bluuebunny/crossref_metadata_2025 huggingface dataset:
Future climate change-related decreases in food quality may affect juvenile Chinook salmon growth and survival
Authors: Garzke Jessica , Forster Ian , Graham Caroline , Costalago David , Hunt Brian P.V.
Published: August 2022

The global temperature increase due to global change is predicted to be between 3.3 – 5.7°C by 2100 leading to changes at the base of the marine food web in species composition, abundance, and quality at the base of the marine food web leading to flow-on effects of higher trophic levels such as fish and humans. Changes in marine prey availability and nutritional quality can affect juvenile salmon conditions (i.e., growth, condition, and mortality) during the early marine phase. There is limited knowledge of the interplay between prey availability and prey quality and the importance of food quality under food-satiated conditions. Here, a three-phase feeding experiment measured the effects of nutritional quality (fatty acid composition and ratios) on juvenile Chinook salmon (Oncorhynchus tshawytscha) condition. Experimental diets represented the present three different climate scenarios with a present-day diet (Euphausia pacifica), a control diet (commercial aquaculture diet), and a predicted IPCC worst-case scenario diet with low essential fatty acid concentrations (IPCC SSP5-8.5). We tested how potential future low quality food affects growth rates, body condition, fatty acid composition and mortality rates in juvenile Chinook salmon compared to present-quality prey. Fatty acids were incorporated into the salmon muscle at varying rates but, on average, reflected dietary concentrations. High dietary concentrations of DHA, EPA and high DHA:EPA ratios resulted in increased fish growth and condition. In contrast, low concentrations of DHA and EPA and low DHA:EPA ratios in the diets were not compensated for by increased food quantity. This result highlights the importance of considering food quality when assessing fish response to changing ocean conditions.

Highlights

Climate change may decrease the quality of salmon prey through changes in the fatty acid composition.

Low dietary essential fatty acid levels reduce growth and condition and increase mortality rates in juvenile Chinook salmon.

Food quality changes within zooplankton species but also by changes between species.

Results suggest potential cascading effects on higher trophic levels when zooplankton species composition shifts to lower quality species.

Higher food intake cannot compensate for low food quality.
Analysis of the Hamiltonian Monte Carlo genotyping algorithm on PROVEDIt mixtures including a novel precision benchmark
Authors: Susik Mateusz , Sbalzarini Ivo F.
Published: August 2022

We provide an internal validation study of a recently published precise DNA mixture algorithm based on Hamiltonian Monte Carlo sampling [1]. We provide results for all 428 mixtures analysed by Riman et al. [2] and compare the results with two state-of-the-art software products: STRmix™ v2.6 and Euroformix v3.4.0. The comparison shows that the Hamiltonian Monte Carlo method provides reliable values of likelihood ratios (LRs) close to the other methods. We further propose a novel large-scale precision benchmark and quantify the precision of the Hamiltonian Monte Carlo method, indicating its improvements over existing solutions. Finally, we analyse the influence of the factors discussed by Buckleton et al. [3].
Depolarization of astrocytes in the basolateral amygdala restores WFS1 neuronal activity and rescues impaired risk-avoidance behavior in DISC1TM mice
Authors: Zhou Xinyi , Xiao Qian , Chen Shuai , Xu Xirong , Hong Yuchuan , Chen Yuewen , Wang Liping , Chen Yu , Yang Fan , Tu Jie
Published: August 2022

Many mental illnesses are accompanied by abnormal risk-avoidance behavior, yet we have only a limited understanding of the neuronal regulatory mechanisms involved. We previously established an inducible DISC1-N terminal fragment transgenic mouse (DISC1-NTM) model which has exhibited risk-avoidance deficiency. Using this model, we analyzed differentially expressed genes (DEGs) using snRNA-seq and the results indicate impaired neuron-astrocyte interactions. We used optogenetic tools to modulate astrocytes in the basolateral amygdala (BLA) and found that ChR2-expressing astrocytes were able to rescue risk-avoidance impairment in DISC1-NTM mice. Using patch clamp recordings combined with signal-cell qPCR, we found impaired excitability of BLAWFS1 neurons in DISC1-NTM mice and that ChR2-expressing astrocytes can induce action potentials (APs) in WFS1 neurons, which restores WFS1 neuronal activity. WFS1 neurons are necessary for BLA astrocytes to modulate impaired risk-avoidance behavior. These finding provide new insights into mechanisms of astrocyte-neuron interactions and suggest that BLA astrocytes may be a promising target for impaired risk avoidance in mental illness.

Highlights

ChR2-expressing astrocytes in the BLA rescue impaired risk-avoidance behavior in DISC1-NTM mice.

Astrocytes in the BLA modulate different nearby neurons to different degrees. Depolarization of BLA astrocytes restore neuronal activity in WFS1 neurons. Astrocytes in the BLA modulate WFS1 neurons via NMDARs.
Characterising Long Covid: a living systematic review update with controlled studies
Authors: Michelen Melina , Sigfrid Louise , Kartsonaki Christiana , Shemilt Ian , Hastie Claire , O’Hara Margaret E. , Suett Jake C. , Stelson Elisabeth A. , Bugaeva Polina , Dahmash Dania T. , Rigby Ishmeala , Munblit Daniel , Harriss Eli , Burls Amanda , Cheng Vincent , Scott Janet T. , Carson Gail , Olliaro Piero , Stavropoulou Charitini
Published: August 2022

Statement

The authors have withdrawn their manuscript owing to a reporting error that we have identified in the conduct of this updated systematic review. On 7thMarch 2022 we made changes to the original protocol published in F1000, to highlight the need to keep up with the evolving landscape of Covid-19 and Covid-19 research and focus on comparative, controlled studies. The revisions included also changes in data extraction and analysis that would be needed to do so. These changes were done in consultation with members of the Long COVID Support Group. However, we omitted to publicize these changes in an accessible, modified version of our protocol, and/or by updating our preregistered PROSPERO record (CRD42020211131) and F1000 publication, prior to commencing and completing these stages of the process. In this manuscript, which reports the revised analyses, we have consequently also omitted to explicitly describe these changes as important deviations from the published protocol. Additionally, following rapid, sustained, and continuous growth in the conduct and reporting of eligible primary studies, it has become clear that, with or without the changes described above, we do not have sufficient capacity or resources to transition our baseline systematic review to being regularly updated using a living systematic review approach. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Not4-dependent targeting ofMMF1mRNA to mitochondria limits its expression via ribosome pausing, Egd1 ubiquitination, Caf130, No-Go-Decay and autophagy
Authors: Chen Siyu , Allen George , Panasenko Olesya O. , Collart Martine A.
Published: August 2022

The Ccr4-Not complex is a conserved multi protein complex with diverse roles in the mRNA life cycle. Recently we determined that the Not1 and Not4 subunits of Ccr4-Not inversely regulate mRNA solubility and thereby impact dynamics of co-translation events. One mRNA whose solubility is limited by Not4 isMMF1encoding a mitochondrial matrix protein. In this work we determine that Not4 promotes the co-translational docking ofMMF1mRNA to mitochondria via the mitochondrial targeting sequence of the Mmf1 nascent chain, the Egd1 chaperone, the Om14 mitochondrial outer membrane protein and the co-translational import machinery. We observe thatMMF1mRNA is translated with ribosome pausing and uncover a mechanism that depends upon its targeting to the mitochondria and limits its overexpression. We have named this mechanism Mito-ENCay. It relies onEgd1 ubiquitination byNot4, theCaf130 subunit of the Ccr4-Not complex, the mitochondrial outer membrane proteinCis1, No-Go-Decayas well as autophagy. We propose that in fermenting yeast, mRNAs whose encoded proteins depend upon co-translational folding and/or assembly are regulated by Caf130-dependent quality control mechanisms similar to Mito-ENCay.
Alignment, Segmentation and Neighborhood Analysis in Cyclic Immunohistochemistry Data Using CASSATT
Authors: Brockman Asa A. , Khurana Rohit , Bartkowiak Todd , Thomas Portia L. , Sivagnanam Shamilene , Betts Courtney B , Coussens Lisa M. , Lovly Christine M. , Irish Jonathan M. , Ihrie Rebecca A.
Published: August 2022

Cyclic immunohistochemistry (cycIHC) uses sequential rounds of colorimetric immunostaining and imaging for quantitative mapping of location and number of cells of interest. In addition, cycIHC benefits from the speed and simplicity of brightfield microscopy for data collection, making the collection of entire tissue sections and slides possible at a trivial cost compared to other high dimensional imaging modalities. However, large cycIHC datasets (greater than 50 GB) currently require an expert data scientist to concatenate separate open-source tools for each step of image pre-processing, registration, and segmentation, or the use of proprietary software. Here, we present a unified and user-friendly pipeline for processing, aligning, and analyzing cycIHC data - Cyclic Analysis of Single-Cell Subsets and Tissue Territories (CASSATT). CASSATT registers scanned slide images across all rounds of staining, segments individual nuclei, and measures marker expression on each detected cell. Beyond straightforward single cell data analysis outputs, CASSATT explores the spatial relationships between cell populations. By calculating the logodds of interaction frequencies between cell populations within tissues and tissue regions, this pipeline helps users identify populations of cells that interact - or do not interact - at frequencies that are greater than those occurring by chance. It also identifies specific neighborhoods of cells based on the assortment of neighboring cell types that surround each cell in the sample. The presence and location of these neighborhoods can be compared across slides or within distinct regions within a tissue. CASSATT was first tested using a newly generated cycIHC dataset consisting of six GBM tissue sections processed through eight cycles of AEC based IHC staining. Further validation was completed on a previously published lung cancer tissue microarray dataset consisting of 107 cores processed through eighteen cycles of staining and imaging. CASSATT is a fully open-source workflow tool developed to process cycIHC data and will allow greater utilization of this powerful staining technique.
Revisiting the impact of synthetic ORF sequences on engineered LINE-1 retrotransposition
Authors: Chan Dorothy , Workman Stephanie , Gerdes Patricia , Han Jeffrey S , Boeke Jef D , Faulkner Geoffrey J , Richardson Sandra R
Published: August 2022

The retrotransposon Long Interspersed Element 1 (L1) contains adenosine rich ORFs, a characteristic that limits its expression in mammalian cells. A synthetic mouse L1 (smL1) with ORF adenosine content decreased from 40% to 26% showed increased mRNA expression and retrotransposed far more efficiently than the native parental element, L1spa (1). Here, we observe two nonsynonymous substitutions between the L1spa and smL1 ORF1 sequences, and note that the smL1 3’UTR lacks a conserved guanosine-rich region (GRR) which could potentially take on a G-quadruplex secondary structure. We find that the combined effect of a single amino acid change and the GRR 3’UTR deletion, rather than synthetic ORF sequences, accounts for the increase in smL1 retrotransposition efficiency over L1spa. Furthermore, we demonstrate that the position of the GRR within the L1 reporter construct impacts retrotransposition efficiency. Our results prompt a reevaluation of synthetic L1 activity and suggest native mouse L1 mobility has in some cases been underestimated in engineered retrotransposition assays.

Author Summary

L1 retrotransposons are mobile DNA elements or “jumping genes” that can copy- and-paste their sequences to new locations in the host genome. The jumping ability, or retrotransposition efficiency, of individual L1 elements can be evaluated using a cultured cell assay in which the L1 is tagged in its 3’ untranslated region (3’UTR) with a reporter gene that becomes expressed upon successful retrotransposition. In a previous study, authors Han and Boeke reported that the retrotransposition efficiency of a mouse L1 element could be enhanced dramatically by synthetically increasing the GC content of the L1 ORFs without changing their amino acid sequence. Curiously, a similarly constructed synthetic human L1 achieved only a modest increase in retrotransposition efficiency over the native element. Here, we find that two coding changes and partial deletion of the mouse L1 3’UTR sequence which occurred during construction of the synthetic mouse L1 reporter actually are responsible for the increased jumping of this construct. We also find that changing the placement as well as the presence of this deleted 3’UTR region within the reporter construct determines its impact on engineered retrotransposition efficiency. Together, our study reconciles the disparate impacts of synthetic sequences upon human and mouse L1 retrotransposition efficiency, prompts a reconsideration of numerous studies using synthetic L1 constructs, and will inform the ongoing use of synthetic and natural mouse L1 reporter constructs in vivo and in vitro.
A Large-Scale ENIGMA Multisite Replication Study of Brain Age in Depression
Authors: Han Laura K.M. , Dinga Richard , Leenings Ramona , Hahn Tim , Cole James H. , Aftanas Lyubomir , Amod Alyssa R. , Besteher Bianca , Colle Romain , Corruble Emmanuelle , Couvy-Duchesne Baptiste , Danilenko Konstantin , Fuentes-Claramonte Paola , Gonul Ali Saffet , Gotlib Ian H. , Goya-Maldonado Roberto , Groenewold Nynke A. , Hamilton Paul , Ichikawa Naho , Ipser Jonathan C. , Itai Eri , Koopowitz Sheri-Michelle , Li Meng , Okada Go , Okamoto Yasumasa , Olga Churikova , Osipov Evgeny , Penninx Brenda W.J.H. , Pomarol-Clotet Edith , Rodríguez-Cano Elena , Sacchet Matthew D. , Shinzato Hotaka , Sim Kang , Stein Dan J. , Uyar-Demir Aslihan , Veltman Dick J. , Schmaal Lianne
Published: August 2022

Background

Several studies have evaluated whether depressed persons have older appearing brains than their nondepressed peers. However, the estimated neuroimaging-derived “brain age gap” has varied from study to study, likely driven by differences in training and testing sample (size), age range, and used modality/features. To validate our previously developed ENIGMA brain age model and the identified brain age gap, we aim to replicate the presence and effect size estimate previously found in the largest study in depression to date (N=2,126 controls & N=2,675 cases; +1.08 years [SE 0.22], Cohen’s d=0.14, 95% CI: 0.08-0.20), in independent cohorts that were not part of the original study.

Methods

A previously trained brain age model (www.photon-ai.com/enigma_brainage) based on 77 FreeSurfer brain regions of interest was used to obtain unbiased brain age predictions in 751 controls and 766 persons with depression (18-75 years) from 13 new cohorts collected from 20 different scanners.

Results

Our ENIGMA MDD brain age model generalized reasonably well to controls from the new cohorts (predicted age vs. age:r= 0.73,R2=0.47, MAE=7.50 years), although the performance varied from cohort to cohort. In these new cohorts, on average, depressed persons showed a significantly higher brain age gap of +1 year (SE 0.35) (Cohen’s d□=□□.15, 95% CI: 0.05–0.25) compared with controls, highly similar to our previous finding.

Conclusions

This study further validates our previously developed ENIGMA brain age algorithm. Importantly, we replicated the brain age gap in depression with a comparable effect size. Thus, two large-scale independent mega-analyses across in total 32 cohorts and >3,400 patients and >2,800 controls worldwide show reliable but subtle effects of brain aging in adult depression.
Reactivation of an errantivirus inDrosophilaovarian somatic tissue: from germline invasion to taming
Authors: Yoth Marianne , Maupetit-Méhouas Stéphanie , Akkouche Abdou , Gueguen Nathalie , Bertin Benjamin , Jensen Silke , Brasset Emilie
Published: August 2022

Most Drosophila transposable elements (TEs) are LTR retrotransposons, some of which belong to the genus Errantivirus and share structural and functional characteristics with vertebrate endogenous retroviruses (ERVs). These virus-derived elements occupy a large part of the genome, but it is unclear whether and how they can be reactivated and if they retain their replication capacity. We created conditions where control of the DrosophilaZAMerrantivirus through the piRNA pathway was abolished leading to its reactivation in real time in somatic gonadal cells. We show that ZAM may remain active in these cells indicating that errantiviruses may hide from the efficient germline piRNA pathway by being expressed exclusively in somatic cells. After reactivation,ZAMinvaded the oocytes and severe fertility defects were observed. The germline then set up its own adaptive genomic immune response against the constantly invading errantivirus, restricting invasion and restoring fertility. Our results not only highlight how errantiviruses and their host adapt to each other but also reveal a time window during oogenesis that may be favourable for viral germline invasion and endogenization.
Structures of ferroportin in complex with its specific inhibitor vamifeport
Authors: Lehmann Elena F. , Liziczai Márton , Drożdżyk Katarzyna , Altermatt Patrick , Manolova Vania , Sundstrom Hanna , Dürrenberger Franz , Dutzler Raimund , Manatschal Cristina
Published: August 2022

A central regulatory mechanism of iron homeostasis in humans involves ferroportin (FPN), the sole cellular iron exporter, and the peptide hormone hepcidin, which inhibits Fe2+ transport and induces internalization and degradation of FPN. Dysregulation of the FPN/hepcidin axis leads to diverse pathological conditions, and consequently, pharmacological compounds that inhibit FPN-mediated iron transport are of high clinical interest. Here, we describe the cryo-EM structures of human FPN in complex with synthetic nanobodies and vamifeport (VIT-2763), the first clinical-stage oral FPN inhibitor. Vamifeport competes with hepcidin for FPN binding and is currently in clinical development for β-thalassemia and sickle cell disease. The structures display two distinct conformations of FPN, representing outward-facing and an occluded states of the transporter. The vamifeport site is located in the center of the protein, where the overlap with hepcidin interactions underlies the competitive relationship between the two molecules. The introduction of point mutations in the binding pocket of vamifeport reduces its affinity to FPN, emphasizing the relevance of the structural data. Together, our study reveals the conformational rearrangements of FPN on its transport cycle and it provides initial insight into the pharmacological targeting of this unique iron efflux transporter.
Comparing different computational approaches for detecting long-term vertical transmission in host-associated microbiota
Authors: Perez-Lamarque Benoît , Morlon Hélène
Published: August 2022

Long-term vertical transmissions of gut bacteria are thought to be frequent and functionally important in mammals. Several phylogenetic-based approaches have been proposed to detect, among species-rich microbiota, the bacteria that have been vertically transmitted during a host clade radiation. Applied to mammal microbiota, these methods have sometimes led to conflicting results; in addition, how they cope with the slow evolution of markers typically used to characterize bacterial microbiota remains unclear. Here, we use simulations to test the statistical performances of two widely-used global-fit approaches (ParaFit and PACo) and two event-based approaches (ALE and HOME). We find that these approaches have different strengths and weaknesses depending on the amount of variation in the bacterial DNA sequences and are therefore complementary. In particular, we show that ALE performs better when there is a lot of variation in the bacterial DNA sequences, whereas HOME performs better when there is not. Global-fit approaches (ParaFit and PACo) have higher type-I error rates (false positives) but have the advantage to be very fast to run. We apply these methods to the gut microbiota of primates and our results suggest that only a small fraction of their gut bacteria is vertically transmitted.
A systematic scoping review of the ethics of contributor role ontologies and taxonomies
Authors: Hosseini Mohammad , Gordijn Bert , Wafford Q. Eileen , Holmes Kristi L.
Published: August 2022

Contributor Role Ontologies and Taxonomies (CROTs) provide a standard list of roles to specify individual contributions to publications. Due to the recent uptake of CROTs – the CRediT taxonomy in particular– researchers from different disciplinary backgrounds have anticipated a positive impact on ethical issues related to the attribution of credit and responsibilities. Yet, they have also voiced concerns about CROTs shortcomings and ways in which they could be misunderstood or misused and have provided suggestions to improve them. These discussions have never been collated and consolidated. To fill this gap, the current scoping review collates and explores published viewpoints about the ethics of CROTs. Ovid Medline, Scopus, Web of Science, and Google Scholar were searched. In total, 30 papers met the inclusion criteria and were subsequently analyzed using an inductive approach. We identified eight themes and 20 specific issues related to the ethics of CROTs and provided four recommendations for CROT developers: 1) Compile comprehensive instructions that explain how CROTs should be used and that note common pitfalls of employing them in practice; 2) Improve the coherence of used terms, 3) Provide translations of roles in languages other than English, and 4) Communicate a clear vision about future development plans.
Effects of human-wildlife Conflicts on Local People’s Livelihoods and Wildlife Conservation in and around Alitash National Park, Northwest Ethiopia
Authors: Ayalew Mekuriaw Zewdie , Melese Getahun Tassew
Published: August 2022

Human-wildlife conflict becomes one of the fundamental aspects of wildlife management because it threatens both wildlife and human. People injured, abused, and killed wildlife in response to the perceived and/or actual damages from wildlife. Such negative interaction between humans and wildlife exists everywhere but more intense and costly in adjacent protected areas. This study aimed to assess the effects of human-wildlife conflicts on local people’s livelihood and wildlife conservation in and around Alitash National Park. The primary data were collected using multi-stage sampling techniques by employing a combination of social survey methods involving participatory techniques (focus group discussions and key informant interviews) and structured household interviewers. The survey questionnaire consisted of both open-ended and fixed-response questions designed to solicit information mainly for wildlife-caused damages and other costs to the local community along with human-induced wildlife decline and perceptions towards wildlife conservation. The results revealed that 59.6% of the respondents encountered at least a single type of damage. More than half (54%) of respondents encountered crop damage, of which 34.4% lost up to 25% of their crop fields whereas the amount of loss to the remaining (18.7%) was to 75% of the crop fields. The livestock loss during the last five years of the period prior to the survey administration was 287.89 tropical livestock units which were shared by 47.5% of the respondents. Wildlife attacks on humans were rare but eighteen attacks were caused by Panther leo, Crocuta crocuta and Panthera pardus were encountered when the victims cross the habitats of the species. The responses of the victims to the wildlife imposed the damage was negative and full of anger and resentment. This has been undermining conservation efforts and the socio-economic welfare of the local people around Alitash National Park. Providing alternative livelihood opportunities and creating a context-based conservation scheme along with continuous conservation education would help to reduce the negative effect of human-wildlife conflicts on both wildlife and people in the study area.
The claudin-like apicomplexan microneme protein is required for gliding motility and infectivity of Plasmodium sporozoites
Authors: Loubens Manon , Marinach Carine , Paquereau Clara-Eva , Hamada Soumia , Hoareau-Coudert Bénédicte , Akbar David , Franetich Jean-François , Silvie Olivier
Published: August 2022

Invasion of host cells by apicomplexan parasites such as Toxoplasma and Plasmodium spp requires the sequential secretion of the parasite apical organelles, the micronemes and the rhoptries. The claudin-like apicomplexan microneme protein (CLAMP) is a conserved protein that plays an essential role during invasion in Toxoplasma gondii tachyzoites and Plasmodium falciparum merozoites. CLAMP is also expressed in Plasmodium sporozoites, the mosquito-transmitted forms of the malaria parasite, but its role in this stage is still unknown. CLAMP is essential for Plasmodium blood stage growth and is refractory to conventional gene deletion. To circumvent this obstacle and study the function of CLAMP in sporozoites, we used a conditional genome editing strategy based on the dimerisable Cre recombinase in the rodent malaria model parasite P. berghei. We successfully deleted clamp gene in P. berghei transmission stages and analyzed the functional consequences on sporozoite infectivity. In mosquitoes, sporozoite development and egress from oocysts was not affected in conditional mutants. However, invasion of the mosquito salivary glands was dramatically reduced upon deletion of clamp gene. In addition, CLAMP-deficient sporozoites were impaired in cell traversal and productive invasion of mammalian hepatocytes. This severe phenotype was associated with major defects in gliding motility and with reduced shedding of the sporozoite adhesin TRAP. These results demonstrate that CLAMP is essential across invasive stages of the malaria parasite, and strongly suggest that the protein acts upstream of host cell invasion, possibly by regulating the secretion or function of adhesins in Plasmodium sporozoites.

Author summary

Plasmodium parasites, the causative agents of malaria, are transmitted during the bite of an infected mosquito. Infectious parasite stages known as sporozoites are released from the insect salivary glands and injected into the host skin. Sporozoites rapidly migrate to the host liver, invade hepatocytes and differentiate into the next invasive forms, the merozoites, which invade and replicate inside red blood cells. Sporozoite motility and host cell invasion rely on the secretion of apical organelles called micronemes and rhoptries. Here we characterize the function of a microneme protein expressed both in merozoites and sporozoites, the claudin-like protein CLAMP. We used a conditional genome editing strategy in a rodent malaria model to generate CLAMP-deficient sporozoites. In the absence of CLAMP, sporozoites failed to invade mosquito salivary glands and mammalian hepatocytes, and showed defects in gliding motility and microneme secretion. Our data establish that CLAMP plays an essential role across Plasmodium invasive stages, and might represent a potential target for transmission-blocking antimalarial strategies.
Antimicrobial activity of cationic antimicrobial peptides against stationary phase bacteria
Authors: Rodríguez-Rojas Alexandro , Rolff Jens
Published: August 2022

Antimicrobial peptides (AMPs) are ancient antimicrobial weapons used by multicellular organisms as components of their innate immune defences. Because of the antibiotic crisis, AMPs have also become candidates for developing new drugs. Here, we show that five different AMPs of different classes are effective against non-dividing E. coli and S. aureus. By comparison, three conventional antibiotics from the main three classes of antibiotics poorly kill non-dividing bacteria at clinically relevant doses. The killing of fast-growing bacteria by AMPs is faster than that of slow-dividing bacteria and, in some cases, without any difference. Still, non-dividing bacteria are effectively killed over time. Our results point to a general property of AMPs, which might explain why selection has favoured AMPs in the evolution of metazoan immune systems. The ability to kill non-dividing cells is another reason that makes AMPs exciting candidates for drug development.
Stable isotopomers of myo-inositol to uncover the complex MINPP1-dependent inositol phosphate network
Authors: Trung Minh Nguyen , Kieninger Stefanie , Fandi Zeinab , Qiu Danye , Liu Guizhen , Saiardi Adolfo , Jessen Henning , Keller Bettina , Fiedler Dorothea
Published: August 2022

The water-soluble inositol phosphates (InsPs) represent a functionally diverse group of small-molecule messengers central to a myriad of cellular processes. However, we have an incomplete understanding of InsP metabolism because the available analytical toolset for inositol phosphates is rather limited. Here, we have synthesized and utilized fully and unsymmetrically 13C-labeled myo-inositol and inositol phosphates. These probes were applied in combination with nuclear magnetic resonance spectroscopy (NMR) and capillary electrophoresis mass spectrometry (CE-MS) to further annotate central aspects of InsP metabolism in human cells. The labeling strategy provided detailed structural information via NMR – down to individual enantiomers – which overcomes a crucial blind spot in the analysis of InsPs. We uncovered a novel branch of InsP dephosphorylation in human cells which is dependent on MINPP1, a phytase-like enzyme, that contributes to cellular homeostasis. Full characterization of MINPP1 activity in vitro and in cells, provided a clear picture of this multifunctional phosphatase. Metabolic labeling with stable isotopomers thus constitutes a powerful tool for investigating InsP networks in a variety of different biological contexts.
Sequential And Directional Insulation By Conserved CTCF Sites Underlies The Hox Timer In Pseudo-Embryos
Authors: Rekaik Hocine , Lopez-Delisle Lucille , Hintermann Aurélie , Mascrez Bénédicte , Bochaton Célia , Duboule Denis
Published: August 2022

During development, Hox genes are activated in a time sequence following their relative positions on their clusters, leading to the proper identities of structures along the rostral to caudal axis. To understand the mechanism operating this Hox timer, we used ES-cells derived stembryos and show that the core of the process involves the start of transcription at the 3’ part of the cluster, following Wnt signaling, and the concomitant loading of cohesin complexes on the transcribed DNA segments, i.e., with an asymmetric distribution along the gene cluster. Chromatin extrusion then occurs with successively more posterior CTCF sites acting as transient insulators, thus generating a progressive time-delay in the activation of more 5’-located genes due to long-range contacts with a flanking TAD. Mutant stembryos support this model and reveal that the iterated presence of evolutionary conserved and regularly spaced intergenic CTCF sites control the precision and the pace of this temporal mechanism.
Persistent virus-specific and clonally expanded antibody secreting cells respond to induced self antigen in the CNS
Authors: Agrafiotis Andreas , Dizerens Raphael , Vincenti Ilena , Wagner Ingrid , Kuhn Raphael , Shlesinger Danielle , Manero-Carranza Marcos , Cotet Tudor-Stefan , Hong Kai-Lin , Page Nicolas , Fonta Nicolas , Shammas Ghazal , Mariotte Alexandre , Piccinno Margot , Kreutzfeldt Mario , Gruntz Benedikt , Ehling Roy , Genovese Alessandro , Pedrioli Alessandro , Dounas Andreas , Franzenburg Sören , Kavaka Vladyslav , Gerdes Lisa Ann , Dornmair Klaus , Beltrán Eduardo , Oxenius Annette , Reddy Sai T. , Merkler Doron , Yermanos Alexander
Published: August 2022

B cells contribute to the pathogenesis of both cellular- and humoral-mediated central nervous system (CNS) inflammatory diseases through a variety of mechanisms. In such conditions, B cells may enter the CNS parenchyma and contribute to local tissue destruction. It remains unexplored, however, how infection and autoimmunity drive transcriptional phenotypes, repertoire features, and antibody functionality. Here, we profiled B cells from the CNS of murine models of intracranial (i.c.) viral infections and autoimmunity. We identified a population of clonally expanded, antibody secreting cells (ASCs) that had undergone class-switch recombination and extensive somatic hypermutation following i.c. infection with attenuated lymphocytic choriomeningitis virus (rLCMV). Recombinant expression and characterisation of these antibodies revealed specificity to viral antigens (LCMV glycoprotein GP), correlating with ASC persistence in the brain weeks after resolved infection. Furthermore, these virus-specific ASCs upregulated proliferation and expansion programs in response to the conditional and transient induction of the LCMV GP as a neo-self antigen by astrocytes. This class-switched, clonally expanded, and mutated population persisted and was even more pronounced when peripheral B cells were depleted prior to autoantigen induction in the CNS. In contrast, the most expanded B cell clones in mice with persistent expression of LCMV GP in the CNS did not exhibit neo-self antigen specificity, potentially a consequence of local tolerance induction. Finally, a comparable population of clonally expanded, class-switched, proliferating ASCs was detected in the cerebrospinal fluid of multiple sclerosis patients. Taken together, our findings support the existence of B cells that populate the CNS and are capable of responding to locally encountered autoantigens.

Graphical abstract
Statistical modelling of aquatic size spectra: integrating data from multiple taxa and sampling methods
Authors: Giacomini Henrique Corrêa , de Kerckhove Derrick T. , Kopf Victoria , Chu Cindy
Published: August 2022

Size spectra are used to assess the status and functioning of marine and freshwater ecosystems worldwide. Its use is underpinned by theory linking the dynamics of trophic interactions to a power-law decline of abundance with body size in ecological communities. Recent papers on empirical size spectrum estimation have argued for Maximum Likelihood Estimation (MLE) of power-law probability distributions as a more accurate alternative to traditional linear regression approaches. One major limitation of currently used size spectrum estimators from MLE is that they cannot account for the use of multiple sampling protocols, nor the distortions caused by gear size selectivity, and therefore they become restricted to a relatively narrow taxonomic group and size range. Further progress in the field requires new methods that are flexible enough to combine multiple trophic groups and sampling gears into a single size spectrum estimate, while taking advantage of more accurate distributional approaches. The method we propose in this paper fills this gap by deriving the distribution of observed sizes explicitly from the underlying power-law spectrum and gear selectivity functions. It specifies likelihoods as a product of two components: (i) the probability of belonging to a given group and (ii) the probability distribution within the group. Using Bayesian estimation, we applied the method to surveys of phytoplankton, zooplankton, and fishes in lakes of Quetico Provincial Park, northwestern Ontario, using Van Dorn samplers, zooplankton nets, gillnets, and hydroacoustics. The results show that the spectra estimated from subsets of trophic groups or gears are weak predictors of more complete spectra, highlighting the importance of using more inclusive community data. The two-component partitioning of likelihoods also helped demonstrating the existence of between-group spectrum slopes that were overall steeper than within-group slopes, indicating that heterogeneity of trophic transfers across the size spectrum is an important factor structuring these ecosystems.
«Application of RT-LAMP-CRISPR-Cas13a technology to the detection of OXA-48 producing Klebsiella pneumoniae»
Authors: Ortiz-Cartagena Concha , Blasco Lucia , Fernández-García Laura , Pacios Olga , Bleriot Ines , López María , Fernández-Cuenca Felipe , Cantón Rafael , Tomás María
Published: August 2022

Carbapenem-resistant pathogens have been recognized as a health concern because of their ability to cause severe infections and because they are difficult to detect in laboratories. Researchers are making great efforts to develop a diagnostic technique with high levels of sensitivity and specificity, as accurate, early diagnosis is required to prevent the spread of these microorganisms and improve the prognosis of patients. In this context, CRISPR-Cas systems are proposed as promising tools for the development of diagnostic techniques due to their high specificity: Cas13 endonuclease discriminates single nucleotide changes and displays collateral activity against single-stranded RNA molecules. This technology is usually combined with isothermal pre-amplification reactions in order to increase the sensitivity of diagnosis. We have developed an RT-LAMP-CRISPR-Cas13a-based assay for the detection of Klebsiella pneumoniae OXA-48 producer strains in clinical samples without the need for RNA extraction. The assay exhibited 100 % specificity, sensitivity, positive predictive value and negative predictive value.
Proteomics unveil a central role for peroxisomes in butyrate assimilation of the heterotrophic Chlorophyte alga Polytomella sp
Authors: Lacroux J. , Atteia A. , Brugière S. , Couté Y. , Vallon O. , Steyer J.-P. , van Lis R.
Published: August 2022

Volatile fatty acids found in effluents of the dark fermentation of biowastes can be used for mixotrophic growth of microalgae, improving productivity and reducing the cost of the feedstock. Microalgae can use the acetate in the effluents very well, but butyrate is poorly assimilated and can inhibit growth above 1 gC.L-1. The non-photosynthetic chlorophyte alga Polytomella sp. SAG 198.80 was found to be able to assimilate butyrate fast. To decipher the metabolic pathways implicated in butyrate assimilation, quantitative proteomics study was developed comparing Polytomella sp. cells grown on acetate and butyrate at 1 gC.L-1. After statistical analysis, a total of 1772 proteins were retained, of which 119 proteins were found to be overaccumulated on butyrate vs. only 46 on acetate, indicating that butyrate assimilation necessitates additional metabolic steps. The data show that butyrate assimilation occurs in the peroxisome via the β-oxidation pathway to produce acetyl-CoA and further tri/dicarboxylic acids in the glyoxylate cycle. Concomitantly, reactive oxygen species defense enzymes as well as the branched amino acid degradation pathway were strongly induced.Although no clear dedicated butyrate transport mechanism could be inferred, several membrane transporters induced on butyrate are identified as potential condidates. Metabolic responses correspond globally to the increased needs for central cofactors NAD, ATP and CoA, especially in the peroxisome and the cytosol.
Bacterial Microbiome and Host Inflammatory Gene Expression in Foreskin Tissue
Authors: Maust Brandon S. , Petkov Stefan , Herrera Carolina , Feng Colin , Brown Bryan P. , Lebina Limakatso , Opoka Daniel , Ssemata Andrew , Pillay Natasha , Serwanga Jennifer , Seatlholo Portia , Namubiru Patricia , Odoch Geoffrey , Mugaba Susan , Seiphetlo Thabiso , Gray Clive M. , Kaleebu Pontiano , Webb Emily L. , Martinson Neil , Chiodi Francesca , Fox Julie , Jaspan Heather B.
Published: August 2022

As part of the CHAPS randomized clinical trial, we sequenced a segment of the bacterial 16S rRNA gene from foreskin tissue of 144 adolescents from South Africa and Uganda collected during surgical penile circumcision after receipt of 1 to 2 doses of placebo, emtricitabine with tenofovir disoproxil fumarate, or emtricitabine with tenofovir alafenamide. We found a large proportion ofCorynebacteriumin addition to other anaerobic species.Cutibacterium acneswas more abundant among participants from South Africa than Uganda, though this made no difference in surgical recovery. We did not find a difference in bacterial populations by treatment received nor bacterial taxa that were differentially abundant between participants who received placebo versus active drug. Using RNAseq libraries from foreskin tissue of the same participants, we found negative correlations between the relative abundance of bacterial taxa and the expression of genes downstream of the innate response to bacteria and regulation of the inflammatory response. When participants were divided into clusters based on bacterial community composition, two main clusters emerged which were distinguished by high and low bacterial diversity. Random forest classification showed higher expression ofNFATC3andSELENOSand lower expression ofSTAP1andNLRP6in the higher diversity group compared to the lower. Our results show no difference in the tissue microbiome of the foreskin with short-course PrEP but that bacterial taxa were largely inversely correlated with gene expression, consistent with non-inflammatory colonization.

Author Summary

We investigated the bacterial community of the foreskin of the penis. Previous studies found increased inflammation with certain anaerobic bacteria from swabs taken under the foreskin, but we found that higher relative abundances of the bacteria were correlated with lower expression of inflammatory genes. We did not find different bacteria in participants who received medicine to prevent HIV. Understanding the relationship between bacteria and inflammation in the penis will help us to understand how interventions like penile circumcision reduce the risk of acquiring sexually transmitted infections such as HIV.
Expression and Splicing Mediate Distinct Biological Signals
Authors: Dam Søren Helweg , Olsen Lars Rønn , Vitting-Seerup Kristoffer
Published: August 2022

Background

Through alternative splicing, most human genes produce multiple isoforms in a cell-, tissue-, and disease-specific manner. Numerous studies show that alternative splicing is essential for development, diseases and their treatments. Despite these important examples, the extent and biological relevance of splicing are currently unknown.

Results

To solve this problem, we developed pairedGSEA and used it to profile transcriptional changes in 100 representative RNA-seq datasets. Our systematic analysis demonstrates that changes in splicing, on average, contribute to 48.1% of the biological signal in expression analyses. Gene-set enrichment analysis furthermore indicates that expression and splicing both convey shared and distinct biological signals.

Conclusion

These findings establish alternative splicing as a major regulator of the human condition and suggest that most contemporary RNA-seq studies likely miss out on critical biological insights. We anticipate our results will contribute to the transition from a gene-centric to an isoform-centric research paradigm.
The neural signature of magnitude integration between time and numerosity
Authors: Togoli I. , Fornaciai M. , Visibelli E. , Piazza M. , Bueti D.
Published: August 2022

Magnitude dimensions such as time and numerosity are fundamental components of our visual experience, allowing us to understand the environment and interact with it. Different magnitudes are however not processed independently from each other, but show a relationship whereby the perception of one dimension depends on the others (“magnitude integration”). In this study, we use electroencephalography (EEG) to address whether such integration may arise from a shared brain processing stage where different dimensions are integrated together, or from independent parallel processes interfering with each other. In the experiment, participants judged either the average numerosity or duration of dynamic dot-array stimuli concurrently modulated in both dimensions. First, the behavioural results show a magnitude integration effect in both tasks, with duration affecting the judgement of numerosity and vice versa. The EEG results further show that both numerosity and duration significantly modulate event-related potentials at several distinct latencies. Crucially, however, we identified a significant interaction between numerosity and duration emerging in a specific latency window (360-460 ms) irrespective of the task performed by participants. In this latency window, the modulation of ERPs provided by the interfering magnitude dimension can be predicted by the strength of the behavioural bias. Our results thus support the idea of different magnitude dimensions converging onto a shared perceptual processing stage mediating their integration. Overall, our results demonstrate a clear electrophysiological signature of magnitude integration between numerosity and time, and provide new evidence for a shared representational system encompassing different magnitude dimensions.
Evolutionary Divergence in the Conformational Landscapes of Tyrosine vs Serine/Threonine Kinases
Authors: Gizzio Joan , Thakur Abhishek , Haldane Allan , Levy Ronald M.
Published: August 2022

Inactive conformations of protein kinase catalytic domains where the DFG motif has a “DFG-out” orientation and the activation loop is folded present a druggable binding pocket that is targeted by FDA-approved “type-II inhibitors” in the treatment of cancers. Tyrosine Kinases (TKs) typically show strong binding affinity with a wide spectrum of type-II inhibitors while Serine/Threonine Kinases (STKs) usually bind more weakly which we suggest here is due to differences in the folded to extended conformational equilibrium of the activation loop between TKs vs. STKs. To investigate this, we use sequence covariation analysis with a Potts Hamiltonian statistical energy model to guide absolute binding free-energy molecular dynamics simulations of 74 protein-ligand complexes. Using the calculated binding free energies together with experimental values, we estimated free-energy costs for the large-scale (∼17-20Å) conformational change of the activation loop by an indirect approach, circumventing the very challenging problem of simulating the conformational change directly. We also used the Potts statistical potential to thread large sequence ensembles over active and inactive kinase states. The structure-based and sequence-based analyses are consistent; together they suggest TKs evolved to have free-energy penalties for the classical “folded activation loop” DFG-out conformation relative to the active conformation that is, on average, 4-6 kcal/mol smaller than the corresponding values for STKs. Potts statistical energy analysis suggests a molecular basis for this observation, wherein the activation loops of TKs are more weakly “anchored” against the catalytic loop motif in the active conformation, and form more stable substrate-mimicking interactions in the inactive conformation. These results provide insights into the molecular basis for the divergent functional properties of TKs and STKs, and pharmacological implications for the target selectivity of type-II inhibitors.