bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of andrenine bees reveals a long and complex history of faunal interchanges between the Americas during the Mesozoic and Cenozoic
Authors: Ramos Kelli S. , Martins Aline C. , Melo Gabriel A. R.
Published: August 2021

Bees are presumed to have arisen in the early to mid-Cretaceous coincident with the fragmentation of the southern continents and concurrently with the early diversification of the flowering plants. Among the main groups of bees, Andreninae sensu lato comprise about 3000 species widely distributed with greatest and disjunct diversity in arid areas of North America, South America, and the Palearctic region. Here, we present the first comprehensive dated phylogeny and historical biogeographic analysis for andrenine bees, including representatives of all currently recognized tribes. Our analyses rely on a dataset of 106 taxa and 7952 aligned nucleotide positions from one mitochondrial and six nuclear loci. Andreninae is strongly supported as a monophyletic group and the recovered phylogeny corroborates the commonly recognized clades for the group. Thus, we propose a revised tribal classification that is congruent with our phylogenetic results. The time-calibrated phylogeny and ancestral range reconstructions of Andreninae reveal a fascinating evolutionary history with Gondwana patterns that are unlike those observed in other subfamilies of bees. Andreninae arose in South America during the Late Cretaceous around 90 Million years ago (Ma) and the origin of tribes occurred through a relatively long time-window from this age to the Miocene. The early evolution of the main lineages took place in South America until the beginning of Paleocene with North American fauna origin from it and Palearctic from North America as results of multiple lineage interchanges between these areas by long-distance dispersal or hopping through landmass chains. Overall, our analyses provide strong evidence of amphitropical distributional pattern currently observed in Andreninae in the American continent as result at least three periods of possible land connections between the two American landmasses, much prior to the Panama Isthmus closure. The andrenine lineages reached the Palearctic region through four dispersal events from North America during the Eocene, late Oligocene and early Miocene, most probably via the Thulean Bridge. The few lineages with Afrotropical distribution likely originated from a Palearctic ancestral in the Miocene around 10 Ma when these regions were contiguous, and the Sahara Desert was mostly vegetated making feasible the passage by several organisms. Incursions of andrenine bees to North America and then onto the Old World are chronological congruent with distinct periods when open-vegetation habitats were available for trans-continental dispersal and at the times when aridification and temperature decline offered favorable circumstances for bee diversification.
A graph-theoretical approach to DNA similarity analysis
Authors: Nguyen Dong Quan Ngoc , Xing Lin , Le Phuong Dong Tan , Lin Lizhen
Published: August 2021

One of the very active research areas in bioinformatics is DNA similarity analysis. There are several approaches using alignment-based or alignment-free methods to analyze similarities/dissimilarities between DNA sequences. In this work, we introduce a novel representation of DNA sequences, using n-ary Cartesian products of graphs for arbitrary positive integers n. Each of the component graphs in the representing Cartesian product of each DNA sequence contain combinatorial information of certain tuples of nucleotides appearing in the DNA sequence. We further introduce a metric space structure to the set of all Cartesian products of graphs that represent a given collection of DNA sequences in order to be able to compare different Cartesian products of graphs, which in turn signifies similarities/dissimilarities between DNA sequences. We test our proposed method on several datasets including Human Papillomavirus, Human rhinovirus, Influenza A virus, and Mammals. We compare our method to other methods in literature, which indicates that our analysis results are comparable in terms of time complexity and high accuracy, and in one dataset, our method performs the best in comparison with other methods.
Naked mole-rat and Damaraland mole-rat exhibit lower respiration in mitochondria, cellular and organismal levels
Authors: Yap Kang Nian , Wong Hoi Shan , Ramanathan Chidambaram , Rodriguez-Wagner Cristina Aurora , Roberts Michael D. , Freeman David A , Buffenstein Rochelle , Zhang Yufeng
Published: August 2021

Naked mole-rats (NMR) and Damaraland mole-rats (DMR) are the only two eusocial mammals known. Both species exhibit extraordinary longevity for their body size, high tolerance to hypoxia and oxidative stress and high reproductive output; these collectively defy the concept that all life-history traits should be negatively correlated. However, when life-history traits share similar underpinning physiological mechanisms, these may be positively associated with each other. Here, we propose that the bioenergetic properties of mole-rats share a potential common mechanism. We adopted a top-down perspective measuring the bioenergetic properties at the organismal, cellular, and molecular level in both species and the biological significance of these properties were compared with the same measures in Siberian hamsters and C57BL/6 mice, chosen for their similar body size to the mole-rat species. We found mole-rats shared several bioenergetic properties that differed from their comparator species, including low basal metabolic rates, a high dependence on glycolysis rather than on oxidative phosphorylation for ATP production, and low proton conductance across the mitochondrial inner membrane. These shared mole-rat features could be a result of evolutionary adaptation to tolerating variable oxygen atmospheres, in particular hypoxia, and may in turn be one of the molecular mechanisms underlying their extremely long lifespans.
Knockout of circRNAs by base editing back-splice sites of circularized exons
Authors: Gao Xiang , Ma Xu-Kai , Li Xiang , Li Guo-Wei , Liu Chu-Xiao , Zhang Jun , Wang Ying , Wei Jia , Chen Jia , Chen Ling-Ling , Yang Li
Published: August 2021

A large number of circular RNAs (circRNAs) are produced from back-splicing of exon(s) of precursor mRNAs and generally co-expressed with their cognate linear RNAs from the same gene loci. Methods for circRNA-specific knockout are lacking, largely due to complete sequence-overlaps between circular and cognate linear RNAs. Here, we report to use base editors (BEs) for circRNA depletion. By targeting splice sites involved in both back-splicing and canonical splicing, BEs can repress both circular and linear RNAs expression, which confirms the requirement of canonical splice site signals for back-splice. Importantly, by targeting back-splice sites predominantly for circRNA biogenesis, BEs could efficiently repress the production of circular, but not linear cognate RNAs. As hundreds of exons were found to be predominantly back-spliced to produce circRNAs, this study provides an efficient method to deplete circRNAs for function study.
A Novel Mouse Wound Model for Scar Tissue Formation in Abdominal-Muscle Wall
Authors: Jimi Shiro , Saparov Arman , Koizumi Seiko , Miyazaki Motoyasu , Takagi Satoshi
Published: August 2021

Scar tissue formation is a result of excess healing reactions after wounding. Hypertrophic scars scarcely develop in a mouse. In the present study, we established a novel experimental model of a scar-forming wound by resecting a small portion of the abdominal wall on the lower center of the abdomen, which exposed contractive forces by the surrounding muscle tissue. As a tension-less control, a back-skin excision model was used with a splint fixed onto the excised skin edge, and granulation tissue formed on the muscle facia supported by the back skeleton. One week after the resection, initial healing reactions such as fibroblast proliferation took place in both models.

However, after 21 days, lesions with collagen-rich granulation tissues forming multiple nodular/spherical-like structures developed only in the abdominal-wall model. The lesions are analogous to scar lesions in humans. Such lesions, however, did not develop in the back-skin excision model. Therefore, this animal model is unique in that fibrous scar tissues form under a physiological condition without using any artificial factors and is valuable for studying the pathogenesis and preclinical treatment of scar lesions.

Summary Statement

Scar lesions are hardly developed in animals. We thus developed a scar lesion in mice without using any artificial factors. The model is reliable, reproducible, and valuable.
An Intrinsically Disordered Peptide Tag that Confers an Unusual Solubility to Aggregation-Prone Proteins
Authors: Jo Byung Hoon
Published: August 2021

There is a high demand for the production of recombinant proteins in Escherichia coli for biotechnological applications but their production is still limited by their insolubility. Fusion tags have been successfully used to enhance the solubility of aggregation-prone proteins; however, smaller and more powerful tags are desired for increasing the yield and quality of target proteins. Herein, NEXT tag, a 53 amino acid-length solubility enhancer, is described. The NEXT tag showed outstanding ability to improve both in vivo and in vitro solubilities with minimal effect on passenger proteins. The C-terminal region of the tag was mostly responsible for in vitro solubility, while the N-terminal region was essential for in vivo soluble expression. The NEXT tag appeared to be intrinsically disordered and seemed to exclude neighboring molecules and prevent protein aggregation by acting as an entropic bristle. This novel peptide tag should have general use as a fusion partner to increase the yield and quality of difficult-to-express proteins.

IMPORTANCE

Production of recombinant protein in Escherichia coli still suffers from the insolubility problem. Conventional solubility enhancers with large sizes represented by maltose-binding protein (MBP) have remained as the first-choice tags, however, the success in the soluble expression of tagged protein is largely unpredictable. In addition, the large tags can negatively affect the function of target proteins. In this work, NEXT tag, an intrinsically disordered peptide, was introduced as a small but powerful alternative to MBP. The NEXT tag could significantly improve both expression level and solubility of target proteins including a thermostable carbonic anhydrase and a polyethylene terephthalate (PET)-degrading enzyme that are remarkable enzymes for environmental bioremediation.
Nontypeable Haemophilus influenzae infection impedes Pseudomonas aeruginosa colonization and persistence in mouse respiratory tract
Authors: Lindgren Natalie , Novak Lea , Hunt Benjamin C. , McDaniel Melissa S. , Swords W. Edward
Published: August 2021

Patients with cystic fibrosis (CF) experience lifelong respiratory infections which are a significant cause of morbidity and mortality. These infections are polymicrobial in nature, and the predominant bacterial species undergo a predictable series of changes as patients age. Young patients have populations dominated by opportunists that are typically found within the microbiome of the human nasopharynx, such as nontypeable Haemophilus influenzae (NTHi); these are eventually supplanted and the population within the CF lung is later dominated by pathogens such as Pseudomonas aeruginosa (Pa). In this study, we investigated how initial colonization with NTHi impacts colonization and persistence of Pa in the respiratory tract.

Analysis of polymicrobial biofilms in vitro by confocal microscopy revealed that NTHi promoted greater levels of Pa biofilm volume and diffusion. However, sequential respiratory infection of mice with NTHi followed by Pa resulted in significantly lower Pa as compared to infection with Pa alone. Coinfected mice also had reduced airway tissue damage and lower levels of inflammatory cytokines as compared with Pa infected mice. Similar results were observed after instillation of heat-inactivated NTHi bacteria or purified NTHi lipooligosaccharide (LOS) endotoxin prior to Pa introduction. Based on these results, we conclude that NTHi significantly reduces susceptibility to subsequent Pa infection, most likely due to priming of host innate immunity rather than a direct competitive interaction between species. These findings have potential significance with regard to therapeutic management of early life infections in patients with CF.
Quality of life profile of methadone maintenance treatment patients in Ho Chi Minh City, Vietnam
Authors: Trang Vu Thu , Tu Le Ngoc , Tuong Vi Vu Thi , Long Khuong Quynh , Cam Hong Le Huynh Thi , Thu Van Tieu Thi , Van Dung Do
Published: August 2021

Aim

To determine the health-related quality of life (HRQoL) of methadone maintenance treatment patients in Ho Chi Minh City, Vietnam.

Subject and Methods

A cross-sectional study was conducted in 967 patients treating at two methadone clinics in Ho Chi Minh City, in 2018. Patient’s health-related quality of life was estimated using the EQ-5D-5L and Visual analogue scale (VAS). Tobit regressions were used to identify factors related to patient’s health-related quality of life.

Results

Overall, the mean EQ-5D-5L utility and EQ-VAS indexes were 0.96 (SD = 0.12) and 75.8 (SD=15.5), respectively. Factors related with a higher EQ-5D-5L score included peoples who are single, and have a higher monthly income (more than 4 million VND per month), while patients aged under 30 years old, have full-time employment, and have higher education were associated with a higher EQ-VAS score. HIV was associated with lower scores of both EQ-5D-5L and EQ- VAS (β = -0.07 (95%CI: -0.13; -0.01), and β = -7.10 (95%CI: -9.23; -4.98), respectively).

Conclusion

HRQoL measurement provides valuable information for the policymaker to adopt suitable decisions on opioid dependence treatment. The finding shows that patients with education, job situation, and socioeconomic status are the related elements with higher HRQoL, which suggested that the policymakers and physicians should pay more attention to these aspects while working on treatment plan for drug users.
Factorial Structure of the Transactional eHealth Literacy Among Vietnamese Youth: An Instrument Validation Study
Authors: Vu Giang Thu , Vu Thuc Minh Thi , van Kessel Robin , Han Wong Brian Li , Nguyen Tham Thi , Thi Nguyen Thao Phuong , Nguyen Son Hoang , Do Ha Ngoc , Tran Bach Xuan , Latkin Carl A. , Ho Cyrus , Ho Roger
Published: August 2021

The progression into the Digital Age has brought an array of novel skill requirements. Unlike traditional literacy, there are currently few measures that can reliably measure eHealth literacy. The Transactional Model of eHealth Literacy and subsequent Transactional eHealth Literacy Instrument may provide a feasible option for measuring eHealth literacy. However, this instrument has yet to be validated, which is the aim of this study. We conducted an online cross-sectional study among 236 Vietnamese young people. Using exploratory factor analysis, we ensured that a model consisting of four factors had the best fit (RMSEA = 0.116; CFI = 0.907) and the highest internal consistency (Cronbach’s α = 0.96). A confirmatory factor analysis tested measurement invariance at four levels: configural, metric, scalar, and strict invariance. Only metric invariance was partially invariant, while the rest tested fully invariant. Even with partial metric invariance, there is reason to assume that functional, communicative, critical, and translational eHealth literacy (the four levels according to the transactional model) are consistently measured when deploying the Transactional eHealth Literacy Instrument across groups. In other words, this study suggests the instrument can be used for comparisons across groups and has the potential to generate high-quality data usable for informing change agents as to whether a particular population is proficient enough to adopt novel eHealth innovations.
Prevalence and effect of bacterial co-infections on clinical outcomes in hospitalized COVID-19 patients at a tertiary care centre of India
Authors: Pathak Ashutosh , Singh Sweta , Singh Sanjay , Patel Sangram Singh , Fatima Nida , Garg Atul , Ghoshal Ujjala , Sahu Chinmoy
Published: August 2021

Background

Bacterial co-infections are a leading cause of morbidity and mortality during viral infections including COVID-19. Systematic testing of COVID-19 patients having bacterial co-infections is essential to select the correct antibiotic for treatment in order to reduce mortality and also prevent spread of antimicrobial resistance (AMR). The present study aims to evaluate the prevalence, demographic parameters, antibiotic sensitivity patterns and outcomes in hospitalized COVID-19 patients with bacterial co-infections.

Methods

A total of 1019 COVID-19 patients were selected for the study. We analyzed the prevalence, antibiotic sensitivity pattern and clinical outcomes in COVID-19 patients having bacterial co-infections.

Results

Out of a total 1019 COVID-19 patients screened, 5.2% of patients demonstrated clinical signs of bacterial co-infection. Bacteremia was found in majority of the patients followed by respiratory and urinary infections. Escherichia coli, Pseudomonas aeruginosa and Klebsiella spp. were most common isolates among the Gram-negative and Coagulase-negative Staphylococci (CONS) and Staphylococcus aureus among the Gram-positive bacterial infections. Antibiotic sensitivity profiling revealed that colistin, imipenem and fosfomycin were the most effective drugs against the Gram-negative isolates while vancomycin, teicoplanin and doxycycline against the Gram-positive isolates. Analysis of clinical outcomes revealed that the mortality rate was higher (39%) among the patients with bacterial co-infections as compared to the group without co-infection (17%).

Conclusions

This study reveals that the rate of bacterial co-infections is significantly increasing among COVID-19 patients and leading to increase in mortality. Systematic testing of bacterial co-infections is therefore essential in COVID-19 patients for better clinical outcomes and to reduce AMR.
Serendipitous COVID-19 Vaccine-Mix in Uttar Pradesh, India: Safety and Immunogenicity Assessment of a Heterologous Regime
Authors: Kant Rajni , Dwivedi Gaurav , Zaman Kamran , Sahay Rima R , Sapkal Gajanan , Kaushal Himanshu , Nyayanit Dimpal A. , Yadav Pragya D , Deshpande Gururaj , Singh Rajeev , Chaowdhary Sandeep , Gupta Nivedita , Kumar Sanjay , Abraham Priya , Panda Samiran , Bhargava Balram
Published: August 2021

Immunization program against COVID-19 in India started with two vaccines; AstraZeneca’s ChAdOx1-nCov-19 (termed Covishield in India) and inactivated whole virion BBV152 (Covaxin); homologous prime-boost approach was followed. However, eighteen individuals, under the national program, inadvertently received Covishield as the first jab and Covaxin as the second. We compared the safety and immunogenicity profile of them against that of individuals receiving either Covishield or Covaxin (n=40 in each group). Lower and similar adverse events following immunization in all three groups underlined the safety of the combination vaccine-regime. Immunogenicity profile against Alpha, Beta and Delta variants in heterologous group was superior; IgG antibody and neutralising antibody response of the participants was also significantly higher compared to that in the homologous groups. The findings suggest that immunization with a combination of an adenovirus vector platform-based vaccine followed by an inactivated whole virus vaccine was not only safe but also elicited better immunogenicity.
Trends in accident-related admissions to pediatric intensive care units during the first COVID-19 lockdown in Germany
Authors: Bruns Nora , Willemsen Lea , Holtkamp Katharina , Kamp Oliver , Dudda Marcel , Kowall Bernd , Stang Andreas , Hey Florian , Blankenburg Judith , Hemmen Sabir , Eifinger Frank , Fuchs Hans , Haase Roland , Andrée Clemens , Heldmann Michael , Potratz Jenny , Kurz Daniel , Schumann Anja , Müller-Knapp Merle , Mand Nadine , Doerfel Claus , Dahlem Peter , Rothoeft Tobias , Ohlert Manuel , Silkenbäumer Katrin , Dohle Frank , Indraswari Fithri , Niemann Frank , Jahn Peter , Merker Michael , Braun Nicole , Nunez Francisco Brevis , Engler Matthias , Heimann Konrad , Wolf Gerhard , Wulf Dominik , Hollborn Claudia , Freymann Holger , Allgaier Nicolas , Knirsch Felix , Dercks Martin , Reinhard Julia , Hoppenz Marc , Felderhoff-Müser Ursula , Dohna-Schwake Christian
Published: August 2021

Objective

To compare the number of accident- and injury-related admissions to pediatric intensive care units (PICU) during the first German COVID-19 lockdown with previous years. To investigate if shifts in types of accidents or injuries occurred, especially regarding non-accidental injuries.

Design

Retrospective observational multicenter study.

Setting

37 German PICUs.

Patients

1444 children and adolescents < 18 years admitted to German PICUs due to trauma or injuries during the first German lockdown period (16.3.-31.5.2020) and during the same periods of the years 2017-2019.

Interventions

None.

Measurements and main results

Standardized morbidity ratios (SMR) and 95% confidence intervals (CI) were calculated for the severity of disease, admission reasons, types of accidents, injury patterns, surgeries and procedures, and outcomes. Disease severity did not differ from previous years. We found an increase in ingestions (SMR 1.41 (CI 0.88 – 2.16)) and a decrease in aspirations (0.77 (0.41 – 1.32)) and burns (0.82 (0.59 – 1.12)). The total number of admissions for trauma remained constant, but traffic accidents (0.76 (0.56 – 1.01) and school/kindergarten accidents (0.25 (0.05 – 0.74) decreased. Household (1.32 (1.05 – 1.64)) and leisure accidents (1.32 (1.05 – 1.65)) increased. Injured structures did not change, but less neurosurgeries (0.69 (0.42 – 1.07)) and more visceral surgeries (2.00 (1.14 – 3.24)) were performed. Non-accidental non-suicidal injuries declined (0.85 (0.50 – 1.37)). Suicide attempts increased in adolescent boys (1.57 (0.58 – 3.42)), while there was a decrease in adolescent girls (0.86 (0.53 – 1.31)).

Conclusions

Our study showed shifts in trauma types and associated surgeries during the lockdown period that are generally in line with current literature. The decreased number of non-accidental non-suicidal injuries we observed does not suggest a fundamental increase in severe child abuse during the lockdown period. The decrease in suicide attempts among adolescent girls confirms previous findings, while the increase among boys has not been described yet and deserves further investigation.
Functional roles of multiple Ton complex genes in a Sphingobium degrader of lignin-derived aromatic compounds
Authors: Fujita Masaya , Yano Shodai , Shibata Koki , Kondo Mizuki , Hishiyama Shojiro , Kamimura Naofumi , Masai Eiji
Published: August 2021

TonB-dependent transporters (TBDTs) mediate outer membrane transport of nutrients using the energy derived from proton motive force transmitted from the TonB−ExbB−ExbD complex localized in the inner membrane. Recently, we discovered ddvT encoding a TBDT responsible for the uptake of a 5,5-type lignin-derived dimer in Sphingobium sp. strain SYK-6. Furthermore, overexpression of ddvT in an SYK-6-derivative strain enhanced its uptake capacity, improving the rate of platform chemical production. Thus, understanding the uptake system of lignin-derived aromatics is fundamental for microbial conversion-based lignin valorization. Here we examined whether multiple tonB-, exbB-, and exbD-like genes in SYK-6 contribute to the outer membrane transport of lignin-derived aromatics. The disruption of tonB2−6 and exbB3 did not reduce the capacity of SYK-6 to convert or grow on lignin-derived aromatics. In contrast, the introduction of the tonB1−exbB1−exbD1−exbD2 operon genes into SYK-6, which could not be disrupted, promoted the conversion of β-O-4-, β-5-, β-1-, β-β-, and 5,5-type dimers and monomers, such as ferulate, vanillate, syringate, and protocatechuate. These results suggest that TonB-dependent uptake involving the tonB1 operon genes is responsible for the outer membrane transport of the above aromatics. Additionally, exbB2/tolQ and exbD3/tolR were suggested to constitute the Tol-Pal system that maintains the outer membrane integrity.
Structural characterization of a Thorarchaeota profilin indicates eukaryotic-like features but with an extended N-terminus
Authors: Inturi Raviteja , Lara Sandra , Derweesh Mahmoud , Chi Celestine N.
Published: August 2021

The emergence of the first eukaryotic cell was preceded by evolutionary events which are still highly debatable. Recently, comprehensive metagenomics analysis has uncovered that the Asgard super-phylum is the closest yet known archaea host of eukaryotes. However, it remains to be established if a large number of eukaryotic signature proteins predicated to be encoded by the Asgard super-phylum are functional at least, in the context of a eukaryotic cell. Here, we determined the three-dimensional structure of profilin from Thorarchaeota by nuclear magnetic resonance spectroscopy and show that this profilin has a rigid core with a flexible N-terminus which was previously implicated in polyproline binding. In addition, we also show that thorProfilin co-localizes with eukaryotic actin in cultured HeLa cells. This finding reaffirm the notion that Asgardean encoded proteins possess eukaryotic-like characteristics and strengthen likely existence of a complex cytoskeleton already in a last eukaryotic common ancestor.
Mitochondrial membrane proteins and VPS35 orchestrate selective removal of mtDNA
Authors: Pla-Martin David , Sen Ayesha , Kallabis Sebastian , Nüchel Julian , Maliphol Kanjanamas , Hofmann Julia , Krüger Marcus , Wiesner Rudolf J.
Published: August 2021

Integrity of mitochondrial DNA (mtDNA), encoding several subunits of the respiratory chain, is essential to maintain mitochondrial fitness. Mitochondria, as a central hub for metabolism, are affected in a wide variety of human diseases but also during normal ageing, where mtDNA integrity is compromised. Mitochondrial quality control mechanisms work at different levels, and mitophagy and its variants are critical to remove dysfunctional mitochondria together with mtDNA to maintain cellular homeostasis. Understanding the mechanisms governing a selective turnover of mutation-bearing mtDNA without affecting the entire mitochondrial pool is fundamental to design therapeutic strategies against mtDNA diseases and ageing. Here we show that mtDNA depletion after expressing a dominant negative version of the mitochondrial helicase Twinkle, or by chemical means, is due to an exacerbated mtDNA turnover. Targeting of nucleoids is controlled by Twinkle which, together with the mitochondrial transmembrane proteins ATAD3 and SAMM50, orchestrate mitochondrial membrane remodeling to form extrusions. mtDNA removal depends on autophagy and requires the vesicular trafficking protein VPS35 which binds to Twinkle-enriched mitochondrial subcompartments upon mtDNA damage. Stimulation of autophagy by rapamycin selectively removes mtDNA deletions which accumulated during muscle regenerationin vivo, but without affecting mtDNA copy number. With these results we unveil a new complex mechanism specifically targeting and removing mutant mtDNA which occurs outside the mitochondrial network. We reveal the molecular targets involved in a process with multiple potential benefits against human mtDNA related diseases, either inherited, acquired or due to normal ageing.
Immunomodulatory properties of umbilical cord blood-derived small extracellular vesicles and their therapeutic potential for inflammatory skin disorders
Authors: Rodrigues Sílvia C. , Cardoso Renato M. S. , Freire Patricia C. , Gomes Cláudia , Duarte Filipe , Neves Ricardo , Simões-Correia Joana
Published: August 2021

Umbilical cord blood (UCB) has long been seen as a rich source of naïve cells with strong regenerative potential, likely mediated by small extracellular vesicles (sEV). More recently, small extracellular vesicles (sEV), such as exosomes, have been shown to play essential roles in cell-to-cell communication, via the transport of numerous molecules, including small RNAs. Often explored for their potential as biomarkers, sEV are now known to have regenerative and immunomodulating characteristics, particularly if isolated from stem cell-rich tissues. In this study, we aim to characterize the immunomodulating properties of umbilical cord blood mononuclear cell sEV (herein referred as Exo-101), and explore their therapeutic potential for inflammatory skin diseases. Exo-101 was shown to shift macrophages toward an anti-inflammatory phenotype, which in turn exert paracrine effects on fibroblasts, despite previous inflammatory stimuli. Additionally, the incubation of PBMC with Exo-101 resulted in an reduction of total CD4+and CD8+T-cell proliferation and cytokine release, while specifically supporting the development of regulatory T-cells (Treg), by influencing FOXP3 expression. In a 3D model of psoriatic skin, Exo-101 reduced the expression of inflammatory and psoriatic markers IL-6, IL-8, CXCL10, COX-2, S100A7 and DEFB4.In vivo, Exo-101 significantly prevented or reversed acanthosis in imiquimod-induced psoriasis, and tendentially increased the number of Treg in skin, without having an overall impact on disease burden. This work provides evidence for the anti-inflammatory and tolerogenic effect of Exo-101, which may be harnessed for the treatment of Th17-driven inflammatory skin diseases, such as psoriasis.
The darkest place is under the candlestick - healthy urogenital tract as a source of UTI-relatedEscherichia colilineages
Authors: Ksiezarek Magdalena , Novais Angela , Peixe Luisa
Published: August 2021

Since the discovery of the urinary microbiome, including identification ofEscherichia coliin healthy hosts, its involvement in UTI development is a subject of high interest.

We explored population diversity and antimicrobial resistance ofE. colifrom urogenital microbiome of asymptomatic and recurrent UTI (rUTI) women. We also evaluated the genomic relationship between extraintestinal pathogenicE. coli(ExPEC) strains from healthy and diseased hosts, particularly of the ST131 lineage.

E. coliwas highly prevalent in asymptomatic women (48%) with slightly higher prevalence in vaginal samples comparing to urine, and occasionally with multiclonal population in the same individual. B2 was the most frequent phylogenetic group, with most strains classified as ExPEC. We demonstrated that virulence associated genes profile does not allow to distinguish strains isolated from healthy and rUTI host. We identifiedE. coliwidespread lineages e.g., sequence types (ST) 127, ST131 (asymptomatic cohort) and ST73, ST131 (rUTI), frequently resistant to at least one antibiotic. Phylogenomics of ST131 and other ExPEC lineages revealed close relatedness between healthy and diseased host.

These findings demonstrate that healthy urogenital microbiome is a source of potentially pathogenic and antibiotic resistantE. colistrains, including globally spreadE. colilineages causing UTI including ST131.
Scaffolding protein GspB/OutB facilitates assembly of the Dickeya dadantii type 2 secretion system by anchoring the outer membrane secretin pore to the inner membrane and to the peptidoglycan cell wall
Authors: Zhang Shiheng , Gu Shuang , Rycroft Piers , Ruaudel Florence , Delolme Frederic , Robert Xavier , Ballut Lionel , Pickersgill Richard W. , Shevchik Vladimir E.
Published: August 2021

The phytopathogenic proteobacterium Dickeya dadantii secretes an array of plant cell wall degrading enzymes and other virulence factors via the type 2 secretion system (T2SS). T2SSs are widespread among important plant, animal and human bacterial pathogens. This multi-protein complex spans the double membrane cell envelope and secretes fully folded proteins through a large outer membrane pore formed by 15 subunits of the secretin GspD. Secretins are also found in the type 3 secretion system and the type 4 pili. Usually, specialized lipoproteins termed as pilotins assist the targeting and assembly of secretins into the outer membrane. Here, we show that in Dickeya, the pilotin acts in concert with the scaffolding protein GspB. Deletion of gspB profoundly impacts secretin assembly, pectinase secretion, and virulence. Structural studies reveal that GspB possesses a conserved periplasmic Homology Region domain that interacts directly with the N-terminal secretin domain. Site-specific photo cross-linking unravels molecular details of the GspB-GspD complex in vivo. We show that GspB facilitates outer membrane targeting and assembly of the secretin pores and anchors them to the inner membrane while the C-terminal extension of GspB scaffolds the secretin channel in the peptidoglycan cell wall. Phylogenetic analysis shows that in other bacteria, GspB homologs vary in length and domain composition and act in concert with either a cognate ATPase GspA or a pilotin GspS.

Importance

Gram-negative bacteria have two cell membranes sandwiching a peptidoglycan net that form together a robust protective cell envelope. To translocate effector proteins across this multilayer envelope, bacteria have evolved several specialized secretion systems. In the type 2 secretion system and some other bacterial machineries, secretins form large multimeric pores that allow transport of effector proteins or filaments across the outer membrane. The secretins are essential for nutrient acquisition and pathogenicity and constitute a target for development of new antibacterials. Targeting of secretin subunits into the outer membrane is often facilitated by a special class of lipoproteins called pilotins. Here, we show that in Dickeya and some other bacteria, the scaffolding protein GspB acts in concert with pilotin, facilitating the assembly of the secretin pore and its anchoring to both the inner membrane and the bacterial cell wall. GspB homologs of varied domain composition are present in many other T2SSs.
An engineered, orthogonal auxin analog/AtTIR1(F79G) pairing improves both specificity and efficacy of the auxin degradation system inCaenorhabditis elegans
Authors: Hills-Muckey Kelly , Martinez Michael A. Q. , Stec Natalia , Hebbar Shilpa , Saldanha Joanne , Medwig-Kinney Taylor N. , Moore Frances E. Q. , Ivanova Mariia , Morao Ana , Ward Jordan D. , Moss Eric G. , Ercan Sevinc , Zinovyeva Anna Y. , Matus David Q. , Hammell Christopher M.
Published: August 2021

The auxin-inducible degradation system inC. elegansallows for spatial and temporal control of protein degradation via heterologous expression of a singleArabidopsis thalianaF-box protein, transport inhibitor response 1 (AtTIR1). In this system, exogenous auxin (Indole-3-acetic acid; IAA) enhances the ability ofAtTIR1 to function as a substrate recognition component that adapts engineered degron-tagged proteins to the endogenousC. elegansE3 ubiquitin ligases complex (SKR-1/2-CUL-1-F-box (SCF)), targeting them for degradation by the proteosome. While this system has been employed to dissect the developmental functions of manyC. elegansproteins, we have found that several auxin-inducible degron (AID)-tagged proteins are constitutively degraded byAtTIR1 in the absence of auxin, leading to undesired loss-of-function phenotypes. In this manuscript, we adapt an orthogonal auxin-derivative/mutantAtTIR1 pair (C. elegansAID version 2 (C.e.AIDv2)) that transforms the specificity of allosteric regulation of TIR1 from IAA to one that is dependent on an auxin derivative harboring a bulky aryl group (5-Ph-IAA). We find that a mutantAtTIR1(F79G) allele that alters the ligand binding interface of TIR1 dramatically reduces ligand-independent degradation of multiple AID*-tagged proteins. In addition to solving the ectopic degradation problem for some AID targets, addition of 5-Ph-IAA to culture media of animals expressingAtTIR1(F79G) leads to more penetrant loss-of-function phenotypes for AID*-tagged proteins than those elicited by theAtTIR1-IAA pairing at similar auxin analog concentrations. The improved specificity and efficacy afforded by the mutantAtTIR1(F79G) allele expands the utility of the AID system and broadens the number of proteins that can be effectively targeted with it.

ARITCLE SUMMARY

Implementation of the auxin induced degradation (AID) system has increased the power if theC. elegansmodel through its ability to rapidly degrade target proteins in the presence of the plant hormone auxin (IAA). The currentC.e.AID system is limited in that a substantial level of target degradation occurs in the absence of ligand and full levels of target protein degradation require high levels of auxin inducer. In this manuscript, we modify the AID system to solve these problems.
Single-cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and stellate cell activation phenotypes with human liver
Authors: Morrison Joshua K. , DeRossi Charles , Alter Isaac L. , Nayar Shikha , Giri Mamta , Zhang Chi , Cho Judy H. , Chu Jaime
Published: August 2021

Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated (1). The mechanisms of fibrogenesis are multi-faceted and remain elusive with no approved antifibrotic treatments available (2). Here we use single-cell RNA sequencing (scRNA-seq) of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single-cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA-seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA-seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells (HSCs), the driver cell in liver fibrosis (3), specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel, conserved marker for zebrafish HSCs. To demonstrate the power of scRNA-seq to study liver fibrosis, we performed scRNA-seq on our zebrafish model of a pediatric liver disease with characteristic early, progressive liver fibrosis caused by mutation in mannose phosphate isomerase (MPI) (4–6). Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor-ligand interactions within normal and fibrotic states. This study establishes the first scRNA-seq atlas of the adult zebrafish liver, highlights the high degree of similarity to the human liver, and strengthens its value as a model to study liver fibrosis.

Significance Statement

To our knowledge, this is the first single-cell characterization of the adult zebrafish liver, both in a normal physiologic state and in the setting of liver fibrosis. We identify transcriptionally distinct zebrafish liver cell populations and a high degree of transcriptional conservation between human and zebrafish cells across the majority of hepatic cell types. Furthermore, using this scRNA transcriptome, we identify key signaling pathways in zebrafish HSCs that are replicated in human HSCs and implicated in the regulation of liver fibrosis. Our work provides a useful resource that can be used to aid research using the zebrafish liver and asserts the usefulness of the adult zebrafish to study liver fibrosis.
The cortical bone metabolome of C57BL/6J mice is sexually dimorphic
Authors: Welhaven Hope D. , Vahidi Ghazal , Walk Seth T. , Bothner Brian , Martin Stephen A. , Heveran Chelsea M. , June Ronald K.
Published: August 2021

Cortical bone quality, which is sexually dimorphic, depends on bone turnover and therefore the activities of remodeling bone cells. However, sex differences in cortical bone metabolism are not yet defined. Adding to the uncertainty about cortical bone metabolism, the metabolomes of whole bone, isolated cortical bone without marrow, and bone marrow have not been compared. We hypothesized that the metabolome of isolated cortical bone would be distinct from that of bone marrow and would reveal sex differences. Metabolite profiles from LC-MS of whole bone, isolated cortical bone, and bone marrow were generated from humeri from 20-week-old female C57Bl/6J mice. The cortical bone metabolomes were then compared for 20-week-old female and male C57Bl/6J mice. Femurs from male and female mice were evaluated for flexural material properties and were then categorized into bone strength groups. The metabolome of isolated cortical bone was distinct from both whole bone and bone marrow. We also found sex differences in the isolated cortical bone metabolome. Based on metabolite pathway analysis, females had higher lipid metabolism, and males had higher amino acid metabolism. High-strength bones, regardless of sex, had greater tryptophan and purine metabolism. For males, high strength bones had upregulated nucleotide metabolism, whereas lower strength bones had greater pentose phosphate pathway metabolism. Since the higher strength groups (females compared with males, high strength males compared with lower strength males) had higher serum CTX1/P1NP, we estimate that the metabolomic signature of bone strength in our study at least partially reflects differences in bone turnover. These data provide novel insight into bone bioenergetics and the sexual dimorphic nature of bone material properties in C57Bl/6 mice.
Visual modulation of spectrotemporal receptive fields in mouse auditory cortex
Authors: Bigelow James , Morrill Ryan J. , Olsen Timothy , Bazarini Stephanie N. , Hasenstaub Andrea R.
Published: August 2021

Recent studies have established significant anatomical and functional connections between visual areas and primary auditory cortex (A1), which may be important for perceptual processes such as communication and spatial perception. However, much remains unknown about the microcircuit structure of these interactions, including how visual context may affect different cell types across cortical layers, each with diverse responses to sound. The present study examined activity in putative excitatory and inhibitory neurons across cortical layers of A1 in awake male and female mice during auditory, visual, and audiovisual stimulation. We observed a subpopulation of A1 neurons responsive to visual stimuli alone, which were overwhelmingly found in the deep cortical layers and included both excitatory and inhibitory cells. Other neurons for which responses to sound were modulated by visual context were similarly excitatory or inhibitory but were less concentrated within the deepest cortical layers. Important distinctions in visual context sensitivity were observed among different spike rate and timing responses to sound. Spike rate responses were themselves heterogeneous, with stronger responses evoked by sound alone at stimulus onset, but greater sensitivity to visual context by sustained firing activity following transient onset responses. Minimal overlap was observed between units with visual-modulated firing rate responses and spectrotemporal receptive fields (STRFs) which are sensitive to both spike rate and timing changes. Together, our results suggest visual information in A1 is predominantly carried by deep layer inputs and influences sound encoding across cortical layers, and that these influences independently impact qualitatively distinct responses to sound.

Significance statement

Multisensory integration is ubiquitous throughout the brain, including primary sensory cortices. The present study examined visual responses in primary auditory cortex, which were found in both putative excitatory and inhibitory neurons and concentrated in the deep cortical layers. Visual-modulated responses to sound were similarly observed in excitatory and inhibitory neurons but were more evenly distributed throughout cortical layers. Visual modulation moreover differed substantially across distinct sound response types. Transient stimulus onset spike rate changes were far less sensitive to visual context than sustained spike rate changes during the remainder of the stimulus. Spike timing changes were often modulated independently of spike rate changes. Audiovisual integration in auditory cortex is thus diversely expressed among cell types, cortical layers, and response types.
Paracrine granules are cytoplasmic RNP granules distinct from stress granules that assemble in response to viral infection
Authors: Iadevaia Valentina , Burke James M. , Eke Lucy , Moller-Levet Carla , Parker Roy , Locker Nicolas
Published: August 2021

To rapidly respond and adapt to stresses, such as viral infections, cells have evolved several mechanisms, which include the activation of stress response pathways and the innate immune response. These stress responses result in the rapid inhibition of translation and condensation of stalled mRNAs, together with RNA-binding proteins and signalling components, into cytoplasmic biocondensates called stress granules. Increasing evidence suggests that stress granules contribute to antiviral defense and thus viruses need to evade these response pathways to propagate. In addition, the stress granule pathway is proposed to be dynamic and adaptable to specific stresses. We previously showed that Feline Calicivirus (FCV) impairs SGs assembly by cleaving the scaffolding protein G3BP1. We also observed that uninfected bystander cells assembled G3BP1-granules, suggesting a paracrine response trigged by the infection. We now present evidence that virus-free supernatant generated from infected cells can induce the formation of paracrine granules. They are different from canonical stress granules and exhibit specific kinetics of assembly-disassembly, protein and RNA composition and are linked to antiviral activity. We propose that this paracrine induction reflects a novel cellular defence mechanism to limit viral propagation and promote stress responses in bystander cells.

Summary statement

We describe a novel type of paracrine induced RNA granules associated with viruses, highlighting how different stresses results in heterogeneous stress granule-like condensates with specific cellular functions.
Homeobox transcription factor MNX1 is crucial for restraining the expression of pan-neuronal genes in motor neurons
Authors: Sun Ming-an , Ralls Sherry , Wu Warren , Demmerle Justin , Jiang Jiayao , Miller Carson , Wolf Gernot , Macfarlan Todd S.
Published: August 2021

Motor neurons (MNs) control muscle movement and are essential for breathing, walking and fine motor skills. Motor Neuron and Pancreas Homeobox 1 (MNX1) has long been recognized as a key marker of the MN lineage. Deficiency of the Mnx1 gene in mice results in early postnatal lethality – likely by causing abnormal MN development and respiratory malfunction. However, the genome-wide targets and exact regulatory function of Mnx1 in MNs remains unresolved. Using an in vitro model for efficient MN induction from mouse embryonic stem cells, we identified about six thousand MNX1-bound loci, of which half are conserved enhancers co-bound by the core MN-inducing factors ISL1 and LHX3, while the other half are promoters for housekeeping-like genes. Despite its widespread binding, disruption of Mnx1 affects the activity of only a few dozen MNX1-bound loci, and causes mis-regulation of about one hundred genes, the majority of which are up-regulated pan-neuronal genes with relatively higher expression in the brain compared to MNs. Integration of genome-wide binding, transcriptomic and epigenomic data in the wild-type and Mnx1-disrupted MNs predicts that Pbx3 and Pou6f2 are two putative direct targets of MNX1, and both are homeobox transcription factors highly expressed in the central nervous system. Our results suggest that MNX1 is crucial for restraining the expression of many pan-neuronal genes in MNs, likely in an indirect fashion. Further, the rarity of direct targets in contrast to the widespread binding of MNX1 reflects a distinctive mode of transcriptional regulation by homeobox transcriptional factors.