bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural analysis and conformational dynamics of a holo-adhesion GPCR reveal interplay between extracellular and transmembrane domains
Authors: Kordon Szymon P. , Cechova Kristina , Bandekar Sumit J. , Leon Katherine , Dutka Przemysław , Siffer Gracie , Kossiakoff Anthony A. , Vafabakhsh Reza , Araç Demet
Published: February 2024

Adhesion G Protein-Coupled Receptors (aGPCRs) are key cell-adhesion molecules involved in numerous physiological functions. aGPCRs have large multi-domain extracellular regions (ECR) containing a conserved GAIN domain that precedes their seven-pass transmembrane domain (7TM). Ligand binding and mechanical force applied on the ECR regulate receptor function. However, how the ECR communicates with the 7TM remains elusive, because the relative orientation and dynamics of the ECR and 7TM within a holoreceptor is unclear. Here, we describe the cryo-EM reconstruction of an aGPCR, Latrophilin3/ADGRL3, and reveal that the GAIN domain adopts a parallel orientation to the membrane and has constrained movement. Single-molecule FRET experiments unveil three slow-exchanging FRET states of the ECR relative to the 7TM within the holoreceptor. GAIN-targeted antibodies, and cancer-associated mutations at the GAIN-7TM interface, alter FRET states, cryo-EM conformations, and receptor signaling. Altogether, this data demonstrates conformational and functional coupling between the ECR and 7TM, suggesting an ECR-mediated mechanism of aGPCR activation.
Exploring Arylidene-Indolinone Ligands of Autophagy Proteins LC3B and GABARAP
Authors: Leveille Alexandria N. , Schwarzrock Thomas , Brown Hawley , True Bennett , Plasencia Joanet , Neudecker Philipp , Üffing Alina , Weiergräber Oliver H. , Willbold Dieter , Kritzer Joshua A.
Published: February 2024

We report the first structure-activity studies of arylidene-indolinone compoundGW5074which was reported as a ligand of autophagy-related protein LC3B. The literature has conflicting information on the binding affinity of this compound and there is some debate regarding its use as a component of autophagy-dependent degrader compounds. We developed an AlphaScreen assay to measure competitive inhibition of the binding of known peptide ligands to LC3B and its paralog GABARAP. 18 analogs were synthesized and tested against both proteins. Inhibitory potencies were found to be in the mid- to high micromolar range. 2D-NMR data revealed the binding site on GABARAP as hydrophobic pocket 1, where native peptide ligands bind with an aromatic side chain. Our results suggest thatGW5074binds LC3B and GABARAP with micromolar affinity. These affinities could support further exploration in targeted protein degradation, but only if off-target effects and poor solubility can be appropriately addressed.
Local ecdysone synthesis in a wounded epithelium sustains developmental delay and promotes regeneration inDrosophila
Authors: Terry Douglas , Schweibenz Colby , Moberg Kenneth
Published: February 2024

Regenerative ability often declines as animals mature past embryonic and juvenile stages, suggesting that regeneration requires redirection of growth pathways that promote developmental growth. Intriguingly, theDrosophilalarval epithelia require the hormone ecdysone (Ec) for growth but require a drop in circulating Ec levels to regenerate. Examining Ec dynamics more closely, we find that transcriptional activity of the Ec-receptor (EcR) drops in uninjured regions of wing discs, but simultaneously rises in cells around the injury-induced blastema. In parallel, blastema depletion of genes encoding Ec biosynthesis enzymes blocks EcR activity and impairs regeneration but has no effect on uninjured wings. We find that local Ec/EcR signaling is required for injury-induced pupariation delay following injury and that key regeneration regulatorsupd3andEts21crespond to Ec levels. Collectively, these data indicate that injury induces a local source of Ec within the wing blastema that sustains a transcriptional signature necessary for developmental delay and tissue repair.
Oxytocin and shared intentionality drive variation in cooperation in children
Authors: McClung Jennifer , Triki Zegni , Lancheros Pompeyo Monica , Fassier Romain , Emery Yasmin , Bangerter Adrian , Clément Fabrice , Bshary Redouan
Published: February 2024

While humans cooperate with unrelated individuals to an extent that far outstrips any other species, we also display extreme variation in decisions about whether to cooperate or not. A diversity of cognitive, affective, social, and physiological mechanisms interact to shape these decisions. For example, group membership, shared intentionality talk (i.e. talk about shared goals), and natural initial oxytocin levels affect cooperation in adults in an optimal foraging paradigm that is loosely modelled on the iterated prisoner’s dilemma. In this ‘egg hunt’, shared intentionality talk was key to achieve cooperation, and it occurred more between participants who shared the same group membership and had higher initial oxytocin levels. Such complex interactions raise the question of the age at which humans develop the necessary mechanisms to cooperate effectively in the egg hunt game. Here, we tested children in secondary school aged between 10 and 14 years. We found that, as for adults, shared intentionality talk was crucial for successful cooperation. Furthermore, initial oxytocin levels affected cooperation through shared intentionality talk. In contrast, group membership did not affect behaviour. Finally, pre- and post-experiment oxytocin levels showed various interactions with group membership and gender. Thus, children’s performance was relatively similar to adults while showing some differences with respect to underlying mechanisms. Our study is a rare contribution to further our understanding of the role of oxytocin in early adolescent social behaviour.
Stabilization of Integrator/INTAC by the small but versatile DSS1 protein
Authors: Xu Congling , Zhou Qian-Xing , Zheng Hai , Song Aixia , Zhao Wen-Ying , Xiong Yan , Huang Zixuan , Xu Yanhui , Cheng Jingdong , Chen Fei Xavier
Published: February 2024

Integrator-PP2A (INTAC) is a highly modular complex orchestrating the transition of paused RNA polymerase II into productive elongation or promoter-proximal premature termination, with its loss resulting in transcription dysregulation and genome instability. Here, we identify human DSS1—a flexible 70-residue protein found in multiple functionally diverse complexes including the 26S proteasome—as an integral subunit of the INTAC backbone. Structural analysis of DSS1–INTAC, both alone and in association with paused polymerase, demonstrates intimate interactions between DSS1 and the INTAC backbone subunit INTS7. We identify tryptophan 39 of DSS1 as being critical for interacting with INTAC and find that mutating this residue disrupts DSS1’s interaction with INTAC, while maintaining DSS1’s interaction with the proteasome. This substitution not only destabilizes INTAC and therefore INTAC-dependent transcriptional regulation, but also reveals that INTAC is DSS1’s major chromatin-bound form. Together, our findings reveal the essential role of the versatile DSS1 protein in the structure and regulatory functions of INTAC.
Grapevine Rootstock and Scion Genotypes’ Symbiosis with Soil Microbiome: A Machine Learning Revelation for Climate-Resilient Viticulture
Authors: Anand Lakshay , Gentimis Thanos , Downie Allan Bruce , Lopez Carlos M. Rodriguez
Published: February 2024

Given the impact of climate change on agriculture, the development of resilient crop cultivars is imperative. A healthy plant microbiota is key to plant productivity, influencing nutrient absorption, disease resistance, and overall vigor. The plant genetic factors controlling the assembly of microbial communities are still unknown. Here we examine if Machine Learning can predict grapevine rootstock and scion genotypes based on soil microbiota, despite environmental variability. The study utilized soil microbial bacteriome datasets from 281 vineyards across 13 countries and five continents, featuring 34 differentVitis viniferacultivars grafted onto, often ambiguous, rootstocks. Random Forests, Adaptive Boost, Gradient Boost, Support Vector Machines, Gaussian and Bernoulli Naïve Bayes, k-Nearest Neighbor, and Neural Networks algorithms were employed to predict continent, country, scion, and rootstock cultivar, under two filtering criteria: retaining sparse classes, ensuring class diversity, and excluding sparse classes assessing model robustness against overfitting. Both criteria showed remarkable F1-weighted scores (>0.8) for all classes, for most algorithms. Moreover, successful rootstock and scion genotype prediction from soil microbiomes confirms that genotypes of both plant parts shape the microbiome. These insights pave the way for identifying plant genes for use with breeding programs that enhance plant productivity and sustainability by improving the plant-microbiota relationship.
RNA-binding tunes the conformational plasticity and intradomain stability of TDP-43 tandem RNA recognition motifs
Authors: Ozguney Busra , Mohanty Priyesh , Mittal Jeetain
Published: February 2024

TAR DNA binding protein 43 (TDP-43) is a nuclear RNA/DNA-binding protein with pivotal roles in RNA-related processes such as splicing, transcription, transport, and stability. The high binding affinity and specificity of TDP-43 towards its cognate RNA sequences (GU-rich) is mediated by highly conserved residues in its tandem RNA recognition motif (RRM) domains (aa:104-263). Importantly, the loss of RNA-binding to the tandem RRMs caused by physiological stressors and chemical modifications promotes cytoplasmic mislocalization and pathological aggregation of TDP-43. Despite the substantial implications of RNA in TDP-43 function and pathology, a comprehensive characterization of the effect of RNA-binding on conformational dynamics, interdomain interactions and intradomain stability of the tandem RRMs has not yet been conducted. Here, we employed all-atom molecular dynamics (MD) simulations to assess the effect of RNA-binding on the conformational landscape and intradomain stability of TDP-43 tandem RRMs. Our simulations reveal a high intrinsic conformational plasticity of the tandem RRMs in the absence of RNA which surprisingly, is accompanied by a tendency of RRM1 to adopt partially-unfolded conformations. While binding to RNA limits the overall conformational space of the tandem RRMs and promotes intradomain stability, several RRM-RNA contacts mediated by highly conserved residues are observed to be far more dynamic than previously inferred from NMR structural ensemble. Overall, our simulations reveal how RNA dynamically tunes the structural and conformational landscape of TDP-43 tandem RRMs, contributing to physiological function and mitigating pathological aggregation.

SIGNIFICANCE

The cytoplasmic mislocalization and aggregation of TDP-43 due to loss of its RNA-binding capability is associated with the onset and progression of neurodegenerative diseases such as Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Due to the flexible nature of RNA and the presence of a disordered linker between RRM domains, characterizing the dynamic interactions between RRMs-RNA and/or RRM1-RRM2 by experiments alone has remained challenging. In this study, we performed all-atom simulations initiated from the NMR conformers of RNA-bound tandem RRMs of TDP-43 to investigate their underlying structural and conformational dynamics. Our findings indicate that RNA binding effectively reduces conformational heterogeneity in the tandem RRMs and acts as a protective factor for the unfolding and aggregation of RRM1. These effects are achieved through a combination of stable and dynamic protein-RNA interactions which involve highly conserved amino acids.
Genome Report: The reference genome of an endangered Asteraceae,Deinandra increscenssubsp.villosa, endemic to the Central Coast of California
Authors: McEvoy Susan L. , Meyer Rachel S. , Hasenstab-Lehman Kristen E. , Guilliams C. Matt
Published: February 2024

We present a high-quality reference genome of the federally endangered Gaviota tarplant,Deinandra increscenssubsp.villosa(Madiinae, Asteraceae), an annual herb endemic to the Central California coast. Stewards of remaining populations have planned to apply conservation strategies informed by whole genome approaches. Generating PacBio Hifi, Oxford Nanopore Technologies, and Dovetail Omni-C data, we assembled a genome of 1.67 Gbp as 28.7 K scaffolds with a scaffold N50 of 74.9 Mb. BUSCO completeness for the final assembly was 98.1% with 15.7% duplicate copies. We annotated repeat content in 74.8% of the genome. Long terminal repeats (LTR) covered 44.0% of the genome withCopiafamilies predominant at 22.9% followed byGypsyat 14.2%. BothGypsyandCopiaelements were common in ancestral peaks of LTR, and the most abundant element was aGypsyelement containing nestedCopia/Angelasequenced similarity, reflecting a complex evolutionary history of repeat activity. Gene annotation produced 41,039 genes and 69,563 transcripts, of which >99% were functionally annotated. BUSCO duplication rates remained very high with proteins at 50.4% complete duplicates and 46.0% single copy. Whole genome duplication (WGD) synonymous mutation rates of Gaviota tarplant and sunflower (Helianthus annuus) shared peaks that correspond to the last Asteraceae polyploidization event and subsequent divergence from a common ancestor at ∼27 mya. Tandem genes were twice as prevalent as WGD genes suggesting tandem genes could be an important strategy of environmental adaptation in this species.

Article Summary

We introduce a high-quality reference genome for the endangered Gaviota tarplant. The assembly is 1.67 Gbp with 98.1% BUSCO completeness and 41 K annotated genes. We find extensiveCopialong terminal repeat sequences and tandem genes that suggest environmental adaptation strategies. Comparisons with sunflower suggest a shared polyploidization event around 27 million years ago, close to the date of the common ancestor divergence. This work underlines the importance of genomic studies in accurately understanding adaptations and conservation needs.
Meiotic DSB repair DNA synthesis tracts inArabidopsis thaliana
Authors: Hernández Sánchez-Rebato Miguel , Schubert Veit , White Charles I.
Published: February 2024

We report here the successful labelling of meiotic prophase I DNA synthesis in the flowering plant,Arabidopsis thaliana. Incorporation of the thymidine analogue, EdU, enables visualisation of the footprints of recombinational repair of programmed meiotic DNA double-strand breaks (DSB), with ∼400 discrete, SPO11-dependent, EdU-labelled chromosomal foci clearly visible at pachytene and later stages of meiosis. This number equates well with previous estimations of 200-300 DNA double-strand breaks per meiosis in Arabidopsis, confirming the power of this approach to detect the repair of most or all SPO11-dependent meiotic DSB repair recombination. The chromosomal distribution of these DNA-synthesis foci accords with that of early recombination markers and MLH1, which marks Class I crossover sites, colocalises with the EdU foci.

It is currently estimated that ∼10 cross-overs (CO) and an equivalent number of non-cross-overs (NCO) occur in each Arabidopsis male meiosis. Thus, at least 90% of meiotic recombination events, and very probably more, have not previously been accessible for analysis. Visual examination of the patterns of the foci on the synapsed pachytene chromosomes corresponds well with expectations from the different mechanisms of meiotic recombination and notably, no evidence for long Break-Induced Replication DNA synthesis tracts was found. Labelling of meiotic prophase I, SPO11-dependent DNA synthesis holds great promise for further understanding of the molecular mechanisms of meiotic recombination, at the heart of reproduction and evolution of eukaryotes.

Author Summary

Sexual reproduction involves the fusion of two cells, one from each parent. To maintain a stable chromosome complement across generations, these specialized reproductive cells must be produced through a specialized cell division called meiosis. Meiosis halves the chromosome complement of gametes and recombines the parental genetic contributions in each gamete, generating the genetic variation that drives evolution. The complex mechanisms of meiotic recombination have been intensely studied for many years and we now know that it involves the repair of programmed chromosomal breaks through recombination with intact template DNA sequences on another chromatid. At the molecular level, this is known to involve new DNA synthesis at the sites of repair/recombination and we report here the successful identification and characterisation of this DNA neo-synthesis during meiosis in the flowering plant, Arabidopsis. Both the characteristics and numbers of these DNA synthesis tracts accord with expectations from theory and earlier studies. Potentially applicable to studies in many organisms, this approach provides indelible footprints in the chromosomes and has the great advantage of freeing researchers from dependence on indirect methods involving detection of proteins involved in these dynamic processes.
Establishing and evaluating the gradient of item naming difficulty in post-stroke aphasia and semantic dementia
Authors: Nørkær Erling , Halai Ajay D. , Woollams Anna , Lambon Ralph Matthew A. , Schumacher Rahel
Published: February 2024

Anomia is a common consequence following brain damage and a central symptom in semantic dementia (SD) and post-stroke aphasia (PSA), for instance. Picture naming tests are often used in clinical assessments and experience suggests that items vary systematically in their difficulty. Despite clinical intuitions and theoretical accounts, however, the existence and determinants of such a naming difficulty gradient remain to be empirically established and evaluated. Seizing the unique opportunity of two large-scale datasets of semantic dementia and post-stroke aphasia patients assessed with the same picture naming test, we applied an Item Response Theory (IRT) approach and we (a) established that an item naming difficulty gradient exists, which (b) partly differs between patient groups, and is (c) related in part to a limited number of psycholinguistic properties - frequency and familiarity for SD, frequency and word length for PSA. Our findings offer exciting future avenues for new, adaptive, time-efficient, and patient-tailored approaches to naming assessment and therapy.
Scenarios for the long-term efficacy of amyloid-targeting therapies in the context of the natural history of Alzheimer’s disease
Authors: Raket Lars Lau , Cummings Jeffrey , Moscoso Alexis , Villain Nicolas , Schöll Michael
Published: February 2024

Importance

Recent clinical trials of Aβ-targeting therapies in Alzheimer’s disease (AD) have demonstrated clinical benefit over 18-months, but their long-term impact on disease trajectory is not yet understood. We propose a framework for evaluating realistic long-term scenarios.

Objective

To integrate data from recent phase 3 trials of the high-clearance Aβ-targeting antibodies with an estimate of the long-term patient-level natural history trajectory of the Clinical Dementia Rating-Sum of Boxes (CDR-SB) score, to explore realistic long-term efficacy scenarios.

Data Sources

Published results from recent phase 3 randomized clinical trials of high-clearance Aβ-targeting antibodies with completion between 2019 and 2023.

Study Selection

All phase 3 studies of aducanumab, lecanemab, gantenerumab, and donanemab were included.

Main Outcomes and Measures

Reported study results on CDR-SB estimated using categorical-time models.

Results

Three distinct long-term efficacy scenarios were examined, ranging from conservative (enduring short-term delay), over intermediate (fading stage-dependent slowing), to optimistic (continued stage-independent slowing). In a hypothetical framework, we found that even modestly effective therapies with fading stage-dependent slowing could result in major delays of disease progression if initiated in the earliest stages of AD. In long-term scenarios for the treatment effects observed in recent positive phase 3 trials, we found that initiating the treatments in the early symptomatic stages, defined by the respective trial inclusion criteria, could delay the onset of severe dementia by 0.3-0.6 years (conservative), 1.1-1.9 years (intermediate), and 2.0-4.2 years (optimistic).

Conclusion and Relevance

The findings provide insights into hypothetical long-term impact of Aβ-targeting treatments, highlighting the potential of maximizing clinical benefit with earlier intervention. This study underscores some of the complexities of evaluating and comparing Aβ-targeting therapies in the context of AD’s nonlinear disease trajectory and the need for considering both differences in trial populations and duration. Our work calls for studies with longer follow-up and results from early intervention trials to provide a comprehensive assessment of these therapies’ true long-term impact.
Exploring what lies beneath the tip of the gender-based violence iceberg
Authors: Moriña David , Millán Isabel , Fernández-Fontelo Amanda , Puig Pedro , Toran Pere , Gómez-Maldonado Meritxell , Falguera Gemma
Published: February 2024

Gender-based violence refers to violence directed against a person because of that person’s gender or violence that affects persons of a particular gender disproportionately. It is estimated that 30% of women worldwide have suffered either physical and/or sexual violence in their lifetime. Primary Health Care could be one of the ideal places for the detection of these situations, but most of the cases remain undetected as the victims often decline to seek for medical care after suffering an event. This work shows that public primary health care system in Catalonia might be registering only around 50% of the cases currently, and it will take more than 20 years to see the whole picture of the phenomenon, and the situation could be the same in countries with similar socioeconomic contexts. We found in previous studies that gender-based violence cases are severely underregistered from the public health and judicial perspectives, on the basis of qualitative analyses and survey data. Furthermore, we propose a statistical modelling approach able to estimate the actual burden of this issue accurately. Our results show that awareness training campaigns focused on primary healthcare professionals are very effective in reducing the underreporting issue but should be conducted repeatedly and not only once.
Differential expression analyses on aortic tissue reveal novel genes and pathways associated with abdominal aortic aneurysm onset and progression
Authors: Temprano-Sagrera Gerard , Soto Begoña , Dilmé Jaume , Peypoch Olga , Juscafresa Laura Calsina , Davtian David , Nieto Lluís , Brown Andrew , Escudero José Román , Viñuela Ana , Camacho Mercedes , Sabater-Lleal Maria
Published: February 2024

Background

Abdominal aortic aneurysms (AAA) are focal dilatations of the abdominal aorta. They are normally asymptomatic and progressively expand, increasing their risk of rupture. Rupture of an AAA is associated with high mortality rates, but the mechanisms underlying the initiation, expansion and rupture of AAA are not yet fully understood. This study aims to characterize and identify new genes associated with the pathophysiology of AAA through differential expression analyses between dilated and non-dilated aortic tissue samples, and between AAA of different diameters. Our study used RNA-seq data on 140 samples, becoming the largest RNA-seq dataset for differential expression studies of AAA.

Results

We identified 7,454 differentially expressed genes (DEGs) between AAA and controls, 2,851 of which were new compared to previous microarray studies. Notably, a novel cluster on adenosine triphosphate synthesis regulation emerged as strongly associated with AAA. Additionally, exploring AAA of different diameters identified eight genes (EXTL3,ZFR,DUSP8,DISP1,USP33,VPS37C,ZNF784,RFX1) that overlapped with the DEGs between AAA and controls, implying roles in both disease onset and progression. Seven genes (SPP1,FHL1,GNAS,MORF4L2,HMGN1,ARL1,RNASE4) with differential splicing patterns were also DEGs between AAA and controls, suggesting that splicing differences contribute to the observed expression changes and the disease development.

Conclusions

This study identified new genes and pathways associated with AAA onset and progression and validated previous relevant roles of inflammation and intracellular calcium regulation. These findings provide insights into the complex mechanisms underlying AAA and indicate potential targets to limit AAA progression and mortality risk.
Health and economic impacts of Lassa vaccination campaigns in West Africa
Authors: Smith David R M , Turner Joanne , Fahr Patrick , Attfield Lauren A , Bessell Paul R , Donnelly Christl A , Gibb Rory , Jones Kate E , Redding David W , Asogun Danny , Ayodeji Oladele Oluwafemi , Azuogu Benedict N , Fischer William A , Jan Kamji , Olayinka Adebola T , Wohl David A , Torkelson Andrew A , Dinkel Katelyn A , Nixon Emily J , Pouwels Koen B , Hollingsworth T Déirdre
Published: February 2024

Lassa fever is a zoonotic disease identified by the World Health Organization (WHO) as having pandemic potential. This study estimates the health-economic burden of Lassa fever throughout West Africa and projects impacts of a series of vaccination campaigns. We also model the emergence of “Lassa-X” – a hypothetical pandemic Lassa virus variant – and project impacts of achieving 100 Days Mission vaccination targets. Our model predicted 2.7M (95% uncertainty interval: 2.1M-3.4M) Lassa virus infections annually, resulting over ten years in 2.0M (793.8K-3.9M) disability-adjusted life years (DALYs). The most effective vaccination strategy was a population-wide preventive campaign primarily targeting WHO-classified “endemic” districts. Under conservative vaccine efficacy assumptions, this campaign averted $20.1M ($8.2M-$39.0M) in lost DALY value and $128.2M ($67.2M-$231.9M) in societal costs (International dollars 2021). Reactive vaccination in response to local outbreaks averted just one-tenth the health-economic burden of preventive campaigns. In the event of Lassa-X emerging, spreading throughout West Africa and causing approximately 1.2M DALYs within two years, 100 Days Mission vaccination averted 22% of DALYs given a vaccine 70% effective against disease, and 74% of DALYs given a vaccine 70% effective against both infection and disease. These findings suggest how vaccination could alleviate Lassa fever’s burden and assist in pandemic preparedness.
Open Science Practices Among Authors Published in Complementary, Alternative, and Integrative Medicine Journals: An International, Cross-Sectional Survey
Authors: Ng Jeremy Y , Lin Brenda , Kreuder Liliane , Cramer Holger , Moher David
Published: February 2024

Background

Open science practices aim to increase transparency in research and increase research availability through open data, open access platforms, and public access. Due to the increasing popularity of complementary, alternative, and integrative medicine (CAIM) research, our study aims to explore current open science practices and perceived barriers among CAIM researchers in their own respective research articles.

Methods

We conducted an international cross-sectional online survey that was sent to authors that published articles in MEDLINE-indexed journals categorized under the broad subject of “Complementary Therapies” or articles indexed under the MeSH term “Complementary Therapies”. Articles were extracted to obtain the names and emails of all corresponding authors. 8,786 researchers were emailed our survey, which included questions regarding participants’ familiarity with open science practices, their open science practices, and perceived barriers to open science in CAIM with respect to participants’ most recently published article. Basic descriptive statistics was generated based on the quantitative data.

Results

The survey was completed by 292 participants (3.32% response rate). Results indicate that the majority of participants were “very familiar” (n = 83, 31.68%) or “moderately familiar” (n = 83, 31.68%) with the concept of open science practices while creating their study. Open access publishing was the most familiar to participants, with 51.96% (n = 136) of survey respondents publishing with open access. Despite participants being familiar with other open science practices, the actual implementation of these practices was low. Common barriers participants experienced in implementing open science practices include not knowing where to share the study materials, where to share the data, or not knowing how to make a preprint.

Conclusions

Although participants responded that they were familiar with the concept of open science practices, the actual implementation and uses of these practices were low. Barriers included a lack of overall knowledge about open science, and an overall lack of funding or institutional support. Future efforts should aim to explore how to implement methods to improve open science training for CAIM researchers.
Spatial patterning of the epigenome during vertebrate gastrulation
Authors: Azambuja Ana Paula , Rothstein Megan , Kanno Tatiane Y. , Simoes-Costa Marcos
Published: February 2024

Embryonic patterning relies on the ability of cells to interpret the spatial information they receive from the environment. In vertebrates, this process begins with the localized activation of signaling systems that mediate axial specification. How embryonic cells record these spatial coordinates within their regulatory states has remained unclear. Here, we report that positional information is encoded within the chromatin landscape of embryonic cells. By utilizing spatially resolved genomic analysis in the avian gastrula, we found that the epigenome is organized in gradients of accessibility along the embryonic axes. Positional gradients of chromatin activation are established at thelociof developmental genes at the onset of gastrulation and can be used to predict the location of cells in amniote embryos. Our results show that axial specification involves the spatial patterning of the epigenome and support the existence of a Cartesian system of chromatin activation in the developing embryo.
The emergence and evolution of gene expression in genome regions replete with regulatory motifs
Authors: Fuqua Timothy , Sun Yiqiao , Wagner Andreas
Published: February 2024

Gene regulation is essential for life and controlled by regulatory DNA. Mutations can modify the activity of regulatory DNA, and also create new regulatory DNA, a process called regulatory emergence. Non-regulatory and regulatory DNA contain motifs to which transcription factors may bind. In prokaryotes, gene expression requires a stretch of DNA called a promoter, which contains two motifs called -10 and -35 boxes. However, these motifs may occur in both promoters and non-promoter DNA in multiple copies. They have been implicated in some studies to improve promoter activity, and in others to repress it. Here, we ask whether the presence of such motifs in different genetic sequences influences promoter evolution and emergence. To understand whether and how promoter motifs influence promoter emergence and evolution, we start from 50 “promoter islands”, DNA sequences enriched with -10 and -35 boxes. We mutagenize these starting “parent” sequences, and measure gene expression driven by 240’000 of the resulting mutants. We find that the probability that mutations create an active promoter varies more than 200-fold, and is not correlated with the number of promoter motifs. For parent sequences without promoter activity, mutations created over 1’500 new -10 and -35 boxes at unique positions in the library, but only ∼0.3% of these resulted in de-novo promoter activity. Only ∼13% of all -10 and -35 boxes contribute to de-novo promoter activity. For parent sequences with promoter activity, mutations create new -10 and -35 boxes in 11 specific positions that partially overlap with preexisting ones to modulate expression. We also find that -10 and -35 boxes do not repress promoter activity. Overall, our work demonstrates how promoter motifs influence promoter emergence and evolution. It has implications for predicting and understanding regulatory evolution, de-novo genes, and phenotypic evolution.
TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics
Authors: Chen Chin-Wen , Lin Pei-Yi , Lai Ying-Mi , Lin Miao-Hsia , Lin Shu-Yu , Hsu Chuan-Chih
Published: February 2024

Protein post-translational modifications (PTMs) are crucial in plant cellular processes, particularly in protein folding and signal transduction. N-glycosylation and phosphorylation are notably significant PTMs, playing essential roles in regulating plant responses to environmental stimuli. However, current sequential enrichment methods for simultaneous analysis of phosphoproteome and N-glycoproteome are labor-intensive and time-consuming, limiting their throughput. Addressing this challenge, this study introduces a novel tandem S-Trap-IMAC-HILIC (S-Trap: suspension trapping; IMAC: immobilized metal ion affinity chromatography; HILIC: hydrophilic interaction chromatography) strategy, termed TIMAHAC, for simultaneous analysis of plant phosphoproteomics and N-glycoproteomics. This approach integrates IMAC and HILIC into a tandem tip format, streamlining the enrichment process of phosphopeptides and N-glycopeptides. The key innovation lies in the use of a unified buffer system and an optimized enrichment sequence to enhance efficiency and reproducibility. The applicability of TIMAHAC was demonstrated by analyzing the Arabidopsis phosphoproteome and N-glycoproteome in response to abscisic acid (ABA) treatment. Up to 1,954 N-glycopeptides and 11,255 phosphopeptides were identified from Arabidopsis, indicating its scalability for plant tissues. Notably, distinct perturbation patterns were observed in the phosphoproteome and N-glycoproteome, suggesting their unique contributions to ABA response. Our results reveal that TIMAHAC offers a comprehensive approach to studying complex regulatory mechanisms and PTM interplay in plant biology, paving the way for in-depth investigations into plant signaling networks.
Phylogenomics resolves a 100-year-old debate regarding the evolutionary history of caddisflies (Insecta: Trichoptera)
Authors: Ge Xinyu , Peng Lang , Morse John C , Wang Jingyuan , Zang Haoming , Yang Lianfang , Sun Changhai , Wang Beixin
Published: February 2024

Trichoptera (caddisfly) phylogeny provides an interesting example of aquatic insect evolution, with rich ecological diversification, especially for underwater architecture. Trichoptera provide numerous critical ecosystem services and are also one of the most important groups of aquatic insects for assessing water quality. The phylogenetic relationships of Trichoptera have been debated for nearly a century. In particular, the phylogenetic position of the cocoon-makers within Trichoptera has long been contested. Here, we designed a universal single-copy orthologue and sets of ultraconserved element markers specific for Trichoptera for the first time. Simultaneously, we reconstructed the phylogenetic relationship of Trichoptera based on genome data from 111 species, representing 29 families and 71 genera. Our phylogenetic inference clarifies the probable phylogenetic relationships of cocoon-makers within Integripalpia. Hydroptilidae is considered as the basal lineage within Integripalpia, and the families Glossosomatidae, Hydrobiosidae, and Rhyacophilidae formed a monophyletic clade, sister to the integripalpian subterorder Phryganides. The resulting divergence time and ancestral state reconstruction suggest that the most recent common ancestor of Trichoptera appeared in the early Permian and that diversification was strongly correlated with habitat change.
Concatenation of segmented viral genomes for reassortment analysis
Authors: Ivanova A. , Volchkov P. , Deviatkin A.
Published: February 2024

Most reassortment identification methods are based on searching for phylogenetic discrepancies between phylogenetic trees for different segments. Other methods use pairwise genetic distances or compare the position of individual genome components in a tree relative to a reference component of the viral genome. However, such approaches are labour-intensive and hardly scalable.

Recent advances in the availability of viral sequencing technologies have led to the sequencing of large numbers of pathogen genomes, making manual processing of this large data difficult. At the same time, recombination analysis methods can process almost any number of sequences simultaneously. Such approaches are not suitable for the simultaneous analysis of multiple segments and are therefore not used to search for reassortment events. However, in the case of sequential concatenation of all segments, the methods of recombination analysis can be used to detect traces of reassortment events.

The code is available athttps://github.com/melibrun/Concatenation-of-segmented-viral-genomes-for-reassortment-analysis. The service is implemented as a web applicationhttps://melibrun.shinyapps.io/viralsegmentconcatenator1/. It concatenates segmented viral genomes for reassortment analysis. The tool accepts files in GenBank format as input and generates a set of sequences in fasta format that are sequentially concatenated sequences of viral segments named in accordance with the “strain” field of the GenBank record annotation.

In order to use recombination search algorithms in the study of reassortment events, we have developed a method (Virus Segment Concatenator, VSC) to automatically concatenate the sequences of all segments of a virus into a single sequence.

The applicability of VSC for automated searches for reassortment events was demonstrated using CCHFV, an H5N5 subtype of influenza virus.
Transcriptomic analysis of the human habenula in schizophrenia
Authors: Yalcinbas Ege A. , Ajanaku Bukola , Nelson Erik D. , Garcia-Flores Renee , Eagles Nicholas J. , Montgomery Kelsey D. , Stolz Joshua M. , Wu Joshua , Divecha Heena R. , Chandra Atharv , Bharadwaj Rahul A. , Bach Svitlana , Rajpurohit Anandita , Tao Ran , Pertea Geo , Shin Joo-Heon , Kleinman Joel E. , Hyde Thomas M. , Weinberger Daniel R. , Huuki-Myers Louise A. , Collado-Torres Leonardo , Maynard Kristen R.
Published: February 2024

Pathophysiology of many neuropsychiatric disorders, including schizophrenia (SCZD), is linked to habenula (Hb) function. While pharmacotherapies and deep brain stimulation targeting the Hb are emerging as promising therapeutic treatments, little is known about the cell type-specific transcriptomic organization of the human Hb or how it is altered in SCZD. Here we define the molecular neuroanatomy of the human Hb and identify transcriptomic changes in individuals with SCZD compared to neurotypical controls. Utilizing Hb-enriched postmortem human brain tissue, we performed single nucleus RNA-sequencing (snRNA-seq; n=7 neurotypical donors) and identified 17 molecularly defined Hb cell types across 16,437 nuclei, including 3 medial and 7 lateral Hb populations, several of which were conserved between rodents and humans. Single molecule fluorescentin situhybridization (smFISH; n=3 neurotypical donors) validated snRNA-seq Hb cell types and mapped their spatial locations. Bulk RNA-sequencing and cell type deconvolution in Hb-enriched tissue from 35 individuals with SCZD and 33 neurotypical controls yielded 45 SCZD-associated differentially expressed genes (DEGs, FDR < 0.05), with 32 (71%) unique to Hb-enriched tissue. eQTL analysis identified 717 independent SNP-gene pairs (FDR < 0.05), where either the SNP is a SCZD risk variant (16 pairs) or the gene is a SCZD DEG (7 pairs). eQTL and SCZD risk colocalization analysis identified 16 colocalized genes. These results identify topographically organized cell types with distinct molecular signatures in the human Hb and demonstrate unique genetic changes associated with SCZD, thereby providing novel molecular insights into the role of Hb in neuropsychiatric disorders.

One Sentence Summary

Transcriptomic analysis of the human habenula and identification of molecular changes associated with schizophrenia risk and illness state.
Isolation and characterization of the newStreptomycesphages Kamino, Geonosis, Abafar and Scarif infecting a broad range of host species
Authors: Rackow Bente , Rolland Clara , Mohnen Isabelle , Wittmann Johannes , Müsken Mathias , Overmann Jörg , Frunzke Julia
Published: February 2024

Streptomyces, a multifaceted genus of soil-dwelling bacteria within the phylum Actinobacteria, features intricate phage-host interactions shaped by its complex life cycle and the synthesis of a diverse array of specialized metabolites. Here, we describe the isolation and characterization of four novelStreptomycesphages infecting a variety of different host species. While phage Kamino, isolated onStreptomyces kasugaensis, is predicted to be temperate and encodes a serine integrase in its genome, phages Geonosis (isolated onS. griseus) and phages Abafar and Scarif, isolated onS. albidoflavus, are virulent phages. Phages Kamino and Geonosis were shown to amplify well in liquid culture leading to a pronounced culture collapse already at low titres. Determination of the host range by testing >40 differentStreptomycesspecies identified phages Kamino, Abafar and Scarif as broad host range phages, with Kamino showing productive infections on 15 different species. Isolated phages were further tested regarding their sensitivity to antiphage molecules. Here, the strongest effects were observed for the DNA-intercalating molecule daunorubicin. Overall, the phages described in this study expand the publicly available portfolio of phages infectingStreptomycesand will be instrumental for advancing the mechanistic understanding of the intricate antiviral strategies employed by these multicellular bacteria.
Thermal plasticity in protective wing pigmentation is modulated by genotype and food availability in an insect model of seasonal polyphenism
Authors: van Bergen E , Atencio G , Saastamoinen M , Beldade P
Published: February 2024

Developmental plasticity refers to the phenomenon whereby an organism’s phenotype depends on the environmental conditions experienced during development. This plasticity can match phenotype to ecological conditions and help organisms to cope with environmental heterogeneity, including differences between alternating seasons. Experimental studies of developmental plasticity often focus on the impact of individual environmental cues and do not take explicit account of genetic variation. In contrast, natural environments are complex, comprising multiple variables with combined effects that are poorly understood and may vary among genotypes. We investigated the effects of multifactorial environments on the development of the seasonally plastic eyespots ofBicyclus anynanabutterflies. Eyespot size is known to depend on developmental temperature and to be involved in alternative seasonal strategies for predator avoidance. In nature, both temperature and food availability undergo seasonal fluctuations. However, our understanding of whether thermal plasticity in eyespot size varies in relation to food availability and across genotypes remains limited. To address this, we investigated the combined effects of temperature (T; two levels: 20°C and 27°C) and food availability (N; two levels: control and limited) during development. We examined their impact on wing and eyespot size in adult males and females from multiple genotypes (G; 28 families). We found evidence of thermal and nutritional plasticity, and of temperature-by-nutrition interactions (significant TxN) on the size of eyespots in both sexes. Food limitation resulted in relatively smaller eyespots and tempered the effects of temperature. Additionally, we found differences among families for thermal plasticity (significant GxT effects), but not for nutritional plasticity (non-significant GxN effects) nor for the combined effects of temperature and food limitation (non-significant GxTxN effects). Our results reveal the context dependence of thermal plasticity, with the slope of thermal reaction norms varying across genotypes and across nutritional environments. We discuss these results in light of the ecological significance of pigmentation and the value of considering thermal plasticity in studies of the biological impact of climate change.
Population genomics resolves cryptic species of the ecologically flexible genusLaspinema(cyanobacteria)1
Authors: Dvořák Petr , Skoupý Svatopluk , Jarošová Hana , Páleníčková Kateřina , Stanojković Aleksandar
Published: February 2024

Cyanobacterial taxonomy is entering the genomic era, but only a few taxonomic studies have employed population genomics, which provides a framework and a multitude of tools to understand species boundaries. Phylogenomic and population genomic analyses previously suggested that several cryptic lineages emerged within the genusLaspinema. Here, we apply population genomics to define boundaries between these lineages and propose new cryptic species,Laspinema olomoucenseandLaspinema palackyanum. Moreover, we sampled soil and puddles across Central Europe and sequenced the 16S rRNA and 16S-23S ITS of the isolatedLaspinemastrains. Together with database mining of 16S rRNA sequences, we found that the genusLaspinemahas a cosmopolitan distribution and inhabits a wide variety of habitats, including freshwater, saline water, mangroves, soil crusts, soils, puddles, and the human body.
Overexpressing NRT2.7 induces nitrate export from the vacuole and increases growth of Arabidopsis
Authors: Armengaud Patrick , De Angeli Alexis , Berquin Patrick , Bréhaut Virginie , Durand Mickaël , Daniel-Vedele Françoise , Krapp Anne , Filleur Sophie
Published: February 2024

Nitrogen nutrition is essential for crop yield but applying fertilizers has detrimental effects on the environment. Compartmenting nitrate into vacuoles is one of the options to develop Nitrogen-efficient crop adapted to less fertilizers. Only few proteins involved in nitrate transport on the tonoplast have been identified. CLCa is the major transporter involved in nitrate storage in Arabidopsis but it can also facilitate nitrate remobilization from the vacuole in guard cells. Several other nitrate transporters amongst NRT2.7 have been localized in this membrane. The transport mechanism of NRT2.7 has not yet been defined as this protein is present mainly in seed cells that are not easily amenable for electrophysiology analysis. Here, we investigated NRT2.7 function through its ectopic overexpression in aclcaknock-out mutant. Although the growth diminution ofclcaon nitrogen sufficient medium was complemented, nitrate homeostasis was not restored by NRT2.7 activity. Moreover, NRT2.7 ectopic overexpression in wild-type background (WT) increased growth under limiting nitrogen supply, suggesting that NRT2.7 stimulates nitrate efflux from vacuoles. This hypothesis was demonstrated by electrophysiological nitrate flux measurements on isolated vacuoles. This discovery of NRT2.7 function and more largely the coupling of vacuolar nitrate fluxes with growth under low nitrate supply, will enable new strategies for engineering better NUE for a more sustainable agriculture.

Highlight

The overexpression of the nitrate transporter NRT2.7 stimulates growth by increasing the export of nitrate from the vacuole, the main cell compartment for nitrate storage.