bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection shapes the landscape of functional variation in wild house mice
Authors: Lawal Raman Akinyanju , Arora Uma P. , Dumont Beth L. 
Published: May 2021

AbstractBackgroundThrough human-aided dispersal, house mice have recently colonized new and diverse habitats across the globe, promoting the emergence of new traits that confer adaptive advantages in distinct environments. Despite their status as the premiere mammalian model system, the impact of this demographic and selective history on the global patterning of disease-relevant trait variation in wild mouse populations is poorly understood.ResultsHere, we leveraged 154 whole-genome sequences from diverse wild house mouse populations, subspecies, and species to survey the geographic organization of functional variation and systematically identify signals of positive selection. We show that a significant proportion of wild mouse variation is private to single populations, including numerous predicted functional alleles. In addition, we report strong signals of positive selection at numerous genes associated with both complex and Mendelian diseases in humans. Notably, we detect a significant excess of selection signals at disease-associated genes relative to null expectations, pointing to the important role of adaptation in shaping the landscape of functional variation in wild mouse populations. We also uncover strong signals of selection at multiple genes involved in starch digestion, including Mgam and Amy1. We speculate that the successful emergence of the human-mouse commensalism may have been facilitated, in part, by dietary adaptations at these loci. Finally, our work uncovers multiple cryptic structural variants that manifest as putative signals of positive selection, highlighting an important and under-appreciated source of false-positive signals in genome-wide selection scans.ConclusionsOverall, our findings underscore the role of adaptation in shaping wild mouse genetic variation at human disease-associated genes. Our work highlights the biomedical relevance of wild mouse genetic diversity and unsdercores the potential for targeted sampling of mice from specific populations as a strategy for developing effective new mouse models of both rare and common human diseases.
The population frequency of human mitochondrial DNA variants is highly dependent upon mutational bias
Authors: Dunn Cory D. 
Published: May 2021

AbstractNext-generation sequencing can quickly reveal genetic variation potentially linked to heritable disease. As databases encompassing human variation continue to expand, rare variants have been of high interest, since the frequency of a variant is expected to be low if the genetic change leads to a loss of fitness or fecundity. However, the use of variant frequency when seeking genomic changes linked to disease remains very challenging. Here, we explore the role of selection in controlling human variant frequency using the HelixMT database, which encompasses hundreds of thousands of mitochondrial DNA (mtDNA) samples. We find that a substantial number of synonymous substitutions, which have no effect on protein sequence, were never encountered in this large study, while many other synonymous changes are found at very low frequencies. Further analyses of human and mammalian mtDNA datasets indicate that the population frequency of synonymous variants is predominantly determined by mutational biases rather than by strong selection acting upon nucleotide choice. Our work has important implications that extend to the interpretation of variant frequency for non-synonymous substitutions.
Human immunocompetent Choroid-on-Chip: a novel tool for studying ocular effects of biological drugs
Authors: Cipriano Madalena , Schlünder Katharina , Probst Christopher , Linke Kirstin , Weiss Martin , Fischer Mona J. , Mesh Lena , Achberger Kevin , Liebau Stefan , Mesquida Marina , Nicolini Valeria , Schneider Anneliese , Giusti Anna Maria , Kustermann Stefan , Loskill Peter 
Published: May 2021

AbstractDisorders of the eye leading to visual impairment are a major issue that affects millions of people. On the other side ocular toxicities were described for e.g. molecularly targeted therapies in oncology and may hamper their development. Current ocular model systems feature a number of limitations affecting human-relevance and availability. To find new options for pharmacological treatment and assess mechanisms of toxicity, hence, novel complex model systems that are human-relevant and readily available are urgently required. Here, we report the development of a human immunocompetent Choroid-on-Chip (CoC), a human cell-based in vitro model of the choroid layer of the eye integrating melanocytes and microvascular endothelial cells, covered by a layer of retinal pigmented epithelial cells. Immunocompetence is achieved by perfusion of peripheral immune cells. We demonstrate controlled immune cell recruitment into the stromal compartments through a vascular monolayer and in vivo-like cytokine release profiles. To investigate applicability for both efficacy testing of immunosuppressive compounds as well as safety profiling of immunoactivating antibodies, we exposed the CoCs to cyclosporine and tested CD3 bispecific antibodies.Abstract FigureGraphical Abstract
8-azaadenosine and 8-chloroadenosine are not selective inhibitors of ADAR
Authors: Cottrell Kyle A. , Torres Luisangely Soto , Weber Jason D. 
Published: May 2021

AbstractThe RNA editing enzyme ADAR, is an attractive therapeutic target for multiple cancers. Through its deaminase activity, ADAR edits adenosine to inosine in dsRNAs. Loss of ADAR in some cancer cell lines causes activation of the type I interferon pathway and the PKR translational repressor, leading to inhibition of proliferation and stimulation of cell death. As such, inhibition of ADAR function is a viable therapeutic strategy for many cancers. However, there are no FDA approved inhibitors of ADAR. Two small molecules have been previously described as inhibitors of ADAR: 8-azaadenosine and 8-chloroadenosine. Here we show that neither molecule is a selective inhibitor of ADAR. Both 8-azaadenosine and 8-chloroadenosine show similar toxicity to ADAR-dependent and independent cancer cell lines. Furthermore, the toxicity of both small molecules is comparable between cell lines with knockdown of ADAR and cells with unperturbed ADAR expression. Treatment with neither molecule causes activation of PKR. Finally, treatment with either molecule has no effect on A-to-I editing of an ADAR substrate. Together these data show that 8-azaadenosine and 8-chloroadenosine are not suitable small molecules for therapies that require selective inhibition of ADAR, and neither should be used in preclinical studies as ADAR inhibitors.
Preclinical characterization and target validation of the antimalarial pantothenamide MMV693183
Authors: de Vries Laura E. , Jansen Patrick A.M. , Barcelo Catalina , Munro Justin , Verhoef Julie M.J. , Pasaje Charisse Flerida A. , Rubiano Kelly , Striepen Josefine , Bolscher Judith M. , Henderson Rob , Huijs Tonnie , Koolen Karin M.J. , Tumwebaze Patrick K. , Yeo Tomas , Aguiar Anna C.C. , Angulo-Barturen Iñigo , Churchyard Alisje , Baum Jake , Fernández Benigno Crespo , Gamo Francisco-Javier , Guido Rafael V.C. , Jiménez-Diaz María Belén , Pereira Dhelio B. , Rochford Rosemary , Sanz Laura M. , Trevitt Graham , Wittlin Sergio , Cooper Roland A. , Rosenthal Philip J. , Sauerwein Robert W. , Schalkwijk Joost , Hermkens Pedro H.H. , Bonnert Roger , Campo Brice , Fidock David A. , Llinás Manuel , Niles Jacquin C. , Kooij Taco W.A. , Dechering Koen J. 
Published: May 2021

AbstractDrug resistance and a dire lack of transmission-blocking antimalarials hamper malaria elimination. Here, we present the pantothenamide MMV693183 as a first-in-class acetyl-CoA synthetase (ACS) inhibitor to enter preclinical development. Our studies demonstrated attractive drug-like properties and in vivo efficacy in a humanized mouse model of Plasmodium falciparum infection. The compound showed exceptional in vitro activity against P. falciparum and P. vivax clinical isolates, and potently blocked P. falciparum transmission to Anopheles mosquitoes. Genetic and biochemical studies identified ACS as the target of the MMV693183-derived antimetabolite, CoA-MMV693183. MMV693183 was well adsorbed after oral administration in mice, rats and dogs. Pharmacokinetic – pharmacodynamic modelling predicted that a single 30 mg oral dose is sufficient to cure a malaria infection in humans. In conclusion, the ACS-targeting compound MMV693183 represents a promising addition to the portfolio of antimalarials in (pre)clinical development with a novel mode of action for the treatment of malaria and blocking transmission.
Evidence against altered excitatory/inhibitory balance in the posteromedial cortex of young adult APOE E4 carriers: a resting state 1H-MRS study
Authors: Costigan AG , Umla-Runge K , Evans CJ , Raybould R , Graham KS , Lawrence AD 
Published: May 2021

AbstractA strategy to gain insight into early changes that may predispose people to Alzheimer’s disease is to study the brains of younger cognitively healthy people that are at increased genetic risk of AD. The Apolipoprotein (APOE) E4 allele is the strongest genetic risk factor for AD, and several neuroimaging studies comparing APOE E4 carriers with non-carriers at age ~20-30 have detected hyperactivity (or reduced deactivation) in posteromedial cortex (PMC), a key hub of the default network (DN) which has a high susceptibility to early amyloid deposition in AD. Transgenic mouse models suggest such early network activity alterations may result from altered excitatory/inhibitory (E/I) balance, but this is yet to be examined in humans. Here we test the hypothesis that PMC fMRI hyperactivity could be underpinned by altered levels of excitatory (glutamate) and/or inhibitory (GABA) neurotransmitters in this brain region. Forty-seven participants (20 APOE E4 carriers and 27 non-carriers) aged 18-25 underwent resting-state proton magnetic resonance spectroscopy (1H-MRS), a non-invasive neuroimaging technique to measure glutamate and GABA in vivo. Metabolites were measured in a PMC voxel of interest and in a comparison voxel in the occipital cortex (OCC). There was no difference in either glutamate or GABA between the E4 carriers and non-carriers in either MRS voxel, nor in the ratio of glutamate to GABA, a measure of E/I balance. Default Bayesian t-tests revealed evidence in support of this null finding. Results suggest that PMC hyperactivity in APOE E4 carriers is unlikely to be associated with, or indeed may precede, alterations in local resting-state PMC neurotransmitters, thus informing the spatio-temporal order and the cause/effect dynamic of neuroimaging differences in APOE E4 carriers.HighlightsHyperactivity in posteromedial (PM) network in people at AD genetic risk (APOE E4)Such PM network hyperactivity may initiate pathogenic cascade that triggers ADAPOE mouse models suggest hyperactivity driven by excitatory/inhibitory imbalanceUsing 1H-MRS at 3T we studied PMC E/I balance in young adult APOE E4 carriersFound evidence against altered E/I balance in young adult APOE E4 carriers
Diet effects on mouse meiotic recombination: a warning for recombination studies
Authors: Tebar Angela Belmonte , San Martin Perez Estefania , Nam-Cha Syong Hyun , Soler Valls Ana Josefa , Singh Nadia D. , de la Casa-Esperon Elena 
Published: May 2021

ABSTRACTMeiotic recombination is a critical process for sexually reproducing organisms. This exchange of genetic information between homologous chromosomes during meiosis is important not only because it generates genetic diversity, but also because it is often required for proper chromosome segregation. Consequently, the frequency and distribution of crossovers are tightly controlled to ensure fertility and offspring viability. However, in many systems it has been shown that environmental factors can alter the frequency of crossover events. Two studies in flies and yeast point to nutritional status affecting the frequency of crossing over. However, this question remains unexplored in mammals. Here we test how crossover frequency varies in response to diet inMus musculusmales. We use immunohistochemistry to estimate crossover frequency in multiple genotypes under two diet treatments. Our results indicate that while crossover frequency was unaffected by diet in some strains, other strains were sensitive even to small composition changes between two common laboratory chows. Therefore, recombination is both resistant and sensitive to certain dietary changes in a strain-dependent manner and, hence, this response is genetically determined. Our study is the first to report a nutrition effect on genome-wide levels of recombination. Moreover, our work highlights the importance of controlling diet in recombination studies and may point to diet as a potential source of variability among studies, which is relevant for reproducibility.
Human alveolar lining fluid from the elderly promotesMycobacterium tuberculosisgrowth in alveolar epithelial cells and bacterial translocation into the cytosol
Authors: Olmo-Fontánez Angélica M. , Scordo Julia M. , Garcia-Vilanova Andreu , Maselli Diego Jose , Peters Jay I. , Restrepo Blanca I. , Clemens Daniel L. , Turner Joanne , Schlesinger Larry S. , Torrelles Jordi B. 
Published: May 2021

ABSTRACTThe elderly population is at significant risk of developing respiratory diseases, including tuberculosis (TB) caused by the airborneMycobacterium tuberculosis(M.tb). OnceM.tbreaches the alveolar space, it contacts alveolar lining fluid (ALF) which dictates host cell interactions. We previously determined that age-associated dysfunctionality in human ALF soluble innate components lead to acceleratedM.tbgrowth within human alveolar macrophages. Here we determined the impact of human ALF onM.tbinfection of alveolar epithelial cells (ATs), another critical cellular determinant of infection. We observed that E-ALF-exposedM.tbhad significantly increased intracellular growth in ATs compared to adult ALF (A-ALF)-exposed bacteria. Despite this, there were no alterations in AT inflammatory mediators or cell activation. However, exposure to E-ALF altered endosomal trafficking ofM.tb, driving bacterial translocation to both endosomal and cytosolic compartments in ATs. Our results indicate that exposure ofM.tbto E-ALF promotes translocation of bacteria into the AT cytosol as a potential favorable niche for rapid bacterial growth and at the same time dampens AT’s immune responses. Thus, our findings highlight the influence of the elderly lung mucosa onM.tbinfection of ATs, an unexplored contributing factor to the elderly population’s increased susceptibility of developing active TB disease.
The effect of developmental pleiotropy on the evolution of insect immune genes
Authors: Ngo Thi Minh , Williams Alissa M. , Tate Ann T. 
Published: May 2021

AbstractThe pressure to survive relentless pathogen exposure explains the frequent observation that immune genes are among the fastest-evolving in the genomes of many taxa, but an intriguing proportion of immune genes also appear to be under purifying selection. Though variance in evolutionary signatures of immune genes is often attributed to differences in gene-specific interactions with microbes, this explanation neglects the possibility that immune genes participate in other biological processes that could pleiotropically constrain adaptive selection. In this study, we analyzed available transcriptomic and genomic data from Drosophila melanogaster and related species to test the hypothesis that there is substantial pleiotropic overlap in the developmental and immunological functions of genes involved in immune signaling and that pleiotropy would be associated with stronger signatures of evolutionary constraint. Our results suggest that pleiotropic immune genes do evolve more slowly than those having no known developmental functions, and that signatures of constraint are particularly strong for pleiotropic immune genes that are broadly expressed across life stages. However, pleiotropic immune genes also contain a significantly higher proportion of positively selected sites and substitutions are more likely to be under positive selection, suggesting a mechanism to circumvent evolutionary constraint. These results support the general yet untested hypothesis that pleiotropy can constrain immune system evolution, raising new fundamental questions about the benefits of maintaining pleiotropy in systems that need to rapidly adapt to changing pathogen pressures.
Histone sequence variation in divergent eukaryotes facilitates diversity in chromatin packaging
Authors: Patwal Indu , Trinh Hien , Golden Aaron , Flaus Andrew 
Published: May 2021

AbstractThe histone proteins defining nucleosome structure are highly conserved in common model organisms and are frequently portrayed as uniform chromatin building blocks. We surveyed over 1700 complete eukaryotic genomes and confirm that almost all encode recognisable canonical core histones. Nevertheless, divergent eukaryotes show unrecognised diversity in histone sequences and offer an opportunity to observe the potential for nucleosome variation. Recombinant histones for Plasmodium falciparum, Giardia lamblia, Encephalitozoon cuniculi and Leishmania major were prepared alongside those for human, Xenopus laevis and Saccharomyces cerevisiae. All could be assembled into nucleosomes in vitro on sequences known to direct positioning with metazoan histones. P. falciparum histones refolded into very stable nucleosomes consistent with a highly regulated transcriptional programme. In contrast, G. lamblia and E. cuniculi histones formed less stable nucleosomes and were prone to aggregation as H3-H4 tetramers. Inspection of the histone fold dimer interface residues suggested a potential to form tetrasomal arrays consistent with polymerisation. DNA binding preferences observed using systematic evolution of ligands by exponential enrichment (SELEX) for human, P. falciparum and E. cuniculi histone octamers were highly similar and reflect a shared capability to package diverse genomic sequences. This demonstrates that nucleosomal organisation is retained across eukaryotes and can accommodate genome variation, but histone protein sequences vary more than commonly recognised to provide the potential for diversity of chromatin features.Significance statementIt is widely assumed that eukaryotes package their genomes using equivalent nucleosome building blocks despite considerable variation in the composition and behaviour of cell nuclei. Our survey of available eukaryote genomes shows that histone proteins from divergent eukaryotes vary much more widely in sequence than is commonly recognised, even in histone fold dimer and DNA interaction interfaces. We demonstrate that divergent eukaryote histones nevertheless form nucleosomes on DNA sequences favoured in metazoans. These nucleosomes vary in stability but share broad DNA sequence preferences. This suggests that histone-dependent packaging does not constrain genome variation, and that chromatin behaviour can adapt by evolution of canonical core histone sequences in addition to other well-known mechanisms.
Chemically modified guide RNAs enhance CRISPR-Cas13 knockdown in human cells
Authors: Méndez-Mancilla Alejandro , Wessels Hans-Hermann , Legut Mateusz , Kadina Anastasia , Mabuchi Megumu , Walker John , Robb G. Brett , Holden Kevin , Sanjana Neville E. 
Published: May 2021

AbstractRNA-targeting CRISPR-Cas13 proteins have recently emerged as a powerful platform to transiently modulate gene expression outcomes. However, protein and CRISPR RNA (crRNA) delivery in human cells can be challenging and knockdown can be transient due to rapid crRNA degradation. Here we compare several chemical RNA modifications at different positions to identify synthetic crRNAs that improve RNA targeting efficiency and half-life in human cells. We show that co-delivery of modified crRNAs and recombinant Cas13 enzyme in ribonucleoprotein (RNP) complexes enables transient gene expression modulation in primary CD4+ and CD8+ T-cells. This system represents a robust and efficient method to transiently modulate transcripts without genetic manipulation.
Nitrogen resorption efficiency in autumn leaves correlated with chlorophyll resorption, not with anthocyanin production
Authors: Pena-Novas Ines , Archetti Marco 
Published: May 2021

AbstractA prominent hypothesis for the adaptive value of anthocyanin production in the autumn leaves of some species of trees is that anthocyanins protect leaves from photooxidative stress at low temperatures, allowing a better resorption of nutrients – in particular, nitrogen – before leaf fall. While there is evidence that anthocyanins enable photoprotection, it is not clear whether this translates to improved nitrogen resorption and how this can explain inter-specific variation in autumn colours. A recent comparative analysis showed no correlation between temperature and anthocyanin production across species but did not analyse nitrogen content and nitrogen resorption efficiency. Here we provide this comparison by comparing the nitrogen content of mature and senescent leaves and their autumn colours in 55 species of trees. We find no correlation between the presence of anthocyanins and the efficiency of nitrogen resorption. We find, instead, that nitrogen resorption is more efficient in species with yellow autumn colours, pointing to chlorophyll resorption, rather than anthocyanin synthesis, as the main determinant of nitrogen resorption efficiency. Hence our results do not corroborate the photoprotection hypothesis as an explanation for the evolution of autumn colours.
Analysis of nucleic acids extracted from rapid diagnostic tests reveals a significant proportion of false positive test results associated with recent malaria treatment
Authors: Hosch Salome , Yoboue Charlene Aya , Donfack Olivier Tresor , Guirou Etienne A. , Dangy Jean-Pierre , Mpina Maxmillian , Nyakurungu Elizabeth , Blöchliger Koranan , Guerra Carlos A. , Phiri Wonder P. , Ayekaba Mitoha Ondo’o , García Guillermo A. , Tanner Marcel , Daubenberger Claudia , Schindler Tobias 
Published: May 2021

AbstractSurveillance programs often use malaria rapid diagnostic tests (RDTs) to determine the proportion of the population carrying parasites in their peripheral blood to assess the malaria transmission intensity. Despite an increasing number of reports on false-negative and false-positive RDT results, there is a lack of systematic quality control activities for RDTs deployed in malaria surveillance programs. Our study provides a larger scale comparative evaluation of RDTs used in the 2018 Malaria Indicator Survey (MIS) conducted on Bioko Island, Equatorial Guinea. We conducted a molecular analysis by extraction of nucleic acids from 1,800 negative and 1,065 positive RDTs followed by qPCR analysis. These results were combined with a dataset collected in a comprehensive questionnaire from each MIS participant. Of the 2,865 RDTs that were collected in 2018 on Bioko Island and analysed in our study, 4.7% had a false-negative result. These false-negative RDT results were associated with low parasite density infections. In a substantial proportion of samples, we identified masked pfhrp2 and pfhrp3 gene deletions in which at least one P. falciparum strain carried a gene deletion. Among all positive RDTs analysed, 28.4% were tested negative by qPCR and therefore considered to be false-positive. Analysing the questionnaire data collected from the participants, this high proportion of false-positive RDT results could be explained by PfHRP2 antigen persistence after recent malaria treatment. We conclude that malaria surveillance depending solely on RDTs needs well-integrated quality control procedures assessing the extend and impact of reduced sensitivity and specificity of RDTs on malaria control programs.