bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal dynamics of microbial transcription in wetted hyperarid desert soils
Authors: León-Sobrino Carlos , Ramond Jean-Baptiste , Coclet Clément , Kapitango Ritha-Meriam , Maggs-Kölling Gillian , Cowan Don A.
Published: May 2021

Rainfall is rare in hyperarid deserts but, when it occurs, it triggers large biological responses which are considered to be essential for the long-term maintenance of biodiversity. In such environments, microbial communities have major roles in nutrient cycling, but their functional responses to short-lived resource opportunities are poorly understood. We used whole community metatranscriptomic data to demonstrate structured and sequential functional responses in desiccated desert soils to a simulated rainfall event over a seven-day time frame. Rapid transcriptional activation of Actinobacteria, Alpha-proteobacteria and phage transcripts was followed by a marked increase in protist and myxobacterial activity, before returning to the original state. In functional terms, motility systems were activated in the early phases, whereas competition-toxicity systems increased in parallel to the activity from predators and the drying of soils. The dispersal-predation dynamic was identified as a central driver of microbial community responses to watering. Carbon fixation mechanisms that were active under dry condition were rapidly down-regulated in wetted soils, and only reactivated on a return to a near-dry state, suggesting a reciprocal balance between carbon fixation and fixed-carbon acquisition processes. Water addition induced a general reduction in the transcription of stress response genes, most prominently HSP20, indicating that this chaperone is particularly important for life in desiccated ecosystems. Based on these data, we propose a rainfall response model for desert soil microbiomes.
Transient ribosome slowdown at the decoding step triggers mRNA degradation independent of Znf598 in zebrafish
Authors: Mishima Yuichiro , Han Peixun , Kimura Seisuke , Iwasaki Shintaro
Published: May 2021

The control of mRNA stability plays a central role in regulating gene expression patterns. Recent studies have revealed that codon composition in the open reading frame (ORF) determines mRNA stability in multiple organisms. Based on genome-wide correlation approaches, this previously unrecognized role of the genetic code is attributable to the kinetics of the codon-decoding process by the ribosome. However, complementary experimental analysis is required to define the codon effects on mRNA stability apart from the related cotranslational mRNA decay pathways such as those triggered by aberrant ribosome stalls. In the current study, we performed a set of reporter-based analyses to define codon-mediated mRNA decay and ribosome stall-dependent mRNA decay in zebrafish embryos. Our analysis showed that the effect of codons on mRNA stability stems from the decoding process, independent of Znf598 and stall-dependent mRNA decay. We propose that codon-mediated mRNA decay is triggered by transiently slowed ribosomes engaging in a productive translation cycle in zebrafish embryos.
Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers
Authors: Verdier Héloïse , Konecny Lara , Marquette Christophe , Reveron Helen , Tadier Solène , Grémillard Laurent , Barthès Amélie , Datry Thibault , Bouchez Agnès , Lefébure Tristan
Published: May 2021

The study of environmental DNA released by aquatic organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Common eDNA sampling methods such as filtration and precipitation are time consuming, require human intervention and are not applicable to a wide range of habitats such as turbid waters and poorly-accessible environments. To circumvent these limitations, we propose to use the binding properties of minerals to create a passive eDNA sampler.

We have designed 3D-printed samplers made of hydroxyapatite (HAp samplers), a mineral known for its high binding affinity with DNA. The shape and the geometry of the samplers have been designed to facilitate their handling in laboratory and field. Here we describe and test the ability of HAp samplers to recover artificial DNA and eDNA.

We show that HAp samplers efficiently recover DNA and are effective even on small amounts of eDNA (<1 ng). However, we also observed large variations in the amount of DNA recovered even under controlled conditions.

By better understanding the physico-chemical interactions between DNA and the HAp sampler surface, one could improve the repeatability of the sampling process and provide an easy-to-use eDNA sampling tool for aquatic environments.
Ecdysteroids as natural doping substances in the blood of insectivorous bats
Authors: Hornok Sándor , Berkecz Róbert , Sós Endre , Sándor Attila D. , Körmöczi Tímea , Solymosi Norbert , Kontschán Jenő , Hunyadi Attila
Published: May 2021

Bats have deserved much scientific attention due to their biological-ecological properties and increasingly recognized epidemiological significance. Ecdysteroids are insect-molting hormones that (under experimental conditions) have stimulating and anabolic effects in mammals, including humans. Therefore, these biologically active compounds are currently under consideration by the World Anti-Doping Agency (WADA) to become doping-controlled substances. Previously we demonstrated that low to high concentrations of ecdysteroids appear in the blood of insectivorous passerine birds. Since passerine birds and echolocating bats share several adaptive mechanisms in connection with flying, and insectivorism is also among their common traits, we hypothesized that ecdysteroids might also be present in the blood of insectivorous bats. To test this hypothesis, blood samples of eight insectivorous bat species were collected and analyzed for the presence of ecdysteroids with highly sensitive targeted ultra-high-performance liquid chromatography coupled to high-resolution quadrupole-orbitrap mass spectrometry method (UHPLC-HRMS). The results supported our hypothesis, because nine ecdysteroids were detected in bat blood. The spectrum of these ecdysteroids was similar in those bat species which have their most preferred food items from the same insect order, supporting insects as the most likely source of these hormones. It was also shown that the spectrum of blood-borne ecdysteroids was broader in the autumn than in the summer, and higher concentrations of 20-hydroxyecdysone were measured in samples of large size bat species in comparison with small size ones. Based on the known physiologic effects of ecdysteroids, we postulate that these results might have implications on the metabolic rate and parasite burdens of insectivorous bats.
Actin isovariant ACT7 controls root meristem development in Arabidopsis through modulating auxin and ethylene responses
Authors: Numata Takahiro , Sugita Kenji , Rahman Arifa Ahamed , Rahman Abidur
Published: May 2021

Meristem is the most functionally dynamic part in a plant body. The shaping of the meristem requires constant cell division and cell elongation, which are influenced by hormones and cell cytoskeletal component, actin. Although the roles of hormones in modulating meristem development have been extensively studied, the role of actin in this process is still elusive. Using the single and double mutants of the vegetative class actin, we demonstrate that actin isovariant ACT7 plays an important role in root meristem development. In absence of ACT7, but not ACT8 and ACT2, depolymerization of actin was observed. Consistently, act7 mutant showed reduced cell division, cell elongation, and meristem length. Intracellular distribution and trafficking of auxin transport proteins in the actin mutants revealed that ACT7 specifically functions in root meristem to facilitate the trafficking of auxin efflux carriers PIN1 and PIN2, and consequently the transport of auxin. Compared with act7, act7act8 double mutant shows slightly enhanced phenotypic response and altered intracellular trafficking. The altered distribution of auxin in act7 and act7act8 affects the response of the roots to ethylene but not to cytokinin. Collectively, our results suggest that ACT7 dependent auxin-ethylene response plays a key role in controlling Arabidopsis root meristem development.
Pulmonary mesenchymal stem cells are engaged in distinct steps of host response to respiratory syncytial virus infection
Authors: Brügger Melanie , Démoulins Thomas , Barut G. Tuba , Zumkehr Beatrice , Oliveira Esteves Blandina I. , Mehinagic Kemal , Haas Quentin , Schögler Aline , Rameix-Welti Marie-Anne , Eléouët Jean-François , Moehrlen Ueli , Marti Thomas M. , Schmid Ralph A. , Summerfield Artur , Posthaus Horst , Ruggli Nicolas , Hall Sean R. R. , Alves Marco P.
Published: May 2021

Lung-resident (LR) mesenchymal stem and stromal cells (MSCs) are key elements of the alveolar niche and fundamental regulators of homeostasis and regeneration. We interrogated their function during virus-induced lung injury using the highly prevalent respiratory syncytial virus (RSV) which causes severe outcomes in infants. We applied complementary approaches with primary pediatric LR-MSCs and a state-of-the-art model of human RSV infection in lamb. Remarkably, RSV-infection of pediatric LR-MSCs led to a robust activation, characterized by a strong antiviral and pro-inflammatory phenotype combined with mediators related to T cell function. In line with this, following in vivo infection, RSV invades and activates LR-MSCs, resulting in the expansion of the pulmonary MSC pool. Moreover, the global transcriptional response of LR-MSCs appears to follow RSV disease, switching from an early antiviral signature to repair mechanisms including differentiation, tissue remodeling, and angiogenesis. These findings demonstrate the involvement of LR-MSCs during virus-mediated acute lung injury and may have therapeutic implications.

AUTHOR SUMMARY

This work identifies a novel function of lung-resident MSCs during virus-induced acute lung injury. These findings contribute to the understanding of host response and lung repair mechanisms during a highly prevalent clinical situation and may have therapeutic implications.
Mechanistic insights into dideoxygenation in gentamicin biosynthesis
Authors: Li Sicong , Bury Priscila dos Santos , Huang Fanglu , Guo Junhong , Sun Guo , Reva Anna , Huang Chuan , Jian Xinyun , Li Yuan , Zhou Jiahai , Deng Zixin , Leeper Finian J. , Leadlay Peter F. , Dias Marcio V. B. , Sun Yuhui
Published: May 2021

Gentamicin is an important aminoglycoside antibiotic used for treatment of infections caused by Gram-negative bacteria. Although most of the biosynthetic pathway of gentamicin has been elucidated, a remaining intriguing question is how the intermediates JI-20A and JI-20B undergo a dideoxygenation to form gentamicin C complex. Here we show that the dideoxygenation process starts with GenP-catalyzed phosphorylation of JI-20A and JI-20Ba. The phosphorylated products are converted to C1a and C2a by concerted actions of two PLP (pyridoxal 5’-phosphate)-dependent enzymes: elimination of water and then phosphate by GenB3 and double bond migration by GenB4. Each of these reactions liberates an imine which hydrolyses to a ketone or aldehyde and is then re-aminated by GenB3 using an amino donor. Crystal structures of GenB3 and GenB4 have guided site-directed mutagenesis to reveal crucial residues for the enzymes’ functions. We propose catalytic mechanisms for GenB3 and GenB4, which shed new light on the already unrivalled catalytic versatility of PLP-dependent enzymes.
A sex-specific evolutionary interaction betweenADCY9andCETP
Authors: Gamache Isabel , Legault Marc-André , Grenier Jean-Christophe , Sanchez Rocio , Rhéaume Eric , Asgari Samira , Barhdadi Amina , Zada Yassamin Feroz , Trochet Holly , Luo Yang , Lecca Leonid , Murray Megan , Raychaudhuri Soumya , Tardif Jean-Claude , Dubé Marie-Pierre , Hussin Julie G.
Published: May 2021

Pharmacogenomic studies have revealed associations between rs1967309 in the adenylyl cyclase type 9 (ADCY9) gene and clinical responses to the cholesteryl ester transfer protein (CETP) modulator dalcetrapib, however, the mechanism behind this interaction is still unknown. Here, we characterized selective signals at the locus associated with the pharmacogenomic response in human populations and we show that rs1967309 region exhibits signatures of positive selection in several human populations. Furthermore, we identified a variant inCETP, rs158477, which is in long-range linkage disequilibrium with rs1967309 in the Peruvian population. The signal is mainly seen in males, a sex-specific result that is replicated in the LIMAA cohort of over 3,400 Peruvians. Analyses of RNA-seq data further suggest an epistatic interaction onCETPexpression levels between the two SNPs in multiple tissues, which also differs between males and females. We also detected interaction effects of the two SNPs with sex on cardiovascular phenotypes in the UK Biobank, in line with the sex-specific genotype associations found in Peruvians at these loci. We propose thatADCY9andCETPcoevolved during recent human evolution due to sex-specific selection, which points towards a biological link between dalcetrapib’s pharmacogeneADCY9and its therapeutic targetCETP.
Do host-consumed resources increase endoparasitic but decrease ectoparasitic infections?
Authors: Shayhorn Brin , Ramsay Chloe , Medina Kristi , Sauer Erin , Rohr Jason R.
Published: May 2021

Habitat loss and disease outbreak play a major role in the decline of biodiversity. Habitat degradation is often associated with reduced food resources, which can lead to less investment in host immunity and increased infections. However, pathogens use host resources for replication and pathogen traits, such as infecting hosts internally or short generation times, might allow pathogens to rapidly capitalize on host-consumed nutrients. Thus, it is unclear whether increased food consumption by hosts should reduce or amplify pathogen levels. We conducted experiments on Cuban treefrogs (Osteopilus septentrionalis) to test how food availability affects infection levels of Ranavirus and the fungal pathogen Batrachochytrium dendrobatidis (Bd), which are both associated with mass die-offs of amphibians. Given that Ranavirus is an endoparasite with a much shorter generation time than the ectoparasitic Bd, we postulated that Ranavirus might be able to capitalize on host-consumed resources more quickly than Bd. We hypothesized that increased food availability to hosts might reduce Bd infections more than Ranavirus infections. As predicted, augmenting food access decreased Bd infection intensity, but increased Ranavirus infection intensity. Future work should assess whether pathogen traits, such as generation time and endo- versus ectoparasitism, generally affect whether food resources more positively benefit hosts or pathogens.
Bilingual speakers’ enhanced monitoring can slow them down
Authors: Markiewicz Roksana , Mazaheri Ali , Krott Andrea
Published: May 2021

Performance differences between bilinguals and monolinguals on conflict tasks can be affected by the balance of various sub-processes such as conflict monitoring and allocation of attentional resources for stimulus categorisation. Here we investigated the effect of bilingualism on these sub-processes during a conflict task with medium monitoring demand. We examined the behavioural responses and evoked potentials from bilinguals and monolinguals during a flanker task with 25% incongruent trials. We analysed behavioural differences by means of averaged response times and ex-Gaussian analyses of response time distributions. For the evoked potentials we focused on N2 (reflecting conflict monitoring) and P3 responses (reflecting allocation of attentional resources for cognitive control). We found that bilinguals had significantly longer response distribution tails compared to monolinguals. Additionally, bilinguals exhibited a more pronounced N2 and smaller P3 components compared to monolinguals, independent of experimental condition, suggesting a different balance of sub-processes for the two groups. It is suggested that bilinguals engaged more strongly in monitoring processes, leading to the allocation of fewer attentional resources during stimulus categorisation. Importantly, N2 amplitudes were positively and P3 amplitudes negatively related to the length of response distribution tails. We postulate that these results reflect an overactive monitoring system in bilinguals. This enhanced monitoring led to reduced engagement of attentional resources for stimulus categorisation, but also occasionally to slow responses. These results suggest that changes of the cognitive control system due to bilingual experience can change the balance of processes during conflict tasks, potentially leading to a small behavioural disadvantage.
Frequency Comb Optoacoustic Tomography
Authors: Stylogiannis Antonios , Prade Ludwig , Glasl Sarah , Mustafa Qutaiba , Zakian Christian , Ntziachristos Vasilis
Published: May 2021

Optoacoustics (OA) is overwhelmingly implemented in the Time Domain (TD) to achieve a high Signal-to-Noise-Ratio (SNR). Implementations in the Frequency Domain (FD) have been proposed, but have not offered competitive advantages over TD methods to reach high dissemination. It is therefore commonly believed that the TD represents the optimal way of performing optoacoustics. Here, we introduce a novel optoacoustic concept based on frequency comb and theoretically demonstrate its superiority to the TD. Then, using recent advances in laser diode illumination, we launch Frequency Comb Optoacoustic Tomography (FCOT), at multiple wavelengths, and experimentally demonstrate its advantages over TD methods in phantoms and in-vivo. We demonstrate that FCOT optimizes the SNR of spectral measurements over TD methods by benefiting from signal acquisition in the TD and processing in the FD, and that it reaches the fastest multi-spectral operation ever demonstrated in optoacoustics while reducing performance compromises present in TD systems.
Anatomy promotes neutral coexistence of strains in the human skin microbiome
Authors: Conwill Arolyn , Kuan Anne C. , Damerla Ravalika , Poret Alexandra J. , Baker Jacob S. , Tripp A. Delphine , Alm Eric J. , Lieberman Tami D.
Published: May 2021

What enables strains of the same species to coexist in a microbiome? Here, we investigate if host anatomy can explain strain co-residence of Cutibacterium acnes, the most abundant species on human skin. We reconstruct on-person evolution and migration using 947 C. acnes colony genomes acquired from 16 subjects, including from individual skin pores, and find that pores maintain diversity by limiting competition. Although strains with substantial fitness differences coexist within centimeter-scale regions, each pore is dominated by a single strain. Moreover, colonies from a pore typically have identical genomes. An absence of adaptive signatures suggests a genotype-independent source of low within-pore diversity. We therefore propose that pore anatomy imposes random single-cell bottlenecks during migration into pores and subsequently blocks new migrants; the resulting population fragmentation reduces competition and promotes coexistence. Our findings imply that therapeutic interventions involving pore-dwelling species should focus on removing resident populations over optimizing probiotic fitness.
in silicoAssessment of Antibody Drug Resistance to Bamlanivimab of SARS-CoV-2 Variant B.1.617
Authors: Zhang Leili , Huynh Tien , Luan Binquan
Published: May 2021

The highly infectious SARS-CoV-2 variant B.1.617 with double mutations E484Q and L452R in the receptor binding domain (RBD) of SARS-CoV-2’s spike protein is worrisome. Demonstrated in crystal structures, the residues 452 and 484 in RBD are not in direct contact with interfacial residues in the angiotensin converting enzyme 2 (ACE2). This suggests that albeit there are some possibly nonlocal effects, the E484Q and L452R mutations might not significantly affect RBD’s binding with ACE2, which is an important step for viral entry into host cells. Thus, without the known molecular mechanism, these two successful mutations (from the point of view of SARS-CoV-2) can be hypothesized to evade human antibodies. Usingin silicoall-atom molecular dynamics (MD) simulation as well as deep learning (DL) approaches, here we show that these two mutations significantly reduce the binding affinity between RBD and the antibody LY-CoV555 (also named as Bamlanivimab) that was proven to be efficacious for neutralizing the wide-type SARS-CoV-2. With the revealed molecular mechanism on how L452R and E484K evade LY-CoV555, we expect that more specific therapeutic antibodies can be accordingly designed and/or a precision mixing of antibodies can be achieved in a cocktail treatment for patients infected with the variant B.1.617.

Abstract Figure
Selection shapes the landscape of functional variation in wild house mice
Authors: Lawal Raman Akinyanju , Arora Uma P. , Dumont Beth L.
Published: May 2021

Background

Through 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.

Results

Here, 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.

Conclusions

Overall, 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

Next-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

Disorders 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 Figure

Graphical 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

The 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

Drug 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

A 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.

Highlights

Hyperactivity in posteromedial (PM) network in people at AD genetic risk (APOE E4)

Such PM network hyperactivity may initiate pathogenic cascade that triggers AD

APOE mouse models suggest hyperactivity driven by excitatory/inhibitory imbalance

Using 1H-MRS at 3T we studied PMC E/I balance in young adult APOE E4 carriers

Found 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

Meiotic 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

The 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

The 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

The 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 statement

It 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

RNA-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

A 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

Surveillance 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.
D-serine induces distinct transcriptomes in diverse Escherichia coli pathotypes
Authors: Connolly James P. R. , Turner Natasha C. A. , Hallam Jennifer C. , Rimbi Patricia T. , Flett Tom , McCormack Mhairi J. , Roe Andrew J. , O’Boyle Nicky
Published: May 2021

Appropriate interpretation of environmental signals facilitates niche specificity in pathogenic bacteria. However, the responses of niche-specific pathogens to common host signals are poorly understood. D-serine (D-ser) is a toxic metabolite present in highly variable concentrations at different colonisation sites within the human host that we previously found is capable of inducing changes in gene expression. In this study, we made the striking observation that the global transcriptional response of three Escherichia coli pathotypes - enterohaemorrhagic E. coli (EHEC), uropathogenic E. coli (UPEC) and neonatal meningitis associated E. coli (NMEC) - to D-ser was highly distinct. In fact, we identified no single differentially expressed gene common to all three strains. We observed the induction of ribosome-associated genes in extraintestinal pathogens UPEC and NMEC only, and the induction of purine metabolism genes in gut-restricted EHEC and UPEC indicating distinct transcriptional responses to a common signal. UPEC and NMEC encode dsdCXA – a genetic locus required for the detoxification and hence normal growth in the presence of D-ser. Specific transcriptional responses were induced in strains accumulating D-ser (WT EHEC and UPEC/NMEC mutants lacking the D-ser-responsive transcriptional activator DsdC), corroborating the notion that D-ser is an unfavourable metabolite if not metabolized. Importantly, many of the UPEC-associated transcriptome alterations correlate with published data on the urinary transcriptome, supporting the hypothesis that D-ser sensing forms a key part of urinary niche adaptation in this pathotype. Collectively, our results demonstrate distinct pleiotropic responses to a common metabolite in diverse E. coli pathotypes, with important implications for niche selectivity.

Importance

The pathogenic Escherichia coli comprise a group of highly specialized bacteria, some of which are capable of disseminating from the intestine and causing disease at other sites within the human host. Chemicals (metabolites) derived from the host and other microorganisms shape the behaviour of E. coli in different environments. Here we investigate the changes in gene expression that occur in E. coli strains capable (UPEC and NMEC) and incapable (EHEC) of metabolizing D-ser – a metabolite specifically enriched in the urine and in regions of the brain. We show that EHEC, UPEC and NMEC – distinct pathotypes associated with disease in the gut, bladder and brain, respectively, respond in a distinct manner to D-ser. Many of the genes affected by D-ser have been shown to be important during disease, highlighting the importance of varied responses to this common signal in host infection.