 2024

Scene perception allows humans to extract information from their environment and plan navigation efficiently. The automatic extraction of potential paths in a scene, also referred to as navigational affordances is supported by scene-selective regions (SSRs) that enable efficient human navigation. Recent evidence suggests that the activity of these SSRs can be influenced by information from adjacent spatial memory areas. However, it remains unexplored how these contextual information could influence the extraction of bottom-up information, such as navigational affordances, from a scene and the underlying neural dynamics. Therefore, we analyzed event-related potentials (ERPs) in 26 young adults performing scene and spatial memory tasks in artificially generated rooms with varying numbers and locations of available doorways. We found that increasing the number of navigational affordances only impaired performance in the spatial memory task. ERP results showed a similar pattern of activity for both tasks, but with increased P2 amplitude in the spatial memory task compared to the scene memory. Finally, we reported no modulation of the P2 component by the number of affordances in either task. This modulation of early markers of visual processing suggests that the dynamics of SSR activity are influenced by a priori knowledge, with increased amplitude when participants have more contextual information about the perceived scene. Overall, our results suggest that prior spatial knowledge about the scene, such as the location of a goal, modulates early cortical activity associated with scene-selective regions, and that this information may interact with bottom-up processing of scene content, such as navigational affordances.
Physiologic media renders human iPSC-derived macrophages permissive forM. tuberculosisby rewiring organelle function and metabolism
Authors: Bussi Claudio , Lai Rachel , Athanasiade Natalia , Gutierrez Maximiliano G.
Published: March 2024

In vitrostudies are crucial for our understanding of the human macrophage immune functions. However, traditionalin vitroculture media poorly reflect the metabolic composition of blood, potentially affecting the outcomes of these studies. Here, we analysed the impact of a physiological medium on human induced pluripotent stem cell (iPSC)-derived macrophages (iPSDM) function. Macrophages cultured in a human plasma-like medium (HPLM) were more permissive toMycobacterium tuberculosis(Mtb) replication and showed decreased lipid metabolism with increased metabolic polarisation. Functionally, we discovered that HPLM-differentiated macrophages showed different metabolic organelle content and activity. Specifically, HPLM-differentiated macrophages displayed reduced lipid droplet and peroxisome content, increased lysosomal proteolytic activity, and increased mitochondrial activity and dynamics. Inhibiting or inducing lipid droplet formation revealed that lipid droplet content is a key factor influencing macrophage permissiveness to Mtb. These findings underscore the importance of using physiologically relevant mediain vitrofor accurately studying human macrophage function.
Celldetective: an AI-enhanced image analysis tool for unraveling dynamic cell interactions
Authors: Torro Rémy , Díaz-Bello Beatriz , Arawi Dalia El , Dervanova Ksenija , Ammer Lorna , Dupuy Florian , Chames Patrick , Sengupta Kheya , Limozin Laurent
Published: March 2024

A current challenge in bioimaging for immunology and immunotherapy research lies in analyzing multimodal and multidimensional data that capture dynamic interactions between diverse cell populations. Here, we introduce Celldetective, an open-source Python-based software designed for high-performance, end-to-end analysis of image-basedin vitroimmune and immunotherapy assays. Purpose-built for multicondition, 2D multichannel time-lapse microscopy of mixed cell populations, Celldetective is optimized for the needs of immunology assays. The software seamlessly integrates AI-based segmentation, Bayesian tracking, and automated single-cell event detection, all within an intuitive graphical interface that supports interactive visualization, annotation, and training capabilities. We demonstrate its utility with original data on immune effector cell interactions with an activating surface, mediated by bispecific antibodies, and further showcase its potential for analyzing extensive sets of pairwise interactions in antibody-dependent cell cytotoxicity events.
CD39 is expressed on functional effector and tissue resident memory CD8+ T cells
Authors: Isaacs Jordan F. , Degefu Hanna N. , Chen Tiffany , Kleist Sierra A. , Musial Shawn C. , Ford Myles A. , Searles Tyler G. , Lin Chun-Chieh , Skorput Alexander G. J. , Shirai Keisuke , Turk Mary Jo , Zanazzi George J. , Rosato Pamela C.
Published: March 2024

The ecto-ATPase CD39 is expressed on exhausted CD8+ T cells in chronic viral infection and has been proposed as a marker of tumor-specific CD8+ T cells in cancer, but the role of CD39 in an effector and memory T cell response has not been clearly defined. We report that CD39 is expressed on antigen-specific CD8+ short-lived effector cells (SLECs), while it’s co-ecto-enzyme, CD73, is found on memory precursor effector cells (MPEC)in vivo. Inhibition of CD39 enzymatic activity duringin vitroT cell priming enhances MPEC differentiationin vivoafter transfer and infection. The enriched MPEC phenotype is associated with enhanced tissue resident memory (TRM) establishment in the brain and salivary gland following an acute intranasal viral infection, suggesting that CD39 ATPase activity plays a role in memory CD8+ T cell differentiation. We also show that CD39 is expressed on human and murine TRMacross several non-lymphoid tissues and melanoma, while CD73 is expressed on both circulating and resident memory subsets in mice. In contrast to exhausted CD39+ T cells in chronic infection, CD39+ TRMare fully functional when stimulatedex vivowith cognate antigen. This work further expands the identity of CD39 beyond a T cell exhaustion marker.
CLigopt: Controllable Ligand Design Through Target-Specific Optimisation
Authors: Li Yutong , Costa Avelar Pedro Henrique da , Chen Xinyue , Zhang Li , Wu Min , Tsoka Sophia
Published: March 2024

ABSTRACT

Motivation

Key challenge in deep generative models for molecular design is to navigate random sampling of the vast molecular space, and produce promising molecules that compromise property controls across multiple chemical criteria. Fragment-based drug design (FBDD), using fragments as starting points, is an effective way to constrain chemical space and improve generation of biologically active molecules. Furthermore, optimisation approaches are often implemented with generative models to search through chemical space, and identify promising samples which satisfy specific properties. Controllable FBDD has promising potential in efficient target-specific ligand design.

Results

We propose a controllable FBDD model, CLigOpt, which can generate molecules with desired properties from a given fragment pair. CLigOpt is a Variational AutoEncoder-based model which utilises co-embeddings of node and edge features to fully mine information from molecular graphs, as well as a multi-objective Controllable Generation Module to generate molecules under property controls. CLigOpt achieves consistently strong performance in generating structurally and chemically valid molecules, as evaluated across six metrics. Applicability is illustrated through ligand candidates for hDHFR and it is shown that the proportion of feasible active molecules from the generated set is increased by 10%. Molecular docking and synthesisability prediction tasks are conducted to prioritise generated molecules to derive potential lead compounds.

Availability and Implementation

The source code is available viahttps://github.com/yutongLi1997/CLigOpt-Controllable-Ligand-Design-through-Target-Specific-Optimisation.
HIV integrase compacts viral DNA into biphasic condensates
Authors: Kolbeck Pauline J. , de Jager Marjolein , Gallano Margherita , Brouns Tine , Bekaert Ben , Frederickx Wout , Konrad Sebastian F. , Van Belle Siska , Christ Frauke , De Feyter Steven , Debyser Zeger , Filion Laura , Lipfert Jan , Vanderlinden Willem
Published: March 2024

The human immunodeficiency virus (HIV) infects non-dividing cells and its genome must be compacted to enter the cell nucleus. Here, we show that the viral enzyme integrase (IN) compacts HIV DNA mimeticsin vitro. Under physiological conditions, IN-compacted genomes are consistent in size with those found for pre-integration complexes in infected cells. Compaction occurs in two stages: first IN tetramers bridge DNA strands and assemble into “rosette” structures that consist of a nucleo-protein core and extruding bare DNA. In a second stage, the extruding DNA loops condense onto the rosette core to form a disordered and viscoelastic outer layer. Notably, the core complex is susceptible towards IN inhibitors, whereas the diffuse outer layer is not. Together, our data suggest that IN has a structural role in viral DNA compaction and raise the possibility to develop inhibitors that target IN-DNA interactions in disordered condensates.

Teaser

Single-molecule studies demonstrate the mechanism, dynamics, and drug-susceptibility of viral genome compaction by HIV integrase.
Heterotypic Seeding Generates Mixed Amyloid Polymorphs
Authors: Banerjee S. , Baghel D. , Edmonds H. O. , Ghosh Ayanjeet
Published: March 2024

Aggregation of the amyloid β (Aβ) peptide into fibrils represents one of the major biochemical pathways underlying the development of Alzheimer’s disease (AD). Extensive studies have been carried out to understand the role of fibrillar seeds on the overall kinetics of amyloid aggregation. However, the precise effect of seeds that are structurally or sequentially different from Aβ on the structure of the resulting amyloid aggregates is yet to be fully understood. In this work, we use nanoscale infrared spectroscopy to probe the spectral facets of individual aggregates formed by aggregating Aβ42 with antiparallel fibrillar seeds of Aβ (16-22) and E22Q Aβ (1-40) Dutch mutant and demonstrate that Aβ can form heterotypic or mixed polymorphs that deviate significantly from its expected parallel cross β structure. We further show that formation of heterotypic aggregates is not limited to coaggregation of Aβ and its isomers, and that the former can form heterotypic fibrils with alpha synuclein and brain protein lysates. These findings highlight the complexity of Aβ aggregation in AD and underscore the need to explore how Aβ interacts with other brain components, which is crucial for developing better therapeutic strategies for AD.
Cholinergic Transmission in an Inducible Transgenic Mouse Model of Paroxysmal Dystonia
Authors: Scarduzio Mariangela , Jaunarajs Karen L Eskow , Standaert David G
Published: March 2024

Altered interaction between striatonigral dopaminergic (DA) inputs and local acetylcholine (ACh) in striatum has long been hypothesized to play a central role in dystonia pathophysiology. Indeed, previous research across various genetic mouse models of human isolated dystonia has identified as a shared endophenotype with paradoxical excitation of striatal cholinergic interneurons (ChIs) activity in response to activation of dopamine D2 receptor (D2R). These mouse models lack a dystonic motor phenotype, which leaves a critical gap in comprehending the role of ACh transmission in the manifestation of dystonia. To tackle this question, we used a combination ofex vivoslice physiology andin vivomonitoring of striatal ACh dynamics in the inducible, phenotypically penetrant, transgenic mouse model of paroxysmal non-kinesigenic dyskinesia (PNKD). We found that, similarly to other genetic models, the PNKD mouse displays D2R-induced paradoxical excitation of ChI firing inex vivostriatal brain slices.In vivo, caffeine triggers dystonic symptoms while reversing the D2R-mediated excitation of ChIs and desynchronizing the striatal cholinergic network. In WT littermate controls, caffeine stimulates spontaneous locomotion through a similar but reversed mechanism involving an excitatory switch of the D2R control of ChI activity, associated with enhanced cholinergic network synchronization. Together these observations suggest that D2Rs may play an important role in synchronizing the ChI network during heightened movement states. The “paradoxical excitation” described in dystonia models could represent a compensatory or protective mechanism that prevents manifestation of movement abnormalities and allows for phenotypic dystonia when lost.
Systematic Analysis of Biological Processes Reveals Gene Co-expression Modules Driving Pathway Dysregulation in Alzheimer’s Disease
Authors: Adeoye Temitope , Shah Syed I , Ullah Ghanim
Published: March 2024

Alzheimer’s disease (AD) manifests as a complex systems pathology with intricate interplay among various genes and biological processes. Traditional differential gene expression (DEG) analysis, while commonly employed to characterize AD-driven perturbations, does not sufficiently capture the full spectrum of underlying biological processes. Utilizing single-nucleus RNA-sequencing data from postmortem brain samples across key regions—middle temporal gyrus, superior frontal gyrus, and entorhinal cortex—we provide a comprehensive systematic analysis of disrupted processes in AD. We go beyond the DEG-centric analysis by integrating pathway activity analysis with weighted gene co-expression patterns to comprehensively map gene interconnectivity, identifying region- and cell-type specific drivers of biological processes associated with AD. Our analysis reveals profound modular heterogeneity in neurons and glia as well as extensive AD-related functional disruptions. Co-expression networks highlighted the extended involvement of astrocytes and microglia in biological processes beyond neuroinflammation, such as calcium homeostasis, glutamate regulation, lipid metabolism, vesicle-mediated transport, and TOR signaling. We find limited representation of DEGs within dysregulated pathways across neurons and glial cells, indicating that differential gene expression alone may not adequately represent the disease complexity. Further dissection of inferred gene modules revealed distinct dynamics of hub DEGs in neurons versus glia, highlighting the differential impact of DEGs on neurons compared to glial cells in driving modular dysregulations underlying perturbed biological processes. Interestingly, we note an overall downregulation of both astrocyte and microglia modules in AD across all brain regions, suggesting a prevailing trend of functional repression in glial cells across these regions. Notable genes, including those of the CALM and HSP90 family genes emerged as hub genes across neuronal modules in all brain regions, indicating conserved roles as drivers of synaptic dysfunction in AD. Our findings demonstrate the importance of an integrated, systems oriented approach combining pathway and network analysis for a comprehensive understanding of the cell-type-specific roles of genes in AD-related biological processes.
Heterogeneous and Novel Transcript Expression in Single Cells of Patient-Derived ccRCC Organoids
Authors: Karakulak Tülay , Zajac Natalia , Bolck Hella Anna , Bratus-Neuenschwander Anna , Zhang Qin , Qi Weihong , Basu Debleena , Oltra Tamara Carrasco , Rehrauer Hubert , von Mering Christian , Moch Holger , Kahraman Abdullah
Published: March 2024

Splicing is often dysregulated in cancer, leading to alterations in the expression of canonical and alternative splice isoforms. This complex phenomenon can be revealed by an in-depth understanding of cellular heterogeneity at the single-cell level. Recent advances in single-cell long- read sequencing technologies enable comprehensive transcriptome sequencing at the single-cell level. In this study, we have generated single-cell long-read sequencing of Patient-Derived Organoid (PDO) cells of clear-cell Renal Cell Carcinoma (ccRCC), an aggressive and lethal form of cancer that arises in kidney tubules. We have used the Multiplexed Arrays Sequencing (MAS-ISO-Seq) protocol of PacBio to sequence full-length transcripts exceptionally deep across 2,599 single cells to obtain the most comprehensive view of the alternative landscape of ccRCC to date. On average, we uncovered 86,182 transcripts across PDOs, of which 31,531 (36.6%) were previously uncharacterized. In contrast to known transcripts, many of these novel isoforms appear to exhibit cell-specific expression. Nonetheless, >50% of these novel transcripts were predicted to possess a complete protein-coding open reading frame. This finding suggests a biological role for these transcripts within kidney cells. Moreover, an analysis of the most dominant transcript switching events between ccRCC and non-ccRCC cells revealed that many switching events were cell and sample-specific, underscoring the heterogeneity of alternative splicing events in ccRCC.

Overall, our research elucidates the intricate transcriptomic architecture of ccRCC, potentially exposing the mechanisms underlying its aggressive phenotype and resistance to conventional cancer therapies.
Hairpin-RNA Spray Confers Resistance to Mungbean Yellow Mosaic India Virus in Mungbean
Authors: Dhobale Kiran Vilas , Sahoo Lingaraj
Published: March 2024

The prevalence of Begomovirus diseases poses a significant threat to legume crops, necessitating the exploration of innovative control measures. This investigation explores the utilization of dsRNA molecules to initiate RNA interference (RNAi) targeting begomovirus, particularly focusing onMungbean yellow mosaic India virus(MYMIV) and its potential threat to mungbean crops. Given the lack of genetic resistance in commercially available mungbean varieties, the study endeavors to employ RNAi as a strategic method for the effective control of MYMIV. The approach involves the preparation of vectors for the transient expression of three dsRNA targeting multiple overlapping ORFs of MYMIV DNA A through agroinoculation, and the selection of a highly efficient construct for dsRNA expression in bacteria, enabling topical application to mungbean plants in growth chamber experiments. Agroinoculation assays demonstrate effective resistance against MYMIV, as confirmed by reduced symptom severity, limited virus accumulation, and the presence of viral mRNAs. The stability of the prepared dsRNA against nucleases is confirmed, showcasing its ability to enter plant cells, move to non treated trifoliate leaves, and form siRNA when sprayed onto mungbean leaves, as validated by qRT-PCR and northern blotting. Varied combinations of the timing of dsRNA spray and virus infection reveal differential resistance against the virus. Notably, spraying two days before or on the same day as virus exposure emerges as the most suitable time to achieve optimal resistance against virus infection. In light of these findings, the topical application of dsRNAs stands out as a promising and effective strategy for MYMIV control in mungbean crops.
Ca2+-independent ZmCPK2 is inhibited by Ca2+-dependent ZmCPK17 during drought response in maize
Authors: Hu Xiaoying , Cheng Jinkui , Lu Minmin , Fang Tingitng , Zhu Yujuan , Li Zhen , Wang Xiqing , Wang Yu , Guo Yan , Yang Shuhua , Gong Zhizhong
Published: March 2024

Calcium oscillations are induced by different stresses. Calcium-dependent protein kinases (CDPKs/CPKs) are one major group of the plant calcium decoders that are involved in various processes including drought response. Some CPKs are calcium-independent. Here, we identified ZmCPK2 as a negative regulator of drought resistance by screening an overexpression transgenic maize pool. We found that ZmCPK2 does not bind calcium, and its activity is modulated likely in an oscillation manner during short time ABA treatment. Interestingly, ZmCPK2 interacts with and is inhibited by calcium-dependent ZmCPK17, a positive regulator of drought resistance, which is activated by ABA. ZmCPK17 activity exhibits opposite patterns relative to ZmCPK2 under ABA treatment, and could prevent the nuclear localization of ZmCPK2 when co-expressed. ZmCPK2 interacts with and phosphorylates ZmYAB15, a negative transcriptional factor for drought resistance. Our results suggest that drought stress-induced Ca2+can be decoded by corresponding CPK17 likely in an oscillation manner, thereby promoting plant adaptation to water deficit.
Atypical retinal function in a mouse model of Fragile X syndrome
Authors: Vlasits Anna L. , Syeda Maria , Wickman Annelise , Guzman Pedro , Schmidt Tiffany M.
Published: March 2024

Altered function of peripheral sensory neurons is an emerging mechanism for symptoms of autism spectrum disorders. Visual sensitivities are common in autism, but whether differences in the retina might underlie these sensitivities is not well-understood. We explored retinal function in the Fmr1 knockout model of Fragile X syndrome, focusing on a specific type of retinal neuron, the “sustained On alpha” retinal ganglion cell. We found that these cells exhibit changes in dendritic structure and dampened responses to light in the Fmr1 knockout. We show that decreased light sensitivity is due to increased inhibitory input and reduced E-I balance. The change in E-I balance supports maintenance of circuit excitability similar to what has been observed in cortex. These results show that loss of Fmr1 in the mouse retina affects sensory function of one retinal neuron type. Our findings suggest that the retina may be relevant for understanding visual function in Fragile X syndrome.
Live imaging of Alu elements reveals non-uniform euchromatin dynamics coupled to transcription
Authors: Chang Yi-Che , Quinodoz Sofia A. , Brangwynne Clifford P.
Published: March 2024

Chromatin structure and dynamics are crucial for eukaryotic nuclear functions. Hi-C and related genomic assays have revealed chromatin conformations, such as A/B compartments, in fixed cells, but the dynamic motion of such structures is not well understood. Moreover, elucidating the relationship between the motion of chromatin and transcriptional activity is hampered by a lack of tools for specifically measuring the mobility of active euchromatin. Here, we introduce a CRISPR-based strategy for live imaging of the gene-rich A compartment by labeling Alu elements — a retrotransposon family enriched within the transcriptionally active A compartment. Surprisingly, within euchromatin, microscopy analysis reveals that Alu-rich regions do not correlate with lower local H2B density, and form irregular foci of a few hundred nanometers in diameter, underscoring the heterogeneity of euchromatin organization. Alu-rich (gene-rich) chromatin is also more mobile than Alu-poor (gene-poor) chromatin, and transcription inhibition by actinomycin D results in decreased chromatin mobility of Alu-rich regions. These observations highlight the complexity of chromatin organization and dynamics and connect them to transcriptional activity on a genome-wide scale.
Social state gates vision using three circuit mechanisms inDrosophila
Authors: Schretter Catherine E. , Sten Tom Hindmarsh , Klapoetke Nathan , Shao Mei , Nern Aljoscha , Dreher Marisa , Bushey Daniel , Robie Alice A. , Taylor Adam L. , Branson Kristin M. , Otopalik Adriane , Ruta Vanessa , Rubin Gerald M.
Published: March 2024

Animals are often bombarded with visual information and must prioritize specific visual features based on their current needs. The neuronal circuits that detect and relay visual features have been well-studied. Yet, much less is known about how an animal adjusts its visual attention as its goals or environmental conditions change. During social behaviors, flies need to focus on nearby flies. Here, we study how the flow of visual information is altered when femaleDrosophilaenter an aggressive state. From the connectome, we identified three state-dependent circuit motifs poised to selectively amplify the response of an aggressive female to fly-sized visual objects: convergence of excitatory inputs from neurons conveying select visual features and internal state; dendritic disinhibition of select visual feature detectors; and a switch that toggles between two visual feature detectors. Using cell-type-specific genetic tools, together with behavioral and neurophysiological analyses, we show that each of these circuit motifs function during female aggression. We reveal that features of this same switch operate in males during courtship pursuit, suggesting that disparate social behaviors may share circuit mechanisms. Our work provides a compelling example of using the connectome to infer circuit mechanisms that underlie dynamic processing of sensory signals.
A Functional Map of the Human Intrinsically Disordered Proteome
Authors: Pritišanac Iva , Alderson T. Reid , Kolarić Đesika , Zarin Taraneh , Xie Shuting , Lu Alex , Alam Aqsa , Maqsood Abdullah , Youn Ji-Young , Forman-Kay Julie D. , Moses Alan M.
Published: March 2024

Intrinsically disordered regions (IDRs) represent at least one-third of the human proteome and defy the established structure-function paradigm. Because IDRs often have limited positional sequence conservation, the functional classification of IDRs using standard bioinformatics is generally not possible. Here, we show that evolutionarily conserved molecular features of the intrinsically disordered human proteome (IDR-ome), termed evolutionary signatures, enable classification and prediction of IDR functions. Hierarchical clustering of the human IDR-ome based on evolutionary signatures reveals strong enrichments for frequently studied functions of IDRs in transcription and RNA processing, as well as diverse, rarely studied functions, ranging from sub-cellular localization and biomolecular condensates to cellular signaling, transmembrane transport, and the constitution of the cytoskeleton. We exploit the information that is encoded within evolutionary conservation of molecular features to propose functional annotations for every IDR in the human proteome, inspect the conserved molecular features that correlate with different functions, and discover frequently co-occurring IDR functions on the proteome scale. Further, we identify patterns of evolutionary conserved molecular features of IDRs within proteins of unknown function and disease-risk genes for conditions such as cancer and developmental disorders. Our map of the human IDR-ome should be a valuable resource that aids in the discovery of new IDR biology.
End resection and telomere healing of DNA double-strand breaks during nematode programmed DNA elimination
Authors: Estrem Brandon , Davis Richard E. , Wang Jianbin
Published: March 2024

Most DNA double-strand breaks (DSBs) are harmful to genome integrity. However, some forms of DSBs are essential to biological processes, such as meiotic recombination and V(D)J recombination. DSBs are also required for programmed DNA elimination (PDE) in ciliates and nematodes. In nematodes, the DSBs are healed with telomere addition. While telomere addition sites have been well-characterized, little is known regarding the DSBs that fragment nematode chromosomes. Here, we used embryos from the nematodeAscaristo study the timing of PDE breaks and examine the DSBs and their end processing. Using END-seq, we characterize the DSB ends and demonstrate that DNA breaks are introduced before mitosis, followed by extensive end resection. The resection profile is unique for each break site, and the resection generates 3’ overhangs before the addition of telomeres. Interestingly, telomere healing occurs much more frequently on retained DSB ends than on eliminated ends. This biased repair of the DSB ends inAscarismay be due to the sequestration of the eliminated DNA into micronuclei, preventing their ends from telomere healing. Additional DNA breaks occur within the eliminated DNA in bothAscarisandParascaris, ensuring chromosomal breakage and providing a fail-safe mechanism for nematode PDE.
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
Authors: Koren Sergey , Bao Zhigui , Guarracino Andrea , Ou Shujun , Goodwin Sara , Jenike Katharine M , Lucas Julian , McNulty Brandy , Park Jimin , Rautianinen Mikko , Rhie Arang , Roelofs Dick , Schneiders Harrie , Vrijenhoek Ilse , Nijbroek Koen , Ware Doreen , Schatz Michael C. , Garrison Erik , Huang Sanwen , McCombie William Richard , Miga Karen H , Wittenberg Alexander H.J. , Phillippy Adam M
Published: March 2024

The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, this approach for complete, "telomere-to-telomere" genome assembly relies on multiple sequencing platforms, limiting its accessibility. ONT "Duplex" sequencing reads, where both strands of the DNA are read to improve quality, promise high per-base accuracy. To evaluate this new data type, we generated ONT Duplex data for three widely-studied genomes: human HG002, Solanum lycopersicum Heinz 1706 (tomato), and Zea mays B73 (maize). For the diploid, heterozygous HG002 genome, we also used "Pore-C" chromatin contact mapping to completely phase the haplotypes. We found the accuracy of Duplex data to be similar to HiFi sequencing, but with read lengths tens of kilobases longer, and the Pore-C data to be compatible with existing diploid assembly algorithms. This combination of read length and accuracy enables the construction of a high-quality initial assembly, which can then be further resolved using the ultra-long reads, and finally phased into chromosome-scale haplotypes with Pore-C. The resulting assemblies have a base accuracy exceeding 99.999% (Q50) and near-perfect continuity, with most chromosomes assembled as single contigs. We conclude that ONT sequencing is a viable alternative to HiFi sequencing for de novo genome assembly, and has the potential to provide a single-instrument solution for the reconstruction of complete genomes.