bluuebunny/crossref_metadata_2025 huggingface dataset:
The heartbeat induces local volumetric compression in the healthy human brain: a 7 T magnetic resonance imaging study on brain tissue pulsations
Authors: van Hulst Ellen , Báez-Yáñez Mario G. , Adams Ayodeji L. , Biessels Geert Jan , Zwanenburg Jacobus J. M.
Published: December 2024

Intracerebral blood volume changes along the cardiac cycle cause volumetric strain in brain tissue, measurable with displacement encoding with stimulated echoes (DENSE) magnetic resonance imaging. Individual volumetric strain maps show compressing and expanding voxels, raising the question whether systolic compressions reflect a physiological phenomenon. In DENSE data from nine healthy volunteers, voxels were grouped into three clusters according to volumetric strain in a tissue mask excluding extracerebral blood vessels and cerebrospinal fluid using a two-stage clustering approach. To confirm the physiological source of the compressions, data from a patient with a cranial opening was analysed. Spatial patterns of compressing and expanding clusters were matched to high-resolution anatomical scans, acquired in one additional individual. All healthy subjects consistently showed a cluster with compressive volumetric strain during systole, covering 10.2% [7.3−13.1%] (mean [95% confidence interval]) of the tissue mask, besides two expansion clusters. In the patient, no compression was observed. Although the compression cluster did not consistently co-localize with intracerebral veins or perivascular spaces on the anatomical scans, the first-stage clustering results suggested that the distinction between the clusters has a (peri)vascular source. In conclusion, brain tissue shows heartbeat-induced volumetric compressions, possibly indicating compression of porous structures such as intracerebral veins or perivascular spaces.
RecN and RecA orchestrate an ordered DNA supercompaction response following
ciprofloxacin exposure inEscherichia coli
Authors: Vikedal Krister , Ræder Synnøve Brandt , Riisnæs Ida Mathilde , Bjørås Magnar , Booth James , Skarstad Kirsten , Helgesen Emily
Published: December 2024

Fluoroquinolones induce double-strand breaks in bacterial DNA, triggering
the SOS response, a major DNA damage response that ensures the expression of
repair proteins but also promotes the emergence and spread of antibiotic
resistance. Fluoroquinolone resistance, particularly inEscherichia
coli, is a growing global health concern. Understanding
bacterial responses to these antibiotics is critical for developing preventive
strategies and novel treatments to combat resistance development. This study
investigates DNA morphology inE. colifollowing
exposure to ciprofloxacin, a fluoroquinolone antibiotic. We show that
ciprofloxacin induces a stepwise DNA reorganization, culminating in a highly
dense nucleoid structure at midcell — a process we term DNA supercompaction.
Live cell imaging revealed that RecN, a structural maintenance of chromosomes
(SMC)-like protein, is required for DNA supercompaction, and that RecN’s
dynamics and activity in this response depend on RecA. Additionally, RecN and
RecA frequently colocalized at nucleoid-associated positions. We suggest that
RecN and RecA play active roles in DNA supercompaction following severe DNA
damage, that their interplay is part of a prompt universal survival response to
DNA double-strand breaks inE. coli,and that the
extent of the compaction response depends on the number of double-strand
breaks.

GRAPHICAL ABSTRACT
Motivations underlying co-use of benzodiazepines and opioids in the UK: a qualitative study
Authors: Vojt G , Family HE , Poulter H , Bailey C , Cavallo D , Abdala Sheikh AP , Karimi S , Booth N , Da Silva P , Aitken L , Stewart S , Hickman M , Henderson G , Scott J , Kesten J
Published: December 2024

Background

Drug-related deaths have substantially increased over the past decade in the UK, particularly in Scotland. Co-using opioids and benzodiazepines (prescribed and/or illicit) is a risk factor contributing to rising mortality. This study identified motivations in people’s co-use with the aim of informing prescribing and harm reduction interventions to address drug-related deaths.

Methods

We interviewed 48 people who co-use opioids and benzodiazepines and/or z-drugs (zopiclone and zolpidem) in Glasgow (n=28), Teesside (n=10) and Bristol (n=10). Most participants self-identified as male (n=37, 77%), white (n=45, 94%) and had a mean age of 43 years (range: 25-61 years). The majority reported at least one overdose experience, and poor mental health including trauma. Interviews were semi-structured, conducted by an academic and/or peer researcher, and analysed using reflexive thematic analysis.

Results

Participants’ motivations for co-using drugs mapped onto two interlinked meta-themes: (1) Functional motivations included co-using to augment drug effects, self-medicate or help to generate income. (2) Experiential motivations described participants’ desires to achieve (a) ‘buzz’ (feeling energised), (b) ‘glow’ (feeling comforted) (c) ‘oblivion’ (escaping trauma and adversity), and (d) feeling ‘gouchy’ (physical and mental sensations of ebbing in and out of glow and oblivion). Those typically seeking a glow or buzz wished to minimise the risks of co-use. Participants aiming to achieve oblivion or feeling ‘gouchy’ felt ambivalent about the risk of overdose.

Conclusions

The importance of assessing motivations to co-use should be recognised and routinised as part of harm reduction, (co-)prescribing and medication assisted treatments to reduce mortality risk.
Neglected predatory insects trigger potential Key Biodiversity Areas in threatened coastal habitats
Authors: Ascenzi Aleida , Nania Dario , Cristiano Andrea , Badano Davide , Pacifici Michela , Cerretti Pierfilippo
Published: December 2024

Key Biodiversity Areas (KBAs) are poised to become a powerful tool for identifying regions that host unique biodiversity. With their great diversity, insects hold significant potential as indicators for global KBA mapping, even in highly specialized and narrowly distributed habitats. For instance, species adapted to fragmented ecosystems like coastal sand dunes-among the most heavily impacted habitats worldwide-can serve as critical indicators to trigger KBAs in these fragile environments. Despite their relevance as indicators, the inclusion of insects in KBA assessments remains limited, especially for neglected insect species such as antlions. We tested selected KBA criteria on 26 antlion and owlfly species (Neuroptera: Myrmeleontidae) in Italy, including dunes specialists, and performed COI based genetic analysis to identify potential weaknesses of the assessment. Several endemic and dune specialist species trigger potential KBAs, showing limited (< 20% of their extent) overlap with the current protected area network, confirming the great value of these taxa in narrowly distributed habitats. Genetic data provides evidence of misidentification for widely distributed species. We advise for the integration of both spatial and genetic data to increase reliability of potential KBA assessments using neglected insect taxa.
The unique morphological basis and parallel evolutionary history of personate flowers inPenstemon
Authors: Depatie Trinity H , Wessinger Carolyn
Published: December 2024

Adaptive radiation in ecologically and morphologically diverse plant lineages presents an opportunity to the rapid evolution of novel floral traits. While some types of floral traits, such as flower color, are well-characterized, other types of complex morphologies remain understudied. One example is occluded personate flowers, dorso-ventrally compressed flowers with obstructed floral passageways, which have evolved in multiple genera, but have only been characterized from snapdragon. Our study examined the morphological basis and evolutionary history of personate flowers in a clade ofPenstemonspecies that includes three personate-flowered species. We characterized floral morphology and inferred phylogenomic relationships for 13 species in this group in order to examine the evolutionary history of personate flowers. We used phylogenomic tests for introgression to examine whether personate-flowered lineages have a history of introgression. Unlike the personate flowers of snapdragon, personate flowers inPenstemonare produced by deep pleats in the ventral petal tissue that curve the ventral petal surface upwards, obstructing the floral tube opening. Our phylogenetic tree suggests that personate flowers evolved in two separate lineages. Phylogenomic analyses indicate incomplete lineage sorting and introgression between certain taxa have contributed to phylogenomic discordance, however we found little evidence of recent introgression between the two personate-flowered lineages. The evolution of personate flowers inPenstemoninvolves a distinct morphological basis than snapdragon. Personate flowers have evolved multiple times inPenstemonon a rapid evolutionary timescale. The source of genetic variation for repeated shifts may be de novo mutations or pre-existing variants.
The comprehensive detection of hemoglobinopathy variants via long-read sequencing
Authors: Xiang Jiale , Peng Jiguang , Sun Xiangzhong , Jiang Chen , Zhao Huiru , Guo Yaya , Xu Haiyan , Gu Shanshan , Ye Haodong , You Long , Huang Xiaoyan , Chen Shiping , Zhu Baosheng , Peng Zhiyu
Published: December 2024

BACKGROUND

The genetic complexity of hemoglobin genes, characterized by high GC content and homologous sequences, poses significant challenges for detecting hemoglobin variants in clinical settings.

METHODS

A long-read indexed PCR method utilizing the novel CycloneSEQ nanopore sequencing platform was developed to detect all variant types, including single nucleotide variants (SNVs), deletions, structural variants (SVs) inHBA, HBB, HBD, andHBGgenes. The method was validated using 507 clinical samples to assess its performance.

RESULTS

The long-read indexed PCR system employed 13 primers targeting the hemoglobin gene clusters. This design enabled the detection of 37 types ofHBAdeletions, 5 SV (3 multicopies (αααα, αααanti3.7, αααanti4.2) and 2 fusion allele (HKαα andanti-HKαα)), 37HBBdeletions, and all SNVs in the targeted regions. Validation across 507 samples (84 withHBAvariants, 60 withHBBvariants, 256 with bothHBAandHBBvariants, and 107 with no known variants) demonstrated 100.0% sensitivity and specificity. Additionally, the long-read sequencing enabled phasing of variants within hemoglobin genes, providing insights critical for clinical interpretation.

CONCLUSIONS

The long-read indexed PCR method, combined with the CycloneSEQ nanopore sequencing platform, proved to be a robust and efficient solution for detecting hemoglobinopathy variants. The integration of indexed primers and barcoding enhances scalability, making this method ideal for large-scale population screening programs in the future.
Separable cognitive and motor decline tracked across adult life-span for goal-directed navigation
Authors: Lancia Gian Luca , D’Alessandro Marco , Eluchans Mattia , Ibáñez-Berganza Miguel , Spiers Hugo J. , Pezzulo Giovanni
Published: December 2024

Spatial navigation is a fundamental cognitive skill, yet our understanding of the strategies people employ in real-world navigation remains incomplete. This study investigates navigation strategies using data from the large-scale Sea Hero Quest (SHQ) game, in which participants face navigational problems consisting in controlling a boat to reach a series of goal locations, within maps having different shapes. By using a combination of behavioral and computational modeling approaches, we report three key findings: First, participants predominantly use goal-directed strategies compared to visibility-based strategies. Second, participants show signatures of sequential planning, both during memorization – as they spend more time looking at difficult levels – and during navigation – as they show primacy effects, suggesting that they remember better the first navigational goal. Third, our results show a significant age-related decline in navigation performance, which depends both on reduced motor skill – as indexed by poorer control of the boat – and decreased cognitive strategy – as indexed by a loss of goal-directedness during spatial navigation. Unexpectedly, the loss of goal-directedness with age is not associated with a shift to visibility-based strategy or to an incorrect sequencing of goals. Taken together, our findings offer a nuanced understanding of spatial navigation strategies in naturalistic conditions and their decline with age. Our computational approach permits distinguishing motoric and cognitive variables, showing that both decline with age. These results align with and extent previous research on spatial memory decline with age, including potential links to neurodegenerative diseases like Alzheimer’s. The computational models developed in this study provide a robust framework for analyzing navigation strategies, applicable to other virtual environments and video games.
GJB3, a gap junction gene, supports cell growth by mediating cystine uptake and regulating cellular stress pathways in SLC7A11 low adenocarcinomas
Authors: Acharya Disha , Chatterjee Annesha , Bhandari Nikita , Roy Payel , Agrawal Monishka , Chaube Bal Krishna , Shukla Sudhanshu
Published: December 2024

Gap junctions are specialized intercellular connections that directly connect the cytoplasm of two cells via protein structure called connexins. Despite extensive research on many cell surface proteins, Gap junction proteins are understudied in cancer. In this study, we used TCGA data to identify genetic and epigenetic changes associated with Gap junction proteins. The analysis identified GJB3 as a key gene with differential methylation and expression patterns, with notable overexpression in COAD and LUAD, correlating significantly with patient survival outcomes. GJB3 knockdown studies revealed reduced cell proliferation and migration. Transcriptomic analysis revealed that GJB3 knockdown induced a cellular stress response, characterized by activation of starvation and autophagy pathways. Western blot analysis confirmed these findings, showing increased phosphorylation of eIF2α and activation of the GCN2-eIF2α-ATF4 signaling axis subsequent autophagy induction. We also found that sustained autophagy induced apoptosis mediated cell death. Metabolic profiling revealed a significant decrease in cystine levels in GJB3-deficient cells. We demonstrated that GJB3 plays a crucial role in cystine uptake, especially in cells with low SLC7A11 expression. Furthermore, we showed that GJB3 can be targeted using specific antibodies, establishing it as a potential therapeutic strategy for GJB3-dependent cancers. These findings highlight the significance of GJB3 in cancer progression and its potential as a therapeutic target, offering new insights into its epigenetic regulation and functional role in cellular stress and survival mechanisms.
Comparative genomics ofRickettsiellabacteria reveal variable metabolic traits involved in symbiotic interactions with arthropods
Authors: Floriano Anna M. , El-Filali Adil , Amoros Julien , Buysse Marie , Jourdan-Pineau Hélène , Sprong Hein , Kohl Robert , Dirks Ron P. , Schaap Peter , Koehorst Jasper , Nijsse Bart , Bouchon Didier , Daubin Vincent , Vavre Fabrice , Duron Olivier
Published: December 2024

Members of theRickettsiellagenus (Legionellales) are emerging as widespread bacteria associated with insects, arachnids, and crustaceans. While someRickettsiellastrains are highly virulent entomopathogens, others are maternally inherited endosymbionts that manipulate arthropod phenotypes, including the induction of defensive symbiosis and cytoplasmic incompatibility. However, the genomic diversity ofRickettsiellaremains largely unexplored, and their genetic potential to induce complex phenotypes in arthropods is only partially understood. In this study, we sequenced five novel Rickettsiella genomes isolated from three tick species. Through comparative genomics, we observed thatRickettsiellamembers share similar metabolic capabilities, and collectively lack virulence genes from pathogenicLegionellales. Additional analysis ofRickettsiellagenomes revealed significant variability in metabolic properties related to endosymbiosis. Specifically, their capacity to biosynthesize certain B vitamins and heme varies, suggesting a functional role of someRickettsiellastrains in the nutrition of their arthropod hosts. SomeRickettsiellagenomes harbour homologs ofWolbachia cifgenes, encoding for the effectors of cytoplasmic incompatibility, suggesting thatRickettsiellamay use a similar molecular mechanism similar to manipulate the reproduction of their arthropod hosts. Phylogenomics further revealed that tick-borneRickettsiellaexhibit distinct evolutionary origins within the genus, indicating thatRickettsiellahave undergone repeated horizontal transfers between ticks and other arthropods.
Blood and tissue correlates of steroid non-response in checkpoint inhibition-induced immune-related adverse events
Authors: van Eijs Mick J.M. , van der Wal M. Marlot , Klotškova Hedi-Britt , Dautzenberg Noël M.M. , Schuiveling Mark , Verheijden Rik J. , van Schaik Fiona D.M. , Oldenburg Bas , Nierkens Stefan ,   the UNICIT Consortium, Suijkerbuijk Karijn P.M. , van Wijk Femke
Published: December 2024

High-dose steroids constitute the cornerstone of first-line treatment for immune-related adverse events (irAEs) associated with immune checkpoint inhibitors, but compromise antitumor immunity. A deeper understanding of irAEs and their response to steroids can contribute to more targeted irAE management regimens. We took a multi-omics approach to identify blood- and tissue-based predictors of steroid response and to explore underlying mechanisms of steroid non-response in irAEs. In the blood, steroid non-response correlated with trends for elevated Tc1/Tc17 CD8+T cells and serum interleukin (IL)-17, IL-6, IL-12 and IL-23 prior to initiation of steroids, along with persistent (CD8+) T cell proliferation and activation after start of steroids. A remarkably fast decrease in inflammatory gene signatures and lymphocyte infiltration was observed in colitis tissue of steroid responders obtained within 24h after initiation of steroids. Peripheral T cell PD-1 receptor occupancy was not associated with steroid response. Colitis tissue of steroid non-responders was enriched for activated CD4+memory T cells and a pronounced type 1/17 immune response. Together, our findings suggest rapid immunological effects of steroids in circulating cells and irAE-affected tissue and support that an enhanced type 1/type 17 response is associated with steroid non-response in irAEs.
Understanding and overcoming innate and acquired MAPK-inhibition resistance in anaplastic thyroid cancer
Authors: Zeng Peter YF , Meens Jalna , Pan Harrison , Cecchini Matthew J. , Jarycki Laura , Ryan Sarah B. , Dawson Alice E. , Karimi Amir , Shaikh Mushfiq H. , Palma David A. , Winquist Eric , Gunaratnam Laksman , Mymryk Joe S. , Barrett John W. , Boutros Paul C. , Ailles Laurie , Nichols Anthony C.
Published: December 2024

Anaplastic thyroid cancer (ATC) is one of the most lethal human cancers, with some patients succumbing to the disease within weeks of diagnosis. Although a subset of patients with ATC with BRAFV600Emutation respond to the monomeric type I RAF inhibitor (RAFi) dabrafenib in combination with MEK inhibitor (MEKi) trametinib, most rapidly develop adaptive or acquired resistance. These patients, along with those who do not harbor the BRAFV600Ealteration, have limited treatment options. To understand the mechanism of resistance to dabrafenib and trametinib, we utilized multi-region whole genome, high-coverage whole exome and single nuclei RNA-sequencing of ATC patient tumours to unravel genomic, transcriptomic, and microenvironmental evolution during type I RAFi and MEKi therapy. Single-cell nuclei RNA sequencing of matched primary and resistant ATC patient tumours identified reactivation of the MAPK-pathway, along with immunosuppressive macrophage proliferation, underlying the development of acquired resistance. Our translational genomics led us that hypothesize that type II RAFi, which inhibit both RAF monomers and dimers, can be efficacious in overcoming treatment resistance. Screening of a panel of type II RAFi revealed that ATC cell lines are exquisitely sensitive to the type II RAFi, naporafenib, by inhibiting EphA2-mediated MAPK-signaling. We further demonstrated that naporafenib, in combination with the MEKi trametinib, can durably and robustly overcome both innate and acquired treatment resistance to dabrafenib and trametinib using ATC cell lines and patient-derived xenograft models. Finally, we describe a novel mechanism of acquired resistance to type II RAFi and MEKi through compensatory mutations inMAST1. Taken together, our work using translational and functional genomics has unraveled the differential mechanisms of treatment resistance to type I and type II RAFi in combination with trametinib and rationalizes the clinical investigation of type II RAFi in the setting of thyroid cancer.
Effects of contrast-medium and vertebral measurement level on computed tomography-based body composition parameters of skeletal muscle and adipose tissue
Authors: Akamatsu Nobuhiko , Gonoi Wataru , Hanaoka Shouhei , Inui Shohei , Kurokawa Mariko , Taguchi Satoru , Sugawara Kotaro , Kume Haruki , Abe Osamu
Published: December 2024

Objective

To comprehensively evaluate the effects of contrast-medium administration and measurement level (L3 and L1) on computed tomography (CT) derived body composition parameters, promising prognostic factors for various diseases.

Methods

203 dynamic contrast-enhanced CT examinations, including unenhanced (phase 0) and early arterial, late arterial, portal, and equilibrium phases (phases 1-4, respectively), were retrospectively enrolled in the study. Areas and mean densities of skeletal muscle (SMA and MSMD), subcutaneous adipose tissue (SATA and MSATD), and visceral adipose tissue (VATA and MVATD) were measured at L3 and L1 levels across five phases (phase 0–4). Measurement changes among phases and levels were assessed statistically.

Results

The rates of SMA, SATA, and VATA on phase 1/2/3/4 compared to those on phase 0 were as follows: L3 SMA +1.1%/+2.1%/+2.8%/+3.5%; L1 SMA, +2.0%/+2.7%/+3.0%/+3.7%; L3 SATA −0.4%/−1.9%/−2.9%/−4.7%; L1 SATA −0.3%/−2.2%/−3.5%/−6.1%; L3 VATA −7.5%/−17.8%/−20.0%/−22.2%; L1 VATA −8.5%/−20.1%/−22.6%/−23.7%. Differences of MSMD, MSATD, and MVATD on phase 1/2/3/4 between those on phase 0 were as follows (Hounsfield Units): L3 MSMD, +2.1/+5.8/+7.8/+9.6; L1 MSMD, +2.9/+7.7/+9.1/+9.8; L3 MSATD, +1.2/+3.7/+4.8/+6.2; L1 MSATD, +1.2/+3.8/+4.7/+5.6; L3 MVATD, +1.5/+4.1/+5.2/+6.1; L1 MVATD, +1.9/+4.9/+5.8/+6.3. The values between L3 and L1 showed a linear solid correlation (coefficient of determination, 0.950–0.999), suggesting interchangeability.

Conclusion

Changes in body composition parameters measured in various contrast phases and two dominant body levels were comprehensively elucidated, promoting the interchangeability of cohorts with mixed CT conditions.
Genome-wide Machine Learning Analysis of Anosmia and Ageusia with COVID-19
Authors: Pietan Lucas , Phillippi Elizabeth , Melo Marcelo , El-Shanti Hatem , Smith Brian J , Darbro Benjamin , Braun Terry , Casavant Thomas
Published: December 2024

The COVID-19 pandemic has caused substantial worldwide disruptions in health, economy, and society, manifesting symptoms such as loss of smell (anosmia) and loss of taste (ageusia), that can result in prolonged sensory impairment. Establishing the host genetic etiology of anosmia and ageusia in COVID-19 will aid in the overall understanding of the sensorineural aspect of the disease and contribute to possible treatments or cures. By using human genome sequencing data from the University of Iowa (UI) COVID-19 cohort (N=187) and the National Institute of Health All of Us (AoU) Research Program COVID-19 cohort (N=947), we investigated the genetics of anosmia and/or ageusia by employing feature selection techniques to construct a novel variant and gene prioritization pipeline, utilizing machine learning methods for the classification of patients. Models were assessed using a permutation-based variable importance (PVI) strategy for final prioritization of candidate variants and genes. The highest held-out test set area under the receiver operating characteristic (AUROC) curve for models and datasets from the UI cohort was 0.735 and 0.798 for the variant and gene analysis respectively and for the AoU cohort was 0.687 for the variant analysis. Our analysis prioritized several novel and known candidate host genetic factors involved in immune response, neuronal signaling, and calcium signaling supporting previously proposed hypotheses for anosmia/ageusia in COVID-19.
GWAS highlights the neuronal contribution to multiple sclerosis susceptibility
Authors: Zeng Lu , Atlas Khan , Lama Tsering ,   the International Multiple Sclerosis Genetics Consortium, Chitnis Tanuja , Weiner Howard , Wang Gao , Fujita Masashi , Zipp Frauke , Taga Mariko , Kiryluk Krzysztof , De Jager Philip L.
Published: December 2024

Multiple Sclerosis (MS) is a chronic inflammatory and neurodegenerative disease affecting the brain and spinal cord. Genetic studies have identified many risk loci, that were thought to primarily impact immune cells and microglia. Here, we performed a multi-ancestry genome- wide association study with 20,831 MS and 729,220 control participants, identifying 236 susceptibility variants outside the Major Histocompatibility Complex, including four novel loci. We derived a polygenic score for MS and, optimized for European ancestry, it is informative for African-American and Latino participants. Integrating single-cell data from blood and brain tissue, we identified 76 genes affected by MS risk variants. Notably, while T cells showed the strongest enrichment, inhibitory neurons emerged as a key cell type, highlighting the importance of neuronal and glial dysfunction in MS susceptibility.
Ubiquitin Ligase ITCH Regulates Life Cycle of SARS-CoV-2 Virus
Authors: Xiang Qiwang , Wouters Camille , Chang Peixi , Lu Yu-Ning , Liu Mingming , Wang Haocheng , Yang Junqin , Pekosz Andrew , Zhang Yanjin , Wang Jiou
Published: December 2024

SARS-CoV-2 infection poses a major threat to public health, and understanding the mechanism of viral replication and virion release would help identify therapeutic targets and effective drugs for combating the virus. Herein, we identified E3 ubiquitin-protein ligase Itchy homolog (ITCH) as a central regulator of SARS-CoV-2 at multiple steps and processes. ITCH enhances the ubiquitination of viral envelope and membrane proteins and mutual interactions of structural proteins, thereby aiding in virion assembly. ITCH-mediated ubiquitination also enhances the interaction of viral proteins to the autophagosome receptor p62, promoting their autophagosome-dependent secretion. Additionally, ITCH disrupts the trafficking of the protease furin and the maturation of cathepsin L, thereby suppressing their activities in cleaving and destabilizing the viral spike protein. Furthermore, ITCH exhibits robust activation during the SARS-CoV-2 replication stage, and SARS-CoV-2 replication is significantly decreased by genetic or pharmacological inhibition of ITCH. These findings provide new insights into the mechanisms of the SARS-CoV-2 life cycle and identify a potential target for developing treatments for the virus-related diseases.
Cryo-EM reveals that cardiac IGLV6-derived AL fibrils can be polymorphic
Authors: Bassett Parker , Nguyen Binh A. , Singh Virender , Garrett Patrick T. , Moresco James J. , Kaur Gurbakhash , Afrin Shumaila , Pękała Maja , Saelices Lorena
Published: December 2024

AL amyloidosis is a systemic disease caused by the aggregation of free antibody light chains (LC) secreted by aberrant plasma cell clones into the bloodstream. These LC aggregates form amyloid fibrils that deposit in multiple organs, leading to organ failure and, ultimately, death. Investigating the structural basis of LC aggregation is a critical avenue for understanding the biopathology of AL amyloidosis. Structural insights into AL fibril formation may reveal mechanisms driving amyloid deposition and inspire novel therapeutic strategies. Previous studies using cryo-electron microscopy have uncovered diverse AL fibril structures extracted from multiple patients, highlighting variability in fibril architecture. Here, we present a novel cryo-EM structure of AL cardiac fibrils from a patient with AL amyloidosis. This structure reveals a unique fibril fold and the coexistence of multiple morphologies, including single- and double-protofilament forms. Notably, some of these double-protofilament fibrils exhibit an uncommon rotational symmetry, raising intriguing questions about the mechanisms governing fibril formation and evolution over time.
Lineage labeling with zebrafish hand2 Cre and CreERT2 recombinase CRISPR knock-ins
Authors: Ming Zhitao , Liu Fang , Moran Hannah R , Lalonde Robert L. , Adams Megan , Restrepo Nicole K , Joshi Parnal , Ekker Stephen C , Clark Karl J , Friedberg Iddo , Yin Chunyue , Sumanas Saulius , Mosimann Christian , Essner Jeffrey J , McGrail Maura
Published: December 2024

Background: The ability to generate endogenous Cre recombinase drivers using CRISPR–Cas9 knock–in technology allows lineage tracing, cell type specific gene studies, and in vivo validation of inferred developmental trajectories from phenotypic and gene expression analyses. This report describes endogenous zebrafish hand2 Cre and CreERT2 drivers generated with GeneWeld CRISPR–Cas9 precision targeted integration. Results: hand2–2A–cre and hand2–2A–creERT2 knock–ins crossed with ubiquitous loxP–based Switch reporters led to broad labeling in expected mesodermal and neural crest–derived lineages in branchial arches, cardiac, fin, liver, intestine, and mesothelial tissues, as well as enteric neurons. Novel patterns of hand2 lineage tracing appeared in venous blood vessels. CreERT2 induction at 24 hours reveals late emerging hand2 progenitors in the 24–48 hour embryo contribute to the venous and intestinal vasculature. Induction in 3 dpf larva restricts hand2 lineage labeling to mesoderm–derived components of the branchial arches, heart, liver and enteric neurons. Conclusions: hand2 progenitors from the lateral plate mesoderm and ectoderm contribute to numerous lineages in the developing embryo. Later emerging hand2 progenitors become restricted to a subset of lineages in the larva. The hand2 Cre and CreERT2 drivers establish critical new tools to investigate hand2 lineages in zebrafish embryogenesis and larval organogenesis.
High-Throughput Epigenetic Profiling Immunoassays for Accelerated Disease Research and Clinical Development
Authors: Van den Ackerveken Priscilla , Hannart Clotilde , Pamart Dorian , Varsebroucq Robin , Wargnies Marion , Thiry Olivia , Lurkin Marie , Vincent Séverine , Chapelier Muriel , Rommelaere Guillaume , Herzog Marielle
Published: December 2024

Epigenetics which examines the regulation of genes without modification of the DNA sequence, plays a crucial role in various biological processes and disease mechanisms. Among the different forms of epigenetic modifications, histone post-translational modifications (PTMs) are important for modulating chromatin structure and gene expression. Aberrant levels of histone PTMs are implicated in a wide range of diseases, including cancer, making them promising targets for biomarker discovery and therapeutic intervention. In this context, blood, tissues, or cells serve as valuable resources for epigenetic research and analysis. Traditional methods such as mass spectrometry and western blotting are widely used to study histone PTMs, providing qualitative and (semi)quantitative information. However, these techniques often face limitations that could include throughput and scalability, particularly when applied to clinical samples. To overcome these challenges, we developed and validated 13 Nu.Q® immunoassays to detect and quantify specific histone PTM-nucleosomes from K2EDTA plasma samples. Then, we tested these assays on other types of samples, including chromatin extracts from frozen tissues, as well as cell lines and white blood cells Our findings demonstrate that the Nu.Q®assays offer high specificity, sensitivity, precision and linearity, making them effective tools for epigenetic profiling. A comparative analysis of HeLa cells using mass spectrometry, Western blot, and Nu.Q®immunoassays revealed a consistent histone PTMs signature, further validating the effectiveness of these assays. Additionally, we successfully applied Nu.Q®assays across various biological samples, including human tissues from different organs and specific white blood cell subtypes, highlighting their versatility and applicability in diverse biological contexts.
Molecular cloning and host range analysis of three cytomegaloviruses fromMastomys natalensis
Authors: Staliunaite Laura , Puhach Olha , Ostermann Eleonore , Rosenke Kyle , Nichols Jenna , Oestereich Lisa , Feldmann Heinz , Davison Andrew J. , Jarvis Michael A. , Brune Wolfram
Published: December 2024

Herpesvirus-based vectors are attractive for use as conventional or transmissible vaccines against emerging zoonoses in inaccessible animal populations. In both cases, cytomegaloviruses as members of the subfamilyBetaherpesvirinaeare particularly suitable for vaccine development as they are highly specific for their natural host species, infect a large proportion of their host population, and cause mild infections in healthy individuals. The Natal multimammate mouse (Mastomys natalensis) is the natural reservoir of Lassa virus, which causes deadly hemorrhagic fever in humans.M. natalensiswas recently reported to harbor at least three different cytomegaloviruses (MnatCMV1, MnatCMV2 and MnatCMV3). Herein, we report the molecular cloning of three complete MnatCMV genomes in a yeast and bacterial artificial chromosome (YAC-BAC) hybrid vector. Purified viral genomes were cloned in yeast by single-step transformation-associated recombination (STAR cloning) and subsequently transferred toEscherichia colifor further genetic manipulation. Integrity of the complete cloned viral genomes was verified by sequencing, and replication fitness of viruses reconstituted from these clones was analyzed by replication kinetics inM. natalensisfibroblasts and kidney epithelial cells. We also found that neither parental nor cloned MnatCMVs replicated in mouse and rat fibroblasts, nor did they show sustained replication in baby hamster kidney cells, consistent with the expected narrow host range for these viruses. We further demonstrated that an exogenous sequence can be inserted by BAC-based mutagenesis between open reading frames M25 and m25.1 of MnatCMV2 without affecting replication fitnessin vitro, identifying this site as potentially suitable for the insertion of vaccine target antigen genes.

Importance

Cytomegaloviruses recently discovered in the Natal multimammate mouse (Mastomys natalensis) are widespread within theM. natalensispopulation. Since these rodents also serve as natural hosts of the human pathogen Lassa virus (LASV), we investigated the potential suitability ofM. natalensisCMVs (MnatCMVs) as vaccine vectors. We describe the cloning of three different MnatCMV genomes as bacterial artificial chromosomes (BACs). Replicative capacity and species specificity of these BAC-derived MnatCMVs were analyzed in multiple cell types. We also identified a transgene insertion site within one of the MnatCMV genomes suitable for the incorporation of vaccine target antigens. Together, this study provides a foundation for the development of MnatCMVs as transmissible MnatCMV-based LASV vaccines to reduce LASV prevalence in hard-to-reachM. natalensispopulations and thereby zoonotic transmission to humans.
E-box independent chromatin recruitment turns MYOD into a transcriptional repressor
Authors: Nicoletti Chiara , Massenet Jimmy , Pintado-Urbanc Andreas P. , Connor Leah J. , Nicolau Monica , Sundar Swetha , Xu Mingzhi , Schmitt Anthony , Zhang Wenxin , Fang Zesen , Chan Tsz Ching Indigo , Tapscott Stephen J. , Cheung Tom H. , Simon Matthew D. , Caputo Luca , Puri Pier Lorenzo
Published: December 2024

MYOD is an E-box sequence-specific basic Helix-Loop-Helix (bHLH) transcriptional activator that, when expressed in non-muscle cells, induces nuclear reprogramming toward skeletal myogenesis by promoting chromatin accessibility at previously silent loci. Here, we report on the identification of a previously unrecognized property of MYOD as repressor of gene expression, via E-box-independent chromatin binding within accessible genomic elements, which invariably leads to reduced chromatin accessibility. MYOD-mediated repression requires the integrity of functional domains previously implicated in MYOD-mediated activation of gene expression. Repression of mitogen-and growth factor-responsive genes occurs through promoter binding and requires a highly conserved domain within the first helix. Repression of cell-of-origin/alternative lineage genes occurs via binding and decommissioning of distal regulatory elements, such as super-enhancers (SE), which requires the N-terminal activation domain as well as two chromatin-remodeling domains and leads to reduced strength of CTCF-mediated chromatin interactions. Surprisingly, MYOD-mediated chromatin compaction and repression of transcription do not associate with reduction of H3K27ac, the conventional histone mark of enhancer or promoter activation, but with reduced levels of the recently discovered histone H4 acetyl-methyl lysine modification (Kacme). These results extend MYOD biological properties beyond the current dogma that restricts MYOD function to a monotone transcriptional activator and reveal a previously unrecognized functional versatility arising from an alternative chromatin recruitment through E-box or non-E-box sequences. The E-box independent repression of gene expression by MYOD might provide a promiscuous mechanism to reduce chromatin accessibility and repress cell-of-origin/alternative lineage and growth factor/mitogen-responsive genes to safeguard the integrity of cell identity during muscle progenitor commitment toward the myogenic lineage.
The capsule and genetic background, rather than specific loci, strongly influence pneumococcal growth kinetics
Authors: Chaguza Chrispin , Arends Daan W. , Lo Stephanie W. , Putri Indri Hapsari , York Anna , Lees John A. , Wyllie Anne L. , Weinberger Daniel M. , Bentley Stephen D. , de Jonge Marien I. , Cremers Amelieke J.H.
Published: December 2024

Bacterial growth characteristics intrinsic to each strain can impact and influence gene expression, antibiotic susceptibility, and disease pathogenesis. However, little is known about specific genomic variations that influence these bacterial growth features. Here, we investigate the impact ofStreptococcus pneumoniaegenetics on itsin vitro growth features to shed light on genes that may be important targets in the development of vaccines and therapeutics. We use statistical models to estimate growth features and show that they varied significantly across capsular serotypes and lineages, strongly correlated with the phylogeny, and were highly heritable, highlighting a strong genetic basis. Despite this, genome-wide association studies revealed no specific genomic loci statistically associated with the growth features independently of the genetic background, including those in the capsular polysaccharide synthesis locus. Our findings show that the serotype and lineage, and possibly a combination of genomic loci, influence intrinsic pneumococcal growth kinetics, which may have implications on pneumococcal disease pathogenesis.
Genetic Analysis of Flagellar-Mediated Surface Sensing byPseudomonas aeruginosaPA14
Authors: Kuchma Sherry , Geiger C.J. , Webster Shanice , Fu Yu , Montoya Robert , O’Toole G.A.
Published: December 2024

Surface sensing is a key aspect of the early stage of biofilm formation. ForP. aeruginosa, the type IV pili (TFP), the TFP alignment complex and PilY1 were shown to play a key role in c-di-GMP signaling upon surface contact. The role of the flagellar machinery in surface sensing is less well understood inP. aeruginosa. Here we show, consistent with findings from other groups, that a mutation in the gene encoding the flagellar hook protein (ΔflgK) or flagellin (ΔfliC) results in a strain that overproduces the Pel exopolysaccharide (EPS) with a concomitant increase in c-di-GMP levels. We use a candidate gene approach and genetic screens, combined with phenotypic assays, to identify key roles for the MotAB and MotCD stators and the FliG protein, a component of the flagellar switch complex, in stimulating the surface-dependent, increased c-di-GMP level noted for these flagellar mutants. These findings are consistent with previous studies showing a role for the stators in surface sensing. We also show that mutations in the genes coding for the diguanylate cyclases SadC and RoeA as well as SadB, a protein involved in early surface colonization, abrogate the increased c-d-GMP-related phenotypes of the ΔflgKmutant. Together, these data indicate that bacteria monitor the status of flagellar synthesis and/or function during surface sensing as a means to trigger the biofilm program.

Importance

Understanding how the flagellum contributes to surface sensing byP. aeruginosais key to elucidating the mechanisms of biofilm initiation by this important opportunistic pathogen. Here we take advantage of the observation that mutations in the flagellar hook protein or flagellin enhance surface sensing. We exploit this phenotype to identify key players in this signaling pathway, a critical first step in understanding the mechanistic basis of flagellar-mediated surface sensing. Our findings establish a framework for the future study of flagellar-based surface sensing.
Automated long-range compensation of an rf quantum dot sensor
Authors: Hickie Joseph , van Straaten Barnaby , Fedele Federico , Jirovec Daniel , Ballabio Andrea , Chrastina Daniel , Isella Giovanni , Katsaros Georgios , Ares Natalia
Published: December 2024

Charge sensing is a sensitive technique for probing quantum devices, of particular importance for spin-qubit readout. To achieve good readout sensitivities, the proximity of the charge sensor to the device to be measured is a necessity. However, this proximity also means that the operation of the device affects, in turn, the sensor tuning and ultimately the readout sensitivity. We present an approach for compensating for this crosstalk effect allowing for the gate voltages of the measured device to be swept in a 1-V × 1-V window while maintaining a sensor configuration chosen by a Bayesian optimizer. Our algorithm will hopefully be a major contribution to the suite of fully automated solutions required for the operation of large quantum device architectures.

Published by the American Physical Society
2024
Impact of Next-to-Leading-Order Weak Standard-Model-Effective-Field-Theory Corrections in
e+e−→ZH
Authors: Asteriadis Konstantin , Dawson Sally , Giardino Pier Paolo , Szafron Robert
Published: December 2024

We present results from a complete next-to-leading order (NLO) calculation of e+e−→ZH in the standard model effective field theory (SMEFT) framework, including all contributions from dimension-six operators. At NLO, there are novel dependencies on CP violating parameters in the gauge sector, on modifications to the Higgs boson self-couplings, on alterations to the top quark Yukawa couplings, and on four-fermion operators involving the electron and the top quark, among others. We show that including only the logarithms resulting from renormalization group scaling can produce misleading results, and further, we explicitly demonstrate the constraining power of combining measurements from different energy scales.

Published by the American Physical Society
2024
How to use DIALS to process chemical crystallography 3D ED rotation data from pixel array detectors
Authors: Vypritskaia Angelina , Zou Xiaodong , Yang Taimin , Waterman David Geoffrey
Published: December 2024

The DIALS package provides a set of tools for crystallographic data processing. The open-source nature of the project, and a flexible interface in which individual command-line programs each have a dedicated job, have enabled the adaptation of DIALS to a wide range of experiment types, including electron diffraction. Here we present detailed instructions for the use of DIALS to process chemical crystallography diffraction data from continuous rotation electron diffraction experiments. We demonstrate processing and structure solution from three different samples from three different instruments, including two commercial instruments dedicated to electron diffraction. Each instrument has a pixel array detector, allowing low-noise data to be obtained, resulting in high quality structures. Various new features were added to DIALS to simplify the workflow for these use cases. These are described in detail, along with useful program options for electron diffraction work.
Cooperative research and development projects: researchers’ motivations for participation and the benefits and barriers they encounter
Authors: Fontes Carla , Franco Mario
Published: December 2024

Purpose

Research and development (R&D) initiatives are fundamental for society to evolve in its social, economic, technological and environmental dimensions. This study aimed to provide a view of what motivates researchers to participate in such projects as well as the benefits and barriers they encounter when cooperating in R&D projects.

Design/methodology/approach

A qualitative methodology was adopted, within which a case study was conducted: R&D project “GreenHealth - Digital Strategies”. This initiative was based on leveraging biological assets to improve well-being and promote health. Data were obtained from 10 interviews with researchers and documentary analysis such as the project’s official website and social media accounts.

Findings

The content analysis led to the conclusion that the researchers’ motivations for participating in R&D projects were the opportunity to contribute to scientific and social evolution, the creation of knowledge and personal factors inherent to the participating researchers. The benefits they derived were related to creating and spreading knowledge, as well as financial incentives. Barriers to participation were related to management, communication, organisational culture, the COVID-19 pandemic.

Practical implications

From this study the research team members can understand the importance of cooperation between institutions, which illustrates the importance of creating and transferring knowledge. This study shows also that, in R&D projects, educational and health institutions access new knowledge, attract highly qualified personnel/researchers, establish networks and share financial risks.

Originality/value

The study’s innovation derives from its demonstration that an R&D project of this nature is important for several organisations to develop the conception and implementation of a long-term strategy centred on human beings and focused on the eco-sustainability of the affected regions.