bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic epidemiology ofCorynebacterium diphtheriaein New Caledonia
Authors: Tessier Eve , Hennart Melanie , Badell Edgar , Passet Virginie , Toubiana Julie , Biron Antoine , Gourinat Ann-Claire , Merlet Audrey , Colot Julien , Brisse Sylvain
Published: October 2022

Objectives

An increasing number of isolations ofCorynebacterium diphtheriaehas been observed in recent years in the archipelago of New Caledonia. We aimed to analyze the clinical and microbiological features of samples withC. diphtheriae.

Methods

AllC. diphtheriaeisolates identified in New Caledonia from May 2015 to May 2019 were included. For each case, a retrospective consultation of the patient files was conducted. Antimicrobial susceptibility phenotypes,toxgene and diphtheria toxin expression, biovar and the genomic sequence were determined. Core genome multilocus sequence typing (cgMLST), 7-gene MLST and search of genes of interest were performed from genomic assemblies.

Results

58 isolates were included, with a median age of patients of 28 years (range: 9 days to 78 years). Cutaneous origin accounted for 51 of 58 (87.9%) isolates, andC. diphtheriaewas associated withStaphylococcus aureusand/orStreptococcus pyogenesin three quarters of cases. Half of cases came either from the main city Noumea (24%, 14/58) or from the sparsely populated island of Lifou (26%, 15/58). Six tox-positive isolates were identified, associated with recent travel to Vanuatu; 5 of these cases were linked and cgMLST confirmed recent transmission. Two cases of endocarditis in young female patients with a history of rheumatic fever involved tox-negative isolates. The 58 isolates were mostly susceptible to commonly used antibiotics. In particular, no isolate was resistant to the first-line molecules amoxicillin or erythromycin. Resistance to tetracycline was found in a genomic cluster of 17 (29%) isolates, 16 of which carried thetetOgene. There were 13 cgMLST sublineages, most of which were also observed in the neighboring country Australia.

Conclusions

Cutaneous infections may harbor non-toxigenicC. diphtheriaeisolates, which circulate largely silently in non-specific wounds. The possible introduction of tox-positive strains from a neighboring island illustrates that diphtheria surveillance should be maintained in New Caledonia, and that immunization in neighboring islands must be improved. Genomic sequencing uncovers how genotypes circulate locally and across neighboring countries.
Eusocial evolution without a nest: kin structure of social aphids forming open colonies on bamboo
Authors: Uematsu Keigo , Yang Man-Miao , Amos William , Foster William A.
Published: October 2022

Living in nests is an almost universal feature of eusocial animals. In some aphids, however, sterile soldier castes have evolved in open colonies without a nest. To clarify the factors promoting the evolution of eusociality in these colonies, we used newly developed microsatellite markers to compare the kin structure of the open colonies of two aphid species on bamboo: the non-eusocial colonies ofAstegopteryx bambucifoliaeand the eusocial colonies ofPseudoregma alexanderionDendrocalamus latiflorus.

Our samples, from over 1,000 hectares, contained 99 clones ofA. bambucifoliaeand 19 ofP. alexanderi. Clonal mixing occurred in both species: average pairwise relatedness within a colony was 0.54 inA. bambucifoliaeand 0.71 inP. alexanderi. Each clone ofA. bambucifoliaeoccurred in a unique location, whereas those ofP. alexanderi occurred in multiple locations and more than 90% of individuals came from just four clones. There was significant genetic variation among different colonies in the same clump (stem-cluster) inA. bambucifoliaebut not inP. alexanderi, indicating thatP. alexandericolonies in a single clump are genetically homogenized, functioning as a large colony. InP. alexanderi, the proportion of sterile soldiers to normal first-instar nymphs was significantly different across the four clones.

Our results indicate that the lack of input of migrants from the primary host and feeding on a large, stable host plant are important ecological factors that might favour the evolution of eusociality, enabling the production of genetically homogenised, large, and long-lived colonies. After eusociality evolves on the secondary host, the optimal strategy of soldier production might vary between different clones.

Significance Statement

Nest-living has often been considered to be a necessary condition for the evolution of eusociality. In a small number of aphid species, however, sterile soldier castes have evolved in open colonies without a nest. To understand why these aphids are unique, we examined the kin structure and genetic relatedness of individuals within eusocial and non-eusocial open colonies of two aphid species on bamboo. We found that clonal mixing occurred in both species, but the eusocial colonies are more genetically homogenized, functioning as a large colony. Our results suggest that ecological conditions that promote genetically homogenized, large and long-lived colonies are important for the evolution of eusociality in these aphids. We propose that the open colonies of social aphids provide an ideal model system in which to study the evolution of altruism.
Microsecond pulse electrical stimulation modulates cell migration
Authors: Xiang Xiao-Wei , Liu Hao-Tian , Liu Wei , Yan Ze-Yao , Zeng Yu-Lian , Wang Ya-Jun , Liu Jing , Chen Yu-Chen , Yu Sai-Xi , Zhu Cai-Hui , Tao Xiao-Nan , Wang Chen , Wu Jin-Tao , Du Yang , Xu Xin-Xin , Gao Hai , Jiu Yaming , Ma Jiong , Qiu Jian , Chang Lingqian , Jing Guangyin , Liu Ke-Fu , Liu Yan-Jun
Published: October 2022

Wound healing is a complicated process for maintaining skin integrity after injury, for which electrical stimulations (ES) are ascribed to promote wound healing by facilitating cell migration. Time-shortening of the stimulation treatment from current hours to minutes for efficient wound healing but free of cell damage in return, is however rather a challenge. Here, a novel mechanism of ultrashort pulse electric field (PEF), microsecond PEF at higher voltage, is proposed and realized to promote wound healing under a much short time (seconds) for the total treatment. We revealed that microsecond PEF regulated actin cytoskeleton reorganization and focal adhesion turnover, promoting fibroblasts migration in 2D cell cultures under the pulse stimulation. This accelerated fibroblast migration was accompanied by the mutual promotion with extracellular matrix (ECM) alignment in 3D microenvironments, which cooperatively benefit the eventual wound healing, and these findings were further confirmed by the enhanced skin wound healing in a classic mouse model. Additionally, we coined an actin- and collagen-dependent mechanism of microsecond PEF-mediated wound healing. The quantitative mechanism proposed here for our novel microsecond pulse electric filed (μsPEF) methodology orients the new practical electric treatment in a wide range of biomedical applications, such as wound healing, regenerative medicine, and tissue engineering.
Astrocytic Sleep Homeostasis Model
Authors: Singh Ghanendra
Published: October 2022

Sleep awake cycle is critical for cognitive and functional abilities. Conventional sleep homeostasis mechanisms are neuronal in nature and recent views indicate glial regulation of the sleep-wake process. Mechanisms of homeostatic regulation of sleep remain to be understood. A simplified astrocytic sleep-awake homeostasis mathematical model with sleep pressure and synaptic strength dynamics is proposed using feedback control loops. The model provides insights into the emergence of two discrete states through sleep and awake promoting neuronal populations giving rise to a homeostatic process S and oscillatory process C is regulated by astrocytic sleep pressure. It also explains the variations seen in synaptic strength dynamics during sleep and awake states.
Defining amino acid pairs as structural units suggests mutation sensitivity to adjacent residues
Authors: Rosenberg Aviv A. , Yehishalom Nitsan , Marx Ailie , Bronstein Alex
Published: October 2022

Proteins fold from chains of amino acids, forming secondary structures, α-helices and β-strands, that, at least for globular proteins, subsequently fold into a three-dimensional structure. A large-scale analysis of high-resolution protein structures suggests that amino acid pairs constitute another layer of ordered structure, more local than these conventionally defined secondary structures. We develop a cross-peptide-bond Ramachandran plot that captures the conformational preferences of the amino acid pairs and show that the effect of a particular mutation on the stability of a protein depends in a predictable manner on the adjacent amino acid context.

One-Sentence Summary

Large-scale protein backbone analysis reveals amino acid pair conformational preferences and predicts how sequence context affects mutant stability.
OPS-γδ: allogeneic opsonin-secreting γδT cell immunotherapy for solid tumours mediates direct and bystander immunity
Authors: Fowler D , Barisa M , Southern A , Nattress C , Hawkins E , Vassalou E , Kanouta A , Counsell J , Rota E , Vlckova P , Draper B , Tape C , Chester K , Anderson J , Fisher J
Published: October 2022

T cell-based cancer immunotherapy has typically relied on membrane-bound cytotoxicity enhancers such as chimeric antigen receptors expressed in autologous αβT cells. These approaches are limited by tonic signalling of synthetic constructs and costs associated with manufacture of bespoke patient products. γδT cells are an emerging alternative chassis for cellular therapy, possessing innate anti-tumour activity, potent antibody-dependent cytotoxicity (ADCC) and minimal alloreactivity. We present an immunotherapeutic platform technology built around the Vγ9Vδ2 γδT cell chassis, harnessing specific characteristics of this cell type and offering an allo-compatible means of delivering cellular therapy that recruits bystander immunity. We engineered γδT cells to secrete synthetic opsonins and stabilized IL15 (stIL15). Using GD2 as a model antigen we show how opsonin-secreting Vγ9Vδ2 (OPS-γδ) have enhanced cytotoxicity and also confer this benefit on lymphoid and myeloid bystander cells. Reflecting the secreted nature of the engineered efficacy modules, the entire product rather than just the gene-modified fraction exhibited enhanced activation and cytotoxic profiles, superior persistence and proliferative capacity even upon repeated tumour challenge. Secretion of stIL15 abrogated the need for exogenous cytokine supplementation during expansion and further mediated functional licensing of bystander NK cells. Compared to unmodified γδT cells, stIL15-OPS-γδ cells exhibited superiorin-vivocontrol of subcutaneous tumour and persistence in the blood. stIL15-OPS-γδ cells were further efficacious in 3D patient-derived osteosarcoma models, where efficacy could be boosted with the addition of immunomodulatory aminobisphosphonate drug, zoledronic acid. Together the data identify stIL15-OPS-γδ cells as a novel allogeneic platform combining direct cytolysis with bystander activation to effect solid tumour control.

One Sentence Summary

Armoured, opsonin-secreting OPS-γδ cell immunotherapy is built on the innate strengths of the Vγ9Vδ2 cell chassis for allogeneic solid tumour targeting.
High Angular Resolution Susceptibility Imaging and Estimation of Fiber Orientation Distribution Functions in Primate Brain
Authors: Gkotsoulias Dimitrios G. , Müller Roland , Jäger Carsten , Schlumm Torsten , Mildner Toralf , Eichner Cornelius , Pampel André , Jaffe Jennifer , Gräßle Tobias , Alsleben Niklas , Chen Jingjia , Crockford Catherine , Wittig Roman , Liu Chunlei , Möller Harald E.
Published: October 2022

Uncovering brain-tissue microstructure including axonal characteristics is a major neuroimaging research focus. Within this scope, anisotropic properties of magnetic susceptibility in white matter have been successfully employed to estimate primary axonal trajectories using mono-tensorial models. However, anisotropic susceptibility has not yet been considered for modeling more complex fiber structures within a voxel, such as intersecting bundles, or an estimation of orientation distribution functions (ODFs). This information is routinely obtained by high angular resolutiondiffusionimaging (HARDI) techniques. In applications to fixed tissue, however, diffusion-weighted imaging suffers from an inherently low signal-to-noise ratio and limited spatial resolution, leading to high demands on the performance of the gradient system in order to mitigate these limitations. In the current work, high angular resolutionsusceptibilityimaging (HARSI) is proposed as a novel, phase-based methodology to estimate ODFs. A multiple gradient-echo dataset was acquired in an entire fixed chimpanzee brain at 61 orientations by reorienting the specimen in the magnetic field. The constant solid angle method was adapted for estimating phase-based ODFs. HARDI data were also acquired for comparison. HARSI yielded information on whole-brain fiber architecture, including identification of peaks of multiple bundles that resembled features of the HARDI results. Distinct differences between both methods suggest that susceptibility properties may offer complementary microstructural information. These proof-of-concept results indicate a potential to study the axonal organization inpost-mortemprimate and human brain at high resolution.

Highlights

Introduction of High Angular Resolution Susceptibility Imaging (HARSI) for advancing Quantitative Susceptibility Mapping (QSM).

HARSI-derived fiber orientation distributions in fixed chimpanzee brain.

HARSI-based visualization of complex fiber configurations.

Comparisons between HARSI and High Angular Resolution Diffusion Imaging.

Potential for high-resolutionpost-mortemimaging of fiber architecture.
Dynamic hippocampal-cortical interactions during event boundaries support retention of complex narrative events
Authors: Barnett Alexander J. , Nguyen Mitchell , Spargo James , Yadav Reesha , Cohn-Sheehy Brendan I. , Ranganath Charan
Published: October 2022

According to most memory theories, encoding involves continuous communication between the hippocampus and neocortex leaving the temporal dynamics of hippocampal-neocortical interactions often overlooked. Recent work has shown that we perceive complex events in our lives as dynamic, with relatively distinct starting and stopping points known as event boundaries. Event boundaries may be important for memory, as they are associated with increased activity in the hippocampus, and extended neocortical regions (the posterior cingulate cortex, lateral parietal cortex, and parahippocampal cortex). Our objective was to determine how functional connectivity between the hippocampus and neocortical regions during the encoding of naturalistic events (movies) related to subsequent retrieval and retention of those events. Participants encoded two 16-minute cartoon movies during fMRI scanning. After encoding, participants freely recalled one of the movies immediately, and the other after a 2-day delay. We quantified hippocampal-neocortical functional connectivity (FC) at time windows around each event onset, middle, and offset, and compared these FC measures with subsequent recall. These analyses revealed that higher FC between the hippocampus and the posterior medial network (PMN) at an event’s offset related to whether that event was subsequently recalled. In contrast, mid-event connectivity between the hippocampus and PMN was associated with poorer memory. Furthermore, hippocampal-PMN offset connectivity predicted not only whether events were retained in memory, but also the degree to which these events could be recalled in detail after a 2-day delay. These data demonstrate that the relationship between memory encoding and hippocampal-neocortical interaction is more dynamic than suggested by most memory theories, and they converge with recent modeling work suggesting that event offset is an optimal time for encoding.
Structural basis for the Rad6 activation by the Bre1 N-terminal domain
Authors: Shi Meng , Zhao Jiaqi , Li Mengfei , Huang Wei , Bai Xue , Zhang Wenxue , Zhang Kai , Chen Xuefeng , Xiang Song
Published: October 2022

The mono-ubiquitination of the histone protein H2B (H2Bub1) is a highly conserved histone post-translational modification that plays critical roles in many fundamental processes. In yeast, this modification is catalyzed by the conserved Bre1-Rad6 complex. Bre1 contains a unique N-terminal Rad6 binding domain (RBD), how it interacts with Rad6 and contributes to the H2Bub1 catalysis is unclear. Here, we present crystal structure of the Bre1 RBD-Rad6 complex and structure-guided functional studies. Our structure provides a detailed picture of the interaction between the dimeric Bre1 RBD and a single Rad6 molecule. We further found that the interaction stimulates Rad6’s enzymatic activity by allosterically increasing its active site accessibility and likely contribute to the H2Bub1 catalysis through additional mechanisms. In line with these important functions, we found that the interaction is crucial for multiple H2Bub1-regulated processes. Our study provides molecular insights into the H2Bub1 catalysis.
Mechanotransduction events at the physiological site of touch detection
Authors: Ziolkowski Luke H. , Gracheva Elena O. , Bagriantsev Sviatoslav N.
Published: October 2022

Afferents of peripheral mechanoreceptors innervate the skin of vertebrates, where they detect physical touch via mechanically gated ion channels (mechanotransducers). While the afferent terminal is generally understood to be the primary site of mechanotransduction, the functional properties of mechanically activated (MA) ionic current generated by mechanotransducers at this location remain obscure. Here, we report patch-clamp recordings from the afferent terminal innervating Grandry (Meissner) corpuscles in the bill skin of a tactile specialist duck. We show that mechanical stimulation evokes MA current in the afferent with fast kinetics of activation and inactivation during the dynamic phases of the mechanical stimulus. These responses trigger rapidly adapting firing in the afferent detected at the terminal and in the afferent fiber outside of the corpuscle. Our findings elucidate the initial electrogenic events of touch detection in the mechanoreceptor nerve terminal.
Gene expression profiling in trigeminal ganglia from Cntnap2-/-and Shank3b-/-mouse models of autism spectrum disorder
Authors: Ciancone-Chama Alessandra G. , Bozzi Yuri , Balasco Luigi
Published: October 2022

Sensory difficulties represent a crucial issue in the life of autistic individuals. The diagnostic and statistical manual of mental disorders describes both hyper- and hypo-responsiveness to sensory stimulation as a criterion for the diagnosis autism spectrum disorders (ASD). Among the sensory domain affected in ASD, altered responses to tactile stimulation represent the most commonly reported sensory deficits. Although tactile abnormalities have been reported in monogenic cohorts of patients and genetic mouse models of ASD, the underlying mechanisms are still unknown. Traditionally, autism research has focused on the central nervous system as the target to infer the neurobiological bases of such tactile abnormalities. Nonetheless, the peripheral nervous system represents the initial site of processing of sensory information and a potential site of dysfunction in the sensory cascade. Here we investigated the gene expression deregulation in the trigeminal ganglion (which directly receives tactile information from whiskers) in two genetic models of syndromic autism (Shank3b and Cntnap2 mutant mice) at both adult and juvenile ages. We found several neuronal and non-neuronal markers involved in inhibitory, excitatory, neuroinflammatory and sensory neurotransmission to be differentially regulated within the trigeminal ganglia of both adult and juvenile Shank3b and Cntnap2 mutant mice. These results may help in entangling the multifaced complexity of sensory abnormalities in autism and open avenues for the development of peripherally targeted treatments for tactile sensory deficits exhibited in ASD.
Epigenetic Priming Enhances Chondrogenic Potential of Expanded Chondrocytes for Cartilage Repair
Authors: Scott Adrienne K. , Gallagher Katie M. , Schneider Stephanie E. , Kurse Abhijit , Neu Corey P.
Published: October 2022

Expansion of chondrocytes presents a major obstacle in the cartilage regeneration procedure matrix-induced autologous chondrocyte implantation (MACI). Dedifferentiation of chondrocytes during the expansion process leads to the emergence of a fibrotic (chondrofibrotic) phenotype that decreases the chondrogenic potential of the implanted cells. We aim to 1) determine the extent that chromatin architecture of H3K27me3 and H3K9me3 remodels during dedifferentiation and persists when expanded chondrocytes are transferred to a 3D culture; and 2) to prevent this persistent remodeling to enhance the chondrogenic potential of expanded chondrocytes. Chromatin architecture remodeling of H3K27me3 and H3K9me3 was observed at 0, 8 and 16 population doublings in a two-dimensional (2D) culture and after encapsulation of the expanded chondrocytes in a three-dimensional (3D) hydrogel culture. Chondrocytes were treated with inhibitors of epigenetic modifiers (epigenetic priming) for 16 population doublings and then encapsulated in 3D hydrogels. Chromatin architecture of chondrocytes and gene expression were evaluated before and after encapsulation. We observed a change in chromatin architecture of epigenetic modifications H3K27me3 and H3K9me3 during chondrocyte dedifferentiation. Although inhibiting enzymes that modify H3K27me3 and H3K9me3 did not alter the dedifferentiation process in 2D culture, applying these treatments during the 2D expansion did increase the expression of select chondrogenic genes and protein deposition of type II collagen when transferred to a 3D environment. Overall, we found that epigenetic priming of expanded chondrocytes alters the cell fate when chondrocytes are later encapsulated into a 3D environment, providing a potential method to enhance the success of cartilage regeneration procedures.
COVID-19 prognostic model using Bayesian networks learnt on patient data
Authors: Bernaola Nikolas , Bielza Concha , Larrañaga Pedro
Published: October 2022

The response to the ongoing second wave of the COVID-19 pandemic can be helped by giving medical professionals access to models learned on patient data. To achieve this, we learned a Bayesian network model to predict risk of ICU admission, death and time of stay in the hospital from patient history, initial vital signs, initial laboratory tests and medication. Data were obtained from patients that were admitted to an HM hospital with suspicion of COVID-19 until 24/04/2020, excluding unconfirmed diagnosis, those who were admitted before the epidemic started in Madrid, had an outcome that was not discharge or death or died within 24 hours of presentation. Relevant variables for the model were selected with help from medical professionals. We learned the model using Bayesian search as implemented in GeNIe. Of 2,307 patients in the dataset, 679 were excluded. With the remaining 1,645 patients, we learned a model that predicted death with 86.4% accuracy. Some of the initial variables were discarded because they were independent of the outcomes of interest conditioned on some of the other variables. This high redundancy might be useful to build simpler tests for the severity of COVID-19. We show how the model can be used at different stages of patient admission and even with only partial information about the patient. This can be done by clinicians that want a fast second opinion or a summary of the available data from previous patients similar to the one at hand. We then include how we plan to improve the model with extra patient data and how it could be expanded to other contexts, like for example, an epidemiological one.
Cell-free urine- and plasma DNA mutational analysis predicts neoadjuvant chemotherapy response and outcome in patients with muscle invasive bladder cancer
Authors: Christensen Emil , Nordentoft Iver , Elbæk Sara K. , Birkenkamp-Demtröder Karin , Taber Ann , Andreasen Tine G. , Strandgaard Trine , Knudsen Michael , Lamy Philippe , Agerbæk Mads , Jensen Jørgen B. , Dyrskjøt Lars
Published: October 2022

Purpose

Investigate and compare the use of plasma- and urine DNA mutation analysis for predicting neoadjuvant chemotherapy (NAC) response and long-term oncological outcome in patients with muscle invasive bladder cancer.

Experimental Design

Whole exome sequencing of tumor and germline DNA was performed for 92 patients treated with NAC followed by radical cystectomy (RC). A custom NGS panel capturing approx. 50 mutations per patient was designed and utilized to track tumor-derived DNA (tdDNA) in liquid biopsies. A total of 447 plasma samples, 281 urine supernatants and 123 urine pellets collected before, during and after treatment were analyzed. Patients were enrolled from 2013-2019 with a median follow-up time of 41.3 months after RC.

Results

We identified tdDNA before initiation of NAC in 89% of urine supernatants, 85% of urine pellets and 43% of plasma samples. tdDNA levels were higher in urine supernatants and urine pellets compared to plasma samples (p<0.001). In plasma, detection of tdDNA before NAC was associated with a lower NAC response rate (p<0.001). Detection of tdDNA after NAC was associated with lower response rates in plasma, urine supernatant and urine pellet (p<0.001, p=0.03, p=0.002). tdDNA dynamics during NAC was predictive of NAC response and outcome in urine supernatant and plasma (p=0.006,p=0.002). A combined measure from plasma and urine supernatant tdDNA dynamics stratified patients by outcome (p=0.003).

Conclusions

Analysis of tdDNA in plasma and urine samples both separately and combined has potential to predict treatment response and outcome.
Impact of COVID-19 on the national development of countries: implications for the public health
Authors: Kuzmenko Olha , Lyeonov Serhiy , Letunovska Nataliia , Kashcha Mariya , Strielkowski Wadim
Published: October 2022

The article focuses on measuring the fluctuations in countries’ development as a result of the COVID-19 pandemic. The obtained measures make it possible to predict the extent of the impact of risks to public health on the economy, financial-budgetary, political-institutional development of states in the future, as well as the social determinants of public health. This assessment represents a new paradigm that makes it possible to effectively evaluate the manifestations of the consequences of COVID-19 and to identify the relevant determinants of the lack of resilience of the medical and social security systems to the coronavirus pandemic around the world. We picked the determinant of national development indicators of the 59 countries in order to measure the fluctuations in their economic development. In addition, we applied the binary response model for identifying the economic, financial-budgetary, and political-institutional development change with the happiness index of the countries being the dependent variable. The analysis of our empirical model made it possible for us to conclude that economic and financial-budgetary components have significantly increased the influence on well-being during the COVID-19 pandemic. In contrast, we observed the decrease in the impact of political and institutional indicators during the same period.
A genetic risk score improves risk stratification for anticoagulation-related intracerebral hemorrhage
Authors: Mayerhofer Ernst , Parodi Livia , Prapiadou Savvina , Malik Rainer , Rosand Jonathan , Georgakis Marios K , Anderson Christopher D
Published: October 2022

Background

Intracerebral hemorrhage (ICH) is the most devastating adverse outcome for patients on anticoagulants. Clinical risk scores (CRS) that quantify bleeding risk can guide decision making in situations when indication or duration for anticoagulation is uncertain. We investigated whether integration of a genetic risk score (GRS) into an existing risk factor-based CRS could improve risk stratification for anticoagulation-related ICH.

Methods

We constructed 153 GRS from genome-wide association data of 1,545 ICH cases and 1,481 controls and validated them in 431 ICH cases and 431 matched controls from the population-based UK Biobank. The score that explained the largest variance in ICH risk was selected and tested for prediction of incident ICH in an independent cohort of 5,530 anticoagulant users. A CRS for major anticoagulation-related hemorrhage, based on 8/9 components of the HAS-BLED score, was compared with an enhanced score incorporating an additional point for high genetic risk for ICH (CRS+G).

Results

Among anticoagulated individuals, 94 ICH occurred over a mean follow-up of 11.9 years. Compared to the lowest GRS tertile, being in the highest tertile was associated with a two-fold increased risk for incident ICH (HR: 2.08 [95% CI 1.22, 3.56]). While the CRS predicted incident ICH with a HR of 1.24 per one point increase (95% CI [1.01, 1.53]), adding a point for high genetic ICH risk led to a stronger association (HR of 1.33 per one point increase, 95% CI [1.11, 1.59]) with improved risk stratification (C-index 0.58 vs. 0.53) and maintained calibration (integrated calibration index 0.001 for both). The new score (CRS+G) showed 20% improvement of high-risk classification among individuals with ICH and a net reclassification improvement of 0.10.

Conclusions

Among anticoagulant users, a prediction score incorporating genomic information is superior to a clinical risk score alone for ICH risk stratification and could serve in clinicaldecision making.
The pervasive association between political ideology and COVID-19 vaccine uptake in Brazil: an ecologic study
Authors: Seara-Morais Gabriel J. , Avelino-Silva Thiago J. , Couto Marcia , Avelino-Silva Vivian I.
Published: October 2022

Background

Studies suggest vaccine hesitancy is an increasingly significant phenomenon in Brazil and other countries. Moreover, political ideologies have emerged as an influencing factor for vaccine hesitancy during the COVID-19 pandemic.

Methods

In this study, we use information from publicly available databases to investigate the association between political alignment, depicted by the percentage of Bolsonaro voters in the presidential elections of 2018 and 2022, and COVID-19 vaccination in Brazilian municipalities, adjusted for human development index (HDI) scores and basic sociodemographic characteristics of voters.

Findings

For both the 2018 and 2022 elections, higher percentages of Bolsonaro voters were significantly associated with a lower vaccination index after adjustment for voters’ sociodemographic characteristics. We also found a statistically significant interaction between the percentage of Bolsonaro voters and HDI, with a more significantly detrimental effect of the right-wing political stance in municipalities in the lower HDI quartile.

Interpretation

Our study highlights what may be the beginning of a new scenario with unforeseen challenges for vaccine programs: the politicization of vaccines. Strategies to face these challenges should include joint efforts from governments and civil society for a common public health goal.

Funding

This manuscript received no specific funding
Lipid Droplets Fuel Small Extracellular Vesicle Biogenesis
Authors: Genard Géraldine C. , Tirinato Luca , Pagliari Francesca , Da Silva Jessica , Giammona Alessandro , Alquraish Fatema , Bordas Marie , Marafioti Maria Grazia , Di Franco Simone , Janssen Jeannette , Garcia-Calderón Daniel , Hanley Rachel , Nistico Clelia , Fukasawa Yoshinori , Müller Torsten , Krijgsveld Jeroen , Todaro Matilde , Costanzo Francesco Saverio , Stassi Giorgio , Nessling Michelle , Richter Karsten , Maass Kendra K. , Liberale Carlo , Seco Joao
Published: October 2022

Despite an increasing gain of knowledge regarding small extracellular vesicle (sEV) composition and functions in cell-cell communication, the mechanism behind their biogenesis remains unclear. Here, we revealed for the first time that the sEV biogenesis and release into the microenvironment are tightly connected with another important organelle: Lipid Droplets (LD). We have observed this correlation using different human cancer cell lines as well as patient-derived colorectal cancer stem cells (CR-CSCs). Our results showed that the use of external stimuli such as radiation, pH, hypoxia, or lipid interfering drugs, known to affect the LD content, had a similar effect in terms of sEV secretion. Additional validations were brought using multiple omics data, at the mRNA and protein levels. Altogether, the possibility to fine-tune sEV biogenesis by targeting LDs, could have a massive impact on the amount, the cargos and the properties of those sEVs, paving the way for new clinical perspectives.

Significance Statement
Validation of ligand tetramers for the detection of antigen-specific lymphocytes
Authors: Fitzpatrick Kristin S. , Degefu Hanna N. , Poljakov Katrina , Bibby Madeleine G. , Remington Allison J. , Searles Tyler G. , Gray Matthew D. , Boonyaratanakornkit Jim , Rosato Pamela C. , Taylor Justin J.
Published: October 2022

The study of antigen-specific lymphocytes has been a key advancement in immunology the past few decades. The development of multimerized probes containing antigens, peptide:MHC complexes, or other ligands was one innovation allowing the direct study antigen-specific lymphocytes by flow cytometry. While these types of studies are now common and performed by thousands of laboratories, quality control and assessment of probe quality is often minimal. In fact, many of these types of probes are made in-house and protocols vary between labs. While peptide:MHC multimers can often be obtained from commercial sources or core facilities, few such services exist for antigen multimers. To ensure high quality and consistency with ligand probes, we have developed an easy and robust multiplexed approach using commercially available beads able to bind antibodies specific for the ligand of interest. Using this assay, we have sensitively assessed the performance of peptide:MHC and antigen tetramers and find considerable batch-to-batch variability in performance and stability over time. This assay can also reveal common production errors such as miscalculation of antigen concentration. Unexpectedly, probes including the fluorochrome allophycocyanin exhibited more rapid performance decline compared to probes including the fluorochrome R-phycoerythrin when both were stored at 4°C. This performance decline was reduced for most, but not all, batches when antigen tetramers were instead stored at −20°C in 50% glycerol. This work could set the stage for the development of standardized assays for all commonly used ligand probes to limit lab-to-lab technical variation, and experimental failure due to probe underperformance.
Multi-Tag: A modular platform of bioorthogonal probes for multi-modal (glyco)protein analysis
Authors: Driessen Marc D. , Junghans Hauke L. , Hartmann Laura , Gerling-Driessen Ulla I. M.
Published: October 2022

Bioorthogonal chemistry is a well-established concept for tagging and analyzing targets of interest even in living cells, tissue or organisms. In particular glycans, which are, as a posttranslational modification, not amenable to genetic engineering, became analytically accessible through the establishment of metabolic oligosaccharide engineering and subsequent bioorthogonal tagging of chemical probes. Since many essential cellular processes involve glycoproteins, it is not surprising that especially aberrant glycosylation has been associated with the pathology of many diseases. Investigation of aberrant glycosylation in a disease background is complicated by the heterogeneity of glycans and dynamic changes in their composition. In order to create a meaningful information depth, it can be beneficial to analyze the same sample with different analytical methods. This becomes even more relevant for samples with limited access. Most of the currently existing bioorthogonal probes are designed for use in only one type of experiment. These design restrictions are mainly based on the limited synthetic accessibility of more complex bioorthogonal probes. Multi-step syntheses are often time consuming and cost-inefficient. Here, we introduce a fast and easily manageable strategy for the synthesis of complex bioorthogonal probes that allow an application in multiple coordinated experiments. Using established principles and conditions of solid-phase peptide synthesis, we combine different functional building blocks to generate multi-functional bioorthogonal probes (namedMulti-Tags). We show the easy synthesis of several multi-modal probes and demonstrate their applicability and versatility in exemplary assays.
GiRAFR improves gRNA detection and annotation in single cell CRISPR screens
Authors: Yu Qian , Van Minsel Paulien , Galle Eva , Thienpont Bernard
Published: October 2022

Novel single cell RNA-seq analysis combined with CRISPR screens enables the high-throughput characterization of transcriptional changes caused by genetic perturbations. Dedicated software to annotate CRISPR guide RNA (gRNA) libraries and associate them with single cell transcriptomes are however lacking. Here, we generated a CRISPR droplet sequencing dataset. We demonstrate that the current default tool fails to detect mutant gRNAs. We therefore developed GiRAFR, a pysam-based software tool to characterize intact and mutant gRNAs. We show that mutant gRNAs are dysfunctional, and failure to detect and annotate them leads to an inflated estimate of the number of untransformed cells as well as an underestimated multiplet frequency. These findings are mirrored in publicly available datasets, where we find that up to 34 % of cells are transduced with a mutant gRNA. Applying GiRAFR hence stands to improve the annotation and quality of single cell CRISPR screens.
Pregranulosa cells engage a distinct transcriptional programme prior to cell-cycle dependent primordial follicle activation
Authors: Taylor Güneş , Frost Emily R , Crow Brendan N , Radley Arthur , Boeing Stefan , Galichet Christophe , Bucinskaite Barbora , Baker Mark A , Sutherland Jessie M , Lovell-Badge Robin
Published: October 2022

Primordial follicles are quiescent ovarian structures comprised of a single oocyte surrounded by a layer of somatic supporting pregranulosa cells. Primordial follicle activation is the first step towards oocyte maturation and, ultimately, ovulation. As the number of quiescent primordial follicles is finite, their rate of activation is a critical parameter of the duration of the female reproductive lifespan. Activation status is established by the presence of cuboidal and proliferative granulosa cells in primary follicles, rather than squamous and quiescent pregranulosa cells in primordial follicles. Here, using a continuous Entropy Sort Feature Weighting approach on single-cell RNA sequencing data, we identify a distinct transcriptomic signature of activating pregranulosa cells in neonatal wildtype mice. This signature contains several genes previously linked with mature granulosa cells as well several novel candidates:Slc18a2, Tnni3,Fam13aandMyo1e. We confirm expression ofSlc18a2and TNNI3 in the granulosa cells of activating follicles in embryonic, neonatal and adult mouse ovaries. Perturbation of cell cycle inhibitor p27kip1inCdkn1b-/-mice results in complete activation of all primordial follicles during this neonatal period. Contrary to previous reports on this established mouse model, we find substantial transcriptomic changes in embryonicCdkn1b-/-ovaries. Upon loss of cell-cycle inhibition we find increased expression of our signature of pregranulosa cell activation, particularly that of cardiac troponin I (Tnni3). We conclude that pregranulosa cells engage a distinct transcriptional programme prior to cell-cycle dependent primordial follicle activation.
A quarter-million-year-old polymorphism drives reproductive mode variation in the pea aphid
Authors: Rimbault M. , Legeai F. , Peccoud J. , Mieuzet L. , Call E. , Nouhaud P. , Defendini H. , Mahéo F. , Marande W. , Théron N. , Tagu D. , Le Trionnaire G. , Simon J.-C. , Jaquiéry J.
Published: October 2022

Although asexual linages evolved from sexual lineages in many different taxa, the genetics of sex loss remains poorly understood. We addressed this issue in the pea aphidAcyrthosiphon pisum,whose natural populations encompass lineages performing cyclical parthenogenesis (CP) and producing one sexual generation per year, as well as obligate parthenogenetic (OP) lineages that can no longer produce sexual females but can still produce males. A SNP-based, whole-genome scan of CP and OP populations sequenced in pools (103 individuals from six populations) showed that a single X-linked region controls the variation in reproductive mode. This 840-kb region is highly divergent between CP and OP populations (FST= 34.9%), with >2000 SNPs or short Indels showing a high degree of association with the phenotypic trait. Comparison ofde novogenome assemblies built from long reads did not reveal large structural rearrangements between CP and OP lineages within the candidate region. This reproductive polymorphism still appears relatively ancient, as we estimated its age at ~0.25 million years from the divergence betweencpandopalleles. The low genetic differentiation between CP and OP populations at the rest of the genome (FST= 2.4%) suggests gene flow between them. Males from OP lineages thus likely transmit their op allele to new genomic backgrounds. This “contagious asexuality”, combined with environment-induced selection (each reproductive mode being favored under different climates) probably contributes to the long-term persistence of thecpandopalleles.

Significance

Asexual taxa occur in all major clades of Eukaryotes and derive from related sexual species. Yet, the genetic basis for these transitions is poorly known because crosses cannot generally be performed to genetically map the ability to propagate asexually. As a result, only one gene responsible for sex loss has been identified in one animal species. Here, using pooled genome sequencing, we identified an 840kb region (carrying 32 genes) that controls the transition to permanent asexuality in the pea aphid. We also revealed that sexual and asexual alleles diverged 0.25 million years ago and that asexual lineages likely persist through contagious asexuality, providing new insights into the mechanisms of coexistence of sexual and asexual lineages.
Cytogenetic screening of chromosomal abnormalities and genetic analysis of FSH receptor Ala307Thr and Ser680Asn genes in amenorrheic patients
Authors: Kanaan Bushra A. , Al-Ouqaili Mushtak T.S. , Murshed Rafal M.
Published: October 2022

Background

Amenorrhea is a rare reproductive medical condition defined by the absence of menstruation during puberty or later life. This study aims to establish the frequency and pattern of chromosomal abnormalities (CA) in both primary amenorrhea (PA) and secondary amenorrhea (SA), and further to detect the genetic changes in exon 10 at nucleotide positions 919 and 2039 of the genotypes Thr307Ala, and Asn680Ser, respectively.

Method

This cross-sectional study was conducted on a sample of seventy amenorrhoeic women according to the Helsinki declaration rules of medical ethics, as divided into 40 (57.14%) with PA and 30 (42.86%) with SA, and 30 healthy women with normal menstruation as the control. The chromosomal karyotyping was performed according to the ISCN, 2020. PCR products were submitted to RFLP and Sanger sequencing for women with normal karyotype and high FSH serum levels.

Result

The classical Turner Syndrome was the most common CA in PA, followed by isochromosome X [46, Xi(X)(q10)], mosaicism of Turner and isochromosome X [45, X /46, Xi(X)(q10)], sex reversal (46, XY) and (46, XX,-3,+der3,-19,del 19 p). Abnormal SA cases were characterized by mosaicism Turner syndrome (45,X/46,XX) and (46,XX,-3,+der3,X,+derX). The homozygous genotypes AA and GG of Ala307Thr (rs6165) in the FSHR gene are most common in PA, while the homozygous genotype AA is more common in SA. GG and AG genotypes of Ser680Asn (rs6166) are more frequent in Iraqi patients with PA and SA compared to the healthy control women. Both PCR-RFLP and Sanger sequencing indicated a marked matching between genotypes.

Conclusions

The study emphasizes the need for cytogenetic analysis to determine the genetic basis of PA and SA. Further, genotyping for women with normal karyotype and high FSH serum concentrations via PCR-RFLP should be considered for the precise diagnosis and development of appropriate management of and counselling for these patients.
A Compensatory RNase E Variation Increases Iron Piracy and Virulence in Multidrug-ResistantPseudomonas aeruginosaduring Macrophage Infection
Authors: Vaillancourt Mylene , Galdino Anna Clara Milesi , Limsuwannarot Sam P. , Celedonio Diana , Dimitrova Elizabeth , Broerman Matthew , Bresee Catherine , Doi Yohei , Lee Janet S. , Parks William C. , Jorth Peter
Published: October 2022

During chronic cystic fibrosis (CF) infections, evolvedPseudomonas aeruginosaantibiotic resistance is linked to increased pulmonary exacerbations, decreased lung function, and hospitalizations. However, the virulence mechanisms underlying worse outcomes caused by antibiotic resistant infections are poorly understood. Here, we investigated evolved aztreonam resistantP. aeruginosavirulence mechanisms. Using a macrophage infection model combined with genomic and transcriptomic analyses, we show that a compensatory mutation in thernegene, encoding RNase E, increased siderophore gene expression, causing macrophage ferroptosis and lysis. Macrophage killing could be eliminated by treatment with the iron mimetic gallium. RNase E variants were abundant in clinical isolates, and CF sputum gene expression data show that clinical isolates phenocopied RNase E variant functions during macrophage infection. Together these data show howP. aeruginosaRNase E variants can cause host damage via increased siderophore production and host cell ferroptosis but may also be targets for gallium precision therapy.
A 3D cell-free bone model shows collagen mineralization is driven and controlled by the matrix
Authors: van der Meijden Robin H.M. , Daviran Deniz , Rutten Luco , Walboomers X. Frank , Macías-Sánchez Elena , Sommerdijk Nico , Akiva Anat
Published: October 2022

Osteons, the main organizational components of human compact bone, are cylindrical structures composed of layers of mineralized collagen fibrils, called lamellae. These lamellae have different orientations, different degrees of organization and different degrees of mineralization where the intrafibrillar and extrafibrillar mineral is intergrown into one continuous network of oriented crystals.

While cellular activity is clearly the source of the organic matrix, recent in vitro studies call into question whether the cells are also involved in matrix mineralization, and suggest that this process could be simply driven by the interactions of the mineral with extracellular matrix.

Through the remineralization of demineralized bone matrix, we demonstrate the complete multiscale reconstruction of the 3D structure and composition of the osteon without cellular involvement. We then explore this cell-free in vitro system as a realistic, functional model for the in situ investigation of matrix-controlled mineralization processes. Combined Raman and electron microscopy indicates that glycosaminoglycans play a more prominent role than generally assumed in the matrix-mineral interactions. Our experiments also show that the organization of the collagen is in part a result of its interaction with the developing mineral.