bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of the gut–skin axis in IgE-mediated food allergy and atopic diseases
Authors: Suaini Noor Hidayatul Aini , Siah Kewin Tien Ho , Tham Elizabeth Huiwen
Published: August 2021

Purpose of review

In recent years, landmark clinical trials investigating the role of early oral exposure to food antigens for food allergy (FA) prevention have highlighted the importance of immunoregulatory pathways in the ‘gut–skin axis’. This review highlights recent literature on the mechanisms of the immune system and microbiome involved in the gut–skin axis, contributing to the development of atopic dermatitis (AD), FA, allergic rhinitis (AR) and asthma. Therapeutic interventions harnessing the gut–skin axis are also discussed.

Recent findings

Epicutaneous sensitization in the presence of AD is capable of inducing Th2 allergic inflammation in the intestinal tract and lower respiratory airways, predisposing one to the development of AR and asthma. Probiotics have demonstrated positive effects in preventing and treating AD, though there is no evident relationship of its beneficial effects on other allergic diseases. Prophylactic skin emollients use has not shown consistent protection against AD, whereas there is some evidence for the role of dietary changes in alleviating AD and airway inflammation. More randomized controlled trials are needed to clarify the potential of epicutaneous immunotherapy as a therapeutic strategy for patients with FA.

The growing understanding of the gut–skin interactions on allergic disease pathogenesis presents novel avenues for therapeutic interventions which target modulation of the gut and/or skin.
Setting the Research Agenda for Nursing Administration and Leadership Science: A Delphi Study
Authors: Chipps Esther Maria , Joseph M. Lindell , Alexander Catherine , Lyman Bret , McGinty Logan , Nelson-Brantley Heather , Parchment Joy , Rivera Reynaldo R. , Schultz Mary Anne , Ward Danielle M. , Weaver Susan
Published: August 2021

OBJECTIVE

The aim of this study was to identify and prioritize research topics for nursing administration and leadership science.

BACKGROUND

Nursing administration and leadership research priorities should provide a framework for building the science needed to inform practice.

METHODS

The Association for Leadership Science in Nursing (ALSN) and American Organization for Nursing Leadership (AONL) Foundation (AONL-F) for Nursing Leadership and Education collaborated on a Delphi study. Initial input on research priority items were received from ALSN and AONL members. National experts participated in a 3-round Delphi study.

RESULTS

Top-ranked priorities included: 1) nurses' health, well-being, resiliency, and safety in the workplace; 2) developing and managing a nursing workforce to meet current and future healthcare needs; 3) healthy work/practice environments for direct care nurses; 4) healthy work/ practice environments for nurse leaders; 5) quantification of nursing's value across the healthcare delivery system; and 6) nurse leader development and essential competencies.

CONCLUSIONS

Researchers and funders should use these priorities to guide future studies.
Recombinant Activated Protein C (rhAPC) Affects Lipopolysaccharide-Induced Mechanical Compliance Changes and Beat Frequency of mESC-Derived Cardiomyocyte Monolayers
Authors: Temiz Artmann Aysegül , Kurulgan Demirci Eylem , Fırat Ipek Seda , Oflaz Hakan , Artmann Gerhard M.
Published: August 2021

Background:

Septic cardiomyopathy increases mortality by 70% to 90% and results in mechanical dysfunction of cells.

Methods:

Here, we created a LPS-induced in-vitro sepsis model with mouse embryonic stem cell-derived cardiomyocytes (mESC-CM) using the CellDrum technology which simultaneously measures mechanical compliance and beat frequency of mESCs. Visualization of reactive oxygen species (ROS), actin stress fibers, and mRNA quantification of endothelial protein C receptor (EPCR) and protease-activated receptor 1 (PAR1) before/after LPS incubation were used for method validation. Since activated protein C (APC) has cardioprotective effects, samples were treated with human recombinant APC (rhAPC) with/-out LPS predamage to demonstrate the application in therapeutic studies.

Results:

Twelve hours LPS treatment (5 μg/mL) increased ROS and decreased actin stress fiber density and significantly downregulated EPCR and PAR1 compared to control samples (0.26, 0.39-fold respectively). rhAPC application (5 μg/mL, 12 h) decreased ROS and recovered actin density, EPCR, and PAR1 levels were significantly upregulated compared to LPS predamaged samples (4.79, 3.49-fold respectively). The beat frequencies were significantly decreased after 6- (86%) and 12 h (73%) of LPS application. Mechanical compliance of monolayers significantly increased in a time-dependent manner, up to eight times upon 12-h LPS incubation compared to controls. rhAPC incubation increased the beat frequency by 127% (6h-LPS) and 123% (12h-LPS) and decreased mechanical compliance by 68% (12h-LPS) compared to LPS predamaged samples.

Conclusion:

LPS-induced contraction dysfunction and the reversal effects of rhAPC were successfully assessed by the mechanical properties of mESC-CMs. The CellDrum technology proved a decent tool to simulate sepsis in-vitro.
Streptomyces xanthii sp. nov. and Streptomyces roseirectus sp. nov. isolated from a Chinese medicinal plant
Authors: Hu Siren , Wang Yinfeng , Wang Junzhen , Liu Keyun , Tang Xinke , Gao Jian
Published: August 2021

Two strains of Actinobacteria, designated CRXT-Y-14T and CRXT-G-22T, were isolated from the healthy leaves and seeds, respectively, of a medicinal plant Xanthium sibiricum. Their taxonomic positions were determined using a polyphasic approach. Strain CRXT-Y-14T produced flexuous chains of smooth-surfaced spores. Strain CRXT-G-22T produced straight chains of smooth-surfaced spores. Their morphological features were consistent with the diagnostic characteristics of members of the genus

Streptomyces

. The results of 16S rRNA gene sequence analyses indicated two strains represented members of the genus

Streptomyces

. CRXT-Y-14T shared 99.3, 98.9, 98.8 % sequence similarities to

Streptomyces atriruber

NRRL B-24165T,

Streptomyces avermitilis

MA-4680T and

Streptomyces davaonensis

JCM 4913T, respectively. Whilst CRXT-G-22T exhibited highest similarity to

Streptomyces acidiscabies

ATCC 49003T (98.9 %). The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the closest phylogenetic neighbours of strains CRXT-Y-14T and CRXT-G-22T were

S. atriruber

NRRL B-24165T and

S. acidiscabies

ATCC 49003T, respectively. The phylogenomic analyses further confirmed the relative relationship between strain CRXT-G-22T and

S. acidiscabies

ATCC 49003T, but indicated that CRXT-Y-14T could represent a novel species of the genus Streptomyce. However, the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between CRXT-Y-14T and strain CRXT-G-22T, between CRXT-Y-14T and

S. atriruber

NRRL B-24165T, and between CRXT-G-22T and

S. acidiscabies

ATCC 49003T were 85.4 and 23.2 %, 85.8 and 23.9 % and 89.1 and 34.1 %, respectively, far below the 95~96 and 70 % cut-off points recommended for delineating species. Furthermore, these two novel isolates were distinctly differentiated from their relatives in the genus

Streptomyces

with respect to phenotypic and chemotaxonomic characteristics. On the basis of these data, CRXT-Y-14T and CRXT-G-22T clearly represent two novel species within the genus

Streptomyces

, for which the names Streptomyces xanthii sp. nov. (type strain CRXT-Y-14T = MCCC 1K04966T= JCM 34527T) and Streptomyces roseirectus sp. nov. (type CRXT-G-22T = MCCC 1K04979T= JCM 34565T) are proposed.
Characterization of an operon required for growth on cellobiose in Clostridioides difficile
Authors: Hasan Md Kamrul , Dhungel Babita Adhikari , Govind Revathi
Published: August 2021

Cellobiose metabolism is linked to the virulence properties in numerous bacterial pathogens. Here, we characterized a putative cellobiose PTS operon of Clostridiodes difficile to investigate the role of cellobiose metabolism in C. difficile pathogenesis. Our gene knockout experiments demonstrated that the putative cellobiose operon enables uptake of cellobiose into C. difficile and allows growth when cellobiose is provided as the sole carbon source in minimal medium. Additionally, using reporter gene fusion assays and DNA pulldown experiments, we show that its transcription is regulated by CelR, a novel transcriptional repressor protein, which directly binds to the upstream region of the cellobiose operon to control its expression. We have also identified cellobiose metabolism to play a significant role in C. difficile physiology as observed by the reduction of sporulation efficiency when cellobiose uptake was compromised in the mutant strain. In corroboration to in vitro study findings, our in vivo hamster challenge experiment showed a significant reduction of pathogenicity by the cellobiose mutant strain in both the primary and the recurrent infection model – substantiating the role of cellobiose metabolism in C. difficile pathogenesis.
KoT: an automatic implementation of theK/θmethod for species delimitation
Authors: Spöri Yann , Stoch Fabio , Dellicour Simon , Birky C. William , Flot Jean-François
Published: August 2021

Abstract

K/θis a method to delineate species that rests on the calculation of the ratio between the average distanceKseparating two putative species-level clades and the genetic diversityθof these clades. Although this method is explicitly rooted in population genetic theory, it was never benchmarked due to the absence of a program allowing automated analyses. For the same reason, its application by hand was limited to small datasets of a few tens of sequences.

We present an automatic implementation of theK/θmethod, dubbed KoT (short for “K over Theta”), that takes as input a FASTA file, builds a neighbour-joining tree, and returns putative species boundaries based on a user-specifiedK/θthreshold. This automatic implementation avoids errors and makes it possible to apply the method to datasets comprising many sequences, as well as to test easily the impact of choosing differentK/θthreshold ratios. KoT is implemented in Haxe, with a javascript webserver interface freely available athttps://eeg-ebe.github.io/KoT/
Safety and efficacy of a new vaginal gel, Feminilove, for the treatment of symptoms associated with vaginal dryness and vulvovaginal atrophy in women: an in vitro and in vivo study
Authors: Gonzalez A , Lee MR , Johnson BA , Booshehri L , Grady D , Vaddi V , Ip C , Mitchell C , Krychman M , Dardik R
Published: August 2021

Vaginal dryness is a common symptom associated with vulvovaginal atrophy of menopause. The impact of vaginal dryness is very significant as it negatively affects quality of life, daily activities, sexual satisfaction as well as on interpersonal relationships. Symptoms of vaginal dryness is often underreported and undertreated. Recently, vaginal lubricants and moisturizers have been applied as one of the alternative and safe approaches to relieve vaginal dryness for women with mild to moderate vaginal dryness. We evaluated the safety and beneficial effects of a new type of estrogen-free vaginal gel, Feminilove BIO-FRESH moisturizing vaginal gel, using in vitro and in vivo experimental tools. Our results suggest that; 1) Feminilove vaginal gel exhibits minimal cell cytotoxicity on various human vaginal cells; 2) Feminilove vaginal gel exhibits minimal side-effects on the structure of vaginal mucosa stratum of experimental animals; 3) Feminiove vaginal gel inhibits the growth of pathogenic vaginal bacteria (E. coli) while promotes the growth of beneficial vaginal bacteria (Lactobacillus spp); 4) Feminilove vaginal gel elicits an anti-inflammatory response on vaginal epithelial cells; and 5) Feminilove vaginal gel promotes the production of tropoelastin and collagen on cultural vaginal smooth muscle and may restore loose vaginal wall (i.e., tightening effects). In summary, our results indicate that Feminilove BIO-FRESH moisturizing vaginal gel is a safe and effective remedy for vaginal dryness and vulvovaginal atrophy in women.
Systemic IgG repertoire as a biomarker for translocating gut microbiota members
Authors: Vujkovic-Cvijin Ivan , Welles Hugh , Ha Connie W.Y. , Huq Lutfi , Mistry Shreni , Brenchley Jason M. , Trinchieri Giorgio , Devkota Suzanne , Belkaid Yasmine
Published: August 2021

While the microbiota has been associated with diseases states, how specific alterations in composition, function, or localization contribute to pathologies remains unclear. The ability of defined microbes to translocate has been linked to diseases including inflammatory bowel disease (IBD) and was shown to promote responses to immune checkpoint therapy. However, scalable and unbiased tools to uncover microbes with enhanced ability to translocate are limited. Herein, we developed an approach to utilize systemic IgG in an unbiased, culture-independent, and high-throughput fashion as a biomarker to identify gut microbiota members that are capable of translocation across the gastrointestinal barrier. We validate these findings in a cohort of human subjects, and highlight a number of microbial taxa against which elevated IgG responses are unique to subjects with IBD includingCollinsella, Bifidobacterium, Faecalibacterium,andBlautia spp.CollinsellaandBifidobacteriumtaxa identified as translocators and targets of immunity in IBD also exhibited heightened bacterial activity and growth rates in Crohn’s disease subjects. Our approach may represent a complementary tool to illuminate privileged interactions between host and its microbiota, and may provide an additional lens by which to uncover microbes linked to disease processes.

One Sentence Summary

Circulating microbiota-specific IgG can identify gut microbiota constituents capable of crossing the gut barrier.
Systems-wide Analysis Revealed Shared and Unique Responses to Moderate and Acute High Temperatures in the Green Alga Chlamydomonas reinhardtii
Authors: Zhang Ningning , Mattoon Erin M. , McHargue Will , Venn Benedikt , Zimmer David , Pecani Kresti , Jeong Jooyeon , Anderson Cheyenne M. , Chen Chen , Berry Jeffrey C. , Xia Ming , Tzeng Shin-Cheng , Becker Eric , Pazouki Leila , Evans Bradley , Cross Fred , Cheng Jianlin , Czymmek Kirk J. , Schroda Michael , Mühlhaus Timo , Zhang Ru
Published: August 2021

Different intensities of high temperatures affect the growth of photosynthetic cells in nature. To elucidate the underlying mechanisms, we cultivated the unicellular green alga Chlamydomonas reinhardtii under highly controlled photobioreactor conditions and revealed systems-wide shared and unique responses to 24-hour moderate (35°C) and acute (40°C) high temperatures and subsequent recovery at 25°C. We identified previously overlooked unique elements in response to moderate high temperature. Heat at 35°C transiently arrested the cell cycle followed by partial synchronization, up-regulated transcripts/proteins involved in gluconeogenesis/glyoxylate-cycle for carbon uptake, promoted growth, and increased starch accumulation. Heat at 40°C arrested the cell cycle, inhibited growth, resulting in carbon uptake over usage and increased starch accumulation. Both high temperatures induced photoprotection, while 40°C decreased photosynthetic efficiency, distorted thylakoid/pyrenoid ultrastructure, and affected the carbon concentrating mechanism. We demonstrated increased transcript/protein correlation during both heat treatments, suggesting reduced post-transcriptional regulation during heat may help coordinate heat tolerance activities efficiently. During recovery after both heat treatments, transcripts/proteins related to DNA synthesis increased while those involved in photosynthetic light reactions decreased. We propose down-regulating photosynthetic light reactions during DNA replication benefits cell cycle resumption by reducing ROS production. Our results provide potential targets to increase thermotolerance in algae and crops.
Mechanics of Live Cell Elimination
Authors: Monfared Siavash , Ravichandran Guruswami , Andrade José E. , Doostmohammadi Amin
Published: August 2021

Cell layers eliminate unwanted cells through the extrusion process, which underlines healthy versus flawed tissue behaviors. Although several biochemical pathways have been identified, the underlying mechanical basis including the forces involved in cellular extrusion remain largely unexplored. Utilizing a phase-field model of a three-dimensional cell layer, we study the interplay of cell extrusion with cell-cell and cell-substrate interactions, in a monolayer. Independent tuning of cell-cell versus cell-substrate adhesion forces in the model reveals that a higher cell-substrate adhesion leads to a lower number of total extrusion events. We find extrusion events to be linked to both half-integer topological defects in the orientation field of the cells and to five-fold disclinations in cellular arrangements. We also show that increasing the relative cell-cell adhesion forces translates into a higher likelihood for an extrusion event to be associated with a five-fold disclination and a weaker correlation with +1/2 topological defects. We unify our findings by accessing mechanical stress fields: an extrusion event acts as a mechanism to relieve localized stress concentration.
Benchmarking PSM identification tools for single cell proteomics
Authors: Van Der Watt Daisha , Boekweg Hannah , Truong Thy , Guise Amanda J , Plowey Edward D , Kelly Ryan T , Payne Samuel H
Published: August 2021

Single cell proteomics is an emerging sub-field within proteomics with the potential to revolutionize our understanding of cellular heterogeneity and interactions. Recent efforts have largely focused on technological advancements in sample preparation, chromatography and instrumentation to enable measuring proteins present in these ultra-limited samples. Although advancements in data acquisition have rapidly improved our ability to analyze single cells, the software pipelines used in data analysis were originally written for traditional bulk samples and their performance on single cell data has not been investigated. We benchmarked five popular peptide identification tools on single cell proteomics data. We found that MetaMorpheus achieved the greatest number of peptide spectrum matches at a 1% false discovery rate. Depending on the tool, we also find that post processing machine learning can improve spectrum identification results by up to ∼40%. Although rescoring leads to a greater number of peptide spectrum matches, these new results typically are generated by 3rd party tools and have no way of being utilized by the primary pipeline for quantification. Exploration of novel metrics for machine learning algorithms will continue to improve performance.
Dietary vitamin B12 deficiency impairs motor function and changes neuronal survival and choline metabolism after ischemic stroke in middle aged male and female mice
Authors: Yahn Gyllian B. , Wasek Brandi , Bottiglieri Teodoro , Malysheva Olga , Caudill Marie A. , Jadavji Nafisa M.
Published: August 2021

Nutrition is a modifiable risk factor for ischemic stroke. As people age their ability to absorb some nutrients decreases, a primary example is vitamin B12. Older individuals with a vitamin B12 deficiency are at a higher risk for ischemic stroke and have worse stroke outcome. However, the mechanisms through which these occur remain unknown. The aim of the study was to investigate the role of vitamin B12 deficiency in ischemic stroke outcome and mechanistic changes in a mouse model. Ten-month-old male and female mice were put on control or vitamin B12 deficient diets for 4-weeks prior to and after ischemic stroke to the sensorimotor cortex. Motor function was measured, and tissues were collected to assess potential mechanisms. All deficient mice had increased levels of total homocysteine in plasma and liver tissues. After ischemic stroke, deficient mice had impaired motor function compared to control mice. There was no difference between groups in lesion volume, however, there was an increase in total apoptosis within the ischemic region of brain tissue in male deficient mice. More neuronal survival was present in ischemic brain tissue of the deficient mice compared to controls. Additionally, there were changes in choline metabolites in ischemic brain tissue because of a vitamin B12 deficiency. The data presented in this study confirms that a vitamin B12 deficiency worsens stroke outcome in male and female mice. The mechanisms driving this change may be a result of neuronal survival and compensation in choline metabolism within the damaged brain tissue.
Monitoring fish communities through environmental DNA metabarcoding in the fish pass system of the second largest hydropower plant in the world
Authors: Pont Giorgi Dal , Ritter Camila Duarte , Agostinis Andre Olivotto , Stica Paula Valeska , Horodesky Aline , Cozer Nathieli , Balsanelli Eduardo , Mäder Netto Otto Samuel , Henn Caroline , Ostrensky Antonio , Pie Marcio Roberto
Published: August 2021

The Itaipu Hydroelectric Power Plant is the second largest in the world in power generation. The artificial barrier created by its dam imposes an obstacle for fish migration. Thus, in 2002, a fish pass system, named Piracema Channel, was built to allow fish to access areas upstream of the reservoir. We tested the potential of environmental DNA metabarcoding to monitor the impact of both the dam and associated fish pass system in the Paraná River fish communities and to compare it with traditional monitoring methods. Using a fragment of the 12S gene, we characterized richness and community composition based on amplicon sequence variants, operational taxonomic units, and zero-radius OTUs. We combined GenBank and in-house data for taxonomic assignment. We found that different bioinformatics approaches showed similar results. Also, we found a decrease in fish diversity from 2019 to 2020 probably due to the recent extreme drought experienced in southeastern Brazil. The highest alpha diversity was recorded in the mouth of the fish pass system, located in a protected valley with the highest environmental heterogeneity. Despite the clear indication that the reference databases need to be continuously improved, our results demonstrate the analytical efficiency of the metabarcoding to monitor fish species.
Preservation of eye movements in Parkinson’s disease is stimulus and task specific
Authors: Fooken Jolande , Patel Pooja , Jones Christina B. , McKeown Martin J. , Spering Miriam
Published: August 2021

Parkinson’s disease (PD) is a neurodegenerative disease that includes motor impairments such as tremor, bradykinesia, and postural instability. Although eye movement deficits are commonly found in saccade and pursuit tasks, preservation of oculomotor function has also been reported. Here we investigate specific task and stimulus conditions under which oculomotor function in PD is preserved. Sixteen PD patients and eighteen healthy, age-matched controls completed a battery of movement tasks that included stationary or moving targets eliciting reactive or deliberate eye movements: pro-saccades, anti-saccades, visually-guided pursuit, and rapid go/no-go manual interception. Compared to controls, patients demonstrated systematic impairments in tasks with stationary targets: pro-saccades were hypometric and anti-saccades were incorrectly initiated toward the cued target in about 35% of trials compared to 14% errors in controls. In patients, task errors were linked to short latency saccades, indicating abnormalities in inhibitory control. However, patients’ eye movements in response to dynamic targets were relatively preserved. PD patients were able to track and predict a disappearing moving target and make quick go/no-go decisions as accurately as controls. Patients’ interceptive hand movements were slower on average but initiated earlier, indicating adaptive processes to compensate for motor slowing. We conclude that PD patients demonstrate stimulus- and task-dependency of oculomotor impairments and propose that preservation of eye and hand movement function in PD is linked to a separate functional pathway through the SC-brainstem loop that bypasses the fronto-basal ganglia network.

Significance Statement

Eye movements are a promising clinical tool to aid in the diagnosis of movement disorders and to monitor disease progression. Although Parkinson’s disease (PD) patients show some oculomotor abnormalities, it is not clear whether previously-described eye movement impairments are task specific. We assessed eye movements in PD under different visual (stationary vs. moving targets) and movement (reactive vs. deliberate) conditions. We demonstrate that PD patients are able to accurately track moving objects but make inaccurate eye movements towards stationary targets. The preservation of eye movements towards dynamic stimuli might enable patients to accurately act upon the predicted motion path of the moving target. These results can inform the development of tools for the rehabilitation or maintenance of functional performance.
Partitioning gene-level contributions to complex-trait heritability by allele frequency identifies disease-relevant genes
Authors: Burch Kathryn S. , Hou Kangcheng , Ding Yi , Wang Yifei , Gazal Steven , Shi Huwenbo , Pasaniuc Bogdan
Published: August 2021

Recent works have shown that SNP-heritability—which is dominated by low-effect common variants—may not be the most relevant quantity for localizing high-effect/critical disease genes. Here, we introduce methods to estimate the proportion of phenotypic variance explained by a given assignment of SNPs to a single gene (genelevel heritability). We partition gene-level heritability across minor allele frequency (MAF) classes to find genes whose gene-level heritability is explained exclusively by “low-frequency/rare” variants (0.5% ≤ MAF < 1%). Applying our method to ~17K protein-coding genes and 25 quantitative traits in the UK Biobank (N=290K), we find that, on average across traits, ~2.5% of nonzero-heritability genes have a rare-variant component, and only ~0.8% (370 gene-trait pairs) have heritability exclusively from rare variants. Of these 370 gene-trait pairs, 37% were not detected by existing gene-level association testing methods, likely because existing methods combine signal from all variants in a region irrespective of MAF class. Many of the additional genes we identify are implicated in phenotypically related Mendelian disorders or congenital developmental disorders, providing further evidence of their trait-relevance. Notably, the rare-variant component of gene-level heritability exhibits trends different from those of common-variant gene-level heritability. For example, while total gene-level heritability increases with gene length, the rare-variant component is significantly larger among shorter genes; the cumulative distributions of gene-level heritability also vary across traits and reveal differences in the relative contributions of rare/common variants to overall gene-level polygenicity. We conclude that the proportion of gene-level heritability attributable to low-frequency/rare variation can yield novel insights into complex-trait genetic architecture.
The SEEL Motif and Members of the MYB-related REVEILLE Transcription Factor Family are Important for the Expression of LORELEI in the Synergid Cells of the Arabidopsis Female Gametophyte
Authors: Noble Jennifer A. , Seddon Alex , Uygun Sahra , Bright Ashley , Smith Steven E. , Shiu Shin-han , Palanivelu Ravishankar
Published: August 2021

Synergid cells in the micropylar end of the female gametophyte are required for critical cell-cell signaling interactions between the pollen tube and the ovule that precede double fertilization and seed formation in flowering plants. LORELEI (LRE) encodes a GPI-anchored protein that is expressed primarily in the synergid cells, and together with FERONIA, a receptor-like kinase, it controls pollen tube reception by the receptive synergid cell. Still, how LRE expression is controlled in synergid cells remains poorly characterized. We identified candidate cis-regulatory elements enriched in LRE and other synergid cell-expressed genes. One of the candidate motifs (‘TAATATCT’) in the LRE promoter was an uncharacterized variant of the Evening Element motif that we named as the Short Evening Element-like (SEEL) motif. Deletion or point mutations in the SEEL motif of the LRE promoter resulted in decreased reporter expression in synergid cells, demonstrating that the SEEL motif is important for expression of LRE in synergid cells. Additionally, we found that LRE expression is decreased in the loss of function mutants of REVEILLE (RVE) transcription factors, which are clock genes known to bind the SEEL and other closely related motifs. We propose that RVE transcription factors regulate LRE expression in synergid cells by binding to the SEEL motif in the LRE promoter. Identification of a cis-regulatory element and transcription factors involved in the expression of LRE will serve as a foundation to characterize the gene regulatory networks in synergid cells and investigate the potential connection between circadian rhythm and fertilization.

One sentence summary

A newly identified SEEL motif in the promoter of LORELEI and at least three members of the REVEILLE transcription factor family are important for LORELEI expression in synergid cells of the Arabidopsis female gametophyte.
Regulation of membrane scission in yeast endocytosis
Authors: Menon Deepikaa , Kaksonen Marko
Published: August 2021

During clathrin-mediated endocytosis, a flat plasma membrane is shaped into an invagination that undergoes scission to form a vesicle. In mammalian cells, the force that drives the transition from invagination to vesicle is primarily provided by the GTPase dynamin that acts in concert with crescent-shaped BAR domain proteins. In yeast cells, the mechanism of endocytic scission is unclear. The yeast BAR domain protein complex Rvs161/167 (Rvs) nevertheless plays an important role in this process: deletion of Rvs dramatically reduces scission efficiency. A mechanistic understanding of the influence of Rvs on scission however, remains incomplete. We used quantitative live-cell imaging and genetic manipulation to understand the recruitment and function of Rvs and other late-stage proteins at yeast endocytic sites. We found that arrival of Rvs at endocytic sites is timed by interaction of its BAR domain with specific membrane curvature. A second domain of Rvs167- the SH3 domain-affects localization efficiency of Rvs. We show that Myo3, one of the two type-I myosins in Saccharomyces cerevisiae, has a role in recruiting Rvs167 via the SH3 domain. Removal of the SH3 domain also affects assembly and disassembly of actin and impedes membrane invagination. Our results indicate that both BAR and SH3 domains are important for the role of Rvs as a regulator of scission. We tested other proteins implicated in vesicle formation in Saccharomyces cerevisiae, and found that neither synaptojanins nor dynamin contribute directly to membrane scission. We propose that recruitment of Rvs BAR domains delays scission and allows invaginations to grow by stabilizing them. We also propose that vesicle formation is dependent on the force exerted by the actin network component of the endocytic machinery.
SOX2-phosphorylation toggles a bistable differentiation-switch in squamous cell carcinoma
Authors: Hoang-Phou Steven , Sastre-Perona Ana , Abbruzzese Matteo , Ying Zhe , Siegle Jasmin , Orgilles Beatriz Aranda , Rocha Pedro P. , Aifantis Iannis , Skok Jane , Beronja Slobodan , Schober Markus
Published: August 2021

The fate choice between stem cell self-renewal and differentiation is regulated by bistable transcriptional networks, which are balanced in homeostasis and imbalanced in tumors. Yet, how stem cells switch from self-renewal to differentiation remains a conundrum. Here, we discover a molecular mechanism that allows stem cell-like tumor propagating cells (TPCs) in squamous cell carcinomas (SCCs) to switch from a mutually exclusive SOX2-PITX1-TP63 self-renewal circuit to a KLF4 driven differentiation program, dependent on the relative occupancy of a novel Klf4-regulatory enhancer cluster (Klf4EC944) by SOX2 or KLF4, respectively. We find SOX2 occupies this site in TPCs to inhibit Klf4 transcription, but upon phosphorylation SOX2 becomes evicted from Klf4EC944, allowing residual KLF4 to occupy this site instead, boost the expression of KLF4 and its downstream targets, and differentiate self-renewing TPCs into post-mitotic SCC cells. This mechanism allows SOX2 to promote self-renewal and tumor formation, while preserving the differentiation potential in SCC cells. Our data suggest that stochastic cell fate decisions depend on the effective concentration of enzymatically regulated transcription factors. The surprising specificity by which SOX2-phosphorylation governs the bistable Klf4EC944 network-switch in SCCs reveals a conceptual framework for the identification of similar switches in other stem cell and cancer types and their potential development into cell type specific differentiation therapies for diseases in which tissue homeostasis has gone awry.
Metabolic and Proteomic Defects in Human Hypertrophic Cardiomyopathy
Authors: Previs Michael J. , O’Leary Thomas S. , Wood Neil B. , Morley Michael P. , Palmer Brad , LeWinter Martin , Yob Jaime , Pagani Francis D. , Petucci Christopher , Kim Min-Soo , Margulies Kenneth B. , Arany Zoltan , Kelly Daniel P. , Day Sharlene M.
Published: August 2021

Rationale

Impaired cardiac energetics in hypertrophic cardiomyopathy (HCM) is thought to result from increased ATP utilization at the sarcomere and is believed to be central to pathophysiology. However, the precise defects in cardiac metabolism and substrate availability in human HCM have not been defined.

Objective

The purpose of this study is to define major disease pathways and determine the pool sizes of intermediary metabolites in human HCM.

Methods and Results

We conducted paired proteomic and metabolomic analyses of septal myectomy samples from patients with HCM and compared results to non-failing control human hearts. Increased abundance of extracellular matrix and intermediate filament / Z-disc proteins, and decreased abundance of proteins involved in fatty acid oxidation and cardiac energetics was evident in HCM compared to controls. Acyl carnitines, byproducts of fatty acid oxidation, were markedly depleted in HCM samples. Conversely, the ketone body 3-hydroxybutyrate, lactate, and the 3 branched chain amino acids, were all significantly increased in HCM hearts, suggesting that they may serve as alternate fuel sources for the production of ATP. ATP, nicotinamide adenine dinucleotide (NADH), NADP and NADPH, and acetyl CoA were also severely depleted in HCM hearts. Based on measurements from human skinned muscle fibers, the magnitude of observed reduction in ATP content in the HCM hearts would be expected to decrease the rate of cross-bridge detachment, implying a direct effect of energy depletion on myofilament function that could contribute to diastolic dysfunction.

Conclusions

HCM hearts display profound deficits in cardiac energetics, marked by depletion of fatty acid derivatives and compensatory increases in other metabolites that could serve as alternate fuel sources. These results lend support to the paradigm that energy depletion contributes to the pathophysiology of HCM and also have important therapeutic implications for the future design of metabolic modulators to treat HCM.
Deep tissue scattering compensation with three-photon F-SHARP
Authors: Berlage Caroline , Tantirigama Malinda , Babot Mathias , Di Battista Diego , Whitmire Clarissa , Papadopoulos Ioannis N. , Poulet James F. A. , Larkum Matthew , Judkewitz Benjamin
Published: August 2021

Optical imaging techniques are widely used in biological research, but their penetration depth is limited by tissue scattering. Wavefront shaping techniques are able to overcome this problem in principle, but are often slow and their performance depends on the sample. This greatly reduces their practicability for biological applications. Here we present a scattering compensation technique based on three-photon (3P) excitation, which converges faster than comparable two-photon (2P) techniques and works reliably even on densely labeled samples, where 2P approaches fail. To demonstrate its usability and advantages for biomedical imaging we apply it to the imaging of dendritic spines on GFP-labeled layer 5 neurons in an anesthetized mouse.
Prediction Under Uncertainty: Dissociating Sensory from Cognitive Expectations in Highly Uncertain Musical Contexts
Authors: Mencke Iris , Quiroga-Martinez David Ricardo , Omigie Diana , Michalareas Georgios , Schwarzacher Franz , Haumann Niels Trusbak , Vuust Peter , Brattico Elvira
Published: August 2021

Predictive models in the brain rely on the continuous extraction of regularities from the environment. These models are thought to be updated by novel information, as reflected in prediction error responses such as the mismatch negativity (MMN). However, although in real life individuals often face situations in which uncertainty prevails, it remains unclear whether and how predictive models emerge in high-uncertainty contexts. Recent research suggests that uncertainty affects the magnitude of MMN responses in the context of music listening. However, musical predictions are typically studied with MMN stimulation paradigms based on Western tonal music, which are characterized by relatively high predictability. Hence, we developed an MMN paradigm to investigate how the high uncertainty of atonal music modulates predictive processes as indexed by the MMN and behavior. Using MEG in a group of 20 subjects without musical training, we demonstrate that the magnetic MMN in response to pitch, intensity, timbre, and location deviants is evoked in both tonal and atonal melodies, with no significant differences between conditions. In contrast, in a separate behavioral experiment involving 39 non-musicians, participants detected pitch deviants more accurately and rated confidence higher in the tonal than in the atonal musical context. These results indicate that contextual tonal uncertainty modulates processing stages in which conscious awareness is involved, although deviants robustly elicit low-level pre-attentive responses such as the MMN. The achievement of robust MMN responses, despite high tonal uncertainty, is relevant for future studies comparing groups of listeners’ MMN responses to increasingly ecological music stimuli.
Metabolomics of healthy and stony coral tissue loss disease affected Montastraea cavernosa corals
Authors: Deutsch Jessica M , Jaiyesimi Olakunle , Pitts Kelly , Houk Jay , Ushijima Blake , Walker Brian K. , Paul Valerie J. , Garg Neha
Published: August 2021

Stony coral tissue loss disease, first observed in Florida in 2014, has now spread along the entire Florida Reef Tract and on reefs in many Caribbean countries. The disease affects a variety of coral species with differential outcomes, and in many instances results in whole-colony mortality. We employed untargeted metabolomic profiling of Montastraea cavernosa corals affected by stony coral tissue loss disease to identify metabolic markers of disease. Herein, extracts from apparently healthy, diseased, and recovered corals, Montastraea cavernosa, collected at a reef site near Ft. Lauderdale, Florida were subjected to liquid-chromatography mass spectrometry-based metabolomics. Unsupervised principal component analysis reveals wide variation in metabolomic profiles of healthy corals of the same species, which differ from diseased corals. Using a combination of supervised and unsupervised data analyses tools, we describe metabolite features that explain variation between the apparently healthy corals, between diseased corals, and between the healthy and the diseased corals. By employing a culture-based approach, we assign sources of a subset of these molecules to the endosymbiotic dinoflagellates, Symbiodiniaceae. Specifically, we identify various endosymbiont-specific lipid classes, such as betaine lipids, glycolipids, and tocopherols, which differentiate samples taken from apparently healthy corals and diseased corals. Given the variation observed in metabolite fingerprints of corals, our data suggests that metabolomics is a viable approach to link metabolite profiles of different coral species with their susceptibility and resilience to numerous coral diseases spreading through reefs worldwide.
Visualizing and manipulating hyperstabilization of T cell microvilli contacts by engineered chimeric antigen receptors
Authors: Beppler Casey , Eichorst John , Marchuk Kyle , Cai En , Castellanos Carlos A. , Sriram Venkataraman , Roybal Kole T. , Krummel Matthew F.
Published: August 2021

T cells typically recognize their ligands using a defined cell biology – the scanning of their membrane microvilli to palpate their environment – while that same membrane scaffolds T cell receptors (TCRs) that can signal upon ligand binding. Chimeric antigen receptors (CARs) present both a therapeutic promise as well as a tractable means to study the interplay between receptor affinity, microvillar dynamics and T cell function. CARs are often built using single-chain variable fragments (scFvs) with far greater affinity than that of natural TCRs. We used high resolution lattice lightsheet (LLS) and total internal reflection fluorescence (TIRF) imaging to visualize microvillar scanning in the context of variations in CAR design. This demonstrated that conventional CARs hyper-stabilized microvillar contacts relative to TCRs. Reducing the affinity and/or avidity of binding brought synapse microvillar dynamics into natural ranges, normalized synapse resolution and improved downstream effector function. This work highlights the importance of understanding the underlying cell biology when designing receptors for optimal antigen engagement.
Fluorogenic EXO-Probe Aptamers for Imaging and Tracking Exosomal RNAs
Authors: Bonacquisti Emily E. , Ferguson Scott W. , Jasiewicz Natalie E. , Wang Jinli , Brown Adam D. , Keeley Daniel P. , Itano Michelle S. , Nguyen Juliane
Published: August 2021

Small extracellular vesicles (sEVs), or exosomes, play important roles in physiological and pathological cellular communication. sEVs contain both short and long non-coding RNAs that regulate gene expression and epigenetic processes. Studying the intricacies of sEV function and RNA-based communication requires tools capable of labeling sEV RNA. Here we developed a novel genetically encodable reporter system for tracking sEV RNAs comprising an sEV-loading RNA sequence, termed the EXO-Code, fused to a fluorogenic RNA Mango aptamer for RNA imaging. This fusion construct allowed the visualization and tracking of RNA puncta and colocalization with markers of multivesicular bodies; imaging RNA puncta within sEVs; and quantification of sEVs. This technology represents a useful and versatile tool to interrogate the role of sEVs in cellular communication via RNA trafficking to sEVs, cellular sorting decisions, and sEV RNA cargo transfer to recipient cells.
Molecular mechanisms underlying enhanced hemichannel function of a cataract-associated Cx50 mutant
Authors: Tong J.J. , Khan U. , Haddad B.G. , Minogue P.J. , Beyer E.C. , Berthoud V.M. , Reichow S.L. , Ebihara L.
Published: August 2021

Connexin-50 (Cx50) is among the most frequently mutated genes associated with congenital cataracts. While most of these disease-linked variants cause loss-of-function due to misfolding or aberrant trafficking, others directly alter channel properties. The mechanistic bases for such functional defects are mostly unknown. We investigated the functional and structural properties of a cataract-linked mutant, Cx50T39R (T39R), in the Xenopus oocyte system. T39R exhibited greatly enhanced hemichannel currents with altered voltage-gating properties compared to Cx50 and induced cell death. Co-expression of mutant T39R with wild-type Cx50 (to mimic the heterozygous state) resulted in hemichannel currents whose properties were indistinguishable from those induced by T39R alone, suggesting that the mutant had a dominant effect. Co-expression with Cx46 also produced channels with altered voltage-gating properties, particularly at negative potentials. All-atom molecular dynamics simulations indicate that the R39 substitution can form multiple electrostatic salt-bridge interactions between neighboring subunits that could stabilize the open-state conformation of the N-terminal domain, while also neutralizing the voltage-sensing residue D3 as well as residue E42 which participates in loop-gating. Together, these results suggest T39R acts as a dominant gain-of-function mutation that produces leaky hemichannels that may cause cytotoxicity in the lens and lead to development of cataracts.

Statement of significance

We investigated the functional and structural properties of a cataract-linked mutant, Cx50T39R (T39R), in the Xenopus oocyte system and showed that T39R exhibited greatly enhanced hemichannel currents with altered voltage-gating properties compared to Cx50 and induced cell death. Consistent with our experimental findings, all-atom equilibrium state molecular dynamics (MD) simulations of T39R show that R39 stabilized the open-state configuration of the N-terminal (NT) domain from an adjacent subunit. These results suggest that T39R causes disease by preventing the hemichannels from closing when present in the plasma membrane in the undocked state and provide an atomistic rationalization for the Cx50 disease-linked phenotype. They also expand our understanding of how connexin hemichannel channel gating is controlled.
Variation in white spruce needle respiration at the species range limits: a potential impediment to northern expansion
Authors: Griffin Kevin L. , Griffin Zoe M. , Schmiege Stephanie C. , Bruner Sarah G. , Boelman Natalie T. , Vierling Lee A. , Eitel Jan U. H.
Published: August 2021

White spruce (Picea glauca) spans a massive range from arctic treeline to temperate forests, yet the variability in respiratory physiology and related implications for tree carbon balance at the extremes of this distribution remain as enigmas. Working at both the most northern and southern extents of the white spruce distribution range more than 5000 km apart, we measured the short- term temperature response of dark respiration (R/T) at upper and lower canopy positions.R/T curves were fit to both polynomial and thermodynamic models so that model parameters could be compared among locations, canopy positions, and with previously published data. Respiration measured at 25°C (R25) was 68% lower at the southern location than at the northern location (0.73±0.15 vs. 2.27±0.02 μmol m-2s-1), resulting in a significantly lower (p< 0.01) intercept inR/T response in temperate trees. Only at the southern location did upper canopy leaves have a steeper temperature response than lower canopy leaves, likely reflecting steeper canopy gradients in light. No differences were observed in the maximum temperature of respiration. At the northern range limit respiration is nearly twice that of the averageR25 reported in a global leaf respiration database. This large carbon cost likely challenges tree survival and contributes to restricting the location of the northern treeline. We predict that without significant thermal acclimation, foliage respiration will increase with projected end-of-the-century warming and will likely constrain the future range limits of this important boreal species.

Summary Statement

White spruce (Picea glauca) needle respiration at the northern limit of the species range is three times higher than at the southern range limit (when measured at 25 °C). This high carbon cost likely challenges tree survival and contributes to the location of the northern treeline.