bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimizing therapeutic outcomes with Mechanotherapy and Ultrasound Sonopermeation in solid tumors
Authors: Koutsi Marina , Stylianopoulos Triantafyllos , Mpekris Fotios
Published: December 2024

Mechanical solid stress plays a pivotal role in tumor progression and therapeutic response. Elevated solid stress compresses intratumoral blood vessels, leading to hypoperfusion, and hypoxia, which impair oxygen and drug delivery. These conditions hinder the efficacy of drugs and promote tumor progression and treatment resistance compromising therapeutic outcomes. To enhance treatment efficacy, mechanotherapeutics and ultrasound sonopermeation have been developed to improve tumor perfusion and drug delivery. Mechanotherapy aims to reduce tumor stiffness and mechanical stress within tumors to normal levels leading to decompression of vessels while simultaneously improving perfusion. On the other hand, ultrasound sonopermeation strategy focuses on increasing non-invasively and transiently tumor vessel wall permeability to boost perfusion and thus, improve drug delivery. Within this framework and aiming to replicate published experimental data in silico, we developed a mathematical model designed to derive optimal conditions for the combined use of mechanotherapeutics and sonopermeation, with the goal of optimizing efficacy of nano-immunotherapy. The model incorporates complex interactions among diverse components that are crucial in the multifaceted process of tumor progression. These components encompass a variety of cell populations in tumor, such as tumor cells and immune cells, as well as components of the tumor vasculature including endothelial cells, angiopoietins, and the vascular endothelial growth factor. A comprehensive validation of the predictions generated by the mathematical model was carried out in conjunction with published experimental data, wherein a strong correlation was observed between the model predictions and the actual experimental measurements of critical parameters, which are essential to reinforce the overall accuracy of the mathematical framework employed. In addition, a parametric analysis was performed with primary objective to investigate the impact of various critical parameters that influence sonopermeation. The analysis provided optimal guidelines for the use of sonopermeation in conjunction with mechanotherapy, that contribute to identify optimal conditions for sonopermeation.
Transient transcription factor depletions explain diverse single-cell responses of LexA target promoters to mild DNA damage
Authors: Galbusera Luca , Bellement-Theroue Gwendoline , Julou Thomas , van Nimwegen Erik
Published: December 2024

In bacteria, the effects of transcription factors (TFs) on the expression of their target genes are highly stochastic at the single-cell level. Not only do TF concentrations fluctuate in time and from cell to cell, in each cell the actual binding and unbinding of TFs to promoters is also stochastic. However, how this ‘noise propagation’ from TFs to their targets determines the expression fluctuations in target genes of the same TF has so far not been quantitatively characterized. Here we use fluorescence time-lapse microscopy in combination with microfluidics and automated image analysis to quantitatively track the single-cell growth and gene expression dynamics of different target promoters of the LexA SOS response regulator inE. coliunder mild DNA damage induced by the antibiotic ciprofloxacin (CIP).

We find that, at the single-cell level, LexA target promoters exhibit stochastic bursts in protein production with specific quantitative characteristics. First, the durations of protein production bursts are short, identical for all promoters, and independent of CIP levels. Second, the heights of the production peaks are exponentially distributed for each promoter, and independent of CIP level, but with different average heights for different promoters. Third, the frequency of the production bursts increases with CIP level for all promoters, but differs across promoters.

Importantly, we show that these observations are inconsistent with popular ‘equilibrium’ models of bacterial gene regulation that assume that the dynamics of binding and unbinding of TFs is fast relative to the time-scale of TF concentration fluctuations. Instead, all observations can be quantitatively fit by a relatively simple model in which DNA damage events lead to short transient dips in LexA concentration, and an expression burst occurs in a cell whenever LexA unbinds from the target promoter during such a short dip in LexA concentration. Moreover, because these transient dips in LexA concentration occur on the same time-scale as the stochastic unbinding of LexA from promoters, the response of a target promoter to an individual DNA damage event is stochastic and depends in a complex manner on the strengths of its LexA binding sites and the duration of the event. Consequently, the expression levels of different LexA target genes in a given cell reflect distinct statistics of the frequency and durations of DNA damage events in the recent history of that cell.

Our results show that, even in the simple scenario where a single TF is induced, different target promoters can exhibit distinct stochastic responses that depend on the precise kinetics of the induction events.
On metrics for subpopulation detection in single-cell and spatial omics data
Authors: Luo Siyuan , Germain Pierre-Luc , von Meyenn Ferdinand , Robinson Mark D
Published: December 2024

Benchmarks are crucial to understanding the strengths and weaknesses of the growing number of tools for single-cell and spatial omics analysis. A key task is to distinguish subpopulations within complex tissues, where evaluation typically relies on external clustering validation metrics. Different metrics often lead to inconsistencies between rankings, highlighting the importance of understanding the behavior and biological implications of each metric. In this work, we provide a framework for systematically understanding and selecting validation metrics for single-cell data analysis, addressing tasks such as creating cell embeddings, constructing graphs, clustering, and spatial domain detection. Our discussion centers on the desirable properties of metrics, focusing on biological relevance and potential biases. Using this framework, we not only analyze existing metrics, but also develop novel ones. Delving into domain detection in spatial omics data, we develop new external metrics tailored to spatially-aware measurements. Additionally, an R package, poem, implements all the metrics discussed.
Editingcis-elements ofOsPHO1;2improved phosphate transport and yield in rice
Authors: Maurya Kanika , Mani Balaji , Singh Bhagat , Sirohi Ujjwal , Jaskolowski Aime , Sharma Sandeep , Tatiparthi Harsha Vardhan , Mangrauthia Satendra Kumar , Pandey Renu , Poirier Yves , Giri Jitender
Published: December 2024

Increasing grain yield is the main aim of crop improvement, which is globally impacted by the low availability of soil phosphate (Pi). Overexpressing Pi transporters for increasing Pi uptake often result in Pi toxicity and growth retardation. Despite advancements in genetic engineering, targetingcis-regulatory motifs of Pi transporters remains underexplored for understanding plant mechanisms and improving Pi status. Here, we demonstrated that the excision of the transcription inhibitor motif from the promoter of Pi transporter,OsPHO1;2,enhanced its expression and increased root-to-shoot Pi transport, leading to improved grain yield. Using,in-silicoand DNA-protein interaction studies, we show the role of OsWRKY6 transcription factor in the negative regulation ofOsPHO1;2expression by binding to thecis-regulatory element (W-box) present in its promoter.oswrky6knockout lines displayed a higherOsPHO1;2expressions, and improved shoot Pi levels. Further, we engineered theOsPHO1;2promoter for precisely removing the W-box and enhancingOsPHO1;2expression. The phenotypic and physiological evaluation at the vegetative stage shows thatOsPHO1;2promoter edited (OsPHO1;2:PE) lines have increased shoot length, plant biomass and more root-shoot Pi export under low and normal P conditions. Notably, the33Pi uptake assay reveals thatOsPHO1;2:PElines exhibited enhanced root Pi uptake, supported by higher root-associated Pi transporters (OsPHTs) expression. An extensive agronomical assessment revealed thatOsPHO1;2:PElines acquire increased seed and panicle numbers, thereby increasing yield without affecting seed quality. Our findings offer valuable insight into the potential of promoter editing to raise plants with better Pi use and improved crop yield.
SafeguardingIguanadiversity: Enabling rapid and low-effort tracking of non-native iguanas through terrestrial eDNA innovations
Authors: van Kuijk Jeroen L. , van den Burg Matthijs P. , Didaskalou Emilie A. , de Boer Mark , Debrot Adolphe O. , Wielstra Ben , Stewart Kathryn A.
Published: December 2024

Reptiles have among the highest extinction risk across terrestrial vertebrates, with habitat fragmentation, habitat destruction, and invasive alien species being the primary causes of reptile species loss on a global scale. Invasive hybridization (i.e. hybridization between native and invasive alien species) is increasing globally, causing the extinction of native genotypes, and this phenomenon is particularly pervasive in Caribbean iguanas. The Lesser Antillean Iguana (Iguana delicatissima), a keystone species of Caribbean coastal ecosystems, has become critically endangered mainly due to ongoing hybridization with the invasive Common Green Iguana (I. iguana). For impactful conservation intervention, the need for early detection of invasive animals and their progeny, or detection of surviving pure native animals, is urgent. We aimed to develop a novel environmental DNA (eDNA) toolkit using Kompetitive Allele Specific PCR (KASP) technology, a method of allele-specific amplification for cost-effective and efficient sampling of terrestrial substrates to aid in mapping the distribution of nativeI. delicatissima, invasiveI. iguana, and signal potential invasive hybridization. We demonstrate proof-of-concept and successfully identifiedI. delicatissima, I. iguana,and their hybrids via blood samples using our primer sets, as well as successful detection ofI. delicatissimain several ex-situ (Rotterdam Zoo) and in-situ (St. Eustatius) eDNA samples, collected with environmental swabs and tape-lifting. We found that sampling potential perching spots yielded the highest number of positive detections via environmental swabbing and tape-lifting. Our toolkit demonstrates the potential of terrestrial eDNA sampling for iguana conservation, enabling faster detection of potential invasive hybridization. Additionally, the method holds promise for other terrestrial cryptic species, contributing to broader collection of population-level information.
ReSCU-Nets: recurrent U-Nets for segmentation of multidimensional microscopy data
Authors: Hawkins Raymond , Balaghi Negar , Rothenberg Katheryn E. , Ly Michelle , Fernandez-Gonzalez Rodrigo
Published: December 2024

Segmenting multi-dimensional microscopy data requires high accuracy across many images (e.g. timepoints or Z slices) and is thus a labour-intensive part of biological image processing pipelines. We present ReSCU-Nets, recurrent convolutional neural networks that use the segmentation results from the previous frame as a prompt to segment the current frame. We demonstrate that ReSCU-Nets outperform state-of-the-art image segmentation models in different segmentation tasks on time-lapse microscopy sequences.
Deconvolution of omics data in Python with Deconomix – cellular compositions, cell-type specific gene regulation, and background contributions
Authors: Mensching-Buhr Malte , Sterr Thomas , Seifert Nicole , Völkl Dennis , Tauschke Jana , Rayford Austin , Zacharias Helena U. , Grellscheid Sushma Nagaraja , Beissbarth Tim , Görtler Franziska , Altenbuchinger Michael
Published: December 2024

Gene expression profiles of heterogeneous bulk samples contain signals from multiple cell populations. Studying variations in their composition can help to identify cell populations relevant for disease. Moreover, analyses, such as the identification of differentially expressed genes, can be confounded by cellular composition, as differences in gene expression may arise from both variations in cellular composition and gene regulation. Here, we present Deconvolution of omics data (Deconomix) – a comprehensive toolbox for the cell-type deconvolution of bulk transcriptomics data. Deconomix stands apart from competing solutions with rich functionality and highly efficient implementations. It facilitates (A) the inference of cellular compositions from bulk transcriptomics data, (B) the machine learning-based optimization of gene weights to resolve small cell populations and to disentangle phenotypically related cells, (C) the inference of background contributions which otherwise would deteriorate cell-type deconvolution, and (D) population estimates of cell-type specific gene regulation.

Availability

Deconomix is available athttps://gitlab.gwdg.de/MedBioinf/MedicalDataScience/Deconomixunder GPLv3 licensing. The Python package can be easily installed via pip. It comes with a comprehensive documentation of all user-relevant functions and example workflows provided as Jupyter notebooks.
Cell-sheet shape transformation by internally-driven, oriented forces
Authors: Huang Junrou , Chen Juan , Luo Yimin
Published: December 2024

During morphogenesis, cells collectively execute directional forces that drive programmed folding and growth of the layers, forming tissues and organs. The ability to recapitulate aspects of these processesin vitrowould constitute a significant leap forward in the field of tissue engineering. Free-standing, self-organizing, cell-laden matrices are fabricated using a sequential deposition approach that uses liquid crystal-templated hydrogel fibers to direct cell arrangements. The orientation of hydrogel fibers is controlled using flow or boundary cues, while their microstructures are controlled by depletion interaction and probed by scattering and microscopy. These fibers effectively direct cells embedded in a collagen matrix, creating multilayer structures through contact guidance and by leveraging steric interactions amongst the cells. In uniformly aligned cell matrices, oriented cells exert traction forces that can induce preferential contraction of the matrix. Simultaneously, the matrix densifies and develops anisotropy through cell remodeling. Such an approach can be extended to create cell arrangements with arbitrary in-plane patterns, allowing for coordinated cell forces and pre-programmed, macroscopic shape changes. This work reveals a fundamentally new path for controlled force generation, emphasizing the role of a carefully designed initial orientational field for manipulating shape transformations of reconstituted matrices.
gplasCC: classification and reconstruction of plasmids from short-read sequencing data for any bacterial species
Authors: Paganini Julian A. , Kerkvliet Jesse J. , Teunis Gijs , Jordan Oscar , Plantinga Nienke L. , Meneses Rodrigo , Willems Rob J.L. , Arredondo-Alonso Sergio , Schürch Anita C.
Published: December 2024

Plasmids play a pivotal role in the spread of antibiotic resistance genes. Accurately reconstructing plasmids often requires long-read sequencing, but bacterial genomic data in publicly accessible repositories has historically been derived from short-read sequencing technology. We recently presented an approach for reconstructingEscherichia coliantimicrobial resistance plasmids using Illumina short reads. This method consisted of combining a robust binary classification tool named plasmidEC with gplas2, which is a tool that makes use of features of the assembly graph to bin predicted plasmid contigs into individual plasmids. Here, we developed gplasCC, a plasmidEC-simplification, capable of classifying plasmid contigs using Centrifuge databases. We have developed seven plasmidCC databases in addition to the database forE. coli: six species-specific models (Acinetobacter baumannii,Enterococcus faecium,Enterococcus faecalis,Klebsiella pneumoniae,Staphylococcus aureusandSalmonella enterica) and one species-independent model for less frequently studied bacterial species. We combined these models with gplas2 (now, gplasCC) to reconstruct plasmids from more than 100 bacterial species. This approach allows comprehensive analysis of the wealth of bacterial short-read sequencing data available in public repositories and advance our understanding of microbial plasmids.
Targeted glycophagy ATG8 therapy for diabetic heart disease
Authors: Mellor K M. , Varma U. , Koutsifeli P. , Curl C.L. , Janssens J.V. , Daniels L.J. , Bernasochi G.B. , Raaijmakers A.J.A. , Annandale M. , Li X. , James S.L. , Taylor D.J. , Raedschelders K. , Weeks K.L. , Mills R.J. , Parton R.G. , Hu X. , Bell J.R. , Porrello E.R. , Hudson J.E. , Xiao R-P. , Van Eyk J.E. , Gottlieb R.A. , Delbridge L.M.D.
Published: December 2024

Diabetic heart disease is highly prevalent1and is associated with the early development of impaired diastolic relaxation.1The mechanisms of diabetic heart disease are poorly understood and it is a condition for which there are no targeted therapies. Recently, disrupted glycogen-autophagy (glycophagy) and glycogen accumulation have been identified in the diabetic heart.2Glycophagy involves glycogen receptor binding and linking with an ATG8 protein to locate and degrade glycogen within an intracellular phago-lysosome.3,4Here we show that glycogen receptor protein STBD1 (starch-binding-domain-protein-1) is mobilized early in the cardiac glycogen response to metabolic challengein vivo, and that deficiency of a specific ATG8 linking protein, Gabarapl1 (γ-aminobutyric-acid-receptor-associated-protein-like-1) is associated with diastolic dysfunction in diabetes. Gabarapl1 gene delivery treatment remediated cardiomyocyte and cardiac diastolic dysfunction in type 2 diabetic mice and diastolic performance of ‘diabetic’ human iPSC-derived cardiac organoids. We identify glycophagy dysregulation as a mechanism and potential treatment target for diabetic heart disease.
Mammalian enhancers and GWASs act proximally and seldom skip active genes
Authors: Narita Takeo , Choudhary Chunaram
Published: December 2024

Enhancers play a critical role in regulating transcription. Nearly 90% of human genetic variants identified in genome-wide association studies (GWAS) are located in distal regions, underscoring the importance of enhancers in human development, diseases, and traits. It is widely suggested that mammalian enhancers frequently skip active genes, and thus, linear proximity is a poor predictor of their targets. A key unresolved question is how often mammalian enhancers skip proximal active genes to specifically target distal genes. Genome-wide enhancer-promoter mapping shows that enhancers frequently bypass active genes, while ultra-deep locus-specific analyses reveal extensive multi-way interactions between enhancers and promoters, forming nested microcompartments. The functional significance of these seemingly contrasting phenomena remains unclear.

Here, we compared hundreds of enhancer-target gene pairs identified using enhancer-promoter chromatin contact maps, enhancer-promoter RNA interaction data, and genome-scale CRISPR interference (CRISPRi) perturbations. Our findings reveal limited overlap between active gene-skipping enhancer-gene pairs identified through physical interaction mapping and CRISPRi. Additionally, promoters involved in multi-way enhancer interactions are not co-regulated by shared coactivators. Notably, gene-skipping and non-skipping enhancers identified via CRISPRi differ fundamentally in chromatin features, gene activation strength, false discovery rates, target gene distance, coactivator requirements, and cell-type specificity of target genes. These results suggest that gene-skipping enhancer-promoter interactions observed in chromatin and RNA-based analyses do not reliably predict functional enhancer-gene relationships. We propose that linear enhancer-promoter proximity and coactivator dependency offer a simple, scalable, and cost-effective method for genome-wide prediction of enhancer and GWAS targets, with accuracy comparable to state-of-the-art experimental techniques. While enhancers can skip active genes, such deliberate skipping appears to be the exception rather than the rule.
Prognostic Model Construction Based on Platinum-Free Interval in Ovarian Cancer and Its Implication for Chemotherapy Resistance
Authors: Zhang Yang , Kang Jihui , Wu Chuling , Xu Huishan , Ling Qin , Tan Hao , Zhang Zuwei , He Weipeng , Yao Shuzhong , Gu Langyu , Yang Guofen
Published: December 2024

Background

While platinum sensitivity and resistance have long been central to treatment decisions in high-grade serous ovarian cancer (HGSOC), these categories are increasingly questioned in real-world clinical settings. This study seeks to develop a prognostic model based on platinum-free interval (PFI) as a reliable indicator of patient prognosis, with additional exploration of chemotherapy resistance-related genes and pathways.

Methods

70 HGSOC patients with varied gene expression profiles and corresponding clinical information of platinum-based chemotherapy responses were analysed. We first identified PFI-related genes (PRGs) that constituted a predictive signature for HGSOC by using univariate COX and LASSO regression analysis. We determined the optimal PFI indicative using linear correlation equations between gene expression levels and PFI. This time point was then employed to categorize patients into cohorts with good and poor prognosis, followed by an analysis of differentially expressed genes (DEGs) and their enriched pathways. Additionally, we utilized public available drug database to evaluate chemotherapeutic agents effective against the poor prognosis group.

Results

A signature comprising 10 PRGs (TUBA4A, ENSG00000232325.3, ENSG00000268080.1, KCNK9, ENSG00000230567.3, CST6, KNTC1, LINC02167, ENSG00000267469.1, NKAIN4) was established. Patients within the high-risk category defined by this signature exhibited a poorer prognosis and earlier recurrence than low-risk group. The prognostic model had a robust accuracy in predicting prognosis with an area under curve value >0.90. We estimated a PFI threshold of 22.37 months, which serves as a cutoff point to further differentiate groups with good and poor prognosis. KEGG pathways enrichment analysis revealed that taurine and hypotaurine metabolism, melanogenesis, Cushing syndrome, and mTOR signaling pathways were enriched in the poor prognosis group. We also performed drug resistance assessment and found that patients from the poor prognosis group were more sensitive to anti-cancer drugs such as Pevonedistat and GDC0810 than the good prognosis group.

Conclusions

Our study constructed a prognostic model based on PFI for HGSOC and further explored its implications for chemotherapy resistance. These findings could enhance clinical applications and inform novel anticancer therapeutic strategies targeting HGSOC.
GWAS of Extended Prescription Analgesic Use Identifies Novel Genetic Loci in Chronic Pain
Authors: Harlow Charli E , Uzochukwu Emeka , Fernando Hazel A , Mordaunt Charles E , Hughey Jordan M , Eicher John D , Robinson Lara , Bowker Nicholas , Howe Laurence , Liu Jimmy , Cortes Adrian , Wilson Paul , Gungabissoon Usha , Tribble Vicky , Nash Anthony , Young Gareth , Addis Laura , Xu Chun-Fang , Webber Caleb , Davitte Jonathan M , Cader M. Zameel
Published: December 2024

Pain–related conditions are the leading cause of disability worldwide. Current genome–wide association studies (GWAS) for chronic pain have mainly focused on individual pain–related disorders, which may not optimally capture the phenotype. Here, we applied a novel method of defining chronic pain based on prescription analgesic use (≥90 days) in two large biobanks (UK Biobank and FinnGen). GWAS meta–analyses of 11 prescription–based pain phenotypes identified 140 associations with chronic pain–78 novel (e.g. ARPP21, CNTNAP2) and 62 previously reported (e.g. SLC39A8, DCC, TRPM8). Integrating these genetic associations with functional data including transcriptome–wide association studies, cell–type and pathway enrichment, and gene enrichment in mouse phenotypes identified novel potential mechanisms involved in chronic pain, implicating oligodendrocyte differentiation, neuronal guidance, endolysosomal function and post–synaptic endosome recycling. Our study showcases how the use of prescription data to identify and characterize pain provides new insights into pain genetics and its underlying biology.
Pushing the boundary of child well-being: A spatial examination of child mortality in transition zones of extreme economic inequality and material hardship
Authors: Barboza-Salerno Gia Elise , Liebhard Brittany , Schockley-McCarthy Karla , Duhaney Sharefa
Published: December 2024

How do patterns of socioeconomic inequality shape the risk of child fatality in urban areas? Studies have demonstrated that intentional and accidental deaths of children are highly clustered into areas of social disadvantage. However, in complex urban settings, the risk of death to children is likely to exhibit a more localized spatial structure characterized by rapid changes in child fatality risk. The present research uses Bayesian hierarchical modeling to detect spatial discontinuities in child fatality risk in transition areas defined by elevated levels of economic hardship and inequality (EHI). The analysis detected 413 neighborhood boundaries characterized by extreme differences in EHI (i.e., a difference of four deciles). Living in proximity to a boundary of extreme difference, called a social frontier, is associated with a 22% higher relative risk of child fatality beyond measures of neighborhood racial segregation, concentrated disadvantage, residential mobility, and immigrant concentration. The significance of identifying neighborhoods characterized as a social frontier where children may benefit from additional preventive interventions is discussed in context.
Direct high-throughput deconvolution of unnatural bases via nanopore sequencing and bootstrapped learning
Authors: Perez Mauricio Lisboa , Kimoto Michiko , Rajakumar Priscilla , Suphavilai Chayaporn , da Silva Rafael Peres , Tan Hui Pen , Xun Ong Nicholas Ting , Nicholas Hannah , Hirao Ichiro , Leong Chew Wei , Nagarajan Niranjan
Published: December 2024

The discovery of synthetic xeno-nucleic acids (XNAs) that can basepair as unnatural bases (UBs) to expand the genetic alphabet has spawned interest in many applications, from synthetic biology to DNA storage. However, the inability to read XNAs in a direct, high-throughput manner has been a significant limitation for xenobiology. Here we demonstrate that XNA-containing templates can be directly and robustly sequenced (>2.3 million reads/flowcell, similar to DNA controls) on a MinION sequencer from Oxford Nanopore Technologies to obtain signal data that is significantly distinct from DNA controls (median fold-change >6×). To enable training of machine learning models that deconvolve these signals and basecall XNAs along with natural bases, we developed a framework to synthesize a complex pool of 1,024 UB-containing oligonucleotides with diverse 6-mer sequence contexts and high XNA purity (>90% UB-insertion on average). Bootstrapped models to enable data preparation, and data augmentation with spliced XNA reads to provide high context diversity, enabled learning of a generalizable model to call natural as well as unnatural bases with high accuracy (>80%) and specificity (99%). These results highlight the versatility of nanopore sequencing as a platform for interrogating nucleic acids for xenobiology applications, and the potential to transform the study of genetic material beyond those that use canonical bases.
Analysis of gene expression inAedes aegyptisuggests changes in early genetic control of mosquito development
Authors: Coutinho-dos-Santos Renata , Santos Daniele G. , Ribeiro Lupis , Mucherino-Muñoz Jonathan J. , Uhl Marcelle , Logullo Carlos , Mendonça-Amarante A , Fantappie M , Nunes-da-Fonseca Rodrigo
Published: December 2024

Aedes aegypti,a critical vector for tropical diseases, poses significant challenges for studying its embryogenesis due to difficulties in removing its rigid chorion and achieving effective fixation for in situ hybridization. Here, we present novel methodologies for fixation, dechorionation, DAPI staining, and in situ hybridization, enabling the detailed analysis of gene expression throughoutAe. aegyptiembryogenesis. By synchronizing eggs at various developmental stages (0–72 h), we localized the transcripts of the gap genemille-pattes (mlpt),the dorsoventral gene cactus(cact),and the pioneer transcription factor (pTF)zelda (zld).In situ hybridization and RT-qPCR analyses revealed thatmlpt and cactare maternally expressed, while zldexpression begins zygotically during cellularization and later becomes prominent in neuroblasts. Analysis of previously published transcriptomes suggests that three other pTFs,CLAMP, grainyheadandGAF,are also maternally expressed and may function as pioneer transcription factors duringAe. aegyptiembryogenesis. These findings suggest that the transcription factors responsible for genome activation in mosquitoes differ from those in fruit flies, highlighting significant divergence in the genetic regulation of early Dipteran embryogenesis.
Microglial engulfing of glutamatergic inputs and diminished excitability of D1 medium spiny neurons of the nucleus accumbens by peripheral inflammatory insult
Authors: Nakajima Shingo , Kabahizi Anita , Aubailly Solal , Naili-Douaouda Samar , Tomita Akari , Bosson Anthony , Murphy-Royal Ciaran , Fulton Stephanie
Published: December 2024

Neuroimmune responses to systemic inflammation can generate anxiodepressive behaviors and psychomotor slowing. The nucleus accumbens (NAc) is a neural hub encoding mood and motivation that contributes to the locomotor and mood dampening effects of neuroinflammation. Dopamine receptor 1 mediums spiny neurons (D1-MSNs) of the NAc regulate locomotor activity, motivated behavior and emotional states and are modulated by microglial reactivity. Here, we evaluated sickness- and anxiety-like behaviors along with D1-MSN activity and microglial responses in the NAc to systemic lipopolysaccharide (LPS) administration. LPS stimulated anxiety-like behavior, blunted locomotion and reduced cFos expression in D1-MSNs of the NAc core and shell of male mice. These effects associated with reduced excitatory inputs (EPSCs) onto D1-MSNs as measured by whole cell patch-clamp. To determine if microglia contribute to changes in MSN activity, Ca2+ imaging of primary cultures containing NAc neurons with or without primary NAc microglia was performed. The presence of microglia decreased the activity of LPS-treated MSNs in response to dopamine and glutamate application and LPS stimulated microglial phagocytosis of MSN processes in co-cultures. Immunohistochemical analyses revealed that in vivo LPS treatment enhanced morphological indices of microglia reactivity and engulfment of vesicular glutamate transporter 1 (VGLUT1) inputs in the NAc. Our results suggest that LPS reduces locomotion and stimulates anxiety via increasing microglia engulfment of excitatory inputs onto D1-MSNs, and highlight changes in NAc microglia phagocytic activity in the behavioral consequences of neuroinflammation.
Expanding the CarD interaction network: CrsL is a novel transcription factor inMycobacterium smegmatis
Authors: Shoman Mahmoud , Jirát Matějčková Jitka , Schwarz Marek , Černý Martin , Borah Nabajyoti , Vaňková Hausnerová Viola , Šiková Michaela , Šanderová Hana , Halada Petr , Hubálek Martin , Dvořáková Věra , Převorovský Martin , Holubová Jana , Staněk Ondřej , Krásný Libor , Žídek Lukáš , Hnilicová Jarmila
Published: December 2024

Bacterial transcription regulation is critical for adaptation and survival. CarD is an essential transcription factor in mycobacteria involved in regulation of gene expression. We searched for CarD interaction partners in the model organismMycobacterium smegmatisand identified two proteins: ApeB (MSMEG_5828) and an uncharacterized protein, which we named CrsL (MSMEG_5890). While ApeB interacted with CarD only when CarD was overexpressed, CrsL associated with CarD at its physiological levels. CrsL is a 5.7 kDa protein shown by NMR to be intrinsically disordered. CrsL homologs are present in actinobacteria including pathogenic species such asMycobacterium tuberculosis. CrsL directly interacts with CarD and binds RNAP. ChIP-seq showed that CrsL associates with promoters of actively transcribed genes and ∼75 % of these regions are also associated with CarD. RNA-seq showed ∼50% and ∼66% overlap in differentially expressed genes between CrsL and CarD knockdowns during exponential and stationary phases, respectively. CrsL represses expression of DesA desaturase (MSMEG_5773) and DEAD/DEAH-box RNA helicaseMSMEG_1930, which are important for adaptation to cold stress. Furthermore, CrsL promotes the growth ofM. smegmatisat elevated temperature. In summary, this study identifies CrsL as a novel actinobacterial transcription factor and provides a basis for its further investigation.
Distinct roles for theStaphylococcus aureusPOT transporter DtpT in di/tripeptide uptake and glutathione utilisation inside human macrophages
Authors: Khan Imran , MacDonald Sandy J , Markusson Sigurbjörn , Robson Callum , Parker Joanne L , Newstead Simon , Boucher Dave , Van Der Woude Marjan , Thomas Gavin H
Published: December 2024

Peptides available in biological niches inhabited by the human pathogenStaphylococcus aureusserve as a rich source of amino acids required for growth and successful host colonisation. Uptake of peptides byS. aureusinvolves at least two transport systems: the POT family di/tri-peptide permease DtpT and the oligopeptide ABC transporter Opp3. Here we study the individual and combined functions of DtpT and Opp3 in enabling utilisation of 282 di-/tri-peptides via a high-throughput phenotypic screen. We reveal that many peptides can be utilised via either transporter, though DtpT appears to be the primary route of uptake for dipeptides. Intriguingly, we demonstrate a preference for Asp/Glu-containing peptides among putative DtpT substrates. To measure DtpT-mediated peptide transport directly, the protein was purified and reconstituted into proteoliposomes and active transport of diverse di- and tri-peptides was demonstrated, supporting the conclusions of the phenotypic screen. During thisin vitroanalysis, we also found that DtpT could transport the biologically prevalent tripeptide reduced glutathione (GSH). In the absence of the known glutathione transporter Gis,dtpTis essential for growth under conditions where GSH is supplied as the sole sulphur source, identifying DtpT as the predicted second GSH uptake system ofS. aureus. Site-directed mutagenesis of the predicted ligand binding site of DtpT suggests GSH binds the protein vertically in a manner dependent on interactions with Gln310. Finally, we demonstrate that GSH transport is required byS. aureusfor complete fitness duringin vitromacrophage infection experiments, and our data suggest that GSH uptake plays a role in modulating host-pathogen interactions in these infections. Together, these data reveal important new functions for DtpT, both in the utilisation of diverse peptides for growth but also providing the first clues toward a distinct role of DtpT during intracellular infection.
Bilingual Exposure and Sex Shape Developmental Trajectories of Brain Responses to Speech-Sound Features in Infants
Authors: Puertollano Marta , Gorina-Careta Natàlia , Ijjou-Kadiri Siham , Mondéjar-Segovia Alejandro , Gómez-Roig María Dolores , Escera Carles
Published: December 2024

As the auditory brain becomes functional during the third trimester of pregnancy, both biological and environmental processes begin shaping its maturation, influencing how speech sounds are perceived. Biological factors, such as sex, introduce early genetic differences, while environmental experiences, like bilingualism, modulate the auditory input that infants receive. Although existing research highlights the impact of sex and bilingualism on the development of speech perception, the neural mechanisms remain unclear. In this study, we recorded frequency-following responses (FFRs) longitudinally, at birth, six months, and twelve months of age in 73 infants exposed to varying degrees of bilingual input. We modeled the developmental trajectories for neural encoding of voice pitch and speech formant structure, finding significant maturation during the first six months, followed by stabilization through the first year. Distinct developmental patterns emerged as a function of sex and bilingualism, revealing their influence on neural attunement to key speech-sound features. Bilingual exposure notably predicted lower neural pitch encoding values at six months, but higher values by twelve months. A positive effect of bilingualism on speech formant encoding was observed throughout the first year. These findings reveal how biological and environmental factors contribute to individual variability in early auditory development and speech acquisition.

Highlights

Bilingualism and sex impact early developmental trajectories in neural speech encoding

Results suggest a female advantage in early neural encoding of speech-sound features

Bilingual exposure positively modulates infant neural speech encoding
Drug screening targeting TREM2-TYROBP transmembrane binding
Authors: Cobas-Carreño M. , Esteban-Martos A. , Tomas-Gallardo L. , Iribarren I. , Gonzalez-Palma L. , Rivera-Ramos A. , Elena-Guerra J. , Alarcon-Martin E. , Ruiz R. , Bravo M.J. , Venero J.L. , Morató X. , Ruiz A. , Royo J.L.
Published: December 2024

TREM2encodes a microglial membrane receptor involved in the disease-associated microglia (DAM) phenotype whose activation requires the transmembrane interaction with TYROBP. Mutations inTREM2represent a high-impact risk factor for Alzheimer’s disease (AD) which turned TREM2 into a significant drug target. We present a bacterial two-hybrid (B2H) system designed for high-throughput screening of modulators for the TREM2-TYROBP transmembrane interaction. In a pilot study, 315 FDA-approved drugs were analyzed to identify potential binding modifiers. Our pipeline includes multiple filtering steps to ensure candidate specificity. The screening suggested two potential candidates that were finally assayed in the human microglial cell line HMC3. Upon stimulation with anti-TREM2 mAb, pSYK/SYK ratios were calculated in the presence of the candidates. As a result, we found that varenicline, a smoking cessation medication, can be considered as a transmembrane agonist of the TREM2-TYROBP interaction.
Explainable AI-guided identification of a novel protein-RNA interactive frame for selective siRNA accumulation in plants
Authors: Enoki Natsumi , Kuwada Eriko , Matsuo Shinnosuke , Fujita Naoko , Noda Saki , Matsubayashi Yoshikatsu , Uchida Seiichi , Akagi Takashi
Published: December 2024

Small interference RNA (siRNA) selectively accumulates and acts in RNA interference (RNAi). Although the components involved in siRNA production have long been the focus of studies to elucidate RNAi processes, the mechanism(s) for selectivity of siRNA (or RNAi effectivity) remains unclear. In a novel approach, we developed a progressive deep learning (DL) framework integrating Transformer and convolutional neural networks to predict the sequences of selectively accumulated siRNAs across various land plant species. These approaches achieved high-accuracy prediction of selectively accumulated 21-nt siRNAs and further identified their key signals, which are positionally and linguistically flexible sequences surrounding the target siRNA. We experimentally validated the contribution of these flexible key signal sequences to siRNA accumulation selectivity using virus-induced gene silencing (VIGS) inNicotiana benthamiana, and identified RNA-binding proteins that directly recognize the key signal sequences to act for selective siRNA accumulation. These insights provide a novel framework for investigating RNAi mechanisms in plants.

One sentence summary

We discovered a novel mechanism centered on RNA-protein interactions involving the selective accumulation of small-RNAs in plants by applying advanced deep learning frames.
Control of Epithelial Tissue Organization by mRNA Localization
Authors: Mason Devon E. , Madsen Thomas D. , Gasparski Alexander N. , Jiwnani Neal , Lechler Terry , Weigert Roberto , Iglesias-Bartolome Ramiro , Mili Stavroula
Published: December 2024

mRNA localization to specific subcellular regions is common in mammalian cells but poorly understood in terms of its physiological roles1–6,7. This study demonstrates the functional importance ofNet1mRNA, which we find prominently localized at the dermal-epidermal junction (DEJ) in stratified squamous epithelia.Net1mRNA accumulates at DEJ protrusion-like structures that interact with the basement membrane and connect to a mechanosensitive network of microfibrils. DisruptingNet1mRNA localization in mouse epithelium alters DEJ morphology and keratinocyte-matrix connections, affecting tissue homeostasis. mRNA localization dictates Net1 protein distribution and its function as a RhoA GTPase exchange factor (GEF). Altered RhoA activity is in turn sufficient to alter the ultrastructure of the DEJ. This study provides a high-resolutionin vivoview of mRNA targeting in a physiological context. It further demonstrates how the subcellular localization of a single mRNA can significantly influence mammalian epithelial tissue organization, thus revealing an unappreciated level of post-transcriptional regulation that controls tissue physiology.
Heat-Induced Phosphatidylserine Changes Drive HSPA1A’s Plasma Membrane Localization
Authors: Low Jensen , Altman Rachel , Badolian Allen , Cuaresma Azalea Blythe , Briseño Carolina , Keshet Uri , Fiehn Oliver , Stahelin Robert V. , Nikolaidis Nikolas
Published: December 2024

Heat shock protein A1A (HSPA1A) is a molecular chaperone crucial in cell survival. In addition to its cytosolic functions, HSPA1A translocates to heat-shocked and cancer cells’ plasma membrane (PM). In cancer, PM-localized HSPA1A (mHSPA1A) is associated with increased tumor aggressiveness and therapeutic resistance, suggesting that preventing its membrane localization could have therapeutic value. This translocation depends on HSPA1A’s interaction with PM phospholipids, including phosphatidylserine (PS). Although PS binding regulates HSPA1A’s membrane localization, the exact trigger for this movement remains unclear. Given that lipid modifications are a cancer hallmark, we hypothesized that PS is a crucial lipid driving HSPA1A translocation and that heat-induced changes in PS levels trigger HSPA1A’s PM localization in response to heat stress. We tested this hypothesis using pharmacological inhibition and RNA interference (RNAi) targeting PS synthesis, combined with confocal microscopy, lipidomics, and western blotting. Lipidomic analysis and PS-specific biosensors confirmed a heat shock-induced PS increase, peaking immediately post-stress. Inhibition of PS synthesis with fendiline and RNAi significantly reduced HSPA1A’s PM localization, while depletion of cholesterol or fatty acids had minimal effects, confirming specificity for PS. Further experiments showed that PS saturation and elongation changes did not significantly impact HSPA1A’s PM localization, indicating that the total PS increase, rather than specific PS species, is the critical factor. These findings reshape current models of HSPA1A trafficking, demonstrating that PS is a crucial regulator of HSPA1A’s membrane translocation during the heat shock response. This work offers new insights into lipid-regulated protein trafficking and highlights the importance of PS in controlling cellular responses to stress.
How much is ‘enough’? Considerations for functional connectivity reliability in pediatric naturalistic fMRI
Authors: Rai Shefali , Godfrey Kate J. , Graff Kirk , Tansey Ryann , Merrikh Daria , Yin Shelly , Feigelis Matthew , Demeter Damion V. , Vanderwal Tamara , Greene Deanna J. , Bray Signe
Published: December 2024

functional connectivity (FC) measurements are important for robust and reproducible findings, yet pediatric functional magnetic resonance imaging (fMRI) faces unique challenges due to head motion and bias toward shorter scans. Passive viewing conditions during fMRI offer advantages for scanning pediatric populations, but FC reliability under these conditions remains underexplored. Here, we used precision fMRI data collected across three passive viewing conditions to directly compare FC reliability profiles between 25 pre-adolescent children and 25 adults, with each participant providing over 2.8 hours of data over four sessions. We found that FC test-retest correlations increased asymptotically with scan length, with children requiring nearly twice the post-censored scan time (24.6 minutes) compared to adults (14.4 minutes) to achieve comparable reliability, and that this effect was only partly attributable to head motion. Reliability differences between lower-motion adults and higher-motion children were spatially non-uniform and largest in ventral anterior temporal and frontal regions. While averaging features within functional networks improved intraclass correlation coefficient (ICC) reliability, values for higher-motion children remained in the poor-to-fair ICC range even with 48 minutes of total scan time. Viewing conditions with greater engagement reduced head motion in children but had lower FC reliability compared to less engaging ‘low-demand’ videos, suggesting complex state- or condition-related trade-offs. These findings have important implications for developmental neuroimaging study design, particularly for higher motion pediatric populations.
Gravitational waves from thermal heavy scalar dark matter
Authors: Ghorbani Parsa
Published: December 2024

We propose a gauge singlet scalar with mass around 1–100 TeV as a thermal heavy dark matter candidate along with a dilaton as a Higgs portal mediator in a dimensionless scalar extension of the Standard Model. We demonstrate analytically that such a model gives rise to very strong first-order electroweak phase transition through supercooling. We calculate the corresponding gravitational wave signals due to bubble collisions during the phase transition. The produced gravitational waves can be detected by future space-based gravitational wave detectors in the frequency range from 10−4  to 0.1 Hz.

Published by the American Physical Society
2024