bluuebunny/crossref_metadata_2025 huggingface dataset:
Reconstructing disease dynamics for mechanistic insights and clinical benefit
Authors: Frishberg Amit , Milman Neta , Alpert Ayelet , Spitzer Hannah , Asani Ben , Schiefelbein Johannes B. , Priglinger Siegfried G. , Schultze Joachim L. , Theis Fabian J. , Shen-Orr Shai S.
Published: November 2021

Diseases change over time, both phenotypically and in underlying driving molecular processes. Though understanding disease progression dynamics is critical for diagnostics and treatment, capturing these dynamics is difficult, due to their complexity and the high heterogeneity between individuals. We developed TimeAx, an algorithm which builds a comparative framework for capturing disease dynamics using high-dimensional short time-series data. We demonstrate TimeAx utility by studying disease progression dynamics for multiple diseases and data types. Notably, for urothelial bladder cancer tumorigenesis, we identified a stromal pro-invasion point on the disease progression axis, characterized by massive immune cell infiltration to the tumor microenvironment and increased mortality. Moreover, the continuous TimeAx model differentiated between early and late tumors within the same tumor subtype, uncovering novel molecular transitions and potential targetable pathways. Overall, we present a powerful approach for studying disease progression dynamics, providing improved molecular interpretability and clinical benefits for patient stratification and outcome prediction.
A new lineage of non-photosynthetic green algae with extreme organellar genomes
Authors: Pánek Tomáš , Barcytė Dovilė , Treitli Sebastian C. , Záhonová Kristína , Sokol Martin , Ševčíková Tereza , Zadrobílková Eliška , Jaške Karin , Yubuki Naoji , Čepička Ivan , Eliáš Marek
Published: November 2021

Background

The plastid genomes of the green algal order Chlamydomonadales tend to expand their non-coding regions, but this phenomenon is poorly understood. Here we shed new light on organellar genome evolution in Chlamydomonadales by studying a previously unknown non-photosynthetic lineage. We established cultures of two new Polytoma-like flagellates, defined their basic characteristics and phylogenetic position, and obtained complete organellar genome sequences and a transcriptome assembly for one of them.

Results

We discovered a novel deeply diverged chlamydomonadalean lineage that has no close photosynthetic relatives and represents an independent case of photosynthesis loss. To accommodate these organisms we establish the new genus Leontynka, with two species (L. pallida and L. elongata) distinguishable through both their morphological and molecular characteristics. Notable features of the colourless plastid of L. pallida deduced from the plastid genome (plastome) sequence and transcriptome assembly include the retention of ATP synthase, thylakoid-associated proteins, the carotenoid biosynthesis pathway, and a plastoquinone-based electron transport chain, the latter two modules having an obvious functional link to the eyespot present in Leontynka. Most strikingly, the ~362 kbp plastome of L. pallida is by far the largest among the non-photosynthetic eukaryotes investigated to date due to an extreme proliferation of sequence repeats. These repeats are also present in coding sequences, with one repeat type found in the exons of 11 out of 34 protein-coding genes, with up to 36 copies per gene, thus affecting the encoded proteins. The mitochondrial genome of L. pallida is likewise exceptionally large, with its >104 kbp surpassed only by the mitogenome of Haematococcus lacustris among all members of Chlamydomonadales hitherto studied. It is also bloated with repeats, though entirely different from those in the L. pallida plastome, which contrasts with the situation in H. lacustris where both the organellar genomes have accumulated related repeats. Furthermore, the L. pallida mitogenome exhibits an extremely high GC content in both coding and non-coding regions and, strikingly, a high number of predicted G-quadruplexes.

Conclusions

With its unprecedented combination of plastid and mitochondrial genome characteristics, Leontynka pushes the frontiers of organellar genome diversity and is an interesting model for studying organellar genome evolution.
Identification of antibiotic resistance proteins via MiCId’s augmented workflow. A mass spectrometry-based proteomics approach
Authors: Alves Gelio , Ogurtsov Aleksey , Karlsson Roger , Jaén-Luchoro Daniel , Piñeiro-Iglesias Beatriz , Salvà-Serra Francisco , Andersson Björn , Moore Edward R.B. , Yu Yi-Kuo
Published: November 2021

Fast and accurate identifications of pathogenic bacteria along with their associated antibiotic resistance proteins are of paramount importance for patient treatments and public health. While mass spectrometry has become an important, technique for diagnostics of infectious disease, there is a need for mass spectrometry workflows offering this capability. To meet this need, we have augmented the previously published Microorganism Classification and Identification (MiCId) workflow for this capability. To evaluate the performance of the newly augmented MiCId workflow, we have used MS/MS datafiles from samples of 10 antibiotic resistance bacterial strains belonging to three different species: Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The evaluation results show that MiCId’s workflow has a sensitivity value around 85% (with a lower bound at about 72%) and a precision greater than 95% in the identification of antibiotic resistance proteins. Using MS/MS datasets from samples of two bacterial clonal isolates, one being antibiotic-sensitive while the other (obtained from the same patient at different times) being multidrug-resistant, we applied MiCId’s workflow to investigate possible mechanisms of antibiotic resistance in these pathogenic bacteria; the results showed that MiCId’s conclusions are in agreement with the published study. Furthermore, we show that MiCId’s workflow is fast. It pro-vides microorganismal identifications, protein identifications, sample biomass estimates, and antibiotic resistance protein identifications in 6–17 minutes per MS/MS sample using computing resources that are available in most desktop and laptop computers, making it a highly portable workflow. This study demonstrated that MiCId’s workflow is fast, portable, and with high sensitivity and high precision, making it a valuable tool for rapid identifications of bacteria as well as detection of their antibiotic resistance proteins. The new version of MiCId (v.07.01.2021) is freely available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.
Phylogenomic analyses using genomes and transcriptomes do not “resolve” relationships among major clades in Phrymaceae
Authors: Morales-Briones Diego F. , Lin Nan , Huang Eileen Y. , Grossenbacher Dena L. , Sobel James M. , Gilmore Caroline D. , Tank David C. , Yang Ya
Published: November 2021

Premise of the study

Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny for a stable taxonomy and for macroevolutionary comparisons.

Methods

We sampled 24 genomes and transcriptomes in Phrymaceae and closely related families, including eight newly sequenced transcriptomes. We reconstructed the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance using PhyParts, Quartet Sampling, and cloudogram, and carried out phylogenetic network analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distance, and gene duplication events.

Key results

Most gene trees support the monophyly of Phrymaceae and each of its tribes. Most gene trees also support the tribe Mimuleae being sister to Phrymeae + Diplaceae + Leucocarpeae, with extensive gene tree discordance among the latter three. Despite the discordance, polyphyly of Mimulus s.l. is strongly supported, and no particular reticulation event among the Phrymaceae tribes is well supported. Reticulation likely occurred among Erythranthe bicolor and close relatives. No ancient WGD event was detected in Phrymaceae. Instead, small-scale duplications are among potential drivers of macroevolutionary diversification of Phrymaceae.

Conclusions

We show that analysis of reticulate evolution is sensitive to taxon sampling and methods used. We also demonstrate that genome-scale data do not always fully “resolve” phylogenetic relationships. They present rich opportunities to investigate reticulate evolution, and gene and genome evolution involved in lineage diversification and adaptation.
Hippocampal Neuropeptide Y2receptor blockade improves spatial memory retrieval and modulates limbic brain metabolism
Authors: Méndez-Couz Marta , González-Pardo Héctor , Arias Jorge L. , Conejo Nélida M.
Published: November 2021

Introduction

The neuropeptide Y (NPY) is broadly distributed in the central nervous system (CNS), and it has been related to neuroprotective functions. NPY seems to be an important component to counteract brain damage and cognitive impairment mediated by drugs of abuse and neurodegenerative diseases, and both NPY and its Y2receptor (Y2R) are highly expressed in the hippocampus, critical for learning and memory. We have recently demonstrated its influence on cognitive functions; however, the specific mechanism and involved brain regions where NPY modulates spatial memory by acting on Y2R remain unclear.

Methods

Here, we examined the involvement of the hippocampal NPY Y2R in spatial memory and associated changes in brain metabolism by bilateral administration of the selective antagonist BIIE0246 into the rat dorsal hippocampus. To further evaluate the relationship between memory functions and neuronal activity, we analysed the regional expression of the mitochondrial enzyme cytochrome c oxidase (CCO) as an index of oxidative metabolic capacity in limbic and non-limbic brain regions.

Results

The acute blockade of NPY Y2R significantly improved spatial memory recall in rats trained in the Morris water maze that matched metabolic activity changes in spatial memory processing regions. Specifically, CCO activity changes were found in the dentate gyrus of the dorsal hippocampus and CA1 subfield of the ventral hippocampus, the infralimbic region of the PFC and the mammillary bodies.

Conclusions

These findings suggest that the NPY hippocampal system, through its Y2R receptor, influences spatial memory recall (retrieval) and exerts control over patterns of brain activation that are relevant for associative learning, probably mediated by Y2R modulation of long-term potentiation and long-term depression.

Highlights

Under hippocampal Y2R antagonism, place preference memory retrieval is enhanced

Spatial retrieval enhancement under Y2R blockade is correlated with changes in regional brain energy metabolism

Enhanced retrieval associated CCO activity increases in the dorsal DG, while decreasing in the ventral CA1, IL cortex and mammillary bodies

Y2R exert control over patterns of brain activation that are relevant for spatial memory expression
Robust temporal map of human in vitro myelopoiesis using single-cell genomics
Authors: Alsinet Clara , Primo Maria , Lorenzi Valentina , Knights Andrew J , Sancho-Serra Carmen , Park Jong-Eun , Wyspianska Beata S , Tough David F , Alvarez-Errico Damiana , Gaffney Daniel J , Vento-Tormo Roser
Published: November 2021

Myeloid cells have a central role in homeostasis and tissue defence. Characterising the current in vitro protocols of myelopoiesis is imperative for their use in research and immunotherapy as well as for understanding the early stages of myeloid differentiation in humans. Here, we profiled the transcriptome of more than 400k cells and generated a robust molecular map of the differentiation of human induced pluripotent stem cells (iPSC) into macrophages. By integrating our in vitro datasets with in vivo single-cell developmental atlases, we found that in vitro macrophage differentiation recapitulates features of in vivo yolk sac hematopoiesis, which happens prior to the appearance of definitive hematopoietic stem cells (HSC). During in vitro myelopoiesis, a wide range of myeloid cells are generated, including erythrocytes, mast cells and monocytes, suggesting that, during early human development, the HSC-independent immune wave gives rise to multiple myeloid cell lineages. We leveraged this model to characterize the transition of hemogenic endothelium into myeloid cells, uncovering poorly described myeloid progenitors and regulatory programs. Taking advantage of the variety of myeloid cells produced, we developed a new protocol to produce type 2 conventional dendritic cells (cDC2) in vitro. We found that the underlying regulatory networks coding for myeloid identity are conserved in vivo and in vitro. Using genetic engineering techniques, we validated the effects of key transcription factors important for cDC2 and macrophage identity and ontogeny. This roadmap of early myeloid differentiation will serve as an important resource for investigating the initial stages of hematopoiesis, which are largely unexplored in humans, and will open up new therapeutic opportunities.
The natural adaptation and human selection history of African sheep genomes
Authors: Ahbara Abulgasim M. , Robert Christelle , Kebede Adebabay , Abeba Ayelle , Latairish Suliman , Agoub Mukhtar Omar , Musa Hassan H. , Wiener Pam , Clark Emily , Hanotte Olivier , Mwacharo Joram M.
Published: November 2021

African sheep manifest diverse but distinct physio-anatomical traits which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous African sheep genomes sequenced at an average depth of ∼54x for 130 samples (Ethiopia, Libya) and ∼10x for 20 samples (Sudan), representing sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups that correspond to altitudinal geographic origins and tail morphotypes. Comparative genomic analysis identified targets of selection spanning conserved haplotype structures overlapping genes and gene families relating to hypoxia responses, caudal vertebrae and tail skeleton length, ear morphology, and tail fat-depot structure. Our findings provide novel insights underpinning variation and response to human selection and environmental adaptation, and possible pleiotropic gene interactions in indigenous African sheep genomes, which guaranteed the successful establishment of the species on the continent.
Monophyly of Diverse Bigyromonadea and their Impact on Phylogenomic Relationships Within Stramenopiles
Authors: Cho Anna , Tikhonenkov Denis V. , Hehenberger Elisabeth , Karnkowska Anna , Mylnikov Alexander P. , Keeling Patrick J.
Published: November 2021

Stramenopiles are a diverse but relatively well-studied eukaryotic supergroup with considerable genomic information available (Sibbald and Archibald, 2017). Nevertheless, the relationships between major stramenopile subgroups remain unresolved, in part due to a lack of data from small nanoflagellates that make up a lot of the genetic diversity of the group. This is most obvious in Bigyromonadea, which is one of four major stramenopile subgroups but represented by a single transcriptome. To examine the diversity of Bigyromonadea and how the lack of data affects the tree, we generated transcriptomes from seven novel bigyromonada species described in this study: Develocauda condao, Develocanicus komovi, Develocanicus vyazemskyi, Cubaremonas variflagellatum, Pirsonia chemainus, Feodosia pseudopoda, and Koktebelia satura. Both maximum likelihood and Bayesian phylogenomic trees based on a 247 gene-matrix recovered a monophyletic Bigyromonadea that includes two diverse subgroups, Developea and Pirsoniales, that were not previously related based on single gene trees. Maximum likelihood analyses show Bigyromonadea related to oomycetes, whereas Bayesian analyses and topology testing were inconclusive. We observed similarities between the novel bigyromonad species and motile zoospores of oomycetes in morphology and the ability to self- aggregate. Rare formation of pseudopods and fused cells were also observed, traits that are also found in members of labyrinthulomycetes, another osmotrophic stramenopiles. Furthermore, we report the first case of eukaryovory in the flagellated stages of Pirsoniales. These analyses reveal new diversity of Bigyromonadea, and altogether suggest their monophyly with oomycetes, collectively known as Pseudofungi, is the most likely topology of the stramenopile tree.
LiveCellMiner: A New Tool to Analyze Mitotic Progression
Authors: Moreno-Andrés Daniel , Bhattacharyya Anuk , Scheufen Anja , Stegmaier Johannes
Published: November 2021

Live-cell imaging has become state of the art to accurately identify the nature of mitotic and cell cycle defects. Low- and high-throughput microscopy setups have yield huge data amounts of cells recorded in different experimental and pathological conditions. Tailored semi-automated and automated image analysis approaches allow the analysis of high-content screening data sets, saving time and avoiding bias. However, they were mostly designed for very specific experimental setups, which restricts their flexibility and usability. The general need for dedicated experiment-specific user-annotated training sets and experiment-specific user-defined segmentation parameters remains a major bottleneck for fully automating the analysis process. In this work we present LiveCellMiner, a highly flexible open-source software tool to automatically extract, analyze and visualize both aggregated and time-resolved image features with potential biological relevance. The software tool allows analysis across high-content data sets obtained in different platforms, in a quantitative and unbiased manner. As proof of principle application, we analyze here the dynamic chromatin and tubulin cytoskeleton features in human cells passing through mitosis highlighting the versatile and flexible potential of this tool set.
Coronary Artery Disease (CAD) - risk factors and causes: In Libyan patients
Authors: Bheleel Osama , Abdulhamid Alaa , Alhadi Ibtisam , Grash Hanaa , almuaket Hajer , Mohamed Abdelhamid Mohamed Hadi
Published: November 2021

Aims

Coronary artery disease (CAD) is the leading cause of death worldwide in both men and women. Accordingly, we retrospectively reviewed the effects of various risk factors on coronary angiographic outcomes.

Methods and Results

Data were collected from the catheter lab through Tripoli university hospital records, whereas the team reviewed clinical data and coronary artery diagrams for one year from 01/04/2019 to 31/03/2020. In our study, the total number of cases was 666; 401 male and 265 female, ranging in age between 27 and 91 years. Considering the data, a significantly increased incidence of coronary artery disease (CAD) among the male who smokes, and who were less than 60 years of age. Furthermore, in the present study, the total number of normal patients was predominantly female. The most common risk factors for women were diabetes mellitus (DM), hypertension (HTN) (12%,13% respectively). While the men share the significant effects of smoking on coronary angiography (C. Angio) findings (40.52%), and most of them underwent a percutaneous coronary intervention (PCI).

Conclusions

In our study, there was evidence that CAD is a prevalent disease among the middle-aged populations with male gender preference. The risk factors including diabetes, hypertension, and smoking are the most contributing factors for the developing CAD in Libya.
Uptake of Covid-19 vaccines among frontline workers in California state prisons
Authors: Prince Lea , Long Elizabeth , Studdert David M. , Leidner David , Chin Elizabeth T. , Andrews Jason R. , Salomon Joshua A. , Goldhaber-Fiebert Jeremy D.
Published: November 2021

Background

Prisons are high-risk environments for Covid-19. Vaccination levels among prison staff remain troublingly low - lower than levels among residents and members of the surrounding community. The situation is troubling because prison staff are a key vector for Covid-19 transmission.

Objective

To assess patterns and timing of staff vaccination in California state prisons and identify individual- and community-level factors associated with being unvaccinated.

Design

We calculated fractions of prison staff and incarcerated residents in California state prisons who remained unvaccinated. Adjusted analyses identified demographic, community, and peer factors associated with vaccination uptake among staff.

Setting

California Department of Corrections and Rehabilitation prisons.

Participants

Custody and healthcare staff who worked in direct contact with residents.

Main Outcomes and Measures

Remaining unvaccinated through June 30, 2021.

Results

A total of 26% of custody staff and 52% of healthcare staff took ≥1 dose in the first two months of vaccine offer; uptake stagnated thereafter. By June 30, 2021, 61% of custody and 37% of healthcare staff remained unvaccinated. Remaining unvaccinated was positively associated with younger age, prior Covid-19, residing in a community with relatively low vaccination rates, and sharing shifts with co-workers who had relatively low vaccination rates.

Conclusions and Relevance

Vaccine uptake among prison staff in California in regular contact with incarcerated residents has plateaued at levels that pose ongoing risks—both of further outbreaks in the prisons and transmission into surrounding communities. Staff decisions to forego vaccination appear to be complex and multifactorial. Achieving safe levels of vaccine protection among frontline staff may necessitate requiring vaccination as condition of employment.
Optimizing one-dose and two-dose cholera vaccine allocation in outbreak settings: A modeling study
Authors: Leung Tiffany , Eaton Julia , Matrajt Laura
Published: November 2021

Background

A global stockpile of oral cholera vaccine (OCV) was established in 2013 for use in outbreak response and are licensed as two-dose regimens. Vaccine availability, however, remains limited. Previous studies have found that a single dose of OCV may provide substantial protection against cholera.

Methods

Using a mathematical model with two age groups paired with optimization algorithms, we determine the optimal vaccination strategy with one and two doses of vaccine to minimize cumulative overall infections, symptomatic infections, and deaths. We explore counterfactual vaccination scenarios in three distinct settings: Maela, the largest refugee camp in Thailand, with high in- and out-migration; N’Djamena, Chad, a densely populated region; and Haiti, where departments are connected by rivers and roads.

Results

Over the short term under limited vaccine supply, the optimal strategies for all objectives prioritize one dose to the older age group (over five years old), irrespective of setting and level of vaccination coverage. As more vaccine becomes available, it is optimal to administer a second dose for long-term protection. With enough vaccine to cover the whole population with one dose, the optimal strategies can avert up to 30% to 90% of deaths and 36% to 92% of symptomatic infections across the three settings over one year. The one-dose optimal strategies can avert 1.2 to 1.8 times as many cases and deaths as a two-dose pro-rata strategy.

Conclusions

In an outbreak setting, speedy vaccination campaigns with a single dose of OCV may avert more cases and deaths than a two-dose pro-rata campaign under a limited vaccine supply.
Effectiveness of digital contact tracing for COVID-19 in New South Wales, Australia
Authors: Vogt Florian , Haire Bridget , Selvey Linda , Kaldor John
Published: November 2021

Background

Digital proximity tracing applications were rolled out early in the COVID-19 pandemic in many countries to complement conventional contact tracing. Empirical evidence about their benefits for pandemic response remains scarce. We evaluated the effectiveness and usefulness of ‘COVIDSafe’, Australia’s national smartphone-based proximity tracing application for COVID-19.

Methods

In this prospective study, conducted in New South Wales, Australia between May and November 2020, we calculated the positive predictive value and sensitivity of COVIDSafe, its additional contact yield, and the number of averted public exposure events. Semi-structured interviews with public health staff were conducted to assess the application’s usefulness.

Results

There were 619 confirmed COVID-19 cases and over 25,300 close contacts during the study period. COVIDSafe was used by 137 (22%) cases and detected 79 (0·3%) close contacts. It had a positive predictive value of 39% and a sensitivity of 15%, and detected 17 (0·07%) additional close contacts that were not identified by conventional contact tracing. The application generated a substantial additional workload for public health staff and was not considered useful.

Conclusions

COVIDSafe was not sufficiently effective to make a meaningful contribution to the COVID-19 response in Australia’s most populous state over a 6-month period. This contrasts optimistic projections from modelling studies about the added value of digitally supported contact tracing. We found no evidence that it adds value to conventional contact tracing, and recommend that their implementation should always include comprehensive effectiveness evaluations.
Vitronectin acts as a key regulator of adhesion and migration in human umbilical cord-derived MSCs under different stress conditions
Authors: Sen Ankita , Ta Malancha
Published: November 2021

Mesenchymal stem cell (MSC)-based therapy gets compromised as adverse microenvironmental conditions like nutrient deprivation, ischemia, hypoxia at the target site affect migration, engraftment and viability, of MSCs post transplantation. To improve the treatment efficacy, it is critical to identify factors involved in regulating migration and adhesion of MSCs under such microenvironmental stress conditions. In our study, we observed that human Wharton’s jelly-derived MSCs (WJ-MSCs) exhibited increase in cell spread area and adhesion, with reduction in cellular migration under serum starvation stress. The changes in adhesion and migration characteristics were accompanied by formation of large number of super mature focal adhesions along with extensive stress fibres and altered ECM gene expression with notable induction in vitronectin (VTN) expression. NF-κβ was found to be a positive regulator of VTN expression while ERK pathway regulated it negatively. Molecular and phenotypic comparison studies with inhibition of these signalling pathways or knocking down of VTN under serum starvation established the correlation between increase in VTN expression and increased cellular adhesion with corresponding reduction in cell migration. VTN knockdown also resulted in reduction of super mature focal adhesions and extensive stress fibres, which were formed under serum starvation. Additionally, VTN induction was not detected in hypoxia-treated WJ-MSCs, and the MSCs showed no significant change in the adhesion or migration properties under hypoxia. However, when VTN expression was induced under hypoxia by ERK pathway inhibition, similar increase in cell spread area and adhesion were observed. Our study thus highlights VTN as a key player which is induced under serum starvation stress and possibly regulates the adhesion and migration properties of WJ-MSCs via focal adhesion signalling.
Common variation in EDN1 regulatory regions highlights the role of PPARγ as a key regulator of Endothelin in vitro
Authors: Lago-Docampo Mauro , Solarat Carlos , Méndez-Martínez Luis , Baloira Adolfo , Valverde Diana
Published: November 2021

Pulmonary Arterial Hypertension (PAH) is a rare disease caused by the obliteration of the pulmonary arterioles, increasing pulmonary vascular resistance and eventually causing right heart failure. Endothelin-1 is a vasoconstrictor peptide whose levels are indicators of disease progression and its pathway is one of the commonest targeted by current treatments.

We sequenced the EDN1 untranslated regions of a small subset of PAH patients, predicted the effect in silico, and used a luciferase assay with the different genotypes to analyze its influence on gene expression. Finally, we used siRNAs against the major transcription factors predicted for these regions (PPARγ, KLF4, and VDR) to assess Endothelin-1 expression in cell culture and validate the binding sites.

First, we detected a SNP in the 5’UTR (rs397751713) and another in the 3’regulatory region (rs2859338) that increased luciferase activity in vitro depending on their genotype. We determined in silico that KLF4/PPARγ could be binding in the rs397751713 and VDR in rs2859338. By using siRNAs and luciferase, we determined that PPARγ binds differentially in rs397751713. PPARγ and VDR Knock-Down, increased EDN1 mRNA levels and Endothelin-1 production in PAECs, while PPARγ and KLF4 Knock-Down increased the Endothelin-1 production in HeLa.

In conclusion, common variants in EDN1 regulatory regions could alter Endothelin-1 levels. We were able to validate that PPARγ binds in rs397751713 and is key to regulate Endothelin-1. Also, KLF4 and VDR regulate Endothelin-1 production in a cell-dependent manner, but for VDR this interaction does not happen by binding directly to the regions we studied.
Methylglyoxal Induces Endothelial Dysfunction via Stunning-like Phenotype
Authors: Fleming Thomas , von Nettelbladt Bastian , Morgenstern Jakob , Campos Marta , Le Marois Maxime , Bartosova Maria , Hausser Ingrid , Schwab Constantin , Fischer Andreas , Nawroth Peter P. , Szendroedi Julia , Herzig Stefan
Published: November 2021

Elevated levels of methylglyoxal (MG) and its associated post-translational modifications have been reported to be associated with progression and development of numerous pathological conditions. Despite such extensive evidence, it still remains unclear what the specific effects of MG are other than that induction of cytotoxicity. Here we evaluated the effects of MG in cardiac endothelial cells in vitro. We found that MG leads to a non-proliferative state and endothelial dysfunction, which is reversible as MG-H1, a major post-translational modification induced by MG, is turned over by lysosomal degradation. MG-induced cellular stunning/paralysis describes a new hallmark for cellular dysfunction which could lead to alterations in tissue homeostasis as well as cell-to-cell interactions, thereby contributing to the pathogenesis of diseases.
Structural basis for Cas9 off-target activity
Authors: Pacesa Martin , Lin Chun-Han , Cléry Antoine , Saha Aakash , Arantes Pablo R. , Bargsten Katja , Irby Matthew J. , Allain Frédéric H.T. , Palermo Giulia , Cameron Peter , Donohoue Paul D. , Jinek Martin
Published: November 2021

The target DNA specificity of the CRISPR-associated genome editor nuclease Cas9 is determined by complementarity to a 20-nucleotide segment in its guide RNA. However, Cas9 can bind and cleave partially complementary off-target sequences, which raises safety concerns for its use in clinical applications. Here we report crystallographic structures of Cas9 bound tobona fideoff-target substrates, revealing that off-target binding is enabled by a range of non-canonical base pairing interactions within the guide–off-target heteroduplex. Off-target sites containing single-nucleotide deletions relative to the guide RNA are accommodated by base skipping or multiple non-canonical base pairs rather than RNA bulge formation. Additionally, PAM-distal mismatches result in duplex unpairing and induce a conformational change of the Cas9 REC lobe that perturbs its conformational activation. Together, these insights provide a structural rationale for the off-target activity of Cas9 and contribute to the improved rational design of guide RNAs and off-target prediction algorithms.
A novel enhancer that regulates Bdnf expression in developing neurons
Authors: Brookes Emily , Alan Au Ho Yu , Varsally Wazeer , Barrington Christopher , Hadjur Suzana , Riccio Antonella
Published: November 2021

Brain derived neurotrophic factor (BDNF) is a critical secreted peptide that promotes neuronal differentiation and survival, and its downregulation is implicated in many neurological disorders. Here, we investigated the regulation of the mouse Bdnf gene in cortical neurons and identified a novel enhancer that promotes the expression of many Bdnf transcript variants during differentiation, increasing total Bdnf mRNA levels. Enhancer activity contributes to Bdnf-mediated effects on neuronal clustering and activity-dependent dendritogenesis. During Bdnf activation, enhancer-promoter contacts increase, and the region moves away from the repressive nuclear periphery. Our findings suggest that changes in nuclear structure may contribute to the expression of essential growth factors during neuronal development.
Transgenic tools for targeted chromosome rearrangements allow construction of balancer chromosomes in non-melanogaster Drosophila species
Authors: Stern David L.
Published: November 2021

Perhaps the most valuable single set of resources for genetic studies of Drosophila melanogaster is the collection of multiply-inverted chromosomes commonly known as balancer chromosomes. Balancers prevent the recovery of recombination exchange products within genomic regions included in inversions and allow perpetual maintenance of deleterious alleles in living stocks and the execution of complex genetic crosses. Balancer chromosomes have been generated traditionally by exposing animals to ionizing radiation and screening for altered chromosome structure or for unusual marker segregation patterns. These approaches are tedious and unpredictable, and have failed to produce the desired products in some species. Here I describe transgenic tools that allow targeted chromosome rearrangements in Drosophila species. The key new resources are engineered reporter genes containing introns with yeast recombination sites and enhancers that drive fluorescent reporter genes in multiple body regions. These tools were used to generate a doubly-inverted chromosome 3R in D. simulans that serves as an effective balancer chromosome.
Cryo soft X-ray tomography to explore Escherichia coli nucleoid remodelling by Hfq master regulator
Authors: Cossa Antoine , Trépout Sylvain , Wien Frank , Le Brun Etienne , Turbant Florian , Pereiro Eva , Arluison Véronique
Published: November 2021

Bacterial chromosomic DNA is packed within a membrane-less structure, the nucleoid, thanks to proteins called Nucleoid Associated Proteins (NAPs). The NAP composition of the nucleoid varies during the bacterial life cycle and is growth phase-dependent. Among these NAPs, Hfq is one of the most intriguing as it plays both direct and indirect roles on DNA structure. Indeed, Hfq is best known to mediate post-transcriptional regulation by using small noncoding RNA (sRNA). Although Hfq presence in the nucleoid has been demonstrated for years, its precise role is still unclear. Recently, it has been shown in vitro that Hfq belongs to the bridging family of NAPs. Its bridging mechanism relies on the formation of the amyloid-like structure of Hfq C-terminal region. Here, using cryo soft X-ray tomography imaging of native unlabelled cells and using a semi-automatic analysis and segmentation procedure, we show that Hfq significantly remodels the Escherichia coli nucleoid, especially during the stationary growth phase. Hfq influences both nucleoid volume and absorbance. Hfq cumulates direct effects and indirect effects due to sRNA-based regulation of other NAPs. Taken together, our findings reveal a new role for this protein in nucleoid remodelling that may serve in response to stress conditions and in adapting to changing environments. This implies that Hfq regulates nucleoid compaction directly via its interaction with DNA, but also at the post-transcriptional level via its interaction with RNA.
Moderate-intensity exercise might be a competitive protocol to prevent obesity and obesity-related metabolic diseases
Authors: Kwon Ryeo-Won , Lee Seung-Jea , Kim Tae-Wook , Lee Jeong Beom
Published: November 2021

To determine effects of exercise intensity on expression levels of cytokines and neurotransmitters beneficial for the prevention and improvement of obesity and obesity-related metabolic diseases. Expression levels of irisin, fibroblast growth factor-21 (FGF21), adiponectin, free fatty acid (FFA), dopamine (DA), and serotonin (5-HT) levels after moderate-intensity (50% of maximal oxygen uptake (VO2max)) and high-intensity treadmill running (80% VO2max) for 30 min in 20 healthy men were compared. Blood samples were collected at three time points: before treadmill running (pre-EX), immediately after treadmill running (post-EX), and at 60 min after treadmill running (60 min post-EX). Expression levels of irisin, FGF21, adiponectin, FFA, DA, and 5-HT were increased after 30 min of treadmill running exercise regardless of exercise intensity. Their levels were increased at 60 min post-EX. They showed no significant difference immediately after exercise regardless of exercise intensity. Only irisin, FGF21, FFA, and DA levels showed significant differences between moderate-intensity (50% VO2max) group and high-intensity group (80% VO2max) at 60 min post-EX. Considering that FFA level at 80% VO2max was significantly lower than that at 50% VO2max during post-EX and side effects of high-intensity exercise, moderate-intensity exercise would be a more competitive method compared to high-intensity for the prevention and improvement of obesity and obesity-related metabolic diseases.
Novel insights into the common heritable liability to addiction: a multivariate genome-wide association study
Authors: Schoeler Tabea , Baldwin Jessie , Allegrini Andrea , Barkhuizen Wikus , McQuillin Andrew , Pirastu Nicola , Kutalik Zoltán , Pingault Jean-Baptiste
Published: November 2021

Addiction to nicotine, alcohol and cannabis commonly co-occurs, which is thought to partly stem from a common heritable liability. To elucidate its genetic architecture, we modelled the common liability to addiction, inferred from genetic correlations among six measures of dependence and frequency of use of nicotine, alcohol and cannabis. Forty-two genetic variants were identified in the multivariate genome-wide association study on the common liability to addiction, of which 67% were novel and not associated with the six phenotypes. Mapped genes highlighted the role of dopamine (e.g., dopamine D2 gene), and showed enrichment for several components of the central nervous systems (e.g., mesocorticolimbic brain regions) and molecular pathways (dopaminergic, glutamatergic, GABAergic) that are thought to modulate drug reinforcement. Genetic correlations with other traits were most prominent for reward-related behaviours (e.g., risk-taking, cocaine and heroin use) and mood (e.g., depression, insomnia). These genome-wide results triangulate and expand previous preclinical and human studies focusing on the neurobiological substrates of addiction, and help to elucidate the common genetic architecture underlying addiction.
Pathway specific polygenic risk scores identify pathways and patient clusters associated with inflammatory bowel disease risk, severity and treatment response
Authors: Bodea Corneliu A. , Macoritto Michael , Liu Yingchun , Zhang Wenliang , Karman Jozsef , King Emily A. , Degner Jacob F. , Levesque Marc C. , Davis J. Wade , Cao Sherry
Published: November 2021

Crohn’s disease (CD) and ulcerative colitis (UC) are inflammatory bowel diseases (IBD) with a strong genetic component [1,2]. Genome-wide association studies (GWAS) have successfully identified over 240 genetic loci that are statistically associated with risk of developing IBD, and these associations provide valuable insights into disease pathobiology. Building on GWAS findings, conventional polygenic risk scores (cPRS) aim to quantify the aggregated disease risk based on DNA variation, and these scores can identify individuals at high risk. While stratifying individuals based on cPRS has the potential to inform clinical care, the development of novel therapeutics requires deep insight into how aggregated genetic risk leads to disruption of specific biological pathways. Here, we developed a pathway-specific PRS (pPRS) methodology to assess IBD common variant genetic risk burden across 31 manually curated pathways. We first prioritized 206 genes based on comprehensive fine-mapping and eQTL colocalization analyses of genome-wide significant IBD GWAS loci and 58 highly penetrant genes based on their involvement in early onset IBD or autoimmunity-related colitis. These 264 genes were assigned to at least one of the 31 pathways based on Gene Ontology annotations and manual curation. Finally, we integrated these inputs into a novel pPRS model and performed an extensive investigation of IBD disease risk, severity, complications, and anti-TNF treatment response by applying our pPRS approach to three complementary datasets encompassing IBD cases and controls. Our analysis identified multiple promising pathways that can inform drug target discovery and provides a patient stratification method that offers insights into the biology of treatment response.
Predictors and consequences of HIV status disclosure to adolescents living with HIV in Eastern Cape, South Africa
Authors: Edun Olanrewaju , Shenderovich Yulia , Zhou Siyanai , Toska Elona , Okell Lucy , Eaton Jeffrey W , Cluver Lucie
Published: November 2021

Introduction

The World Health Organization recommends full disclosure of HIV-positive status to adolescents who acquired HIV perinatally (APHIV) by age 12. However, even among adolescents (aged 10-19) already on antiretroviral therapy (ART), disclosure rates are low. Caregivers often report the child being too young and fear of disclosure worsening adolescents’ mental health as reasons for non-disclosure. Evidence is limited about predictors of disclosure and its association with adherence, viral suppression, and mental health outcomes among adolescents in sub-Saharan Africa.

Methods

Analyses included three rounds (2014-2018) of data collected among a closed cohort of adolescents living with HIV in Eastern Cape, South Africa. We used logistic regression with respondent random-effects to identify factors associated with disclosure, and assess differences in ART adherence, viral suppression, and mental health symptoms between adolescents by disclosure status. We also explored differences in the change in mental health symptoms and ART adherence between study rounds and disclosure groups with logistic regression.

Results

813 APHIV were interviewed at baseline, of whom 769 (94.6%) and 729 (89.7%) were interviewed at the second and third rounds, respectively. The proportion aware of their HIV-positive status increased from 63.1% at the first round to 85.5% by the third round. Older age (adjusted odds ratio (aOR): 1.24; 1.07 – 1.43) and living in an urban location (aOR: 2.76; 1.67 – 4.45) were associated with disclosure between interviews. There was no association between awareness of HIV-positive status and ART adherence, viral suppression, or mental health symptoms among all APHIV interviewed. However, among APHIV not aware of their status at baseline, adherence decreased at the second round among those who were disclosed to (N=131) and increased among those not disclosed to (N=151) (interaction aOR: 0.39; 0.19 – 0.80). There was no significant difference in the change in mental health symptoms between study rounds and disclosure groups.

Conclusions

Awareness of HIV-positive status was not associated with higher rates of mental health symptoms, or lower rates of viral suppression among adolescents. Disclosure was not associated with worse mental health. These findings support the recommendation for timely disclosure to APHIV, however, adherence support post-disclosure is important.
Diagnostic accuracy of three prevailing rapid antigen tests for detection of SARS-CoV-2 infection in the general population: cross sectional study
Authors: Venekamp Roderick P , Veldhuijzen Irene K , Moons Karel G M , van den Bijllaardt Wouter , Pas Suzan D , Lodder Esther B , Molenkamp Richard , Igloi Zsofi , Wijers Constantijn , Oliveira dos Santos Claudy , Debast Sylvia B , Bruins Marjan J. , Polad Khaled , Nagel-Imming Carla R S , Han Wanda G H , van de Wijgert Janneke H H M , van den Hof Susan , Schuit Ewoud
Published: November 2021

Objective

To assess the diagnostic accuracy of three rapid antigen tests (Ag-RDTs) for detecting SARS-CoV-2 infection in the general population.

Design

Cross-sectional study with follow-up using pseudonymised record linkage.

Setting

Three Dutch public health service COVID-19 test sites.

Participants

Consecutively included individuals aged 16 years and older presenting for SARS-CoV-2 testing.

Main outcome measures

Sensitivity, specificity, positive and negative predictive values of BD-VeritortmSystem (Becton Dickinson), PanBio (Abbott), and SD-Biosensor (Roche Diagnostics), applying routinely used sampling methods (combined oropharyngeal and nasal [OP-N] or nasopharyngeal [NP] swab), with molecular testing as reference standard. For SD-Biosensor, the diagnostic accuracy with OP-N sampling was also assessed. A viral load cut-off (≥5.2 log10 SARS-CoV-2 E-gene copies/mL) served as a proxy of infectiousness.

Results

SARS-CoV-2 prevalence and overall sensitivities with 95% confidence intervals were 188/1441 (13.0%) and 129/188 (68.6% [61.5%-75.2%]) for BD-Veritor, 173/2056 (8.4%) and 119/173 (68.8% [61.3%-75.6%]) for PanBio, and 215/1769 (12.2%) and 160/215 (74.4% [68.0%-80.1%]) for SD-Biosensor with routine sampling, and 164/1689 (9.7%) and 123/164 (75.0% [67.7%-81.4%]) for SD-Biosensor with OP-N sampling. In those symptomatic or asymptomatic at sampling, sensitivities were 72.2%-83.4% and 54.0%-55.9%, respectively. With a viral load cut-off, sensitivities were 125/146 (85.6% [78.9%-90.9%]) for BD-Veritor, 108/121 (89.3% [82.3%-94.2%]) for PanBio, 160/182 (87.9% [82.3%-92.3%]) for SD-Biosensor with routine sampling, and 118/141 (83.7% [76.5%-89.4%]) with OP-N sampling. Specificities were >99%, and positive and negative predictive values >95%, for all tests in most analyses. 61.3% of false negative Ag-RDT participants returned for testing within 14 days (median of 3 days, interquartile range 3) of whom 90.3% tested positive.

Conclusions

The overall sensitivities of the three Ag-RDTs were 68.6%-75.0%, increasing to at least 85.6% after the viral load cut-off was applied. For SD-Biosensor, the diagnostic accuracy with OP-N and NP sampling was comparable. Over 55% of false negative Ag-RDT participants tested positive during follow-up.
Unraveling the magnetic softness in Fe–Ni–B-based nanocrystalline material by magnetic small-angle neutron scattering
Authors: Bersweiler Mathias , Adams Michael P. , Peral Inma , Kohlbrecher Joachim , Suzuki Kiyonori , Michels Andreas
Published: November 2021

Magnetic small-angle neutron scattering is employed to investigate the magnetic interactions in (Fe0.7Ni0.3)86B14 alloy, a HiB-NANOPERM-type soft magnetic nanocrystalline material, which exhibits an ultrafine microstructure with an average grain size below 10 nm. The neutron data reveal a significant spin-misalignment scattering which is mainly related to the jump of the longitudinal magnetization at internal particle–matrix interfaces. The field dependence of the neutron data can be well described by micromagnetic small-angle neutron scattering theory. In particular, the theory explains the `clover-leaf-type' angular anisotropy observed in the purely magnetic neutron scattering cross section. The presented neutron data analysis also provides access to the magnetic interaction parameters, such as the exchange-stiffness constant, which plays a crucial role towards the optimization of the magnetic softness of Fe-based nanocrystalline materials.