bluuebunny/crossref_metadata_2025 huggingface dataset:
Keratins determine network stress responsiveness in reconstituted actin-keratin filament systems
Authors: Elbalasy Iman , Mollenkopf Paul , Tutmarc Cary , Herrmann Harald , Schnauß Jörg
Published: December 2020

The cytoskeleton is a major determinant of cell mechanics, a property that is altered during many pathological situations. To understand these alterations, it is essential to investigate the interplay between the main filament systems of the cytoskeleton in the form of composite networks. Here, we investigate the role of keratin intermediate filaments (IFs) in network strength by studyingin vitroreconstituted actin and keratin 8/18 composite networks via bulk shear rheology. We co-polymerized these structural proteins in varying ratios and recorded how their relative content affects the overall mechanical response of the various composites. For relatively small deformations, we found that all composites exhibited an intermediate linear viscoelastic behavior compared to that of the pure networks. In stark contrast, the composites displayed increasing strain stiffening behavior as a result of increased keratin content when larger deformations were imposed. This strain stiffening behavior is fundamentally different from behavior encountered with vimentin IF as a composite network partner for actin. Our results provide new insights into the mechanical interplay between actin and keratin in which keratin provides reinforcement to actin. This interplay may contribute to the overall integrity of cells, providing an explanation for the stability of stressed epithelial tissues due to their high keratin contents. Additionally, this helps us to understand the physiological necessity to exchange IF systems during epithelial-mesenchymal transition (EMT) in order to suppress strain stiffening of the network, making cells more elastic and, thus, facilitating their migration through dense tissues.
Feasibility and safety of a telemetric pulmonary artery pressure monitoring system in acute and chronic porcine models of pulmonary hypertension
Authors: Rothman Alexander M. K. , Arnold Nadine D. , Abou-Hanna Jacob , Forouzan Omid , Swift Andrew J. , Dahaghin Payman , Konganige Shiran , Middleton Jennifer T. , Zafar Hamza , Suvarna S. Kim , Kiely David G , Gunn Julian
Published: December 2020

Aims

Pulmonary hypertension (PH) is associated with significant morbidity and mortality and leads to progressive right heart failure. In patients with PAH, haemodynamic parameters measured at catheterisation relate to clinical worsening events, in patients with heart failure proactive pulmonary artery pressure based therapeutic intervention reduces hospitalisation. We therefore investigated use of a novel implanted pulmonary artery (PA) pressure monitor to detect clinically relevant changes in pressure in large animal models of pulmonary hypertension (PH).

Methods and Results

Prototype pulmonary artery pressure sensors (Endotronix) were implanted using standard interventional techniques. Acute PH was induced by infusion of thromboxane A2 in domestic swine. Over a physiological range pressure monitors remained concordant to reference catheter (bias −0.43, 95%CI-5.3-4.4). Chronic PH was induced by i.p. injection of monocrotaline. Implanted pressure sensors demonstrated a gradual rise in PA pressure over 30 days (baseline: 20.7+/-0.4 vrs day-30: 31.74+/-1.4, p<0.01). Pressure sensor derived readings matched reference catheter at baseline and day-30. Pressure sensors remained stable and no adverse events were identified by clinical and histological examination.

Conclusions

The development of PA pressure monitors provide long-term haemodynamic data that identified clinically meaningful changes in pulmonary artery pressure. In addition to proactive heart failure management, such devices may be used to optimise or personalize patient therapy, investigate aspects of physiology and pathology essential to the understanding of disease and provide the opportunity to assess therapeutic interventions in clinical studies.
Age-related Impairment of Implant Osseointegration is Associated with Immune Activation and Suppression of Angiogenic, Notch, and Wnt Pathways
Authors: Turajane Kathleen , Ji Gang , Chinenov Yurii , Chao Max , Ayturk Ugur , Greenblatt Matthew B. , Ivashkiv Lionel B. , Bostrom Mathias PG. , Yang Xu
Published: December 2020

The number of total joint replacements (TJRs) in the United States is increasing annually. Cementless implants are intended to improve upon traditional cemented implants by allowing bone growth directly on the surface to improve implant longevity. One major complication of TJR is implant loosening, which is related to deficient osseointegration in cementless TJRs. Although poor osseointegration in aged patients is typically attributed to decreased basal bone mass, little is known about the molecular pathways that compromise the growth of bone onto porous titanium implants. To identify the pathways important for osseointegration that are compromised by aging, we developed an approach for transcriptomic profiling of peri-implant tissue in young and aged mice using our murine model of osseointegration. Based on previous findings of changes of bone quality associated with aging, we hypothesized that aged mice have impaired activation of bone anabolic pathways at the bone-implant interface. We found that pathways most significantly downregulated in aged mice relative to young mice are related to angiogenic, Notch and Wnt signaling. Downregulation of these pathways is associated with markedly increased expression of inflammatory and immune genes at the bone-implant interface in aged mice. These results identify osseointegration pathways affected by aging and suggest that an increased inflammatory response in aged mice may compromise peri-implant bone healing. Targeting the Notch and Wnt pathways, promoting angiogenesis, or modulating the immune response at the peri-implant site may enhance osseointegration and improve the outcome of joint replacement in older patients.
Dispensability of the second Cys for phycoviolobilin formation by unusual ring D fixation in the cyanobacteriochrome
Authors: Fushimi Keiji , Narikawa Rei
Published: December 2020

Cyanobacteriochromes are linear tetrapyrrole-binding photoreceptors produced by cyanobacteria. Their chromophore-binding GAF domains are categorized into many lineages. Among them, the DXCF cyanobacteriochrome GAF domains have a “second Cys” within the DXCF motif in addition to a highly conserved “first Cys” stably ligated to C31of the A-ring. It has been long known that the second Cys is crucial for two color-tuning events: isomerization activity (reduction of C4=C5 double bond) from the initially incorporated phycocyanobilin to phycoviolobilin and reversible ligation activity to the C10 of the chromophore. Comprehensive site-directed mutagenesis, however, revealed that the second Cys is dispensable for isomerization activity, in which three residues participate by fixing the C- and D-rings. Fixation of the chromophore on both sides of the C5 bridge is necessary, even though one side of the fixation site is far from this bridge, with the other side at C31fixed by the first Cys.
The autophagy activator Spermidine ameliorates Alzheimer’s disease pathology and neuroinflammation in mice
Authors: Freitag Kiara , Sterczyk Nele , Schulz Julia , Houtman Judith , Fleck Lara , Sigrist Stephan J. , Heppner Frank L. , Jendrach Marina
Published: December 2020

Deposition of amyloid beta (Aβ) and phosphorylated Tau along with microglia- and astrocyte-mediated neuroinflammation are prominent pathogeneic features of Alzheimer’s Disease (AD). In recent years, impairment of autophagy has also been shown to contribute to AD progression. Here, we provide evidence that oral treatment of amyloid-prone AD-like APPPS1 mice with the autophagy activator Spermidine, a small body-endogenous polyamine often used as dietary supplement, decreased neuroinflammation and reduced neurotoxic soluble Aβ at both early and late stages of AD. Mechanistically, Spermidine induced autophagy in microglia as well as in astrocytes, which subsequently impacted TLR3- and TLR4-mediated inflammatory processes by decreasing cytotoxicity, inflammasome activity and NF-κB signalling. Our data highlight that autophagy targets the inflammatory response of glial cells and emphasize the potential of orally administered autophagy-activating drugs such as Spermidine to interfere with AD progression.
Molecular and functional properties of PFC astrocytes during neuroinflammation-induced anhedonia
Authors: Diaz-Castro Blanca , Bernstein Alexander M. , Coppola Giovanni , Sofroniew Michael V. , Khakh Baljit S.
Published: December 2020

Astrocytes are widely implicated in CNS diseases, but their contributions to disease related phenotypes remain incompletely explored. Anhedonia accompanies several neurological and psychiatric diseases, including major depressive disorder (MDD) and Alzheimer’s disease (AD), both of which are associated with neuroinflammation. In order to explore how neuroinflammation affects astrocytes, we assessed medial prefrontal cortex (PFC) and visual cortex (VCX) astrocytic gene expression using a neuroinflammation mouse model that displayed anhedonia as a phenotype. In this model, anhedonia was reversed by the fast acting antidepressant ketamine. Astrocyte specific gene expression alterations included those related to immune cell signaling, intracellular Ca2+signaling, cholesterol biosynthesis, and metabolic pathways. Such changes peaked when anhedonia was greatest, and reversed to normal when anhedonia subsided. However, region-specific molecular identities between PFC and VCX astrocytes were maintained throughout, implying that astrocyte identities do not converge during neuroinflammation. We also mapped anhedonia-related astrocyte and bulk tissue gene expression changes onto published PFC single cell RNA sequencing data, and compared them to MDD and AD post-mortem human tissue samples to identify shared mechanisms. Finally, we assessed how neuroinflammation affected mPFC neuronal properties and detected no alterations at a time point when there was strong astrocyte reactivity. Our data show that neuroinflammation can cause significant and reversible changes in astrocyte gene expression and mouse behaviour without obvious neurotoxicity or loss of essential homeostatic functions. Furthermore, gene expression signatures accompanying neuroinflammation reveal pathways shared with MDD and AD, which display neuroinflammation as a comorbidity in humans.

Significance statement

Astrocytes are widely implicated in brain diseases, but their contributions to disease-related phenotypes remain incompletely explored. To make inroads into this problem, we assessed medial prefrontal cortex (PFC) and visual cortex (VCX) astrocyte gene expression using a peripherally induced neuroinflammation mouse model that produced anhedonia – a phenotype associated with several brain disorders. Neuroinflammation caused reversible changes in mouse behaviour and astrocyte-specific gene expression changes, some of which were related to human post mortem data for major depressive disorder (MDD) and Alzheimer’s disease (AD), but without any clear evidence of neurotoxicity in PFC of mice. The astrocyte molecular alterations accompanying neuroinflammation-induced anhedonia will be informative to explore diverse brain disorders and the effects of neuroinflammation on the CNS more broadly.
Single cell gene fusion detection by scFusion
Authors: Jin Zijie , Huang Wenjian , Shen Ning , Li Juan , Wang Xiaochen , Park Peter J. , Xi Ruibin
Published: December 2020

Gene fusions are widespread in tumor cells and can play important roles in tumor initiation and progression. Using full length single cell RNA sequencing (scRNA-seq), gene fusions can now be detected at single cell level. However, scRNA-seq data has a high noise level and contains various technical artefacts that can lead to spurous fusion discoveries. Here we present a computational tool, scFusion, for gene fusion detection based on scRNA-seq. scFusion can efficiently and sensitively detect fusions with a low false discovery rate. In a T cell data, scFusion detected the invariant TCR gene recombinations in Mucosal-associated invariant T cells that many methods developed for bulk-data failed to detect. In a multiple myeloma data, scFusion detected the known recurrent fusionIgH-WHSC1, which was associated with overexpression of theWHSC1oncogene.
An in vivo CRISPR screening platform for prioritizing therapeutic targets in AML
Authors: Lin Shan , Larrue Clément , Seong Bo Kyung A. , Dharia Neekesh V. , Kuljanin Miljan , Wechsler Caroline , Kugener Guillaume , Robichaud Amanda , Conway Amy , Mashaka Thelma N. , Mouche Sarah , Adane Biniam , Ryan Jeremy , Mancias Joseph D. , Younger Scott T. , Piccioni Federica , Lee Lynn , Wunderlich Mark , Letai Anthony , Tamburini Jérôme , Stegmaier Kimberly
Published: December 2020

CRISPR-Cas9-based genetic screens have successfully identified cell type-dependent liabilities in cancers, including acute myeloid leukemia (AML), a devastating hematologic malignancy with poor overall survival. Because most of these screens have been performed in vitro, evaluating the physiological relevance of these targets is critical. We have established a CRISPR screening approach using orthotopic xenograft models to prioritize AML-enriched dependencies in vivo, complemented by the validation in CRISPR-competent AML patient-derived xenograft (PDX) models tractable for genome editing. Our integrated pipeline has revealed several targets with translational value, includingSLC5A3as a metabolic vulnerability for AML addicted to exogenous myo-inositol andMARCH5as a critical guardian to prevent apoptosis in AML. MARCH5 repression enhanced the efficacy of BCL2 inhibitors such as venetoclax, highlighting the clinical potential of targetingMARCH5in AML. Our study provides a valuable strategy for discovery and prioritization of new candidate AML therapeutic targets.

Statement of significance

There is an unmet need to improve the clinical outcome of AML. We developed an integrated in vivo screening approach to prioritize and validate AML dependencies with high translational potential. We identifiedSLC5A3as a metabolic vulnerability andMARCH5as a critical apoptosis regulator in AML, representing novel therapeutic opportunities.
SARS-CoV-2 escapein vitrofrom a highly neutralizing COVID-19 convalescent plasma
Authors: Andreano Emanuele , Piccini Giulia , Licastro Danilo , Casalino Lorenzo , Johnson Nicole V. , Paciello Ida , Monego Simeone Dal , Pantano Elisa , Manganaro Noemi , Manenti Alessandro , Manna Rachele , Casa Elisa , Hyseni Inesa , Benincasa Linda , Montomoli Emanuele , Amaro Rommie E. , McLellan Jason S. , Rappuoli Rino
Published: December 2020

To investigate the evolution of SARS-CoV-2 in the immune population, we co-incubated authentic virus with a highly neutralizing plasma from a COVID-19 convalescent patient. The plasma fully neutralized the virus for 7 passages, but after 45 days, the deletion of F140 in the spike N-terminal domain (NTD) N3 loop led to partial breakthrough. At day 73, an E484K substitution in the receptor-binding domain (RBD) occurred, followed at day 80 by an insertion in the NTD N5 loop containing a new glycan sequon, which generated a variant completely resistant to plasma neutralization. Computational modeling predicts that the deletion and insertion in loops N3 and N5 prevent binding of neutralizing antibodies. The recent emergence in the United Kingdom and South Africa of natural variants with similar changes suggests that SARS-CoV-2 has the potential to escape an effective immune response and that vaccines and antibodies able to control emerging variants should be developed.

One Sentence Summary

Three mutations allowed SARS-CoV-2 to evade the polyclonal antibody response of a highly neutralizing COVID-19 convalescent plasma.
Therapeutic vulnerability to PARP1/2 inhibition inRB1-mutant osteosarcoma
Authors: Zoumpoulidou Georgia , Mendoza Carlos A , Mancusi Caterina , Ahmed Ritika M , Denman Milly , Steele Christopher D , Manji Jiten , Pillay Nischalan , Strauss Sandra J , Mittnacht Sibylle
Published: December 2020

Background

Loss-of-function mutations of the retinoblastoma tumour suppressorRB1are key drivers in cancer, with prominent involvement in the natural history of Osteosarcoma (OS).RB1loss-of-function compromises genome maintenance in cells and hence could yield vulnerability to therapeutics targeting such processes.

Method

We assessed the response to Poly-ADP-Polymerase1/2 inhibitors (PARPi) in histiotype-matched cancer cell lines differing inRB1status including an extended panel of OS lines, measuring viability, clonogenic activity and inhibition of xenograft growthin vivo. We used mutational signature analysis and RAD51 immunostaining to assess competence for homologous repair defect (HRd).

Results

We report selective hypersensitivity to clinically-approved PARPi in OS lines with RB1 mutation, which extends to other cancer histiotypes and is induced in RB1-normal OS following engineered RB1 loss. PARPi treatment caused extensive cell death in RB1-mutated OS and extended survival of mice carrying human RB1-mutated OS grafts. Sensitivity in OS with natural or engineered RB1 loss surpassed that seen in BRCA-mutated backgrounds where PARPi are showing clinical benefit. PARPi sensitivity was not associated with loss of RAD51 recruitment and HRd-linked mutational signatures, which predict PARPi sensitivity in cancers with BRCA1/2 loss, but linked to rapid activation of replication checkpoint signalling with S phase transit critical for the death response observed.

Conclusion

Our work demonstrates that mutations inRB1causes clinically relevant hypersensitivity to approved PARP1/2-targeting therapeutics and advocates PARP1/2 inhibition as a novel, genome lead strategy forRB1-mutated osteosarcoma.
The SYP123-VAMP727 SNARE complex is involved in the delivery of inner cell wall components to the root hair shank in Arabidopsis
Authors: Hirano Tomoko , Ebine Kazuo , Ueda Takashi , Higaki Takumi , Nakayama Takahiro , Konno Hiroki , Takigawa-Imamura Hisako , Sato Masa H.
Published: December 2020

A root hair is a long tubular protrusion from a root hair cell established via tip growth, which is accomplished by the polarized deposition of membranous and cell wall components at the root hair apex accompanied by simultaneous hardening of the shank. The polarized secretion of materials to the root hair apex is well investigated; however, little is known about the deposition of inner cell wall materials at the root hair shank. We have previously reported that phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P2)/ROP10 signaling is required for the regulation of cortical microtubule construction and the deposition of inner cell wall components at the root hair shank during hardening. To unravel the alternate secretion mechanism for delivery of the inner cell wall components to root hair shank, here, we demonstrate that root hair-specific Qa-SNARE, SYP123, localizes to the subapical zone and shank of elongating root hairs in Arabidopsis. SYP123-mediated root hair elongation was inhibited by the FAB1 inhibitor YM201636, and inhibition of PtdIns(3,5)P2production impaired the plasma membrane localization of SYP123. We also showed that SYP123 forms a SNARE complex with VAMP727 on the plasma membrane, andsyp123andvamp727mutants exhibited lower cell wall stiffness in the root hair shank because of impaired deposition of inner cell wall components. These results indicate that SYP123/VAMP727-mediated secretion is involved in the transport of inner cell wall components for hardening of the root hair shank.
Myofiber / pro-inflammatory macrophage interplay controls muscle damage in mdx mice
Authors: Saclier Marielle , Ben Larbi Sabrina , Moulin Eugénie , Mounier Rémi , Chazaud Bénédicte , Juban Gaëtan
Published: December 2020

Duchenne Muscular Dystrophy is a genetic muscle disease characterized by chronic inflammation and fibrosis, which is mediated by a pro-fibrotic macrophage population expressing pro-inflammatory markers. The aim of this study was to characterize cellular events leading to the alteration of macrophage properties, and to modulate macrophage inflammatory status using the gaseous mediator H2S. We first analyzed the relationship between myofibers and macrophages in the mdx mouse model of Duchenne Muscular Dystrophy using coculture experiments. We showed that normal myofibers derived from mdx mice strongly skewed the polarization of resting macrophages towards a pro-inflammatory phenotype. Treatment of mdx mice with NaHS, an H2S donor, reduced the number of pro-inflammatory macrophages in skeletal muscle, which was associated with a decrease in the number of nuclei per fiber, a reduction of myofiber branching and a reduced fibrosis. These results identify an interplay between myofibers and macrophages where dystrophic myofibers contribute to the maintenance of a highly inflammatory environment that skews the macrophage status, which in turn favors myofiber damage, myofiber branching and fibrosis establishment. They also identify H2S donors as a potential therapeutic strategy to improve dystrophic muscle phenotype by modulating macrophage inflammatory status.
Single-cell Individual Complete mtDNA Sequencing Uncovers Hidden Mitochondrial Heterogeneity in Human and Mouse Oocytes
Authors: Bi Chongwei , Wang Lin , Fan Yong , Ramos-Mandujano Gerardo , Yuan Baolei , Zhou Xuan , Wang Jincheng , Shao Yanjiao , Zhang Pu-Yao , Huang Yanyi , Yu Yang , Izpisua Belmonte Juan Carlos , Li Mo
Published: December 2020

The ontogeny and dynamics of mtDNA heteroplasmy remain unclear due to limitations of current mtDNA sequencing methods. We developed individualMitochondrialGenomesequencing (iMiGseq) of full-length mtDNA for ultra-sensitive variant detection, complete haplotyping, and unbiased evaluation of heteroplasmy levels, all at the individual mtDNA molecule level. iMiGseq uncovers unappreciated levels of heteroplasmic variants in single healthy human oocytes well below the current 1% detection limit, of which numerous variants are detrimental and could contribute to late-onset mitochondrial disease and cancer. Extreme mtDNA heterogeneity among oocytes of the same mouse female, and a strong selection against deleterious mutations in human oocytes are observed. iMiGseq could comprehensively characterize and haplotype single-nucleotide and structural variants of mtDNA and their genetic linkage in NARP/Leigh syndrome patient-derived cells. Therefore, iMiGseq could not only elucidate the mitochondrial etiology of diseases, but also help diagnose and prevent mitochondrial diseases with unprecedented precision.
An open platform for high-resolution light-based control of microscopic collectives
Authors: Rubio Denniss Ana , Gorochowski Thomas E. , Hauert Sabine
Published: December 2020

Engineering microscopic collectives of cells or microrobots is challenging due to the often-limited capabilities of the individual agents, our inability to program their motion and local interactions, and difficulties visualising their behaviours. Here, we present a low-cost, modular and open-source Dynamic Optical MicroEnvironment (DOME) and demonstrate its ability to augment microagent capabilities and control collective behaviours using light. The DOME offers an accessible means to study complex multicellular phenomena and implementde-novomicroswarms with desired functionalities.
Occurrence and associated characteristics of a mutatedant(6’)-Iagene amongEnterococcus faeciumstrains expressing phenotypic susceptibility to high levels of streptomycin
Authors: Rodrigues Souza Stephanie Silva , Faria Adriana Rocha , Rangel Freitas Andréa Andrade , Planet Paul J , Carreira Merquior Vânia Lúcia , Teixeira Lúcia Martins
Published: December 2020

Enterococcal high-level resistance to streptomycin (HLR-S) (MIC ≥ 2000 µg/ml), conferred by production of a variety of aminoglycoside modifying enzymes (AMES), has been reported worldwide and a nucleotidyltransferase (ANT) enzyme encoded by theant(6’)-Iagene is frequently associated with this phenotype. However, during a study conducted by our group on whole genome sequencing (WGS) analyses ofEnterococcus faeciumisolates, we observed that 32E. faeciumstrains identified as susceptible to high-levels of streptomycin by the disk diffusion method had the ofant(6’)-Iagene annotated in their genomes. Antimicrobial susceptibility to streptomycin was reassessed by phenotypic testing and the presence of theant(6’)-Iagene was confirmed by PCR in all the isolates. Alignment of theant(6’)-Iagene with a reference sequence revealed a deletion of the first 48 nucleotides and four nonsynonymous mutations, leading to the substitution of a Glutamine to Methionine and an Aspartic Acid to Asparagine in the amino acid sequence. The protein structure was modelled by using the Phyre2 platform and the results indicated alterations in the N-terminus region leading to changes in the predicted binding site. Also, by searching the NCBI database we identified the genomes of 71 strains carrying the mutated gene. MLST analysis revealed that most strains carrying the mutated gene, including those described in this study belonged to hospital-adapted lineages, suggesting the occurrence of clonal dissemination of a subset of mutated isolates.

HIGHLIGHTS

The presence of a mutatedant(6’)-Iagene was identified amongEnterococcus faeciumisolates expressing phenotypic susceptibility to high levels of streptomycin.

Nonsynonymous mutations and inactivating changes in theant(6’)-Iagene led to incongruities between phenotypes and genotypes.

Alterations in the amino acid sequence had impacts on protein structure, with changes in the N-terminus region and the binding site.
Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions and monocytes for optimal therapeutic protection
Authors: Winkler Emma S. , Gilchuk Pavlo , Yu Jinsheng , Bailey Adam L. , Chen Rita E. , Zost Seth J. , Jang Hyesun , Huang Ying , Allen James D. , Case James Brett , Sutton Rachel E. , Carnahan Robert H. , Darling Tamarand L. , Boon Adrianus C. M. , Mack Matthias , Head Richard D. , Ross Ted M. , Crowe James E. , Diamond Michael S.
Published: December 2020

SARS-CoV-2 has caused the global COVID-19 pandemic. Although passively delivered neutralizing antibodies against SARS-CoV-2 show promise in clinical trials, their mechanism of actionin vivois incompletely understood. Here, we define correlates of protection of neutralizing human monoclonal antibodies (mAbs) in SARS-CoV-2-infected animals. Whereas Fc effector functions are dispensable when representative neutralizing mAbs are administered as prophylaxis, they are required for optimal protection as therapy. When given after infection, intact mAbs reduce SARS-CoV-2 burden and lung disease in mice and hamsters better than loss-of-function Fc variant mAbs. Fc engagement of neutralizing antibodies mitigates inflammation and improves respiratory mechanics, and transcriptional profiling suggests these phenotypes are associated with diminished innate immune signaling and preserved tissue repair. Immune cell depletions establish that neutralizing mAbs require monocytes for therapeutic efficacy. Thus, potently neutralizing mAbs require Fc effector functions for maximal therapeutic benefit during therapy to modulate protective immune responses and mitigate lung disease.
Horizontal and vertical transmission of transgenerational memories via theCer1transposon
Authors: Moore Rebecca S. , Kaletsky Rachel , Lesnik Chen , Cota Vanessa , Blackman Edith , Parsons Lance R. , Gitai Zemer , Murphy Coleen T.
Published: December 2020

Animals face both external and internal dangers: pathogens threaten from the environment, and unstable genomic elements threaten from within. Previously, we discovered thatC. elegansprotects itself from pathogens by “reading” bacterial small RNAs and using this information to both induce avoidance and transmit memories for several generations. Here we found that these memories can be transferred to naïve animals viaCer1retrotransposon-encoded capsids.Cer1functions at the step of transmission of information from the germline to neurons, and is required forC. elegans’learned avoidance ability and for mothers to pass this information on to progeny. The presence of theCer1retrotransposon in wildC. elegansstrains correlates with the ability to learn and inherit small RNA-induced pathogen avoidance. Together, these results suggest thatC. eleganshas co-opted a potentially dangerous retrotransposon to instead protect itself and its progeny from a common pathogen through its inter-tissue signaling ability, hijacking this genomic element for its own adaptive immunity benefit.
Transcriptome-wide high-throughput mapping of protein-RNA occupancy profiles using POP-seq
Authors: Srivastava Mansi , Srivastava Rajneesh , Janga Sarath Chandra
Published: December 2020

Interaction between proteins and RNA is critical for post-transcriptional regulatory processes. Existing high throughput methods based on crosslinking of the protein-RNA complexes and polyA pull down are reported to contribute to biases and are not readily amenable for identifying interaction sites on non polyA RNAs. We present Protein Occupancy Profile-Sequencing (POP-seq), a phase separation based method in three versions, one of which does not require crosslinking, thus providing unbiased protein occupancy profiles on whole cell transcriptome without the requirement of polyA pulldown. Our study demonstrates that ~68% of the total POP-seq peaks exhibited an overlap with publicly available protein-RNA interaction profiles of 97 RNA binding proteins (RBPs) in K562 cells. We show that POP-seq variants consistently capture protein-RNA interaction sites across a broad range of genes including on transcripts encoding for transcription factors (TFs), RNA-Binding Proteins (RBPs) and long non-coding RNAs (lncRNAs). POP-seq identified peaks exhibited a significant enrichment (p value < 2.2e-16) for GWAS SNPs, phenotypic, clinically relevant germline as well as somatic variants reported in cancer genomes, suggesting the prevalence of uncharacterized genomic variation in protein occupied sites on RNA. We demonstrate that the abundance of POP-seq peaks increases with an increase in expression of lncRNAs, suggesting that highly expressed lncRNA are likely to act as sponges for RBPs, contributing to the rewiring of protein-RNA interaction network in cancer cells. Overall, our data supports POP-seq as a robust and cost-effective method that could be applied to primary tissues for mapping global protein occupancies.
Growth‐mediated negative feedback shapes quantitative antibiotic response
Authors: Angermayr S. Andreas , Chevereau Guillaume , Bollenbach Tobias
Published: December 2020

Dose‐response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole‐cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose‐response curves. The shape of the dose‐response curve varies drastically between antibiotics and plays a key role for treatments, drug interactions, and resistance evolution. However, the mechanisms shaping the dose‐response curve remain largely unclear. Here, we show inEscherichia colithat the distinctively shallow dose‐response curve of the antibiotic trimethoprim is caused by a negative growth‐ mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends only on growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose‐response curve in a predictable manner, which we corroborate with a mathematical model. Our results indicate that growth‐mediated feedback loops shape drug responses and could be exploited to design evolutionary traps that enable selection against drug resistance.
Locally adaptive inversions modulate genetic variation at different geographic scales in a seaweed fly
Authors: Mérot Claire , Berdan Emma , Cayuela Hugo , Djambazian Haig , Ferchaud Anne-Laure , Laporte Martin , Normandeau Eric , Ragoussis Jiannis , Wellenreuther Maren , Bernatchez Louis
Published: December 2020

Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes of selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci at a potentially massive scale. In this study, we examined how chromosomal inversions shape genetic variation across a species range, and ask how their contribution to adaptation in the face of gene flow varies across geographic scales. We sampled the seaweed flyCoelopa frigidaalong a bioclimatic gradient stretching across 10° of latitude, a salinity gradient and a range of heterogeneous, patchy habitats. We generated a chromosome-level genome assembly to analyse 1,446 low-coverage whole genomes collected along those gradients. We found several large non-recombining genomic regions, including putative inversions. In contrast to the collinear regions, inversions and low recombining regions differentiated populations more strongly, either along an ecogeographic cline or at a fine-grained scale. These genomic regions were associated with environmental factors and adaptive phenotypes, albeit with contrasting patterns. Altogether, our results highlight the importance of recombination in shaping adaptation to environmental heterogeneity at local and large scales.
Endothelial SOCS3 maintains homeostasis and promotes survival in endotoxemic mice
Authors: Martino Nina , Ramos Ramon Bossardi , Lu Shuhan , Leyden Kara , Tomaszek Lindsay , Sadhu Sudeshna , Fredman Gabrielle , Jaitovich Ariel , Vincent Peter A. , Adam Alejandro P.
Published: December 2020

SOCS3 is the main inhibitor of the JAK/STAT3 pathway. This pathway is activated by interleukin 6 (IL-6), a major mediator of the cytokine storm during shock. To determine its role in the vascular response to shock, we challenged mice lacking SOCS3 in the adult endothelium (SOCS3iEKo) with a non-lethal dose of lipopolysaccharide (LPS). SOCS3iEKomice died 16-24 hours post-injection after severe kidney failure. Loss of SOCS3 led to an LPS-induced type I interferon-like program, and high expression of pro-thrombotic and pro-adhesive genes. Consistently, we observed intraluminal leukocyte adhesion and NETosis, as well as retinal venular leukoembolization. Notably, heterozygous mice displayed an intermediate phenotype, suggesting a gene dose effect. In vitro studies were performed to study the role of SOCS3 protein levels in the regulation of the inflammatory response. In HUVEC, pulse-chase experiments showed that SOCS3 protein has a half-life below 20 minutes. Inhibition of SOCS3 ubiquitination and proteasomal degradation leads to protein accumulation and a stronger inhibition of IL-6 signaling and barrier function loss. Together, our data demonstrates that the regulation of SOCS3 protein levels is critical to inhibit IL-6-mediated endotheliopathy during shock and provides a promising new therapeutic avenue to prevent MODS though stabilization of endothelial SOCS3.

Graphical abstract
YAP1-TAZ/TEAD transcriptional networks restrain differentiation downstream of oncogenic Hedgehog-SMO activity
Authors: Yuan Yao , Parra Natalia Salinas , Chen Qianming , Iglesias-Bartolome Ramiro
Published: December 2020

Disruption of the transcriptional activity of the Hippo pathway members YAP1 and TAZ has become a major target for cancer treatment. However, detailed analysis of the effectivity and networks affected by YAP1/TAZ transcriptional targeting are limited. Here, by comparing the effects of YAP1/TAZ knockdown with those resulting from TEAD blockage, we unveil the consequences of YAP1/TAZ transcriptional inhibition in cancer cells. We utilize TEADi, an inhibitor of the binding of YAP1 and TAZ with their main transcriptional target TEAD. In a mouse model of basal cell carcinoma (BCC) driven by the smoothened oncogene (SmoM2), TEADi and YAP1/TAZ knockdown lead to reduced proliferation and increased differentiation of tumor cells both in vitro and in vivo. We find that TEAD transcriptional networks inactivate differentiation in BCC by regulating KLF4. Furthermore, we determine YAP1/TAZ TEAD-independent effects in cancer cells that impact Stat3 and NF-κB gene networks. Our results reveal the TEAD dependent and independent roles of YAP1/TAZ in cancer and expose potential pitfalls for targeting TEAD transcription in tumors.
Novel integrative elements and genomic plasticity in ocean ecosystems
Authors: Hackl Thomas , Laurenceau Raphaël , Ankenbrand Markus J. , Bliem Christina , Cariani Zev , Thomas Elaina , Dooley Keven D. , Arellano Aldo A. , Hogle Shane L. , Berube Paul , Leventhal Gabriel E. , Luo Elaine , Eppley John , Zayed Ahmed A. , Beaulaurier John , Stepanauskas Ramunas , Sullivan Matthew B. , DeLong Edward F. , Biller Steven J. , Chisholm Sallie W.
Published: December 2020

Horizontal gene transfer accelerates microbial evolution, promoting diversification and adaptation. The globally abundant marine cyanobacteriumProchlorococcushas a highly streamlined genome with frequent gene exchange reflected in its extensive pangenome. The source of its genomic variability, however, remains elusive since most cells lack the common mechanisms that enable horizontal gene transfer, including conjugation, transformation, plasmids and prophages. Examining 623 genomes, we reveal a diverse system of mobile genetic elements – cargo-carrying transposons we named tycheposons – that shapeProchlorococcus’ genomic plasticity. The excision and integration of tycheposons at seven tRNA genes drive the remodeling of larger genomic islands containing most ofProchlorococcus’ flexible genes. Most tycheposons carry genes important for niche differentiation through nutrient acquisition; others appear similar to phage parasites. Tycheposons are highly enriched in extracellular vesicles and phage particles in ocean samples, suggesting efficient routes for their dispersal, transmission and propagation. Supported by evidence for similar elements in other marine microbes, our work underpins the role of vesicle- and virus-mediated transfer of mobile genetic elements in the diversification and adaptation of microbes in dilute aquatic environments – adding a significant piece to the puzzle of what governs microbial evolution in the planet’s largest habitat.
The comprehensive roadmaps of reprogramming and transformation unveiled antagonistic roles for bHLH transcription factors in the control of cellular plasticity
Authors: Huyghe A. , Furlan G. , Schroeder J. , Stüder J. , Mugnier F. , De Matteo L. , Wang J. , Yu Y. , Rama N. , Gibert B. , Wajda P. , Goddard I. , Gadot N. , Brevet M. , Siouda M. , Mulligan P. , Dante R. , Liu P. , Gronemeyer H. , Mendoza-Parra M. , Polo J. , Lavial F.
Published: December 2020

Coordinated changes of cellular identity and plasticity are critical for pluripotent reprogramming (PR) and malignant transformation (MT). However, the molecular circuitries orchestrating these modifications, as well as their degree of analogy during reprogramming and transformation, remain unknown. To address this question, we generated “repro-transformable” mice models and dissected comparatively the early events underpinning PR - mediated by Oct4, Sox2, Klf4, c-Myc - and MT - triggered by oncogenic Ras and c-Myc. Transcriptomic analyses allowed the identification of a unique set of markers - the cell surface glycoprotein Thy1 and the transcription factor (TF) Bcl11b - that are commonly downregulated during PR and MT and delineate cellular intermediates (CI) highly amenable to generate pluripotent or malignant derivatives. Comprehensive transcriptomic, epigenomic and functional analyses of different CI, prone or refractory to PR/MT, unveiled that cellular plasticity acquisition precedes the broad extinction of cellular identity. It also demonstrated the existence of specific and shared molecular features of PR and MT while ensuring the identification of broad-range regulators of cellular plasticity. As a proof-of-concept, we revealed that the basic helix-loop-helix (bHLH) class A TF Atoh8 constrains rodent and human iPS cells generation as well as MT and direct neuron conversion. Mechanistically, this TF hampers the reactivation of the pluripotent network during PR and limits the acquisition of phenotypic plasticity during MT. Furthermore, an integrated analysis of Atoh8 genome-wide binding, alongside the other bHLH TFs c-Myc, Ascl1 and MyoD promoting reprogramming/transdifferentiation, unveiled how Atoh8 constrains cellular plasticity by occupying a specific subset of MEF enhancers and by finetuning WNT signalling activity. Collectively, by deconvoluting the early steps of the reprogramming and transformation roadmaps, this integrated study uncoupled changes of cellular plasticity and identity to shed light on novel insights into reprogramming and cancer biology.

Graphical abstract

One-sentence summary

Comparative roadmaps of cellular plasticity acquisition during pluripotent reprogramming and malignant transformation.
An NF-κB/IRF1 axis programs cDC1s to drive anti-tumor immunity
Authors: Ghislat G , Cheema AS , Baudoin E , Verthuy C , Ballester PJ , Crozat K , Attaf N , Dong C , Milpied P , Malissen B , Auphan-Anezin N , Vu Manh TP , Dalod M , Lawrence T
Published: December 2020

Conventional type 1 dendritic cells (cDC1s) are critical for anti-tumor immunity. They acquire antigens from dying tumor cells and cross-present them to CD8+T cells, promoting the expansion of tumor-specific cytotoxic T cells. However, the signaling pathways that govern the anti-tumor functions of cDC1s are poorly understood. We mapped the molecular pathways regulating intra-tumoral cDC1 maturation using single cell RNA sequencing. We identified NF-κB and IFN pathways as being highly enriched in a subset of functionally mature cDC1s. The specific targeting of NF-κB or IFN pathways in cDC1s prevented the recruitment and activation of CD8+T cells and the control of tumor growth. We identified an NF-κB-dependent IFNγ-regulated gene network in cDC1s, including cytokines and chemokines specialized in the recruitment and activation of cytotoxic T cells. We used single cell transcriptomes to map the trajectory of intra-tumoral cDC1 maturation which revealed the dynamic reprogramming of tumor-infiltrating cDC1s by NF-κB and IFN signaling pathways. This maturation process was perturbed by specific inactivation of either NF-κB or IRF1 in cDC1s, resulting in impaired expression of IFN-γ-responsive genes and consequently a failure to efficiently recruit and activate anti-tumoral CD8+T cells. Finally, we demonstrate the relevance of these findings to cancer patients, showing that activation of the NF-κB/IRF1 axis in association with cDC1s is linked with improved clinical outcome. The NF-κB/IRF1 axis in cDC1s may therefore represent an important focal point for the development new diagnostic and therapeutic approaches to improve cancer immunotherapy.

One Sentence Summary

NF-κB and IRF1 coordinate intra-tumoral cDC1 maturation and control of immunogenic tumor growth.
Does experience with agricultural loans improve farmers' well-being? Evidence from Benin
Authors: Sagbo Nicaise Sheila M. , Kusunose Yoko
Published: December 2020

Purpose

The purpose of this study is to examine the effect of loans provided by Benin's largest microlender.

Design/methodology/approach

A pipeline design and matching techniques contribute for identifying the causal effect. The loan treatment considered is loan experience. It includes program entry timing, take-up frequency and the amount obtained over six years. The study uses a cluster analysis to create comparison groups.

Findings

Experience with agricultural loans has a statistically significantly positive effect on recipients' farm income, food security and women's empowerment. Though unusual, these positive results can be credited to the very low rate of loan repurposing and mostly to the lender's rigorous loan implementation strategy.

Practical implications

The study results validate the hypothesis underlying development strategies that target women regarding loan programs. The study provides a simple yet valuable lesson for future credit impact evaluations: the context of the loan program as well as the evaluation indicators is essential.

Social implications

This study’s findings suggest that microcredit, when offered judiciously and with support, can improve farmers' conditions.

Originality/value

Given the relatively long period studied, the analysis has been innovative in defining loan treatment and creating reliable treatment groups. Also to the best of the authors’ knowledge, this study is the first of its kind in Benin.
Photovoltaic thermal building skin: effect of condensing and evaporating temperature on flow rate and heat transfer
Authors: Riaz Ahmad , Zhou Chao , Liang Ruobing , Zhang Jili
Published: December 2020

Purpose

This paper aims to present a numerical study on the natural convection, which operates either as an evaporator or condenser unit of the heat pump system to pre-cool and pre-heat the ambient fresh air.

Design/methodology/approach

This study focuses on natural air cooling or heating within the air channel considering the double skin configuration. Particular focus is given to the analysis of airflow and the heat transfer processes in an air channel to cool or heat the ambient fresh air. In this study, the physical model consists of one wall, either heated uniformly or cooled uniformly, whereas the other wall is adiabatic.

Findings

The results show that the variation of both velocity and temperature is observed as the flow transition occurs at the evaporator or condenser wall. In either case, the temperature rises in the range of 6.3–8.4°C with an increase in mass flow rate from 0.07–0.08 kg/s in the photovoltaic thermal condenser part, while in the photovoltaic thermal evaporator part, the change in mass flow rate from 0.048–0.061 kg/s causes a decrease in temperature from 7.1–4.5°C.

Practical implications

The solar-assisted photovoltaic thermal heat pump system, in building façade having an air layer application, is feasible for pre-heating and pre-cooling the ambient fresh air and also reduces the energy needed to treat the fresh air.

Originality/value

The influence of condensing and evaporating temperature under natural convection mode in double skin conformation is considered for pre-heating and pre-cooling of ambient fresh air.
Query processing over secure perturbed data over hybrid cloud
Authors: Vulapula Sridhar Reddy , Malladi Srinivas
Published: December 2020

Purpose

Hybrid cloud composing of public and private cloud is seen as a solution for storage of health care data characterized by many private and sensitive data. In many hybrid cloud-based solutions, the data are perturbed and kept in public cloud, and the perturbation credentials are kept in private cloud.

Design/methodology/approach

Hybrid cloud is a model combing private and public cloud. Security for the data is enforced using this distribution in hybrid clouds. However, these mechanisms are not efficient for range query and retrieval of data from cloud. In this work, a secure and efficient retrieval solution combining K-mean clustering, geometric perturbation and R-Tree indexing is proposed for hybrid clouds.

Findings

Compared to existing solution, the proposed indexing on perturbed data is able to achieve 33% reduced retrieval time. The security of indexes as measured using variance of differences was 66% more than existing solutions.

Originality/value

This study is an attempt for efficient retrieval of data with range queries using R-Tree indexing approach.