bluuebunny/crossref_metadata_2025 huggingface dataset:
Acceptability of Community Midwives in rural communities of Pakistan: A qualitative exploratory study
Authors: Khowaja Bakhtawar Muhammad Hanif , Feroz Anam Shahil , Rani Musarrat , Khowaja Quratulain , Khowaja Mehmooda Afroz Ali , Abrejo Farina , Saleem Sarah
Published: February 2023

Introduction

The Government of Pakistan initiated the Community Midwifery program in 2006 to provide skilled birth attendance to women living in rural areas. However, the acceptability of midwives and what impact these community midwives have made on overall maternal morbidity and mortality remains an unanswered question. We explored the perceptions of health officials, midwifery students, midwives and community women about the factors that influence the acceptability of community midwives’ services in the rural district Thatta, Pakistan.

Materials and Methods

A qualitative exploratory study was conducted in the rural district Thatta of Pakistan. In-depth interviews were conducted with health officials, midwifery students who were currently enrolled in the midwifery program of the district; community midwives providing services in district Thatta, and trained community midwives who are not practicing. Interviews were also conducted with community women. Data were analyzed using the qualitative thematic analysis approach and the deductive analysis method.

Results

Two overarching themes were identified: (I) community acceptance and support; and (II) dynamics between CMWs and other health care providers. The major hindering factors to CMWs acceptance included their young age challenging social acceptability, patronizing behavior of doctors, high acceptance of traditional birth attendants working in rural areas, and the community’s reluctance towards referral services. The facilitating factors included clients’ privacy maintained at birth stations and the affordability of community midwives’ services.

Conclusion

There are deep-rooted challenges related to the acceptability of midwifery services at the community level and with other competing healthcare providers which need advocacy to support and accept their services at the community level and by other professionals.
Cultivation of the polyextremophileCyanidioschyzon merolae10D during summer conditions on the coast of the Red Sea and its adaptation to hypersaline sea water
Authors: Villegas Melany V. , González-Portela Ricardo E. , de Freitas Bárbara Bastos , Al Jahdali Abdulaziz , Romero-Villegas Gabriel I. , Malibari Raghdah , Kapoore Rahul Vijay , Fuentes-Grünewald Claudio , Lauersen Kyle J.
Published: February 2023

The west coast of Saudi Arabia borders the Red Sea, which maintains high average temperatures and increased salinity compared to other seas or oceans. Summer conditions in the Arabian Peninsula may exceed the temperature tolerance of most currently cultivated microalgae. The Cyanidiales are polyextremophilic red algae whose native habitats are at the edges of acidic hot springs.Cyanidioschyzon merolae10D has recently emerged as an interesting model organism capable of high-cell density cultivation on pure CO2with optimal growth at 42 °C and low pH between 0.5-2.C. merolaebiomass has an interesting macromolecular composition, is protein rich, and contains valuable bio-products like heat-stable phycocyanin, carotenoids, β-glucan, and starch. Here, photobioreactors were used to modelC. merolae10D growth performance in simulated environmental conditions of the mid-Red Sea coast across four seasons, it was then grown at various scales outdoors in Thuwal, Saudi Arabia during the Summer of 2022. We show thatC. merolae10D is amenable to cultivation with industrial-grade nutrient and CO2inputs outdoors in this location and that its biomass is relatively constant in biochemical composition across culture conditions. We also show the adaptation ofC. merolae10D to high salinity levels of those found in Red Sea waters and conducted further modeled cultivations in nutrient enriched local sea water. It was determined that salt-water adaptedC. merolae10D could be cultivated with reduced nutrient inputs in local conditions. The results presented here indicate this may be a promising alternative species for algal bioprocesses in outdoor conditions in extreme desert summer environments.
Dual MAPK Inhibition Triggers Pro-inflammatory Signals and Sensitizes BRAFV600EGlioma to T Cell-Mediated Checkpoint Therapy
Authors: Xing Yao Lulu , Grossauer Stefan , Park Jong-Whi , Nasajpour Emon , Bui Brandon , Morales Daniella , Panovska Dena , Nirschl Jeffrey J. , Feng Zhi-Ping , Wei Ruolun , Koeck Katharina , Thomason Wes , Xiu Joanna , Harter Patrick N. , Filipski Katharina , Mahaney Kelly , Ji Xuhuai , Mulcahy Levy Jean M. , Grant Gerald A. , Prolo Laura M. , Walsh Kyle M. , Lim Michael , Hambardzumyan Dolores , Petritsch Claudia K.
Published: February 2023

BRAFV600Epediatric low-grade gliomas frequently transform into high-grade gliomas (HGG) and poorly respond to chemotherapy, resulting in high mortality. Although combined BRAF and MEK inhibition (BRAFi+MEKi) outperforms chemotherapy, ∼70% of BRAFV600EHGG patients are therapy resistant and undergo unbridled tumor progression. BRAFV600Eglioma have an immune-rich microenvironment suggesting that they could be responsive to immunotherapy but effects of BRAFi+MEKi on anti-tumor immunity are unclear. Using patient tumor tissue before and after BRAFi+MEKi, two novel syngeneic murine models of BRAFV600EHGG, and patient-derived cell lines, we examined the effects of clinically relevant BRAFi+MEKi with dabrafenib and trametinib on tumor growth, cell states, and tumor-infiltrating T cells. We find that BRAFi+MEKi treatment: i) upregulated programmed cell death protein-1 (PD-1) signaling genes and PD-1 ligand (PD-L1) protein expression in murine BRAFV600EHGG by stimulating IFNγ and IL-27, ii) attenuated T cell activity by IL-23, IL-27 and IL-32 production, which can promote the expansion of regulatory T cells, and iii) induced glial differentiation linked to a therapy-resistant PD-L1+ compartment through Galectin-3 secretion by tumor cells. Murine BRAFV600EHGG shrinkage by BRAFi+MEKi is associated with the upregulation of interferon-gamma response genes, MHC class I/II expression, and antigen presentation and processing programs, indicative of increased anti-tumor immunity. Combined BRAFi+MEKi with therapeutic antibodies inhibiting the PD-1 and cytotoxic T-lymphocyte associated protein 4 (CTLA-4) immune checkpoints re-activate T cells and provide a survival benefit over single therapy in a T cell-dependent manner. The quadruple treatment overcame BRAFi+MEKi resistance by invigorating T cell-mediated anti-tumor immunity in murine BRAFV600EHGG. PD-L1 expression was elevated in human BRAF-mutant versus BRAF-wildtype glioblastoma clinical specimen, complementing experimental findings and suggesting translational relevance for patient care.
Leveraging type 1 diabetes human genetic and genomic data in the T1D Knowledge Portal
Authors: Kudtarkar Parul , Costanzo Maria C. , Sun Ying , Jang Dongkeun , Koesterer Ryan , Mychaleckyj Josyf C , Nayak Uma , Onengut-Gumuscu Suna , Rich Stephen S , Flannick Jason A , Gaulton Kyle J , Burtt Noël P
Published: February 2023

Translating genetic discoveries for type 1 diabetes (T1D) into mechanistic insight can reveal novel biology and therapeutic targets but remains a major challenge. We developed the T1D Knowledge Portal (T1DKP), a disease-specific resource of genetic and functional annotation data that enables users to develop hypotheses for T1D-based research and target discovery. The T1DKP can be used to query genes and genomic regions for genetic associations, identify epigenomic features, access results of bioinformatic analyses, and obtain expert-curated resources. The T1DKP is available athttp://t1d.hugeamp.org.
Comparative multi-omics analyses of cardiac mitochondrial stress in three mouse models of frataxin deficiency
Authors: Sayles Nicole M. , Napierala Jill S. , Anrather Josef , Diedhiou Nadège , Li Jixue , Napierala Marek , Puccio Hélène , Manfredi Giovanni
Published: February 2023

Cardiomyopathy is often fatal in Friedreich Ataxia (FA). However, the FA heart maintains adequate function until disease end stage, suggesting that it can initially adapt to the loss of frataxin (FXN). Conditional knockout mouse models with noFxnexpression show transcriptional and metabolic profiles of cardiomyopathy and mitochondrial integrated stress response (ISRmt). However, ISRmthas not been investigated in models with disease-relevant, partial decrease of FXN. We characterized the heart transcriptomes and metabolomes of three mouse models of partial FXN loss, YG8-800, KIKO-700, and FxnG127V. Few metabolites were significantly changed in YG8-800 mice and did not provide a signature of cardiomyopathy or ISRmt. Instead, several metabolites were altered in FxnG127Vand KIKO-700 hearts. Transcriptional changes were found in all models, but differentially expressed genes consistent with cardiomyopathy and ISRmtwere only identified in FxnG127Vhearts. However, these changes were surprisingly mild even at an advanced age (18-months), despite a severe decrease in FXN levels to 1% of WT. These findings indicate that the mouse heart has extremely low reliance on FXN, highlighting the difficulty in modeling genetically relevant FA cardiomyopathy.

Summary statement

The mitochondrial integrated stress response in the heart of a Friedreich Ataxia mouse model is surprisingly mild, despite a severe decrease in frataxin levels below 1% of normal.
Root cap cell corpse clearance limits microbial colonization inArabidopsis thaliana
Authors: Charura Nyasha M. , Llamas Ernesto , De Quattro Concetta , Vilchez David , Nowack Moritz K. , Zuccaro Alga
Published: February 2023

Programmed cell death occurring during plant development (dPCD) is a fundamental process integral for plant growth and reproduction. Here, we investigate the connection between developmentally controlled PCD and fungal accommodation inArabidopsis thalianaroots, focusing on the root cap-specific transcription factor ANAC033/SOMBRERO (SMB) and the senescence-associated nuclease BFN1. Mutations of both dPCD regulators increase colonization by the beneficial fungusSerendipita indica, primarily in the differentiation zone.smb-3mutants additionally exhibit hypercolonization around the meristematic zone and a delay ofS. indica-induced root-growth promotion. This demonstrates that root cap dPCD and rapid post-mortem clearance of cellular corpses represent a physical defense mechanism restricting microbial invasion of the root. Additionally, reporter lines and transcriptional analysis revealed thatBFN1expression is downregulated duringS. indicacolonization in mature root epidermal cells, suggesting a transcriptional control mechanism that facilitates the accommodation of beneficial microbes in the roots.

Key findings in bullet points

The process of programmed cell death in root development (dPCD) influences the extent and outcomes of fungal symbiosis

Fungal colonization of the root tip and differentiation zone is restricted by SMB-mediated clearance of dead cells, which preserves the meristem and regulates symbiosis

Expression of plant nucleaseBFN1, which is associated with senescence, is modulated to facilitate root accommodation of beneficial microbes
Comprehensive and Comparative Transcriptional Profiling of the Cell Wall Stress Response inBacillus subtilis
Authors: Zhang Qian , Cornilleau Charlene , Müller Raphael R. , Meier Doreen , Flores Pierre , Guérin Cyprien , Wolf Diana , Fromion Vincent , Carballido-Lopez Rut , Mascher Thorsten
Published: February 2023

The bacterial cell wall (CW) is an essential protective barrier and the frontline of cellular interactions with the environment and also a target for numerous antimicrobial agents. Accordingly, its integrity and homeostasis are closely monitored and rapid adaptive responses by transcriptional reprogramming induce appropriate counter-measures against perturbations. Here, we report a comprehensive and comparative transcriptional profiling of the primary cell envelope stress responses (CESR), based on combining RNAseq and high-resolution tiling array studies of the Gram-positive model bacteriumBacillus subtilisexposed to a range of antimicrobial compounds that interfere with cytoplasmic, membrane-coupled or extracellular steps of peptidoglycan (PG) biosynthesis. It revealed the complexity of the CESR ofB. subtilisand unraveled the contribution of extracytoplasmic function sigma factors (ECFs) and two-component signal transduction systems (TCSs) to protect the cell envelope. While membrane-anchored steps are tightly controlled, early cytoplasmic and late extracellular steps of PG biosynthesis are hardly monitored at all. The ECF σ factors σWand particularly σMprovide a general CESR, while σVis almost exclusively induced by lysozyme, against which it provides specific resistance. Remarkably, σXwas slightly repressed by most antibiotics, pointing towards a role in envelope homeostasis rather than CESR. It shares this role with the WalRK TCS, which balances CW growth with controlled autolysis. In contrast, all remaining TCSs are envelope stress-inducible systems. LiaRS is induced by a wide range of PG synthesis inhibitors, while the three paralogous systems BceAB, PsdRS and ApeRS are more compound-specific detoxification modules. Induction of the CssRS TCS by all antibiotics interfering with membrane-anchored steps of PG biosynthesis points towards a physiological link between CESR and secretion stress. Based on the expression signatures, a suite of CESR-specificB. subtiliswhole cell biosensors were developed and carefully evaluated. This is the first comprehensive transcriptomic study focusing exclusively on the primary effects of envelope perturbances that shall provide a reference point for future studies on Gram-positive CESR.
Lost inHELLS: disentangling the mystery ofSALNRexistence in senescence cellular models
Authors: Consiglio Arianna , Venturin Marco , Briguglio Sabrina , Rossi Clara , Grillo Giorgio , Bellosta Stefano , Cattaneo Maria Grazia , Licciulli Flavio , Battaglia Cristina
Published: February 2023

Long non-coding RNAs (lncRNAs) have emerged as key regulators of cellular senescence by transcriptionally and post-transcriptionally modulating the expression of many important genes involved in senescence-associated pathways and processes. Among the different lncRNAs associated to senescence,Senescence Associated Long Non-coding RNA(SALNR) was found to be down-regulated in different cellular models of senescence. Since its release in 2015,SALNRhas not been annotated in any database or public repository, and no other experimental data have been published. TheSALNRsequence is located on the long arm of chromosome 10, at band 10q23.33, and it overlaps the 3’ end of theHELLSgene. This investigation helped to unravel the mystery of the existence ofSALNRby analyzing publicly available short- and long-read RNA sequencing data sets and RT-PCR analysis in human tissues and cell lines. Additionally, the expression ofHELLShas been studied in cellular models of replicative senescence, bothin silicoandin vitro. Our findings, while strongly questioning the actual existence ofSALNRas an independent transcript, support the expression of a predictedHELLSisoform entirely covering theSALNRgenomic region. Furthermore, we observed a strong down-regulation ofHELLSin senescent cells versus proliferating cells, supporting its role in the senescence and aging process.

Graphical abstract
5-HT4 receptor agonists treatment reduces tau pathology and behavioral deficit in the PS19 mouse model of tauopathy
Authors: Jiang Shan , Sydney Eric J. , Runyan Avery M. , Serpe Rossana , Figueroa Helen Y. , Yang Mu , Myeku Natura
Published: February 2023

Accumulation of tau in synapses in Alzheimer’s disease (AD) has been shown to cause synaptic damage, synaptic loss, and the spread of pathology through synaptically connected neurons. Synaptic loss correlates with a decline in cognition, providing an opportunity to investigate strategies to target synaptic tau to rescue or prevent cognitive decline. One of the promising synaptic targets is the 5-HT4 receptor present post-synaptically in the brain areas involved in the memory processes. 5-HT4R activation exerts synaptogenic and pro-cognitive effects involving synapse-to-nucleus signaling essential for synaptic plasticity. However, it is not known whether 5-HT4R activation has a therapeutic effect on tauopathy. The goal of this study was to investigate the impact of stimulation of 5-HT4R in tauopathy mice. Our results show that 5-HT4R agonism led to reduced tauopathy and synaptic tau and correlated with increased proteasome activity and improved cognitive functioning in PS19 mice. Thus, stimulation of 5-HT4R offers a promising therapy to rescue synapses from toxic synaptic tau.
Genetics of continuous colour variation in a pair of sympatric sulphur butterflies
Authors: Hanly Joseph J. , Francescutti Caroline M. , Loh Ling S. , Corning Olaf B. W. H. , Long Derek J. , Nakatani Marshall A , Porter Adam H. , Martin Arnaud
Published: February 2023

Continuous colour polymorphisms can serve as a tractable model for the genetic and developmental architecture of traits, but identification of the causative genetic loci is complex due to the number of individuals needed, and the challenges of scoring continuously varying traits. Here we investigated continuous colour variation inColias eurythemeandC. philodice, two sister species of sulphur butterflies that hybridise in sympatry. Using Quantitative Trait Locus (QTL) analysis of 483 individuals from interspecific crosses and an high-throughput method of colour quantification, we found that two interacting large effect loci explain around 70% of the heritable variation in orange-to-yellow chromaticity. Knockouts ofred Malphighian tubules(red), a candidate gene at the primary QTL likely involved in endosomal maturation, resulted in depigmented wing scales showing disorganised pterin granules. The Z sex chromosome contains a large secondary colour QTL that includes the transcription factorbric-a-brac(bab), which we show can act as a modulator of orange pigmentation in addition to its previously-described role in specifying UV-iridescence. We also describe the QTL architecture of other continuously varying traits, and that wing size maps to the Z chromosome, supporting a Large-X effect model where the genetic control of species-defining traits is enriched on sex chromosomes. This study sheds light on the genetic architecture of a continuously varying trait, and illustrates the power of using automated measurement to score phenotypes that are not always conspicuous to the human eye.

Foreword

The colour phenotypes in this article involve nuanced gradations of yellow and orange that may be difficult to perceive for people who are colour vision deficient. Hue-shifted versions of all main figures are accessible online for dichromat readers (BioRxiv preprint: Supplementary Material).
MpoxRadar: a worldwide Mpox genomic surveillance dashboard
Authors: Nasri Ferdous , Kongkitimanon Kunaphas , Wittig Alice , Cortés Jorge Sánchez , Brinkmann Annika , Nitsche Andreas , Schmachtenberg Anna-Juliane , Renard Bernhard Y. , Fuchs Stephan
Published: February 2023

Monkeypox (Mpox) is mutating at an exceptional rate for a DNA virus and its global spread is concerning, making genomic surveillance a necessity. With MpoxRadar, we provide an interactive dashboard to track virus variants on mutation level worldwide. MpoxRadar allows users to select among different genomes as reference for comparison. The occurrence of mutation profiles based on the selected reference is indicated on an interactive world map that shows the respective geographic sampling site in customizable time ranges to easily follow the frequency or trend of defined mutations. Furthermore, the user can filter for specific mutations, genes, countries, genome types, and sequencing protocols and download the filtered data directly from MpoxRadar. On the server, we automatically download all Mpox genomes and metadata from the National Center for Biotechnology Information (NCBI) on a daily basis, align them with the different reference genomes, generate mutation profiles, which are stored and linked to the available metainformation in a database. This makes MpoxRadar a practical tool for the genomic survaillance of Mpox, supporting users with limited computational resources. MpoxRadar is open-source and freely accessible athttps://MpoxRadar.net.

GRAPHICAL ABSTRACT
Mouthparts of the bumblebee (Bombus terrestris)exhibit poor acuity for the detection of pesticides in nectar
Authors: Parkinson Rachel H. , Scott Jennifer , Dorling Anna L. , Jones Hannah , Haslam Martha , McDermott-Roberts Alex E. , Wright Geraldine A.
Published: February 2023

Bees are important pollinators of agricultural crops, but their populations are at risk when pesticides are used. One of the largest risks bees face is poisoning of floral nectar and pollen by insecticides. Studies of bee detection of neonicotinoids have reported contradictory evidence about whether bees can taste these pesticides in sucrose solutions and hence avoid them. Here, we use an assay for the detection of food aversion combined with single-sensillum electrophysiology to test whether the mouthparts of the buff-tailed bumblebee (Bombus terrestris) detect the presence of pesticides in a solution that mimicked the nectar of oilseed rape (Brassica napus). Bees did not avoid consuming solutions containing concentrations of imidacloprid, thiamethoxam, clothianidin, or sulfoxaflor spanning six orders of magnitude, even when these solutions contained lethal doses. Only extremely high concentrations of the pesticides altered spiking in gustatory neurons through a slight reduction in firing rate or change in the rate of adaptation. These data provide strong evidence that bumblebees cannot detect or avoid field-relevant concentrations of pesticides using information from their mouthparts. As bees rarely contact floral nectar with other body parts, we predict that they are at high risk of unwittingly consuming pesticides in the nectar of pesticide-treated crops.
Early detection of white matter hyperintensities using SHIVA-WMH detector
Authors: Tsuchida Ami , Boutinaud Philippe , Verrecchia Violaine , Tzourio Christophe , Debette Stéphanie , Joliot Marc
Published: February 2023

White matter hyperintensities (WMH) are well-established markers of cerebral small vessel disease (cSVD), and are associated with an increased risk of stroke, dementia, and mortality. Although their prevalence increases with age, small and punctate WMHs have been reported with surprisingly high frequency even in young, neurologically asymptomatic adults. However, most automated methods to segment WMH published to date are not optimized for detecting small and sparse WMH. Here we present the SHIVA-WMH tool, a deep-learning (DL)-based automatic WMH segmentation tool that has been trained with manual segmentations of WMH in a wide range of WMH severity. We show that it is able to detect WMH with high efficiency in subjects with only small punctate WMH as well as in subjects with large WMHs (i.e. with confluency) in evaluation datasets from three distinct databases: MRi-Share consisting of young university students, MICCAI 2017 WMH challenge dataset consisting of older patients from memory clinics, and UK Biobank with community-dwelling middle-aged and older adults. Across these three cohorts with a wide-ranging WMH load, our tool achieved voxel-level and individual lesion cluster-level Dice scores of 0.66 and 0.71, respectively, which were higher than for three reference tools tested: the lesion prediction algorithm implemented in the lesion segmentation toolbox (LST-LPA: Schmidt, 2017), PGS tool, a DL-based algorithm and the current winner of the MICCAI 2017 WMH challenge (Park et al, 2021), and HyperMapper tool (HPM: Mojiri Forooshani et al., 2022), another DL-based method with high reported performance in subjects with mild WMH burden. Our tool is publicly and openly available to the research community to facilitate investigations of WMH across a wide range of severity in other cohorts, and to contribute to our understanding of the emergence and progression of WMH.

Highlights

We propose a novel 3D Unet-based model, SHIVA-WMH detector, with much improved detection of small WMH across subjects with a wide range of WMH burden compared to existing methods

We characterize microstructural properties of small white matter hyperintensities in young adults from MRi-Share study
One does not simply grow well: Performance of grassland plants in home and foreign soil and climate
Authors: Aares Karoline H. , Bockelie-Rosendahl Torunn , Priyadarshi Ribha , Pugnaire Francisco I. , Schöb Christian , Alifriqui Mohamed , Manrique Esteban , Jaakola Laura H. , Bråthen Kari Anne
Published: February 2023

Plant-soil feedbacks (PSF) play a substantial role in determining plant performance in native and foreign habitats. Yet, PSF strength may be altered by climatic parameters, creating synergies. Here, we assess performance of alpine grassland species in their native and in foreign soils in an experiment including different climates.

Using soil and seeds sampled from six alpine grassland sites spreading in a gradient from Northern Africa to Northern Europe, we compared plant performance in home soil and in five foreign soils, as well as home and foreign climates (simulated temperature and photoperiod in growth chambers).

We found that despite a high variability in plant performance between sites, plants generally performed better in their home soil and home climate, than in foreign soil or in foreign climate. However, an interaction between soil and climate effect caused this better performance in home soil to occur only when in foreign climate. Similarly, performance improved in home climate only when plants were also placed in foreign soil.

Synthesis: In contrast to predictions from the literature, no benefit from growing in foreign soils are indicated. At least on the short term, climate change alone is not suggested to affect native grassland plant performance. However, when introduced to a habitat with a similar climate to their native habitat, plants may perform as well as in their native range, but when introduced both to a new soil and climate, plants will do poorly. This finding sheds light on the interactive effect of climate and soil origin, as well as the possible success of plant introductions under a changing climate.
Bilayer charge asymmetry and oil residues destabilize membranes upon poration
Authors: Leomil Fernanda S. C. , Stephan Mareike , Pramanik Shreya , Riske Karin A. , Dimova Rumiana
Published: February 2023

Transmembrane asymmetry is ubiquitous in cells, particularly with respect to lipids, where charged lipids are mainly restricted to one monolayer. We investigate the influence of anionic lipid asymmetry on the stability of giant unilamellar vesicles (GUVs), minimal plasma membrane models. To quantify asymmetry, we apply the fluorescence quenching assay, which is often difficult to reproduce and caution in handling the quencher is generally underestimated. Thus, we first optimize this assay and then apply it to GUVs prepared with the inverted emulsion transfer protocol using increasing fractions of anionic lipids restricted to one leaflet. This protocol is found to produce highly asymmetric bilayers, but with ∼20% interleaflet mixing. To probe the stability of asymmetric vs symmetric membranes, we expose the GUVs to porating electric pulses and monitor the fraction of destabilized vesicles. The pulses open macropores, and the GUVs either completely recover or exhibit leakage or bursting/collapse. Residual oil destabilizes porated membranes and destabilization is even more pronounced in asymmetrically charged membranes. This is corroborated by the measured pore edge tension decrease with increasing charge asymmetry. Using GUVs with membranes with imposed transmembrane pH asymmetry, we confirm that poration-triggered destabilization does not depend on the approach used to generate membrane asymmetry.
Evolution of the jasmonate ligands and their biosynthetic pathways
Authors: Chini Andrea , Monte Isabel , Zamarreño Angel M. , García-Mina José M. , Solano Roberto
Published: February 2023

Jasmonates are phytohormones that regulate multiple aspects of plant development and responses to stress, activating a conserved signaling pathway in land plants. The characterization of jasmonates biosynthetic and signaling pathways revealed that (+)-7-iso-JA-Ile (JA-Ile) is the ligand for the COI1/JAZ receptor in angiosperms, where jasmonates are synthesized through the OPR3-dependent or OPR3-independent pathways. More recently, studies on different model species identified dn-cis-OPDA, dn-iso-OPDA and Δ4-dn-iso-OPDA as the ligands of the COI1/JAZ receptor in the liverwortMarchantia polymorpha, and a receptor-independent role for several jasmonates in streptophytes. To understand the distribution of bioactive jasmonates in the green lineage and how their biosynthetic pathways evolved, we combined phylogenetic analyses and jasmonates metabolomics in representative species from different lineages. We found that both OPDA and dn-cis-OPDA are ubiquitous in land plants and present also in charophyte algae, underscoring their importance as ancestral signalling molecules. In contrast, JA-Ile biosynthesis emerged within lycophytes coincident with the evolutionary appearance of JAR1 function. We show that JA biosynthesis mediated by OPR1/OPR2 appeared in charophytes most likely as a degradation pathway of OPDA/dn-cis-OPDA before OPR3 emergence. Therefore, our results demonstrate that the OPR3-independent JA biosynthesis pathway is ancient and predates the evolutionary appearance of the OPR3-dependent pathway. Moreover, we identified a negative correlation between dn-iso-OPDA and JA-Ile in land plants which supports that dn-iso-OPDA is the relevant form of the hormone perceived by COI1/JAZ in bryophytes and lycophytes.
Non-asymptotic transients away from steady states determine cellular responsiveness to dynamic spatial-temporal signals
Authors: Nandan Akhilesh , Koseska Aneta
Published: February 2023

Majority of the theory on cell polarization and the understanding of cellular sensing and responsiveness to localized chemical cues has been based on the idea that non-polarized and polarized cell states can be represented by stable asymptotic switching between them. The existing model classes that describe the dynamics of signaling networks underlying polarization are formulated within the framework of autonomous systems. However these models do not simultaneously capture both, robust maintenance of polarized state longer than the signal duration, and retained responsiveness to signals with complex spatial-temporal distribution. Based on recent experimental evidence for criticality organization of biochemical networks, we challenge the current concepts and demonstrate that non-asymptotic signaling dynamics arising at criticality uniquely ensures optimal responsiveness to changing chemoattractant fields. We provide a framework to characterize non-asymptotic dynamics of system’s state trajectories through a non-autonomous treatment of the system, further emphasizing the importance of (long) transient dynamics, as well as the necessity to change the mathematical formalism when describing biological systems that operate in changing environments.
Host space, not energy or symbiont size, constrains feather mite abundance across passerine bird species
Authors: del Mar Labrador María , Serrano David , Doña Jorge , Aguilera Eduardo , Arroyo José L. , Atiénzar Francisco , Barba Emilio , Bermejo Ana , Blanco Guillermo , Borràs Antoni , Calleja Juan A. , Cantó José L. , Cortés Verónica , De la Puente Javier , De Palacio Diana , Fernández-González Sofía , Figuerola Jordi , Frías Óscar , Fuertes-Marcos Benito , Garamszegi László Z. , Gordo Óscar , Gurpegui Míriam , Kovács István , Martínez José L. , Meléndez Leandro , Mestre Alexandre , Møller Anders P. , Monrós Juan S. , Moreno-Opo Rubén , Navarro Carlos , Pap Péter L. , Pérez-Tris Javier , Piculo Rubén , Ponce Carlos , Proctor Heather , Rodríguez Rubén , Sallent Ángel , Senar Juan Carlos , Tella José L. , Vágási Csongor I. , Vögeli Matthias , Jovani Roger
Published: February 2023

Comprehending symbiont abundance among host species is a major ecological endeavour, and the metabolic theory of ecology has been proposed to understand what constraints symbiont populations. We parameterized metabolic theory equations to predict how bird species’ body size and the body size of their feather mites relate to mite abundance according to four potential energy (microbial abundance, uropygial gland size) and space constraints (wing area, number of feather barbs). Predictions were compared with the empirical scaling of feather mite abundance from 26,604 birds of 106 passerine species, using phylogenetic modelling and quantile regression. Feather mite populations were strongly constrained by host space (number of feather barbs) and not energy. Moreover, feather mite species’ body size was unrelated to their abundance or to the body size of their host species. We discuss the implications of our results for our understanding of the bird-feather mite system and for symbiont abundance in general.
Novel microRNAs downregulated in breast cancer tumors bind to the 3’UTR of SNAIL, SLUG, ZEB1 and/or TWIST and decrease metastatic behavior in breast cancer cells
Authors: Pérez-Moreno Elisa , Ortega-Hernández Victoria , Zavala Valentina A , Gamboa Jorge , Fernández Wanda , Carvallo Pilar
Published: February 2023

Metastasis, the leading cause of cancer-associated deaths, is promoted by transcription factors SNAIL, SLUG, ZEB1 and TWIST through the activation of epithelial-mesenchymal transition (EMT). MicroRNAs can suppress EMT, emerging as candidate molecular biomarkers and novel therapeutic targets. Herein, we evaluated microRNAs downregulated in breast cancer tissues expressing EMT transcription factors, to find new potential regulators of EMT. MiR-30a, miR-1271, miR-196a, miR-202, miR-210, miR-22, miR-331 and miR-34b were validated. Seven microRNAs downregulated luciferase activity through EMT transcription factors 3’UTR, and all microRNAs decreased cell migration, invasion and/or proliferation. In MDA-MB-231 cells, miR-196a and miR-22 decreased endogenous ZEB1 levels, and miR-30a endogenous CCR7 levels. These results suggest that microRNAs studied are novel regulators of EMT through the control of SNAIL, SLUG, ZEB1 and TWIST. They also regulate the metastatic behavior of cancer cells, and may control the development of lymph node metastasis through the regulation of CCR7.

Graphical abstract
Assignment of molecular origins of NOE signal at −3.5 ppm in the brain
Authors: Zhao Yu , Sun Casey , Zu Zhongliang
Published: February 2023

Purpose

Nuclear Overhauser Enhancement mediated saturation transfer effect, termed NOE(−3.5 ppm), is a major source of chemical exchange saturation transfer (CEST) MRI contrasts at 3.5 ppm in the brain. Previous phantom experiments have demonstrated that both proteins and lipids, two major components in tissues, have substantial contributions to NOE(−3.5 ppm) signals. Their relative contributions in tissues are informative for the interpretation of NOE(−3.5 ppm) contrasts that could provide potential imaging biomarkers for relevant diseases, which remain incompletely understood.

Methods

Experiments on homogenates and supernatants of brain tissues collected from healthy rats, that could isolate proteins from lipids, were performed to evaluate the relative contribution of lipids to NOE(−3.5 ppm) signals. On the other hand, experiments on ghost membranes with varied pH, and reconstituted phospholipids with different chemical compositions were conducted to study the dependence of NOE(−3.5 ppm) on physiological conditions. Besides, CEST imaging on rat brains bearing 9L tumors and healthy rat brains was performed to analyze the causes of the NOE(−3.5 ppm) contrast variations between tumors and normal tissues, and between gray matter and white matter.

Results

Our experiments reveal that lipids have dominant contributions to the NOE (−3.5 ppm) signals. Further analysis suggests that decreased NOE(−3.5 ppm) signals in tumors and higher NOE(−3.5 ppm) signals in white matter than in gray matter are mainly explained by changes in membrane lipids, rather than proteins.

Conclusion

NOE(−3.5 ppm) could be exploited as a highly sensitive MRI contrast for imaging membrane lipids in the brain.
Docking Domain Engineering in a Modular Polyketide Synthase and its Impact on Structure and Function
Authors: Buyachuihan Lynn , Zhao Yue , Schelhas Christian , Grininger Martin
Published: February 2023

Modular polyketide synthases (PKSs) are attractive targets for the directed, biosynthetic production of platform chemicals and pharmaceuticals by protein engineering. In this study, we analyze docking domains from the 6-deoxyerythronolide B synthase, SYNZIP domains, and the SpyCatcher:SpyTag complex as engineering tools to couple the polypeptides VemG and VemH to functional venemycin synthases. Our data show that the high-affinity interaction or covalent connection of modules, enabled by SYNZIP domains and the SpyCatcher:SpyTag complex, can be advantageous, e.g., in synthesis at low protein concentrations, but their rigidity and steric demand decrease synthesis rates. However, we also show that efficiency can be recovered when inserting a hinge region distant from the rigid interface. This study demonstrates that engineering approaches should take the conformational properties of modular PKSs into account and establishes a three-polypeptide split-venemycin synthase as an exquisitein vitroplatform for the analysis and engineering of modular PKSs.
Integrated control of non-motor and motor efforts during decision between actions
Authors: Leroy Élise , Koun Éric , Thura David
Published: February 2023

Humans daily life is characterized by a succession of voluntary actions. Since energy resources are limited, the ability to invest the appropriate amount of effort for selecting and executing these actions is a hallmark of adapted behavior. Recent studies indicate that decisions and actions share important principles, including the exchange of temporal resources when the context requires it. In the present study, we test the hypothesis that the management of energy resources is shared between decision and action too. Healthy human subjects performed a perceptual decision task where they had to choose between two levels of effort to invest in making the decision, and report it with a reaching movement. Crucially, motor difficulty gradually increased from trial to trial depending on participants’ decision performance. Results indicate a relatively mild impact of the increasing motor difficulty on the choice of the non-motor (decision) effort to invest in each trial and on decision performance. By contrast, motor performance strongly decreased depending on both the motor and decisional difficulties. Together, the results support the hypothesis of an integrated management of energy resources between decision and action. They also suggest that in the context of the present task, the mutualized resources are primarily allocated to the decision-making process to the detriment of movements.
Loss of RdDM-independent CHH methylation is sufficient for disruption of chromosome-specific rRNA gene silencing
Authors: McKinlay Anastasia , Enganti Ramya , Puppala Navinchandra V. , Saradadevi Gargi P. , Blevins Todd , Mohannath Gireesha
Published: February 2023

Arabidopsis thaliana has two nucleolus organizer regions (NORs), consisting of long tandem arrays of 45S rRNA genes on chromosomes 2 (NOR2) and 4 (NOR4). The rRNA gene subtypes mapping to NOR2 are mostly silenced during development, whereas those mapping to NOR4 are active. By analyzing DNA methylation-deficient Arabidopsis mutants, we found that the degree of disruption of NOR2 rRNA gene silencing correlates consistently with the loss of rDNA cytosine methylation in the CHH sequence context, rather than with methylation losses in CG or CHG contexts. Comparison of Arabidopsis and tomato NOR sequences revealed that rRNA gene promoter cytosines mostly occur in the CHH context, followed by fewer sites in the CHG context. By contrast, almost no CG dinucleotides occur in plant rRNA gene promoters. This prevalence of CHH sites in plant rDNA promoters suggests a mechanism to explain the stronger disruption of NOR2 gene silencing in CHH methylation mutants lacking CHROMOMETHYLASE 2 (CMT2) or DECREASE IN DNA METHYLATION 1 (DDM1) functions as compared to other DNA methylation-deficient mutant lines. Notably, CMT2 mediates CHH methylation independently of RNA-directed DNA methylation factors but with a requirement for the chromatin remodeler DDM1. Furthermore, we demonstrate that NOR2 genes are hypermethylated and exist in more condensed chromatin than NOR4 genes. Collectively, our data define a critical role for CHH methylation in plant rRNA gene silencing, which is mostly mediated by CG methylation in mammals.

Significance Statement

In plants, DNA cytosine methylation occurs in three sequence contexts (CG, CHG, and CHH), but it was not clear how these distinct contexts contribute to chromosome-specific large-scale rRNA gene silencing. Using rRNA gene expression, methylation assays, and bioinformatic analysis of rDNA promoters and methylation patterns, this study shows that CHH methylation, rather than CG or CHG methylation, plays a critical role in plant rRNA gene silencing, which is mostly mediated by CG methylation in mammals.
Adolescent neurostimulation of dopamine circuit reverses genetic deficits in frontal cortex function
Authors: Mastwal Surjeet , Li Xinjian , Stowell Rianne , Manion Matthew , Zhang Wenyu , Kim Nam-Shik , Yoon Ki-jun , Song Hongjun , Ming Guo-li , Wang Kuan Hong
Published: February 2023

Dopamine system dysfunction is commonly implicated in adolescent-onset neuropsychiatric disorders. Although psychosis symptoms can be alleviated by antipsychotics, cognitive symptoms remain unresponsive to such pharmacological treatments and novel research paradigms investigating the circuit substrates underlying cognitive deficits are critically needed. The frontal cortex and its dopaminergic input from the midbrain are implicated in cognitive functions and undergo maturational changes during adolescence. Here, we used mice carrying mutations in theArcorDISC1genes to model mesofrontal dopamine circuit deficiencies and test circuit-based neurostimulation strategies to restore cognitive functions. We found that in a memory-guided spatial navigation task, frontal cortical neurons were activated coordinately at the decision-making point in wild-type but notArcmutant mice. Chemogenetic stimulation of midbrain dopamine neurons or optogenetic stimulation of frontal cortical dopamine axons in a limited adolescent period consistently reversed genetic defects in mesofrontal innervation, task-coordinated neuronal activity, and memory-guided decision-making at adulthood. Furthermore, adolescent stimulation of dopamine neurons also reversed the same cognitive deficits inDISC1mutant mice. Our findings reveal common mesofrontal circuit alterations underlying the cognitive deficits caused by two different genes and demonstrate the feasibility of adolescent neurostimulation to reverse these circuit and behavioral deficits. These results may suggest developmental windows and circuit targets for treating cognitive deficits in neurodevelopmental disorders.
SIN3 gene regulatory activity is linked to RNA polymerase II pausing
Authors: Soukar Imad , Mitra Anindita , Pile Lori
Published: February 2023

The chromatin environment has a significant impact on gene expression. Chromatin structure is highly regulated by histone modifications and RNA polymerase II binding dynamics. The SIN3 histone modifying complex regulates the chromatin environment leading to changes in gene expression. InDrosophila melanogaster, theSin3Agene is alternatively spliced to produce different protein isoforms, two of which include SIN3 220 and SIN3 187. Both SIN3 isoforms are scaffolding proteins that interact with several other factors to regulate the chromatin landscape. The mechanism through which the SIN3 isoforms regulate chromatin is not well understood. Here, we analyze publicly available data sets to allow us to ask specific questions on how SIN3 isoforms regulate chromatin and gene activity. We determined that genes repressed by the SIN3 isoforms exhibited enrichment in histone H3K4me2 and H3K4me3 near the transcription start site. We observed an increase in the amount of paused RNA polymerase II on the promoter of genes repressed by the isoforms as compared to genes that require SIN3 for maximum activation. Furthermore, we analyzed a subset of genes regulated by SIN3 187 that suggest a mechanism in which SIN3 187 might exhibit hard regulation as well as soft regulation. Data presented here expand our knowledge of how the SIN3 isoforms regulate the chromatin environment and RNA polymerase II binding dynamics.

Summary statement

SIN3 cofactors can activate or repress genes. Using bioinformatic analysis, we find that histone methylation and RNA polymerase II binding profiles differ at SIN3-regulated genes with distinct transcriptional outcomes.
Development of a Robust Consensus Modeling Approach for Identifying Cellular and Media Metabolites Predictive of Mesenchymal Stromal Cell Potency
Authors: Van Grouw Alexandria , Colonna Maxwell B. , Maughon Ty S. , Shen Xunan , Larey Andrew M. , Moore Samuel G. , Yeago Carolyn , Fernández Facundo M. , Edison Arthur S. , Stice Steven L. , Bowles-Welch Annie C. , Marklein Ross A.
Published: February 2023

Mesenchymal stromal cells (MSCs) have shown promise in regenerative medicine applications due in part to their ability to modulate immune cells. However, MSCs demonstrate significant functional heterogeneity in terms of their immunomodulatory function because of differences in MSC donor/tissue source, as well as non-standardized manufacturing approaches. As MSC metabolism plays a critical role in their ability to expand to therapeutic numbersex vivo, we comprehensively profiled intracellular and extracellular metabolites throughout the expansion process to identify predictors of immunomodulatory function (T cell modulation and indoleamine-2,3-dehydrogenase (IDO) activity). Here, we profiled media metabolites in a non-destructive manner through daily sampling and nuclear magnetic resonance (NMR), as well as MSC intracellular metabolites at the end of expansion using mass spectrometry (MS). Using a robust consensus machine learning approach, we were able to identify panels of metabolites predictive of MSC immunomodulatory function for 10 independent MSC lines. This approach consisted of identifying metabolites in 2 or more machine learning models and then building consensus models based on these consensus metabolite panels. Consensus intracellular metabolites with high predictive value included multiple lipid classes (such as phosphatidylcholines, phosphatidylethanolamines, and sphingomyelins) while consensus media metabolites included proline, phenylalanine, and pyruvate. Pathway enrichment identified metabolic pathways significantly associated with MSC function such as sphingolipid signaling and metabolism, arginine and proline metabolism, and autophagy. Overall, this work establishes a generalizable framework for identifying consensus predictive metabolites that predict MSC function, as well as guiding future MSC manufacturing efforts through identification of high potency MSC lines and metabolic engineering.