bluuebunny/crossref_metadata_2025 huggingface dataset:
GABAergic LRP1 is a key link between obesity and memory function
Authors: Uner Aaron Aykut , Hou Zhi-Shuai , Aydogan Ahmet , Rodrigues Kellen C.C. , Young Jennie , Choi Anthony , Yang Won-Mo , Kim Woojin S. , Prevot Vincent , Caldarone Barbara J. , Hyman Bradley T. , Lee Hyon , Kim Young-Bum
Published: September 2022

Objective

Low-density lipoprotein receptor-related protein-1 (LRP1) regulates energy homeostasis, blood-brain barrier integrity, and metabolic signaling in the brain. Loss of LRP1 from inhibitory gamma-aminobutyric acid (GABA)ergic neurons causes severe obesity in mice. Its dysfunction has been associated with cognitive decline, dementia, and Alzheimer’s disease. However, the impact of LRP1 in inhibitory neurons on memory function and cognition in the context of obesity is poorly understood.

Methods

Mice lacking LRP1 in GABAergic neurons (Vgat-Cre; LRP1loxP/loxP) are subjected to conduct behavioral tests of locomotor activity and motor coordination, short/long-term and spatial memory, and fear learning/memory. We evaluated the relationships between behavior and metabolic risk factors.

Results

Deletion of LRP1 in GABAergic neurons caused a significant impairment in memory function. In the spatial Y-maze test,Vgat-Cre; LRP1loxP/loxPmice exhibited decreased travel distance and duration in the novel arm compared with controls (LRP1loxP/loxPmice). In addition, GABAergic neuron-specific LRP1-deficient mice had a diminished capacity for performing learning and memory tasks during the water T-maze test. Moreover, reduced freezing time was observed in these mice when the contextual and cued fear conditioning tests were conducted. These effects were accompanied by increased neuronal necrosis and neuroinflammation in the hippocampus. Importantly, the distance and duration in the novel arm and the performance of the reversal water T-maze test negatively correlated with metabolic risk parameters, including body weight, serum leptin, insulin, and apolipoprotein J.

Conclusions

Our findings demonstrate that LRP1 from GABAergic neurons is important in normal memory function. Metabolically, obesity caused by GABAergic LRP1 deletion negatively regulates memory and cognitive function. Thus, LRP1 in GABAergic neurons may play a crucial role in maintaining normal excitatory/inhibitory balance and impacts memory function, reinforcing the potential importance of LRP1 in neural system integrity.
Rapid protection of nonhuman primates against Marburg virus disease using a single low-dose VSV-based vaccine
Authors: O’Donnell Kyle L. , Feldmann Friederike , Kaza Benjamin , Clancy Chad S. , Hanley Patrick W. , Fletcher Paige , Marzi Andrea
Published: September 2022

Marburg virus (MARV) is the causative agent of Marburg virus disease (MVD) which has a case fatality rate up to ~90% in humans. Recently, there were cases reported in Guinea and Ghana highlighting this virus as a high-consequence pathogen potentially threatening global public health. There are no licensed treatments or vaccines available today.

We used a vesicular stomatitis virus (VSV)-based vaccine expressing the MARV-Angola glycoprotein (VSV-MARV) as the viral antigen. Previously, a single dose of 1×107 plaque-forming units (PFU) administered 7 days before challenge resulted in uniform protection from disease in cynomolgus macaques. Here, we sought to lower the vaccination dose to allow for more doses per vial in an emergency outbreak situation. We administered 1×105 or 1×103 PFU 14 days before challenge and achieved uniform protection in both groups. When we administered 1×103 PFU 7 days before challenge, vaccination resulted in uniform protection with no detectable viremia. Antigen-specific IgG responses were induced by both vaccine concentrations and were sustained until the study endpoint. Neutralizing antibody responses and antibody-dependent cellular phagocytosis were observed with both vaccination doses and timelines. The cellular response after vaccination was characterized by early induction of NK cell activation. Additionally, antigen-specific memory T cell subsets were detected in all vaccination cohorts indicating that while the primary protective mechanism of VSV-MARV is the humoral response, a functional cellular response is also induced.

Overall, this data highlights VSV-MARV as a viable and fast-acting MARV vaccine candidate suitable for deployment in emergency outbreak situations and supports its clinical development.

One Sentence Summary

A single low dose of VSV-MARV administered 14 or 7 days before challenge protects NHPs uniformly from lethal disease.
Digitally managed larviciding as a cost-effective intervention for urban malaria: Operational lessons from a pilot in São Tomé and Príncipe guided by the Zzapp system
Authors: Vigodny Arbel , Ben Aharon Michael , Wharton-Smith Alexandra , Fialkoff Yonatan , Houri Yafin Arnon , Bragança Fernando , Da Graça Flavio Soares , Gluck Dani , D’Abreu João Alcântara Viegas , Rompão Herodes
Published: September 2022

Background

Once a mainstay of malaria elimination operations, larval source management—the treatment of mosquito breeding habitats–has been marginalized in Africa, due to insufficient effectiveness. However, the development of new technologies, and mosquitoes’ growing resistance to insecticides used in bed nets and house spraying raise renewed interest in this method.

Methods

A digitally managed larviciding operation in three of the seven districts of São Tomé and Príncipe (STP) was launched by the Ministry of Health and ZzappMalaria LTD, guided by the Zzapp map-and-GPS mobile application and dashboard. During the operation, quality assurance procedures and field management methods were developed and implemented.

Findings

12,788 water bodies were located and treated a total of 128,864 times. The reduction impact on mosquito population and on malaria cases was 74·90% and 52·65%, respectively. The overall cost per person protected (PPP) was US$0·78 and US$0·41 PPP in the urban areas. Various cost and effectiveness drivers were identified.

Interpretation

Digitally managed larviciding can yield highly cost-effective results, especially in urban areas. Digital tools facilitate standardization of operations, implementation of quality assurance procedures, and monitoring of fieldworkers’ performance. Digitally generated spatial data also have the potential to assist integrated vector management operations. A randomized controlled trial with a larger sample is needed to further substantiate findings.

Funding

The operation was funded by ZzappMalaria LTD and the STP Ministry of Health (MOH).
Post-mating parental behavior trajectories differ across four species of deer mice
Authors: Khadraoui Mehdi , Merritt Jennifer R. , Hoekstra Hopi E. , Bendesky Andres
Published: September 2022

Among species, parental behaviors vary in their magnitude, onset relative to reproduction, and sexual dimorphism. In deer mice (genus Peromyscus), while most species are promiscuous with low paternal care, monogamy and biparental care have evolved at least twice under different ecological conditions. Here, in a common laboratory setting, we monitored parental behaviors of males and females of two promiscuous (eastern deer mouse P. maniculatus and white-footed mouse P. leucopus) and two monogamous (oldfield mouse P. polionotus and California mouse P. californicus) species from before mating to after giving birth. In the promiscuous species, females showed parental behaviors largely after parturition, while males showed little parental care. In contrast, both sexes of monogamous species performed parental behaviors. However, while oldfield mice began to display parental behaviors before mating, California mice showed robust parental care behaviors only postpartum. These different parental-care trajectories in the two monogamous species align with their socioecology. Oldfield mice have overlapping home ranges with relatives, so infants they encounter, even if not their own, are likely to be closely related. By contrast, California mice disperse longer distances into exclusive territories with possibly unrelated neighbors, decreasing the inclusive fitness benefits of caring for unfamiliar pups before parenthood. Together, we find that patterns of parental behaviors in Peromyscus are consistent with predictions from inclusive fitness theory.
Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment
Authors: Betschart Raphael O. , Thiéry Alexandre , Aguilera-Garcia Domingo , Zoche Martin , Moch Holger , Twerenbold Raphael , Zeller Tanja , Blankenberg Stefan , Ziegler Andreas
Published: September 2022

Rapid advances in high-throughput DNA sequencing technologies have enabled the conduct of whole genome sequencing (WGS) studies, and several bioinformatics pipelines have become available. The aim of this study was the comparison of 6 WGS data pre-processing pipelines, involving two mapping and alignment approaches (GATK utilizing BWA-MEM2 2.2.1, and DRAGEN 3.8.4) and three variant calling pipelines (GATK 4.2.4.1, DRAGEN 3.8.4 and DeepVariant 1.1.0). We sequenced one genome in a bottle (GIAB) sample 70 times in different runs, and one GIAB trio in triplicate. The truth set of the GIABs was used for comparison, and performance was assessed by computation time, F1score, precision, and recall. In the mapping and alignment step, the DRAGEN pipeline was faster than the GATK with BWA-MEM2 pipeline. DRAGEN showed systematically higher F1score, precision, and recall values than GATK for single nucleotide variations (SNVs) and Indels in simple-to-map, complex-to-map, coding and non-coding regions. In the variant calling step, DRAGEN was fastest. In terms of accuracy, DRAGEN and DeepVariant performed similarly and both superior to GATK, with slight advantages for DRAGEN for Indels and for DeepVariant for SNVs. The DRAGEN pipeline showed the lowest Mendelian inheritance error fraction for the GIAB trios. Mapping and alignment played a key role in variant calling of WGS, with the DRAGEN outperforming GATK.
Boreal Forest Height Mapping using Sentinel-1 Time Series and improved LSTM model
Authors: Ge Shaojia , Gu Hong , Su Weimin , Rauste Yrjö , Praks Jaan , Antropov Oleg
Published: September 2022

Here, a novel semi-supervised Long Short-Term Memory (LSTM) model is developed and demonstrated for predicting forest tree height using time series of Sentinel-1 images. The model uses a Helix-Elapse (HE) projection approach to capture relationship between forest temporal patterns and Sentinel-1 time series, when the acquisition time intervals are irregular. A skip-link based LSTM block is introduced and a novel backbone network, Helix-LSTM, is proposed to retrieve temporal features at different receptive scales. Additionally, a novel semi-supervised strategy, Cross-Pseudo Regression, is employed to achieve better model performance. The developed model is compared versus basic LSTM model, attention-based bidirectional LSTM and several other established regression approaches used in forest variable mapping, demonstrating consistent improvement of forest height prediction accuracy. The study site is located in Central Finland and represents boreal forestland. At best, the achieved accuracy of forest height mapping was 28.3% rRMSE for pixel-level predictions, and 18.0% rRMSE on stand level. We expect that the developed model can also be used for modeling relationships between other forest variables and satellite image time series.
Conserved whole-brain spatiomolecular gradients shape adult brain functional organization
Authors: Vogel Jacob W , Alexander-Bloch Aaron , Wagstyl Konrad , Bertolero Maxwell , Markello Ross , Pines Adam , Sydnor Valerie J , Diaz-Papkovich Alex , Hansen Justine , Evans Alan C , Bernhardt Boris , Misic Bratislav , Satterthwaite Theodore , Seidlitz Jakob
Published: September 2022

Cortical arealization arises during neurodevelopment from the confluence of molecular gradients representing patterned expression of morphogens and transcription factors. However, how these gradients relate to adult brain function, and whether they are maintained in the adult brain, remains unknown. Here we uncover three axes of topographic variation in gene expression in the adult human brain that specifically capture previously identified rostral-caudal, dorsal-ventral and medial-lateral axes of early developmental patterning. The interaction of these spatiomolecular gradients i) accurately predicts the location of unseen brain tissue samples, ii) delineates known functional territories, and iii) explains the topographical variation of diverse cortical features. The spatiomolecular gradients are distinct from canonical cortical functional hierarchies differentiating primary sensory cortex from association cortex, but radiate in parallel with the axes traversed by local field potentials along the cortex. We replicate all three molecular gradients in three independent human datasets as well as two non-human primate datasets, and find that each gradient shows a distinct developmental trajectory across the lifespan. The gradients are composed of several well known morphogens (e.g., PAX6 and SIX3), and a small set of genes shared across gradients are strongly enriched for multiple diseases. Together, these results provide insight into the developmental sculpting of functionally distinct brain regions, governed by three robust transcriptomic axes embedded within brain parenchyma.
Large variations in afforestation-related climate cooling and warming effects across short distances
Authors: Rohatyn Shani , Rotenberg Eyal , Tatarinov Fyodor , Carmel Yohay , Yakir Dan
Published: September 2022

Climate-related benefits of afforestation depend on the balance of the often-contrasting effects of biogeochemical (carbon sequestration) and biogeophysical (energy balance) effects. These effects are known to vary at the continental scale (e.g., from boreal to tropical regions). Here, we show based on a four-year study that the biogeochemical vs. biogeophysical balance in paired forested and non-forested ecosystems across short distances and steep aridity gradient (∼200Km, aridity index 0.64 to 0.18) can change dramatically. The required time for the forestation cooling effects via carbon sequestration, to surpass its warming effects, associated with the forests reduced albedo and suppressed longwave radiation, decreased from >200 years in the driest sites to ∼70 years in the intermediate and ∼40 years in the wettest sites. Climate-related benefits of forestation, previously considered at large-spatial scales, should be considered at high-spatial resolutions in climate-change mitigation programs aimed at taking advantage of the vast non-forested dry regions.

Teaser

Climate-related effects of afforestation can vary between cooling and warming effects across 200 km.
SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets
Authors: Ginell Garrett M. , Flynn Aidan J. , Holehouse Alex S.
Published: September 2022

The emergence of high-throughput experiments and high-resolution computational predictions has led to an explosion in the quality and volume of protein sequence annotations at proteomic scales. Unfortunately, integrating and analyzing complex sequence annotations remains logistically challenging. Here we present SHEPHARD, a software package that makes large-scale integrative protein bioinformatics trivial. SHEPHARD is provided as a stand-alone package and with a pre-compiled set of human annotations in a Google Colab notebook.
Representing cells as sentences enables natural-language processing for single-cell transcriptomics
Authors: Dhodapkar Rahul M.
Published: September 2022

Abstract

Gene expression matrices commonly used in single-cell transcriptomics, cannot be directly analyzed with tools developed for natural languages. By restructuring these matrices as abundance-ordered sequences of genes, we generate cell sentences: rank-normalized, positionally encoded expression data. We show that these cell sentences can be analyzed using existing tools from natural language processing to unify cell and gene representations across species.
Coupling cellular drug-target engagement to downstream pharmacology with CeTEAM
Authors: Valerie Nicholas C.K. , Sanjiv Kumar , Mortusewicz Oliver , Zhang Si Min , Alam Seher , Pires Maria J. , Stigsdotter Hannah , Rasti Azita , Langelier Marie-France , Rehling Daniel , Throup Adam , Desroses Matthieu , Onireti Jacob , Wakchaure Prasad , Almlöf Ingrid , Boström Johan , Bevc Luka , Benzi Giorgia , Stenmark Pål , Pascal John M. , Helleday Thomas , Page Brent D.G. , Altun Mikael
Published: September 2022

Cellular target engagement technologies are reforming drug discovery by enabling quantification of intracellular drug binding; however, simultaneous assessment of drug-associated phenotypes has proven challenging. CeTEAM (cellular targetengagement byaccumulation ofmutant) is a platform that can concomitantly evaluate drug-target interactions and phenotypic responses for holistic assessment of drug pharmacology using conditionally-stabilized drug biosensors. We observe that drug-responsive proteotypes are prevalent among reported mutants of known drug targets. CeTEAM-compatible mutants follow structural and biophysical logic that permits intra-protein and paralogous expansion of the biosensor pool, as exemplified by alanine scanning of leucines within the PARP1 helical domain and transfer of PARP1 destabilization to the analogous PARP2 residue. We then apply CeTEAM to uncouple target engagement from divergent cellular activities of MTH1 inhibitors, dissect NUDT15-associated thiopurine metabolism with the R139C pharmacogenetic variant, and profile the live-cell dynamics of PARP1/2 binding and DNA trapping by PARP inhibitors. Further, PARP1-derived biosensors facilitated high-throughput screening of drug-like libraries for PARP1 binders, as well as multimodalex vivoanalysis and non-invasive tracking of PARPi binding in live animals. Our data suggests that CeTEAM can facilitate real-time, comprehensive characterization of target engagement by bridging drug binding events and their biological consequences.
A p21-GFP zebrafish model of senescence for rapid testing of senolyticsin vivo
Authors: Morsli Samir , Henriques Catarina M. , Ellis Pamela S , Mortiboys Heather , Baxendale Sarah , Loynes Catherine , Renshaw Stephen A. , Bellantuono Ilaria
Published: September 2022

Senescence drives the onset and severity of multiple ageing-associated diseases as well as frailty. As a result, there has been an increased interest in mechanistic studies and in the search for compounds targeting senescent cells, known as senolytics. Mammalian models are commonly used to test senolytics and generate functional and toxicity data at the level of organs and systems, yet this is expensive and time consuming. Zebrafish share high homology in genes associated with human ageing and disease. They can be genetically-modified relatively easily. In larvae, most organs develop within 5 days of fertilisation and are transparent, which allows tracking of fluorescent cellsin vivoin real time, testing drug off-target toxicity and assessment of cellular and phenotypic changes. Here, we have generated a transgenic zebrafish line that expresses green fluorescent protein (GFP) under the promoter of a key senescence marker, p21. We show an increase in p21:GFP+cells in larvae following exposure to ionising radiation and with natural ageing. p21:GFP+cells display other markers of senescence, including senescence-associated β-galactosidase and IL6. The observed increase in senescent cells following irradiation is associated with a reduction in the thickness of muscle fibres and mobility, two important ageing phenotypes. We also show that quercetin and dasatinib, two senolytics currently in clinical trials, reduce the number of p21:GFP+cells, in a rapid 5-day assay. This model provides an important tool to study senescence in a living organism, allowing the rapid selection of senolytics before moving to more expensive and time-consuming mammalian systems.
Cancer-associated SMARCAL1 loss-of-function mutations promote alternative lengthening of telomeres and tumorigenesis in telomerase-negative glioblastoma cells
Authors: Liu Heng , Xu Cheng , Diplas Bill H. , Brown Alexandrea , Strickland Laura M. , Ling Jinjie , McLendon Roger E. , Keir Stephen T. , Ashley David M. , He Yiping , Waitkus Matthew S.
Published: September 2022

Telomere maintenance mechanisms are a hallmark of cancer and are required to enable the replicative immortality of malignant cells. While most cancers activate the enzyme telomerase for telomere maintenance, a subset of cancers (~10-15%) use telomerase-independent mechanisms termed alternative lengthening of telomeres (ALT). ALT is characterized by elevated replication stress at telomeres, telomere synthesis via homology directed-repair mechanisms, and is frequently associated with mutations in the ATRX gene. Because ALT is absent in non-malignant proliferating cells, therapeutic strategies targeting ALT-mediated telomere synthesis is an area of significant translational and clinical interest. We previously showed that a subset of adult GBM patients with ATRX-expressing ALT-positive tumors harbored loss-of-function mutations in the SMARCAL1 gene. SMARCAL1 is an annealing helicase involved in replication fork remodeling and the resolution of replication stress. In this study, we used a patient-derived ALT-positive GBM cell line with native SMARCAL1 deficiency to investigate the role of SMARCAL1 in ALT-mediated telomere synthesis and gliomagenesis in vivo. Our results show that inducible rescue of SMARCAL1 expression suppresses ALT indicators and inhibits de novo telomere synthesis in GBM and osteosarcoma cells, suggesting that SMARCAL1 deficiency plays a functional role in ALT induction in cancers that natively lack SMARCAL1 function. Further, SMARCAL1-deficient ALT-positive cells can be serially propagated in vivo in the absence of detectable telomerase activity, suggesting that the SMARCAL1-deficient ALT phenotype maintains telomeres in a manner that promotes tumorigenesis. In summary, we show that SMARCAL1 loss-of-function mutations are permissive to ALT and promote gliomagenesis. We also established isogenic model systems that permit the dynamic modulation of ALT activity, which will be valuable for future studies aimed at understanding the molecular mechanisms of ALT and for identifying novel anti-cancer therapeutics that target the ALT phenotype.
Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans
Authors: Locher Veronica , Park Sara , Bunis Daniel , Makredes Stephanie , Burt Trevor D. , Fragiadakis Gabriela K. , Halkias Joanna
Published: September 2022

The development of human adaptive immunity progresses faster than previously appreciated, with the emergence of memory CD4+ T cells alongside regulatory T (Treg) cells by the second trimester of pregnancy. We previously identified a prenatal-specific subset of PLZF+ CD4+ T cells with heightened effector potential that accounted for most memory T cells in the developing intestine and accumulated in the cord blood of infants exposed to prenatal inflammatory pathologies. However, the signals that drive their tissue distribution and effector maturation are unknown. In this report, we define the transcriptional and functional heterogeneity of prenatal PLZF+ CD4+ T cells and identify compartmentalization of Th-like effector function across the small intestine (SI) and mesenteric lymph nodes (MLN). We find that IL-7, which is more abundant in the SI relative to the MLN, drives the preferential expansion of naïve PLZF+ CD4+ T cells via JAK/STAT and MEK/ERK signaling. Exposure to IL-7 induces a subset of PLZF+ CD4+ T cells to acquire a memory-phenotype and rapid effector function, identifying the human analogue of memory-phenotype CD4+ T cells. Further, IL-7 modulates the differentiation of Th1- and Th17-like PLZF+ CD4+ T cells, and thus likely contributes to the anatomic compartmentalization of prenatal CD4+ T cell effector function.
Systems biology illuminates alternative metabolic niches in the human gut microbiome
Authors: Noecker Cecilia , Sanchez Juan , Bisanz Jordan E. , Escalante Veronica , Alexander Margaret , Trepka Kai , Heinken Almut , Liu Yuanyuan , Dodd Dylan , Thiele Ines , DeFelice Brian , Turnbaugh Peter J.
Published: September 2022

Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction. Stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP, traits which could be recapitulated in silico by our updated metabolic model. We compared these in vitro findings with metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying shared signatures across environments and highlighting catabolism of the host signaling metabolite agmatine as an alternative energy pathway. Together, our results elucidate a distinctive metabolic niche filled by E. lenta in the gut ecosystem.
Genomics of PDGFR-rearranged hypereosinophilic syndrome
Authors: Rheinbay Esther , Qi Meifang , Bouyssou Juliette M. , Oler Andrew J. , Thumm Lauren , Makiya Michelle , Maric Irina , Klion Amy D. , Lane Andrew A.
Published: September 2022

A subset of patients with hypereosinophilia have a clonal hematologic neoplasm. These neoplastic hypereosinophilic syndromes (HES) can harbor somatic DNA rearrangements involving a PDGF receptor gene, PDGFRA or PGDFRB, most frequently FIP1L1::PDGFRA. Patients with PDGFR-rearranged HES are overwhelmingly males, and the hypereosinophilia responds robustly to the multi-kinase inhibitor imatinib. Unbiased genomics of PDGFR-rearranged HES have not been comprehensively studied. Here, we compared whole genome sequencing of eosinophil DNA from patients with PDGFR-rearranged HES at diagnosis (tumor) versus matched “normal” DNA. Other than the PDGFR rearrangement itself, we detected no recurrent coding somatic point mutations, insertions/deletions, or DNA copy number alterations in the neoplastic eosinophils; instead, there were additional somatic events private to each tumor. The tumors had a linear clonal structure with the PDGFR rearrangement as the initial driver event. We mapped the breakpoints of a novel IQGAP2::PDGFRB::UVRAG intra- and inter-chromosomal fusion event in one patient. Non-coding analysis found no recurrent abnormalities, including in eosinophilic leukemia-associated promoters or enhancers. The sex chromosomes showed no recurrent alterations to provide an obvious explanation for the disease’s extreme male bias. We conclude that neoplastic HES has relatively simple genomics and that the only unambiguous recurrent driver event is the PDGFR rearrangement itself.

Key Points

PDGFR-rearranged hypereosinophilic neoplasms have simple, linear genetic structure with the rearrangement as the likely initiating event

There are no obvious recurrent additional or sex-biased genomic events that cooperate with PDGFR rearrangement to drive the neoplasm
Thermoplasmonic induced vesicle fusion for investigating membrane protein phase affinity
Authors: Moreno-Pescador Guillermo , Arastoo Mohammad R. , Chiantia Salvatore , Daniels Robert , Bendix Poul Martin
Published: September 2022

Many cellular processes involve the lateral organization of integral and peripheral membrane proteins into nanoscale domains. Despite the biological significance the mechanisms that facilitate membrane protein clustering into nanoscale lipid domains remain enigmatic. In cells the analysis of membrane protein phase affinity is complicated by the size and temporal nature of ordered and disordered lipid domains. To overcome these limitations we developed a method for delivering membrane proteins from transfected cells into phase-separated model membranes that combines optical trapping with thermoplasmonic-mediated membrane fusion and confocal imaging. Using this approach we observed clear phase partitioning following the transfer of GFP-tagged influenza hemagglutinin and neuraminidase from transfected cell membranes to giant unilamellar vesicles. The generic platform presented here allows investigation of the phase affinity of any plasma membrane protein which can be labeled or tagged with a fluorescent marker.
A Novel Gene REPTOR2 Activates the Autophagic Degradation of Wing Disc in Pea Aphid
Authors: Yuan Erliang , Guo Huijuan , Chen Weiyao , Du Bingru , Mi Yingjie , Qi Zhaorui , Yuan Yiyang , Zhu-Salzman Keyan , Ge Feng , Sun Yucheng
Published: September 2022

Wing dimorphism is an evolutionarily adaptive trait to maximize insect fitness under various environments, by which the population could be balanced between migration and reproduction. Most studies concern the regulatory mechanisms underlying the stimulation of wing morph in aphids, but relatively little research addresses the molecular basis of wing loss. Here, we found that the wing disc of wingless-destined pea aphids degenerated 30 h post birth by autophagic rather than apoptotic degeneration, whereas winged-destined aphids developed normally. Activation of autophagy in 1st instar nymphs reduced the proportion of winged aphids, and suppression of autophagy increased the proportion. The REPTOR2 gene associated with TOR signaling pathway was identified by RNA-seq as a differentially expressed gene between the two morphs, with higher expression in the thorax of wingless-destined aphids. Further genetic analysis indicated that REPTOR2 could be a novel gene derived from a gene duplication event exclusively in pea aphid on autosome A1 but translocated to the sex chromosome. Knockdown of REPTOR2 reduced autophagy in the wing disc and increased the proportion of winged aphids. In agreement with REPTOR’s canonical negative regulatory role of TOR on autophagy, winged-destined aphids had higher TOR expression in the wing disc. Suppression of TOR activated autophagy of the wing disc and decreased the proportion of winged aphids, and vice versa. These results revealed that the TOR signaling pathway controlled degradation of the wing disc in pea aphids, and that REPTOR2 could modulate this autophagic degradation.
Endothelial cell-derived, secreted long non-coding RNAsGadlor1andGadlor2aggravate pathological cardiac remodeling via intercellular crosstalk
Authors: Keles Merve , Grein Steve , Froese Natali , Wirth Dagmar , Trogisch Felix A. , Wardman Rhys , Hemanna Shruthi , Weinzierl Nina , Koch Philipp-Sebastian , Uhlig Stefanie , Lomada Santosh , Dittrich Gesine M. , Szaroszyk Malgorzata , Haustein Ricarda , Hegermann Jan , Martin-Garrido Abel , Bauersachs Johann , Frank Derk , Frey Norbert , Bieback Karen , Cordero Julio , Dobreva Gergana , Wieland Thomas , Heineke Joerg
Published: September 2022

Background

Pathological overload triggers maladaptive myocardial remodeling that leads to heart failure. Recent studies have shown that long non-coding RNAs (lncRNAs) regulate cardiac remodeling. This study investigates two recently discovered, secreted lncRNAs,Gadlor1andGadlor2(Gadlor 1/2).

Methods

We generated compoundGadlor1/2 knock-out (KO) mice and compared their response to pressure overload by transverse aortic constriction (TAC) to that of wild-type (WT) littermates. Endothelial cells, fibroblasts and cardiomyocytes were isolated from the hearts of both genotypes after TAC and their transcriptome was investigated by RNA sequencing.Gadlortarget proteins were identified by RNA antisense purification coupled with mass spectrometry (RAP-MS) in cardiomyocytes. In addition, we investigated the effects of cardiac overexpression ofGadlor1/2.

Results

Gadlor1/2are jointly upregulated in failing mouse hearts as well as in the myocardium of heart failure patients. Cardiac overexpression ofGadlor1andGadlor2aggravated myocardial dysfunction and enhanced hypertrophic and fibrotic remodeling in mice exposed to pressure overload. CompoundGadlor1/2KO mice, in turn, exerted markedly reduced myocardial hypertrophy, fibrosis and dysfunction, but more angiogenesis during short and long-standing pressure overload. Paradoxically,Gadlor1/2KO mice suffered from sudden death during prolonged overload, possibly due to cardiac arrhythmia.Gadlor1andGadlor2, which are mainly expressed in endothelial cells (ECs) in the heart, where they inhibit pro-angiogenic gene-expression, are strongly secreted within extracellular vesicles (EVs). These EVs transferGadlorlncRNAs to cardiomyocytes, where they bind and activate calmodulin-dependent kinase II, induce pro-hypertrophic gene-expression and enhance calcium re-uptake into the sarcoplasmic reticulum.

Conclusion

Gadlor1andGadlor2are lncRNAs that are mainly enriched in EC-derived EVs and are jointly upregulated in mouse and human hearts during pathological overload. We reveal a crucial endothelial cell-cardiomyocyte crosstalk, which aims at restoring calcium homeostasis in cardiomyocytes during overload at the cost of aggravated hypertrophy and fibrosis.
Multi-site phosphorylation of the TOPBP1 ATR Activation Domain propels ATR signaling during the response to DNA breaks
Authors: Senebandith Holly , Ruis Kenna , Montales Katrina , Huynh Oanh , Jami-Alahmadi Yasaman , Wohlschlegel James A. , Michael W. Matthew
Published: September 2022

TOPBP1 is a BRCT domain-containing scaffold protein that plays important roles in a diverse array of cellular processes, including DNA damage signaling, DNA repair, DNA replication, and mRNA transcription. For DNA damage signaling, TOPBP1 activates the crucial damage response kinase ATR and this occurs during replication stress as well as during a DNA double-strand break response. ATR signaling allows cells to survive genotoxic issues and represents a formidable barrier to transformation to a tumorigenic state. Despite its importance to genome stability, the biochemical mechanism for how TOPBP1 activates ATR is not fully understood. TOPBP1 uses a discrete domain, termed the ATR activation domain, to stimulate ATR kinase. Recent work has shown that the AAD must be in a multimeric state to activate ATR. Other work has shown that phosphorylation of the AAD on serine 1131 (in Xenopus) is important for its function, and some have suggested that this is linked to the formation of TOPBP1 condensates during a DNA damage response. In this study we examine AAD phosphorylation in detail and we report three important new findings. One, S1131 phosphorylation promotes ATR activation in a manner independent of condensate formation and is instead linked to promoting multimerization of the AAD. Two, we identify a novel sight of AAD phosphorylation, on T1098, and show that is required for ATR activation. Three, we identify additional, candidate phosphorylation sites, some of which fit the consensus for casein kinase 2, and we show that casein kinase 2 activity is required for the AAD to perform its function. These studies show that multi-site phosphorylation of the AAD is an important component of the mechanism by which TOPBP1 activates ATR.
Genetic factors influence behavioural repeatability in juvenile poison frogs
Authors: Sonnleitner Ria , Alanen Emmi , Fouilloux Chloe , Valkonen Janne K. , Rojas Bibiana
Published: September 2022

Individual behaviour is a combination of previous experiences and genetic factors whose interaction can be adaptively adjusted to respond to changes in the surrounding environment. Understanding the continuity of behaviours both within and among individuals can help us disentangle the ecological and evolutionary significance underlying patterns of aggression, activity, boldness, and cooperation. In this study, we examined whether there is repeatability in the activity levels of juvenile dyeing poison frogs (Dendrobates tinctorius). This tropical species, known for its striking coloration and skin toxins, changes upon metamorphosis from an aquatic to a terrestrial habitat where individuals must immediately become active foragers to acquire their chemical defences. We did not find individual behaviour to be repeatable, however, we detected repeatability in activity at the family level, suggesting that behavioural variation may be explained, at least partially, by genetic factors in addition to a common environment. The assumption that activity level is very important for the survival of individuals after metamorphosis is supported by our results in that genetic factors seem to play a role in the formation of activity level. Further experiments are needed to investigate to what extent other areas of the individuals’ lives are affected by the respective activity levels, and what significance this has for the survival of a population.
Evolutionary analysis reveals the role of a non-catalytic domain of peptidyl arginine deiminase 2 in transcriptional regulation
Authors: Villanueva-Cañas José Luis , Fernandez-Fuentes Narcis , Saul Dominik , Kosinsky Robyn Laura , Teyssier Catherine , Rogalska Malgorzata Ewa , Pérez Ferran Pegenaute , Oliva Baldomero , Notredame Cedric , Beato Miguel , Sharma Priyanka
Published: September 2022

Peptidyl arginine deiminases (PADIs) catalyze protein citrullination, a post-translational conversion of arginine to citrulline. The most widely expressed member of this family, PADI2, regulates cellular processes that impact several diseases. We hypothesized that we could gain new insights into PADI2 function through a systematic evolutionary and structural analysis. Here, we identify 20 positively selected PADI2 residues, 16 of which are structurally exposed and maintain PADI2 interactions with cognate proteins. Many of these selected residues reside in non-catalytic regions of PADI2. We validate the importance of a prominent loop in the middle domain that encompasses PADI2 L162, a residue under positive selection. This site is essential for interaction with the transcription elongation factor (P-TEFb) and mediates active transcription of the oncogenesc-MYC, andCCNB1,as well as impacting cellular proliferation. These insights could be key to understanding and addressing the role of the PADI2c-MYCaxis in cancer progression.

Significance Statement

Here we use a systematic evolutionary analysis to identify positively selected residues in the non-catalytic domain of PADI2 and link the positive selection of key residues to a role in transcription. Specifically, a structurally exposed loop in the PADI2 middle domain encompasses the positively selected residue L162 which is linked to transcription and cellular proliferation. This loop contributes to PADI2 interaction with the P-TEFb complex and cellular proliferation. Our results showcase the utility of combining evolutionary and experimental approaches to dissect the evolution of essential functional processes.
The Vap33/Eph/Vav/Cdc42 complex confers temporal specification to the outgrowth of primary dendrites in Drosophila neurons
Authors: Kamiyama Daichi , Nishida Yuri , Kamiyama Rie , Fitch Miyuki , Chihara Takahiro
Published: September 2022

The formation of primary dendrites (dendritogenesis) significantly affects the overall orientation and coverage of dendritic arborization, limiting the number and types of inputs a neuron can receive. Previously we reported how a Drosophila motoneuron spatially controls the positioning of dendritogenesis through the Dscam1/Dock/Pak1 pathway; however, how the neuron defines the timing of this process remains elusive. Here we show that the Eph receptor tyrosine kinase provides a temporal cue. We find that, at the onset of dendritogenesis, the Eph receptor recruits the Rho Family GEF Vav to the intracellular domain of Eph, which transiently activates the Cdc42 family of small GTPase. We also show that vap33 (vesicle-associated membrane protein-associated protein) mutants exhibit defects in Cdc42 activation and dendritic outgrowth, indicating Vap33 may play an upstream role in Eph signaling. Together, our result and previous studies argue that the formation of primary dendrites requires the proximity of active Cdc42 and membrane-anchored Pak1 driven by collaborative action between two distinct signaling complexes, Vap33/Eph/Vav and Dscam1/Dock. Signal integration from multiple input pathways would represent a general mechanism for the spatiotemporal precision of dendrite branch formation.
Organization and regulation of nuclear condensates by gene activity
Authors: Schede Halima H. , Natarajan Pradeep , Chakraborty Arup K. , Shrinivas Krishna
Published: September 2022

Condensation by phase separation has recently emerged as a mechanism underlying many nuclear compartments essential for cellular functions. Nuclear condensates enrich nucleic acids and proteins, localize to specific genomic regions, and often promote gene expression. How diverse properties characteristic of nuclear condensates are shaped by genome organization and activity is poorly understood. Here, we develop a physics-based model to interrogate this interplay between condensation, active transcription, and genome organization. We show that spatial clustering of active genes enables precise localization andde novonucleation of condensates. We find that strong clustering and activity drives aspherical condensate morphologies. Condensates flow towards distant gene clusters and competition between multiple clusters lead to stretched morphologies and activity-dependent repositioning. Overall, our model predicts and recapitulates morphological and dynamical features of diverse nuclear condensates and offers a unified mechanistic framework to study the interplay between non-equilibrium processes, genome structure, and multicomponent condensates in cell biology.
Totem: a user-friendly tool for clustering-based inference of tree-shaped trajectories from single-cell data
Authors: Smolander Johannes , Junttila Sini , Elo Laura L
Published: September 2022

Single-cell RNA-sequencing enables cell-level investigation of cell differentiation, which can be modelled using trajectory inference methods. While tremendous effort has been put into designing these methods, inferring accurate trajectories automatically remains difficult. Therefore, the standard approach involves testing different trajectory inference methods and picking the trajectory giving the most biologically sensible model. As the default parameters are often suboptimal, their tuning requires methodological expertise. We introduce Totem, an open-source, easy-to-use R package designed to facilitate inference of tree-shaped trajectories from single-cell data. Totem generates a large number of clustering results, estimates their topologies as minimum spanning trees, and uses them to measure the connectivity of the cells. Besides automatic selection of an appropriate trajectory, cell connectivity enables to visually pinpoint branching points and milestones relevant to the trajectory. Furthermore, testing different trajectories with Totem is fast, easy, and does not require in-depth methodological knowledge.
Plant and prokaryotic TIR domains generate distinct cyclic ADPR NADase products
Authors: Bayless Adam M. , Chen Sisi , Ogden Sam C. , Xu Xiaoyan , Sidda John D. , Manik Mohammad K. , Li Sulin , Kobe Bostjan , Ve Thomas , Song Lijiang , Grant Murray , Wan Li , Nishimura Marc T.
Published: September 2022

Toll/interleukin-1 receptor (TIR) domain proteins function in cell death and immunity. In plants and bacteria, TIR domains are enzymes that produce isomers of cyclic ADPR (cADPR) as putative immune signaling molecules. The identity and functional conservation of cADPR isomer signals is unclear. A previous report found that a plant TIR could cross-activate the prokaryotic Thoeris TIR-immune system, suggesting the conservation of plant and prokaryotic TIR-immune signals. Here, we generate auto-active Thoeris TIRs and test the converse hypothesis: do prokaryotic Thoeris TIRs also cross-activate plant TIR-immunity? Using in planta and in vitro assays, we find that Thoeris and plant TIRs generate overlapping sets of cADPR isomers, and further clarify how plant and Thoeris TIRs activate the Thoeris system via producing 3’cADPR. This study demonstrates that the TIR-signaling requirements for plant and prokaryotic immune systems are distinct and that TIRs across kingdoms generate a diversity of small molecule products.
Probabilistic 3D-modelling of genomes and genomic domains by integrating high-throughput imaging and Hi-C using machine learning
Authors: Castillo David , Mendieta-Esteban Julen , Marti-Renom Marc A.
Published: September 2022

Among the existing techniques for interrogating the genome structure, Hi-C assays have become the most performed experiments and constitute the majority of the publicly available datasets. As a result, there is a continuous demand to create and improve algorithms and methods to assist the scientific community in the interpretation of Hi-C experimental data. Here we introduce probabilistic TADbit (pTADbit), a new approach that combines Deep Learning and restraint-based modelling to infer the three-dimensional (3D) structure of genome and genomic domains interrogated by Hi-C experiments. pTADbit uses thousands of microscopy-based distances between genomic loci to train a neural network model that aims at predicting the population distribution of the spatial distance between two genomic loci based solely on their Hi-C interaction frequency. pTADbit produces more accurate chromatin models compared to the original TADbit as well as other available 3D modeling methods, while drastically reducing the required computation time. The resulting ensemble of models not only agree consistently with independent measures obtained by imaging experiments but also better capture the heterogeneity of the cell population. The development of pTADbit lays the basis for the integration of data produced from high-throughput imaging assays into the 3D modelling genomes and genomic domains.