bluuebunny/crossref_metadata_2025 huggingface dataset:
Hidden paths to endless forms most wonderful: parasite-blind diversification of host quality
Authors: Freund Lisa , Vasse Marie , Velicer Gregory J.
Published: April 2021

Evolutionary diversification can occur in allopatry or sympatry, can be driven by selection or unselected, and can be phenotypically manifested immediately or remain latent until manifested in a newly encountered environment. Diversification of host–parasite interactions is frequently studied in the context of intrinsically selective coevolution, but the potential for host–parasite interaction phenotypes to diversify latently during parasite-blind host evolution is rarely considered. Here, we use a social bacterium experimentally adapted to several environments in the absence of phage to analyse allopatric diversification of host quality—the degree to which a host population supports a viral epidemic. Phage-blind evolution reduced host quality overall, with some bacteria becoming completely resistant to growth suppression by phage. Selective-environment differences generated only mild divergence in host quality. However, selective environments nonetheless played a major role in shaping evolution by determining the degree of stochastic diversification among replicate populations within treatments. Ancestral motility genotype was also found to strongly shape patterns of latent host-quality evolution and diversification. These outcomes show that (i) adaptive landscapes can differ in how they constrain stochastic diversification of a latent phenotype and (ii) major effects of selection on biological diversification can be missed by focusing on trait means. Collectively, our findings suggest that latent-phenotype evolution should inform host–parasite evolution theory and that diversification should be conceived broadly to include latent phenotypes.
Meta-analytic evidence for quantitative honesty in aposematic signals
Authors: White Thomas E. , Umbers Kate D. L.
Published: April 2021

The combined use of noxious chemical defences and conspicuous warning colours is a ubiquitous anti-predator strategy. That such signals advertise the presence of defences is inherent to their function, but their predicted potential for quantitative honesty—the positive scaling of signal salience with the strength of protection—is the subject of enduring debate. Here, we systematically synthesized the available evidence to test this prediction using meta-analysis. We found evidence for a positive correlation between warning colour expression and the extent of chemical defences across taxa. Notably, this relationship held at all scales; among individuals, populations and species, though substantial between-study heterogeneity remains unexplained. Consideration of the design of signals revealed that all visual features, from colour to contrast, were equally informative of the extent of prey defence. Our results affirm a central prediction of honesty-based models of signal function and narrow the scope of possible mechanisms shaping the evolution of aposematism. They suggest diverse pathways to the encoding and exchange of information, while highlighting the need for deeper knowledge of the ecology of chemical defences to enrich our understanding of this widespread anti-predator adaptation.
Lipopolysaccharide from biofilm-forming Pseudomonas aeruginosa PAO1 induces macrophage hyperinflammatory responses
Authors: Wang Sufei , Xiang Dandan , Tian Fangbing , Ni Ming
Published: April 2021

Introduction. Macrophages polarization is essential in infection control. Llipopolysaccharide (LPS) plays an essential role in host innate immune system–pathogen interaction. The LPS structure of

Pseudomonas aeruginosa

modifies in the adaptation of this pathogen to biofilm-related chronic infection.

Gap statement. There have been several studies on LPS induced polarization of human and mouse macrophages with different results. And it was reported that the lipid A structure of the LPS derived from biofilm-forming

Pseudomonas aeruginosa

strain PAO1 was modified.

Aim. This study aimed to investigate the effect and the involved pathway of LPS from biofilm-forming PAO1 on human and murine macrophage polarization.

Methodology. LPS was isolated from biofilm-forming and planktonic PAO1 and quantified. Then the LPS was added to PMA-differentiated human macrophage THP-1 cells and Raw264.7 murine macrophage cells. The expression of iNOS, Arg-1, IL4, TNF-α, CCL3, and CCL22 was analysed in the different cell lines. The expression of TICAM-1 and MyD88 in human THP-1 macrophages was quantified by Western blot. PAO1 infected macrophages at different polarization states, and the intracellular bacterial growth in macrophages was evaluated.

Results. LPS from biofilm-forming PAO1 induced more marked hyperinflammatory responses in THP-1 and Raw264.7 macrophages than LPS derived from planktonic PAO1, and these responses were related to the up-regulation of MyD88. Intracellular growth of PAO1 was significantly increased in THP-1 macrophages polarized by LPS from biofilm-forming PAO1, but decreased both in THP-1 and Raw264.7 macrophages polarized by LPS from planktonic PAO1.

Conclusion. The presented in vitro study indicates that LPS derived from biofilm-forming PAO1 induces enhanced M1 polarization in human and murine macrophage cell lines than LPS from planktonic PAO1.
Analysis of fragment ends in plasma DNA from patients with cancer
Authors: Budhraja Karan K. , McDonald Bradon R. , Stephens Michelle D. , Contente-Cuomo Tania , Markus Havell , Farooq Maria , Favaro Patricia F. , Connor Sydney , Byron Sara A. , Egan Jan B. , Ernst Brenda , McDaniel Timothy K. , Sekulic Aleksandar , Tran Nhan L. , Prados Michael D. , Borad Mitesh J. , Berens Michael E. , Pockaj Barbara A. , LoRusso Patricia M. , Bryce Alan , Trent Jeffrey M. , Murtaza Muhammed
Published: April 2021

Fragmentation patterns observed in plasma DNA reflect chromatin accessibility in contributing cells. Since DNA shed from cancer cells and blood cells may differ in fragmentation patterns, we investigated whether analysis of genomic positioning and nucleotide sequence at fragment ends can reveal the presence of tumor DNA in blood and aid cancer diagnostics. We analyzed whole genome sequencing data from >2700 plasma DNA samples including healthy individuals and patients with 11 different cancer types. We observed higher fractions of fragments with aberrantly positioned ends in patients with cancer, driven by contribution of tumor DNA into plasma. Genomewide analysis of fragment ends using machine learning showed overall area under the receiver operative characteristic curve of 0.96 for detection of cancer. Our findings remained robust with as few as 1 million fragments analyzed per sample, suggesting that analysis of fragment ends can become a cost-effective and accessible approach for cancer detection and monitoring.

One-sentence summary

Analyzing the positioning and nucleotide sequence at fragment ends in plasma DNA may enable cancer diagnostics.
Stimulation of vascular organoids with SARS-CoV-2 antigens increases endothelial permeability and regulates vasculopathy
Authors: Khan Abdullah O. , Reyat Jasmeet S. , Bourne Joshua H. , Colicchia Martina , Newby Maddy L. , Allen Joel D. , Crispin Max , Youd Esther , Murray Paul G. , Taylor Graham , Stamataki Zania , Richter Alex G. , Cunningham Adam F. , Pugh Matthew , Rayes Julie
Published: April 2021

Objective

Thrombotic complications and vasculopathy have been extensively associated with severe COVID-19 infection, however the mechanisms by which endotheliitis is induced remain poorly understood. Here we investigate vascular permeability in the context of SARS-CoV-2-mediated endotheliitis in patient samples and a vascular organoid model.

Methods and Results

We report the presence of the Spike glycoprotein in pericytes associated with pericyte activation and increased endothelial permeability in post-mortem COVID-19 lung autopsies. A pronounced decrease in the expression of the adhesion molecule VE-cadherin is observed in patients with thrombotic complications. Interestingly, fibrin-rich thrombi did not contain platelets, did not colocalize with tissue factor and have heterogenous levels of Von Willebrand factor, suggesting a biomarker-guided therapy might be required to target thrombosis in severe patients. Using a 3D vascular organoid model, we observe that ACE2 is primarily expressed in pericytes adjacent to vascular networks, consistent with patient data, indicating a preferential uptake of the S glycoprotein by these cells. Exposure of vascular organoids to SARS-CoV-2 or its antigens, recombinant trimeric Spike glycoprotein and Nucleocapsid protein, reduced endothelial cell and pericyte viability as well as CD144 expression with no additive effect upon endothelial activation via IL-1β.

Conclusions

Our data suggest that pericyte uptake of SARS-CoV-2 or Spike glycoprotein contributes to vasculopathy by altering endothelial permeability increasing the risk of thrombotic complications.
A prospective longitudinal study of chronic pulmonary aspergillosis in pulmonary tuberculosis in Indonesia (APICAL)
Authors: Setianingrum Findra , Rozaliyani Anna , Adawiyah Robiatul , Syam Ridhawati , Tugiran Mulyati , Sari Cut Yulia I. , Nandipinto Finny , Ramnath Johannes , Arifin Arief Riadi , Handayani Diah , Burhan Erlina , Rumende Martin C. , Wahyuningsih Retno , Rautemaa-Richardson Riina , Denning David W.
Published: April 2021

Objectives

Chronic pulmonary aspergillosis (CPA) can complicate recovery from pulmonary tuberculosis (TB). CPA may also be misdiagnosed as bacteriologically-negative TB. This study aimed to determine the incidence of CPA in patients treated for TB in Indonesia; a country with a high incidence of TB.

Methods

In this prospective, longitudinal cohort study in patients treated for pulmonary TB, clinical, radiological and laboratory findings were analysed. Sputum was collected for fungal culture and TB PCR. Patients were assessed at baseline (0-8 weeks) and at the end (5-6 months) of TB therapy. CPA diagnosis was based on symptoms (>3 months), characteristic radiological features and positive Aspergillus serology, and categorized as proven, probable and possible.

Results

Of the 216 patients recruited, 128 (59%) were followed up until end of TB therapy. At baseline, 91 (42%) had microbiological evidence for TB. Aspergillus-specific IgG was positive in 64 (30%) patients and went from negative to positive in 16 (13%) patients during TB therapy. The incidence of proven and probable CPA at baseline was 6% (n=12) and 2% (n=5) and end of TB therapy 8% (n=10) and 5% (n=7), respectively. Six patients (2 with confirmed TB) developed an aspergilloma. Diabetes mellitus was a significant risk factor for CPA (p=0.040). Persistent cough (n=5, 50%; p=0.005) and fatigue (n=6, 60%; p=0.001) were the most common symptoms in CPA.

Conclusion

CPA should be considered a relatively frequent differential diagnosis in patients with possible or proven TB in Indonesia. Lack of awareness and limited access to Aspergillus-specific IgG tests and CT imaging are obstacles in establishing a CPA diagnosis.

Key messages

What is the key question?

Do what extent is chronic pulmonary aspergillosis (CPA) both a) mistaken for TB and b) co-exists with TB during the course of 6 months therapy

What is the bottom line?

Features consistent with CPA were present in 6% of patients when starting TB therapy and 8% at the end of therapy, with some resolving and some developing CPA de novo during TB therapy. At the end of B therapy symptoms, cavitations with Aspergillus-specific IgG detectable were the key features of CPA.

Why read on?

Co-existence of TB and CPA is present in a substantial minority of patients starting and ending TB therapy, and needs addressing in terms of diagnosis, dual therapy and follow up.
Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants
Authors: Fattel Leila , Psaroudakis Dennis , Yanarella Colleen F. , Chiteri Kevin O. , Dostalik Haley A. , Joshi Parnal , Starr Dollye C. , Vu Ha , Wimalanathan Kokulapalan , Lawrence-Dill Carolyn J.
Published: April 2021

Background

Genome-wide gene function annotations are useful for hypothesis generation and for prioritizing candidate genes potentially responsible for phenotypes of interest. We functionally annotated the genes of 18 crop plant genomes across 14 species using the GOMAP pipeline.

Results

By comparison to existing GO annotation datasets, GOMAP-generated datasets cover more genes, contain more GO terms, and produce datasets similar in quality (based on precision and recall metrics using existing gold standards as the basis for comparison). From there, we sought to determine whether the datasets across multiple species could be used together to carry out comparative functional genomics analyses in plants. To test the idea and as a proof of concept, we created dendrograms of functional relatedness based on terms assigned for all 18 genomes. These dendrograms were compared to well-established species-level evolutionary phylogenies to determine whether trees derived were in agreement with known evolutionary relationships, which they largely are. Where discrepancies were observed, we determined branch support based on jack-knifing then removed individual annotation sets by genome to identify the annotation sets causing unexpected relationships.

Conclusions

GOMAP-derived functional annotations used together across multiple species generally retain sufficient biological signal to recover known phylogenetic relationships based on genome-wide functional similarities, indicating that comparative functional genomics across species based on GO data hold promise for generating novel hypotheses about comparative gene function and traits.
Ensemble of deep masked language models for effective named entity recognition in multi-domain corpora
Authors: Naderi Nona , Knafou Julien , Copara Jenny , Ruch Patrick , Teodoro Douglas
Published: April 2021

The health and life science domains are well known for their wealth of entities. These entities are presented as free text in large corpora, such as biomedical scientific and electronic health records. To enable the secondary use of these corpora and unlock their value, named entity recognition (NER) methods are proposed. Inspired by the success of deep masked language models, we present an ensemble approach for NER using these models. Results show statistically significant improvement of the ensemble models over baselines based on individual models in multiple domains - chemical, clinical and wet lab - and languages - English and French. The ensemble model achieves an overall performance of 79.2% macro F1-score, a 4.6 percentage point increase upon the baseline in multiple domains and languages. These results suggests that ensembles are a more effective strategy for tackling NER. We further perform a detailed analysis of their performance based on a set of entity properties.
Assisted reproductive technology and association with childhood cancer subtypes
Authors: Gulrajani Natalie B. , Montes Samuel , McGough Dan , Wimberly Courtney E. , Khattab Ameera , Semmes Eleanor C. , Towry Lisa , Cohen Jennifer L. , Hurst Jillian H. , Landi Daniel , Hill Sherika N. , Walsh Kyle M.
Published: April 2021

Objectives

Use of assisted reproductive technology (ART) may alter the typical course of fetal development. We sought to investigate the association between ART use and childhood cancer subtype.

Study design

We surveyed 1701 parents of children with cancer about ART use, demographics, and gestational and perinatal factors. Multivariable logistic regression modeled the association between ART use and childhood cancer subtypes, birthweight and multiple gestation status.

Results

Among childhood cancer patients, ART use was highest among children with osteosarcoma (OR=2.81; 95% CI=1.2-6.4; P=0.01). ART use was also elevated among children with hepatoblastoma, and this relationship appeared mediated by low birthweight. No specific type of ART appeared to drive these associations. Low birthweight was itself strongly associated with increased hepatoblastoma risk, even after adjustment for ART use, multiple gestation status, sex, and parental income (P<0.001). Birthweight was higher in patients with germ cell tumors (P=0.02) and with neuroblastoma (P=0.06). Multiple gestation status was associated with neuroblastoma among females (OR=3.6, 95% CI=1.2-10.5, P=0.02), but not among males (OR=0.97, 95% CI=0.27-3.4, P=0.96) (Pinteraction=0.02).

Conclusions

Associations between ART use and hepatoblastoma risk may be mediated by birthweight, a strong hepatoblastoma risk factor that was replicated in our study. ART use may also be associated with osteosarcoma independent of birthweight, an association not previously observed in studies limited to cancers diagnosed before adolescence. Evaluating long-term health outcomes in children conceived by ART, throughout adolescence and potentially into adulthood, appears warranted.
A fructo-oligosaccharide prebiotic is well-tolerated in adults undergoing allogeneic hematopoietic stem cell transplantation: a phase I dose-escalation trial
Authors: Andermann Tessa. M. , Fouladi Farnaz , Tamburini Fiona B. , Sahaf Bita , Tkachenko Ekaterina , Greene Courtney , Buckley Matthew T. , Brooks Erin F. , Hedlin Haley , Arai Sally , Mackall Crystal L. , Miklos David , Fodor Anthony A. , Rezvani Andrew R. , Bhatt Ami S.
Published: April 2021

Background

Alterations of the gut microbiota after allogeneic hematopoietic cell transplantation (allo-HCT) are a key factor in the development of transplant-related complications such as graft-versus-host disease (GVHD). Interventions that preserve the gut microbiome hold promise to improve HCT-associated morbidity and mortality. Murine models demonstrate that prebiotics such as fructo-oligosaccharides (FOS) may increase gut levels of short-chain fatty acids (SCFAs) such as butyrate, and consequently induce proliferation of immunomodulatory CD4+ FOXP3+ T-regulatory cells (Tregs), that impact GVHD risk.

Methods

We conducted a pilot Phase I trial to assess the investigate the maximum tolerated dose of FOS in patients undergoing reduced-intensity (RIC) allo-HCT (n=15) compared to concurrent controls (n=16). We administered FOS starting at pretransplant conditioning and continuing for a total of 21 days. We characterized the gut microbiome using shotgun metagenomic sequencing, measured stool SCFAs using LC-MS, and determined peripheral T-cell concentrations using CyTOF.

Results

We found that FOS was safe and well-tolerated at 10g per day without significant adverse effects in patients undergoing reduced-intensity conditioning allo-HCT. Community-level gut microbiota composition was significantly different on the day of transplant (day 0) between patients receiving FOS compared to concurrent controls, however FOS-associated alterations of the gut microbiota were not sustained after transplant. Although the impact of FOS was fleeting, transplantation itself impacted a substantial number of taxa over time. In our small pilot trial, no significant differences were observed in gut microbial metabolic pathways, stool SCFAs, or in peripheral Tregs although Tregs trended higher in those patients who received FOS. Early alterations in gut microbiota composition in those receiving FOS are especially intriguing although it remains unclear what impact this has on outcomes following transplantation and larger studies are required to investigate the use of prebiotics in HCT recipients.

Conclusions

FOS is well-tolerated at 10g per day in patients undergoing RIC allo-HCT.
ILK play a key role in partial bladder outler obstruction (PBOO) by regulation TLR4/NF-κB(p65) pathway
Authors: Zhou Yiduo , Huang Yi , Gao Jie , Shu Le , Zhang Sicong , Chen Zhengsen , Shen Baixin , Wei Zhongqing , Ding Liucheng
Published: April 2021

Aim

The purpose of this research was to discuss the effects and relative mechanisms of ILK in PBOO by vivo and vitro study.

Materials and methods

The SD rats were divided into Normal, Sham and Model groups. Collecting Bladder outlet tissue, observation pathology and fibrosis levels by H&E and Masson staining. Measuring cell apoptosis and cell viability by TUNEL and p-histone H3 staining, ILK protein were evaluated by WB and IHC assay in Bladder outlet tissue. Using TGF-β1 stimulating BSMC cell to make PBOO cell model. Measuring cell proliferation by CCK-8 assay; Relative gene and proteins expression were evaluated by immunofluorescence, WB and RT-qPCR assay.

Results

Compared with Normal group, bladder weight, collage fiber area, apoptosis cell number and cell viability were significantly difference with ILK protein significantly increasing in bladder outer tissues of Model group (P < 0.05, respectively). In vitro cell experiment, ILK overexpression had effects to stimulate cell proliferation via TLR4/NF-κB(p65) pathway; however, with ILK knockdown, the cell proliferation was significantly depressed via regulation TLR4/NF-κB(p65).

Conclusion

ILK play an important role in PBOO induced cell proliferation, ILK knockdown had effects to improve PBOO induced cell hyper-proliferation via depressing TLR4/NF-κB(p65) pathway.
Gambogic acid and gambogenic acid induce a thiol-dependent heat shock response and disrupt the interaction between HSP90 and HSF1 or HSF2
Authors: Pesonen Linda , Svartsjö Sally , Bäck Viktor , de Thonel Aurélie , Mezger Valérie , Sabéran-Djoneidi Délara , Roos-Mattjus Pia
Published: April 2021

Cancer cells rely on heat shock proteins (HSPs) for growth and survival. Especially HSP90 has multiple client proteins and plays a critical role in malignant transformation, and therefore different types of HSP90 inhibitors are being developed. The bioactive natural compound gambogic acid (GB) is a prenylated xanthone with antitumor activity and it has been proposed to function as an HSP90 inhibitor. However, there are contradicting reports whether GB induces a heat shock response (HSR), which is cytoprotective for cancer cells and therefore a potentially problematic feature for an anticancer drug. In this study, we show that GB and a structurally related compound, called gambogenic acid (GBA), induce a robust HSR, in a thiol-dependent manner. Using heat shock factor 1 (HSF1) orHSF2knockout cells, we show that the GB or GBA-induced HSR is HSF1-dependent. Intriguingly, using closed form ATP-bound HSP90-mutants that can be co-precipitated with HSF1, a known facilitator of cancer, we show that also endogenous HSF2 binds to the HSP90-HSF1 complex. GB and GBA treatment disrupt the interaction between HSP90 and HSF1 and HSF2. Our study implies that these compounds should be used cautiously if developed for cancer therapies, since GB and its derivative GBA are strong inducers of the HSR, in multiple cell types, by involving the dissociation of a HSP90-HSF1-HSF2 complex.
Genetic characteristics of human papillomavirus type 16, 18, 52 and 58 in southern China
Authors: Zu Yuee , Ou Zhihua , Wu Dan , Liu Wei , Liu Liwen , Wu Di , Zhao Yanping , Ren Peidi , Zhang Yanqing , Li Wangsheng , Fu Shujin , Wen Yongchun , Cai Xianchu , Liao Wenbo , Geng Chunyu , Zhou Hongcheng , Wang Xiaman , Lu Haorong , Peng Huanhuan , Liu Na , Zhu Shida , Liu Jiyang , Wang Dongbo , Li Junhua
Published: April 2021

Persistent infections of high-risk human papillomaviruses (HPVs) are the leading cause of cervical cancers. We collected cervical exfoliated cell samples from females in Changsha city, Hunan Province and obtained 358 viral genomes of four major HPV types, including HPV 16 (n=82), 18 (n=35), 52 (n=121) and 58 (n=100). The lineage/sublineage distribution of the four HPVs confirmed previous epidemiological reports, with the predominant prevailing sublineage as A4 (50%), A1 (37%) and A3 (13%) for HPV16, A1 (83%) for HPV18, B2 (86%) for HPV52 and A1 (65%), A3 (19%) and A2 (12%) for HPV58. We also identified two potentially novel HPV18 sublineages, i.e. A6 and A7. Virus mutation analysis further revealed the presence of HPV16 and HPV58 strains associated with potentially high oncogenicity. These findings expanded our knowledge on the HPV genetic diversity in China, providing valuable evidence to facilitate HPV DNA screening, vaccine effectiveness evaluation and control strategy development.
Phospholipid exchange shows insulin receptor activity is supported by both the propensity to form wide bilayers and ordered domains (rafts)
Authors: Suresh Pavana , Miller W. Todd , London Erwin
Published: April 2021

Using efficient methyl-alpha-cyclodextrin mediated lipid exchange, we studied the effect of altering plasma membrane outer leaflet phospholipid composition upon the activity of insulin receptor (IR) in mammalian cells. After substitution of endogenous lipids with lipids having an ability to form liquid ordered (Lo) domains (sphingomyelins) or liquid disordered (Ld) domains (unsaturated phosphatidylcholines (PCs)), we found that the propensity of lipids to form ordered domains is required for high IR activity. Additional substitution experiments using a series of saturated PCs showed that IR activity increased substantially with increasing acyl chain length. Increasing acyl chain length increases both bilayer width and the propensity to form ordered domains. To distinguish the effects of membrane width and domain formation, we incorporated purified IR into alkyl maltoside micelles with increasing hydrocarbon lengths. IR activity increases with increased chain length, but more modestly than by increasing lipid acyl chain length in cells. This suggests that the ability to form Lo domains as well as wide bilayer width contributes to increased IR activity. Inhibition of phosphatases with sodium orthovanadate showed that some of the lipid dependence of IR activity upon lipid structure reflected protection from phosphatases by lipids that support Lo domain formation. The results are consistent with a model in which a combination of bilayer width and ordered domain formation modulate IR activity via effects upon IR conformation and accessibility to phosphatases.

Significance

This study shows how methyl-α-cyclodextrin mediated lipid exchange can be used to probe the influence of lipid structure upon the functioning of a transmembrane receptor. Plasma membranes having a propensity to form Lo domains are required to support a high level of IR activity. The studies indicate this may reflect an effect of lipid environment upon IR domain localization, which in turn alters its conformation and vulnerability to phosphatases. Alterations in lipid composition could conceivably regulate IR activityin vivo.
Circulating miRNA diversity, origin and response to changing metabolic and reproductive states, new insights from the rainbow trout
Authors: Emilie Cardona E , Cervin Guyomar C , Desvignes Thomas , Jérôme Montfort J , Guendouz Samia , Postlethwait John H. , Sandrine Skiba-Cassy S , Bobe Julien
Published: April 2021

Circulating miRNAs (c-miRNAs) are found in most, if not all, biological fluids and are becoming well established biomarkers of many human pathologies. The aim of the present study was to investigate the potential of c-miRNAs as biomarkers of reproductive and metabolic states in fish, a question that has received little attention. Plasma was collected throughout the reproductive cycle from rainbow trout females subjected to two different feeding levels to trigger contrasting metabolic states; ovarian fluid was sample at ovulation. Fluid samples were subjected to small RNA-seq analysis followed by quantitative PCR validation for a subset of promising c-miRNA biomarkers. A comprehensive miRNA repertoire, which was lacking in trout, was first established to allow subsequent analysis. We first showed that biological fluids miRNAomes are complex and encompass a high proportion of the overall species miRNAome. While sharing a high proportion of common miRNAs, plasma and ovarian fluid miRNAomes exhibited strong fluid-specific signatures. We further showed that the plasma miRNAome exhibited major significant changes depending on metabolic and reproductive state. We subsequently identified three (miR-1-1/2-3p, miR-133-a-1/2-3p and miR-206-3p) evolutionarily conserved muscle-specific miRNA that accumulate in the plasma in response to high feeding rates, making these myomiRs strong candidate biomarkers of active myogenesis. We also identified miR-202-5p as a candidate biomarker for reproductive success that could be used to predict ovulation and/or egg quality. These highly promising results reveal the high potential of c-miRNAs as physiologically relevant biomarkers and pave the way for the use of c-miRNAs for non-invasive phenotyping in various fish species.
Proteomic signature of the Dravet syndrome in the geneticScn1a-A1783V mouse model
Authors: Miljanovic Nina , Hauck Stefanie M. , van Dijk R. Maarten , Liberto Valentina Di , Rezaei Ali , Potschka Heidrun
Published: April 2021

Background

Dravet syndrome is a rare, severe pediatric epileptic encephalopathy associated with intellectual and motor disabilities. Proteomic profiling in a mouse model of Dravet syndrome can provide information about the molecular consequences of the genetic deficiency and about pathophysiological mechanisms developing during the disease course.

Methods

A knock-in mouse model of Dravet syndrome withScn1ahaploinsufficiency was used for whole proteome, seizure and behavioral analysis. Hippocampal tissue was dissected from two-(prior to epilepsy manifestation) and four-(following epilepsy manifestation) week-old male mice and analyzed using LC-MS/MS with label-free quantification. Proteomic data sets were subjected to bioinformatic analysis including pathway enrichment analysis. The differential expression of selected proteins was confirmed by immunohistochemical staining.

Results

The findings confirmed an increased susceptibility to hyperthermia-associated seizures, the development of spontaneous seizures, and behavioral alterations in the novelScn1a-A1873V mouse model of Dravet syndrome. As expected, proteomic analysis demonstrated more pronounced alterations following epilepsy manifestation. In particular, proteins involved in neurotransmitter dynamics, receptor and ion channel function, synaptic plasticity, astrogliosis, neoangiogenesis, and nitric oxide signaling showed a pronounced regulation in Dravet mice. Pathway enrichment analysis identified several significantly regulated pathways at the later time point, with pathways linked to synaptic transmission and glutamatergic signaling dominating the list.

Conclusion

In conclusion, the whole proteome analysis in a mouse model of Dravet syndrome demonstrated complex molecular alterations in the hippocampus. Some of these alterations may have an impact on excitability or may serve a compensatory function, which, however, needs to be further confirmed by future investigations. The proteomic data indicate that, due to the molecular consequences of the genetic deficiency, the pathophysiological mechanisms may become more complex during the course of the disease. Resultantly, the management of Dravet syndrome may need to consider further molecular and cellular alterations. Ensuing functional follow-up studies, this data set may provide valuable guidance for the future development of novel therapeutic approaches.
Inositol Polyphosphate-5-phosphatase K (Inpp5k) enhances sprouting of corticospinal tract axons after CNS trauma
Authors: Kauer Sierra D. , Fink Kathren L. , Li Elizabeth H.F. , Evans Brian P. , Golan Noa , Cafferty William BJ
Published: April 2021

Failure of CNS neurons to mount a significant intrinsic growth response after trauma results in chronic functional deficits after spinal cord injury. Approaches to identify novel axon growth activators include transcriptional and repressor screening of embryonic cortical and retinal ganglion neuronsin vitro. These high throughput approaches have identified several candidates; however, their inability to comprehensively model the adult CNS has resulted in their exploitationin vivofailing to stimulate significant anatomical and functional gains. To identify novel cell autonomous axon growth activators while maintaining CNS complexity, we screened intact adult corticospinal neurons (CSNs) undergoing functional plasticity after unilateral pyramidotomy. RNA-seq of intact sprouting corticospinal tract (CST) axons showed an enrichment of genes in the 3-phosphoinositide degradation pathways, including six 5-phosphatases. We explored whether Inositol Polyphosphate-5-phosphatase K (Inpp5k) could enhance CST axon growth in clinical models of CNS trauma. Overexpression ofInpp5kin intact adult CSNs enhanced sprouting of intact CST terminals into the denervated cervical cord after pyramidotomy and cortical stroke lesion.Inpp5koverexpression also stimulated sprouting of CST axons in the cervical cord after acute and chronic severe thoracic spinal contusion. We show thatInpp5kstimulates axon growth by elevating the density of active cofilin in the cytosol of labile growth cones, thus stimulating actin polymerization and enhancing microtubule protrusion into distal filopodia. This study identifiesInpp5kas a novel CST growth activator and underscores the veracity of usingin vivotranscriptional screening to identify the next generation of cell autonomous factors capable of repairing the damaged CNS.

SIGNIFICANCE STATEMENT

Neurological recovery is limited after spinal cord injury as CNS neurons are incapable of self-repair post trauma.In vitroscreening strategies exploit the intrinsically high growth capacity of embryonic CNS neurons to identify novel axon growth activators. While promising candidates have been shown to stimulate axon growthin vivo, concomitant functional recovery remains incomplete. Using transcriptional profiling of intact adult corticospinal tract neurons undergoing functional plasticity, we identifiedInpp5kas a novel axon growth activator capable of stimulating CST axon growth after pyramidotomy, stroke and acute and chronic contusion injuries. These data support usingin vivoscreening approaches to identify novel axon growth activators.
Stochastic dynamics of single molecules across phase boundaries
Authors: Bo Stefano , Hubatsch Lars , Bauermann Jonathan , Weber Christoph A. , Julicher Frank
Published: April 2021

We discuss the stochastic trajectories of single molecules in a phase-separated liquid, when a dense and a dilute phase coexist. Starting from a continuum theory of macroscopic phase separation we derive a stochastic Langevin equation for molecular trajectories that takes into account thermal fluctuations. We find that molecular trajectories can be described as diffusion with drift in an effective potential, which has a steep gradient at phase boundaries. We discuss how the physics of phase coexistence affects the statistics of molecular trajectories and in particular the statistics of displacements of molecules crossing a phase boundary. At thermodynamic equilibrium detailed balance imposes that the distributions of displacements crossing the phase boundary from the dense or from the dilute phase are the same. Our theory can be used to infer key phase separation parameters from the statistics of single-molecule trajectories. For simple Brownian motion, there is no drift in the presence of a concentration gradient. We show that interactions in the fluid give rise to an average drift velocity in concentration gradients. Interestingly, under non-equilibrium conditions, single molecules tend to drift uphill the concentration gradient. Thus, our work bridges between single-molecule dynamics and collective dynamics at macroscopic scales and provides a framework to study single-molecule dynamics in phase-separating systems.
Multiple generations of antibiotic exposure and isolation influence host fitness and the microbiome in a model zooplankton species
Authors: Cooper Reilly O. , Tjards Sarah , Rischling Jessica , Nguyen David T. , Cressler Clayton E.
Published: April 2021

Background

Chronic antibiotic exposure impacts host health through changes to the microbiome, increasing disease risk and reducing the functional repertoire of community members. The detrimental effects of antibiotic perturbation on microbiome structure and function after one host generation of exposure have been well-studied. However, much less is understood about the multigenerational effects of antibiotic exposure and how the microbiome may recover across host generations.

Results

In this study, we examined microbiome composition and host fitness across five generations of exposure to a suite of three antibiotics in the model zooplankton hostDaphnia magna. By utilizing a split-brood design where half of the offspring from antibiotic-exposed parents were allowed to recover and half were maintained in antibiotics, we aimed to examine recovery and resilience of the microbiome. Unexpectedly, we discovered that experimental isolation of single host individuals across generations also exerted a strong effect on microbiome composition, with composition becoming less diverse over generations regardless of treatment. Simultaneously,Daphnia magnabody size and cumulative reproduction increased across generations while survival decreased. Though antibiotics did cause substantial changes to microbiome composition, the microbiome generally became similar to the no antibiotic control treatment within one generation of recovery no matter how many prior generations were spent in antibiotics.

Conclusions

Contrary to results found in vertebrate systems,Daphnia magnamicrobiome composition recovers quickly after antibiotic exposure. However, our results suggest that the isolation of individual hosts leads to the stochastic extinction of rare taxa in the microbiome, indicating that these taxa are likely maintained via transmission in host populations rather than intrinsic mechanisms. This may explain the intriguing result that microbiome diversity loss increased host fitness.
Antarctic Teleosts With and Without Haemoglobin Behaviourally Mitigate Deleterious Effects of Acute Environmental Warming
Authors: Ismailov Iskander I. , Scharping Jordan B. , Andreeva Iraida E. , Friedlander Michael J.
Published: April 2021

Recent studies forecast that many ectothermic animals, especially aquatic stenotherms, may not be able to thrive or even survive predicted climate change. These projections, however, generally do not call much attention to the role of behaviour, an essential thermoregulatory mechanism of many ectotherms. Here we characterize species-specific locomotor and respiratory responses to acute ambient warming in two highly stenothermic Antarctic Notothenioid fishes, one of which (Chaenocephalus aceratus) lacks haemoglobin and appears to be less tolerant to thermal stress as compared to the other (Notothenia coriiceps), which expresses haemoglobin. At the onset of ambient warming, both species perform distinct locomotor manoeuvres that appear to include avoidance reactions. In response to unavoidable progressive hyperthermia, fishes demonstrate a range of species-specific manoeuvres, all of which appear to provide some mitigation of the deleterious effects of obligatory thermoconformation and to compensate for increasing metabolic demand by enhancing the efficacy of branchial respiration. As temperature continues to rise,Chaenocephalus aceratussupplements these behaviours with intensive pectoral fin fanning which may facilitate cutaneous respiration through its scaleless integument, andNotothenia coriicepsmanifests respiratory-locomotor coupling during repetitive startle-like manoeuvres which may further augment gill ventilation. The latter behaviours, found only inNotothenia coriiceps, have highly stereotyped appearance resembling Fixed Action Pattern sequences. Altogether, this behavioural flexibility could contribute to the reduction of the detrimental effects of acute thermal stress within a limited thermal range. In an ecologically relevant setting, this may enable efficient thermoregulation of fishes by habitat selection, thus facilitating their resilience in persistent environmental change.
Real time observation of chaperone-modulated talin mechanics with single molecule resolution
Authors: Chakraborty Soham , Chaudhuri Deep , Banerjee Souradeep , Bhatt Madhu , Haldar Shubhasis
Published: April 2021

Recent single-molecule studies have recognized talin as a mechanosensitive hub in focal adhesion, where its function is strongly regulated by mechanical force. For instance, at low force (below 5 pN), folded talin binds RIAM for integrin activation; whereas at high force (above 5 pN), it unfolds to activate vinculin binding for focal adhesion stabilization. Being a cytoplasmic protein, talin might interact with several cytosolic chaperones: however, the role of chaperones in talin mechanics is unknown.

To address this question, we investigated the force response of a mechanically stable talin domain with a set of well-known holdase (DnaJ, DnaK, Hsp70, and Hsp40) and foldase (DnaKJE, DsbA) chaperones, using single-molecule magnetic tweezers. Our findings demonstrate that chaperone could affect adhesion proteins stability by changing their folding mechanics; while holdase chaperones reduce their unfolding force to ∼6 pN, foldase chaperones shift it up to ∼15 pN. Since talin is mechanically synced within 2 pN force ranges, these changes are significant in cellular condition. Furthermore, we determined the fundamental mechanism of this altered mechanical stability, where chaperones directly reshape their energy landscape: unfoldase chaperone (DnaK) decreases the unfolding barrier height from 26.8 to 21.7 kBT, while foldase chaperone (DsbA) increases it to 33.5 kBT. We reconciled our observations with eukaryotic Hsp70 and Hsp40 chaperones and observed their similar function of decreasing the talin unfolding barrier to 23.1 kBT. The quantitative mapping of this chaperone-induced talin folding landscape directly illustrates that chaperones perturb the adhesion protein stability under physiological force, thereby influencing their force-dependent interactions and adhesion dynamics.
Video-rate remote refocusing through continuous oscillation of a membrane deformable mirror
Authors: Wright Terry , Sparks Hugh , Paterson Carl , Dunsby Chris
Published: April 2021

This paper presents the use of a deformable mirror (DM) configured to rapidly refocus a microscope employing a high numerical aperture objective lens. An Alpao DM97-15 membrane DM was used to refocus a 40×/0.80 NA water-immersion objective through a defocus range of −50 to 50 μm at 26.3 sweeps per second. We achieved imaging with a mean Strehl metric of > 0.6 over a field of view in the sample of 200×200 μm2over a defocus range of 77 μm. We describe an optimisation procedure where the mirror is swept continuously in order to avoid known problems of hysteresis associated with the membrane DM employed. This work demonstrates that a DM-based refocusing system could in the future be used in light-sheet fluorescence microscopes to achieve video-rate volumetric imaging.
Metaviromes reveal the dynamics of Pseudomonas host-specific phages cultured and uncultured by plaque assay
Authors: Skov Alanin Katrine Wacenius , Forero Junco Laura Milena , Jørgensen Jacob Bruun , Kjærgaard Nielsen Tue , Rasmussen Morten Arendt , Kot Witold , Hansen Lars Hestbjerg
Published: April 2021

Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or the ones with highest ability to plaque on solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in envi-ronmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community’s shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media corresponds to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum 2-fold change above 0 in read abundance when adding a Pseudomonas syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, was highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlights how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.
Kinase activity of TBK1 is required for its binding to STING, but not for its recruitment to the Golgi
Authors: Kemmoku Haruka , Kuchitsu Yoshihiko , Mukai Kojiro , Taguchi Tomohiko
Published: April 2021

Stimulator of interferon genes (STING) is an innate immune protein for DNA pathogens. In response to the emergence of DNA in the cytosol, STING relocates from the endoplasmic reticulum (ER) to the Golgi and induces the type I interferon response through cytosolic TANK-binding kinase 1 (TBK1). The molecular mechanism underlying TBK1 activation by STING remains poorly understood. Here we report a cell system by which STING and TBK1 are simultaneously monitored. The system utilizes STING/TBK1-double knockout (KO) cells, fluorescent protein-tagged TBK1 and STING, and super-resolution microscopy. After STING stimulation, TBK1 is directly recruited to the trans-Golgi network (TGN), not to the other parts of the Golgi. The recruitment of TBK1 does not require its kinase activity. C-terminal STING variants (ΔC9 and L373A), in which the TBK1-STING binding interface is mutated or deleted, induce the recruitment of TBK1. These results indicate that the kinase activity of TBK1 or the C-terminal motif of STING is not required for its recruitment to TGN, but rather for the formation of the stable STING signalling complex at TGN.
A nanoscale reciprocating rotary mechanism with coordinated mobility control
Authors: Bertosin Eva , Maffeo Christopher M. , Drexler Thomas , Honemann Maximilian N. , Aksimentiev Aleksei , Dietz Hendrik
Published: April 2021

Biological molecular motors transform chemical energy into mechanical work by coupling a cycle of catalytic reactions to large scale structural transitions. Mechanical deformation can be surprisingly efficient in realizing such coupling, as demonstrated by the celebrated example of F1FoATP synthase. Here, we describe a synthetic molecular mechanism that transforms a rotary motion of an asymmetric camshaft into reciprocating large-scale transitions in the structure of the surrounding stator orchestrated by mechanical deformation. We designed the mechanism using DNA origami, characterized the structure of the components and the entire mechanism using cryo-electron microscopy, and examined the mechanism’s dynamic behavior using single-particle fluorescence microscopy and molecular dynamics simulations. The data indicates that, while the camshaft can rotate inside the stator by diffusion, mechanical deformation of the stator makes the camshaft pause at a set of preferred orientations. By changing the mechanical stiffness of the stator, we could accelerate or suppress the Brownian rotation within the mechanism, thereby demonstrating an allosteric coupling between the movement of the camshaft and of the stator, and the ability to tailor the free energy landscape that governs the rotary motion. Our mechanism provides a framework for the manufacture of artificial nanomachines that, just like the man-made machines in the macroscopic world, function because of coordinated movements of their components.