bluuebunny/crossref_metadata_2025 huggingface dataset:
Demographic and Epidemiological Characteristics Associated With Reduced Antimicrobial Susceptibility to Neisseria gonorrhoeae in the United States, Strengthening the US Response to Resistant Gonorrhea, 2018 to 2019
Authors: Gieseker Karen E. , Learner Emily R. , Mauk Kerry , Barbee Lindley A. , McNeil Candice J. , Hasty Gerald L. , Black Jamie M. , Johnson Kimberly , Nguyen Trang Quyen , Shrestha Dhana , Pham Cau D. , St. Cyr Sancta , Schlanger Karen , Kirkcaldy Robert D. ,   for the SURRG Working Group
Published: August 2021

Background

Jurisdictions participating in Strengthening the US Response to Resistant Gonorrhea (SURRG) implemented specimen collection for culture and antimicrobial susceptibility testing from a sample of persons of all genders (at multiple anatomic sites) attending sexually transmitted disease clinics and community clinics. We describe the percentage and characteristics of patients whose isolates demonstrated reduced susceptibility (RS) to azithromycin, ceftriaxone, or cefixime.

Methods

We included patients from clinics that participated in SURRG whose isolates underwent antimicrobial susceptibility testing by Etest. We defined RS as azithromycin minimum inhibitory concentrations (MICs) ≥2 μg/mL (AZM-RS), ceftriaxone MICs ≥0.125 μg/mL (CRO-RS), or cefixime MICs ≥0.25 μg/mL (CFX-RS). Patients with repeated infections appeared >1 time in the data. We calculated the frequency and percentage of patients with an isolate demonstrating RS by epidemiological characteristics.

Results

During the period 2018–2019, 10,013 patients from 8 jurisdictions provided 10,735 isolates. Among 10,013 patients, 11.0% (n = 1099) had ≥1 isolate with AZM-RS (range by jurisdiction, 2.5%–18.0%). Approximately 11.3% of 8771 of patients visiting sexually transmitted disease clinics and approximately 8.8% of 1242 patients visiting community clinics had an AZM-RS isolate. Nearly 6% of 1013 females had an AZM-RS isolate; among males, the percents of patients with an AZM-RS isolate were 17.7% among 4177 men who have sex only with men and 6.1% among 3581 men who have sex only with women. Few (0.4%) patients had isolates with CFX-RS (n = 40) or CRO-RS (n = 43).

Conclusions

Although infections with reduced cephalosporin susceptibility were rare, AZM-RS infections were prevalent in this sample of patients in multiple jurisdictions and across gender and gender of sex partner categories.
Case Report: Two Genetically Distinct Choroidal Melanomas in the Same Eye Treated with Endolaser Therapy
Authors: Saigal Khushi , El Hamichi Sophia , Gold Aaron S. , Murray Timothy G.
Published: August 2021

SIGNIFICANCE

This case report highlights the merits of using fine needle aspiration biopsy to obtain gene expression profiling of individual choroidal melanomas when more than one tumor arises in the same eye. It is also the first such case to document laser ablation therapy as the primary treatment.

PURPOSE

This report describes a case of two primary choroidal melanomas with different genetic profiles in the same eye.

CASE REPORT

An 80-year-old man presented to the office with a neoplasm of uncertain behavior in the left eye. The patient's visual acuity and IOP in the left eye, respectively, at the time of his first visit to the office were 20/25 and 8 mmHg. A dilated fundus examination revealed that there were two choroidal lesions in the left eye. The macular lesion was classified as type 1A, and the ciliochoroidal lesion was classified as type 1B. The patient underwent a vitrectomy of the left eye, followed by endolaser ablation of the tumors. The patient was also injected with bevacizumab. To date, the patient is free of known metastasis. Most recently, his visual acuity and IOP in the left eye were 20/30 and 14 mmHg, respectively.

CONCLUSIONS

Although rare, multiple melanomas in the same eye may have differing genetic profiles, which may alter prognosis and management, depending on the class of tumor detected.
Alphaviruses: Host pathogenesis, immune response, and vaccine & treatment updates
Authors: Guerrero-Arguero Israel , Tellez-Freitas Claudia M. , Weber K. Scott , Berges Bradford K. , Robison Richard A. , Pickett Brett E.
Published: August 2021

Human pathogens belonging to theAlphavirusgenus, in theTogaviridaefamily, are transmitted primarily by mosquitoes. The signs and symptoms associated with these viruses include fever and polyarthralgia, defined as joint pain and inflammation, as well as encephalitis. In the last decade, our understanding of the interactions between members of the alphavirus genus and the human host has increased due to the re-appearance of the chikungunya virus (CHIKV) in Asia and Europe, as well as its emergence in the Americas. Alphaviruses affect host immunity through cytokines and the interferon response. Understanding alphavirus interactions with both the innate immune system as well as the various cells in the adaptive immune systems is critical to developing effective therapeutics. In this review, we summarize the latest research on alphavirus-host cell interactions, underlying infection mechanisms, and possible treatments.
Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes
Authors: Petitjean Marie , Condamine Bénédicte , Burdet Charles , Denamur Erick , Ruppé Etienne
Published: August 2021

Escherichia coli

is a ubiquitous bacterium that has been widely exposed to antibiotics over the last 70 years. It has adapted by acquiring different antibiotic-resistance genes (ARGs), the census of which we aim to characterize here. To do so, we analysed 70 301

E. coli

genomes obtained from the EnteroBase database and detected 1 027 651 ARGs using the AMRFinder, Mustard and ResfinderFG ARG databases. We observed a strong phylogroup and clonal lineage specific distribution of some ARGs, supporting the argument for epistasis between ARGs and the strain genetic background. However, each phylogroup had ARGs conferring a similar antibiotic class resistance pattern, indicating phenotypic adaptive convergence. The G+C content or the type of ARG was not associated with the frequency of the ARG in the database. In addition, we identified ARGs from anaerobic, non-

Proteobacteria

bacteria in four genomes of

E. coli

, supporting the hypothesis that the transfer between anaerobic bacteria and

E. coli

can spontaneously occur but remains exceptional. In conclusion, we showed that phylum barrier and intra-species phylogenetic history are major drivers of the acquisition of a resistome in

E. coli

.
Identification and Mitigation of High-Risk Pregnancy with the Community Maternal Danger Score Mobile Application in Gboko, Nigeria
Authors: Bola Rajan , Ujoh Fanan , Lett Ronald
Published: August 2021

Introduction

Nigeria constitutes 1% of the world’s population yet accounts for 10% of global maternal mortality. Risk analyses within rural regions of Nigeria are not routinely conducted, yet could help inform access to skilled birth care. The objectives of this study were to assess the proportion of women at risk for mortality or morbidity in Benue State, Nigeria by analysing data collected during routine antenatal visits and through the Community Maternal Danger Score (CMDS), a validated risk-analysis tool.

Methods

Two cohorts, comprised of pregnant women presenting to primary healthcare centres within Gboko, Benue State between 2015-2017 and 2020-2021, were included in this study. The 2015-2017 cohort had their risk assessed retrospectively through analysis of routinely collected data. Identification of risk was based on their age, parity, and disease status (HIV and diabetes). The 2020-2021 cohort had their risk assessed prospectively using the CMDS.

Results

Routinely collected data from 2015-2017 demonstrated that up to 14.9% of women in Gboko were at risk for mortality or morbidity. The CMDS reported that up to 21.5% of women were at a similar level of risk; a significant difference of 6.6% (p=0.006). The CMDS was more efficient in obtaining and assessing this data, and the identification was available in real-time for midwives and pregnant women.

Conclusion

Routine data collected in Gboko identifies a high proportion of pregnant women at risk for mortality or morbidity. The CMDS is an evidence-based risk analysis tool that expands on this assessment by also estimating individual and community-level risk, which allows for more efficient mitigation and prevention strategies of maternal mortality.
Overcoming the pitfalls of NGS-based molecular diagnosis of Shwachman-Diamond syndrome
Authors: Peng Xiaomin , Dong Xinran , Wang Yaqiong , Wu Bingbing , Wang Huijun , Lu Wei , Xiao Feifan , Yang Lin , Li Gang , Zhou Wenhao , Liu Bo , Lu Yulan
Published: August 2021

Purpose

Shwachman-Diamond syndrome (SDS) is predominately caused by biallelic mutations in the SBDS gene and is characterized by exocrine pancreatic insufficiency, skeletal abnormalities and pancytopenia. Gene conversion between SBDS and its pseudogene SBDSP1 is the major cause. We established an efficient approach, HapICE, to infer the haplotype of SBDS based on short-read next-generation sequencing (NGS).

Methods

HapICE based on the Expectation-Maximization algorithm was developed to detect variants in exon 2 of SBDS arising from gene conversion. We retrospectively analyzed two common pathogenic variants (c.183_184delinsCT and c.258+2T>C) in suspected SDS patients and compared the results with those from conventional NGS analysis.

Results

In 47 SDS high-risk individuals and 64 available parents, HapICE improved the diagnostic rate by 27.7% compared with conventional methods and revealed 100% (95% CI: 92.5%-100%) concordance with Sanger sequencing. In addition to eighteen patients having consistent genetic results by both methods, HapICE further reported 8 patients with more accurate variant detection and 13 cases with the c.183_184delinsCT variant missing by conventional methods. HapICE also showed better performance in screening for carrier and wild-type status.

Conclusion

We have developed a novel SBDS variant detection tool through regular NGS data that demonstrated precise variant detection performance in clinical scenarios.
Misinformation can prevent the suppression of epidemics
Authors: Sontag Andrei , Rogers Tim , Yates Christian
Published: August 2021

Abstract

The effectiveness of non-pharmaceutical interventions, such as mask-wearing and social distancing, as control measures for pandemic disease relies upon a conscientious and well-informed public who are aware of and prepared to follow advice. Unfortunately, public health messages can be undermined by competing misinformation and conspiracy theories, spread virally through communities that are already distrustful of expert opinion. In this article, we propose and analyse a simple model of the interaction between disease spread and (mis-) information dynamics in a heterogeneous population composed of both trusting individuals who seek quality information and will take precautionary measures, and distrusting individuals who are susceptible to misinformation. We show that, as the density of the distrusting population increases, the model passes through a phase transition to a state in which major outbreaks cannot be suppressed. Our work highlights the urgent need for effective measures to combat the spread of misinformation.
GWAS meta-analysis reveals dual neuronal and immunological etiology for pain susceptibility
Authors: Mocci Evelina , Ward Kathryn , Dorsey Susan G. , Ament Seth A.
Published: August 2021

Chronic pain is at epidemic proportions in the United States, represents a significant burden on our public health system and is coincident with a growing opioid crisis. While numerous genetic risk factors have been identified, its genetic basis remains poorly understood. Here, we conducted a meta-analysis of genome-wide association study (GWAS) summary statistics from seventeen pain susceptibility traits in the UK Biobank. This analysis revealed 99 genome-wide significant risk loci, of which 62 have not been previously associated with a pain-related trait. Risk loci were enriched for genes involved in neurological and inflammatory pathways. Two-sample Mendelian randomization indicated that depression, neuroticism, and immunological traits mediate many of these effects. These analyses double the number of known risk loci for pain susceptibility and support dual causation from neuronal and immunological genes, providing leads toward targets for novel pain medications.
Development of affinity beads-based in vitro metal-ligand binding assay reveals dominant cadmium affinity of thiol-rich small peptides phytochelatins beyond glutathione
Authors: Uraguchi Shimpei , Nagai Kenichiro , Naruse Fumii , Otsuka Yuto , Ohshiro Yuka , Nakamura Ryosuke , Takanezawa Yasukazu , Kiyono Masako
Published: August 2021

For a better understanding of metal-ligand interaction and its function in cells, we developed an easy, sensitive, and high-throughput method to quantify ligand-metal(loid) binding affinity under physiological conditions by combining ligand-attached affinity beads and inductively coupled plasma-optical emission spectrometry (ICP-OES). Glutathione (GSH) and two phytochelatins (PC2 and PC3, small peptides with different numbers of free thiols) were employed as model ligands and attached to hydrophilic beads. The principle of the assay resembles that of affinity purification of proteins in biochemistry: metals binding to the ligand on the beads and the rest in the buffer are separated by a spin-column and quantified by ICP-OES. The binding assay using the GSH-attached beads and various metal(loid)s suggested the different affinity of the metal-GSH interactions, in accordance with the order of the Irving–Williams series and the reported stability constants. The binding assay using PC2 or PC3-attached beads suggested positive binding between PCs and Ni(II), Cu(II), Zn(II), Cd(II), and As(III) in accordance with the number of thiols in PC2 and PC3. We then conducted the competition assay using Cd(II), Mn(II), Fe(II), Cu(II), and Zn(II) and the results suggested a better binding affinity of PC2 with Cd(II) than with the essential metals. Another competition assay using PC2 and GSH suggested a robust binding affinity between PCs and Cd(II) compared to GSH and Cd(II). These results suggested the dominance of PC-Cd complex formation in vitro, supporting the physiological importance of PCs for the detoxification of cadmium in vivo. We also discuss the potential application of the assay.
Sex differences in incidence and mortality of bloodstream infections. Results from the population-based HUNT study in Norway
Authors: Mohus Randi Marie , Gustad Lise T. , Furberg Anne Sofie , Moen Martine Kjølberg , Liyanarachi Kristin Vardheim , Askim Åsa , Åsberg Signe E. , DeWan Andrew T. , Rogne Tormod , Simonsen Gunnar Skov , Nilsen Tom Ivar Lund , Åsvold Bjørn Olav , Damås Jan Kristian , Solligård Erik
Published: August 2021

Objective

To examine the effect of sex on risk of bloodstream infections (BSI) and BSI mortality and to assess to what extent known risk factors for BSI mediate this association in the general population.

Participants

The prospective, population-based HUNT2 Survey (1995-97) in Norway invited 93,898 inhabitants ≥20 years in the Nord-Trøndelag region, whereof 65,237 (69.5%) participated. 46.8% of the participants were men.

Exposures

Sex and potential mediators between sex and BSI; health behaviours (smoking, alcohol consumption), education attainment, cardiovascular risk factors (systolic blood pressure, non-HDL cholesterol, body mass index) and previous or current comorbidities.

Main outcome measures

Sex differences in risk of first-time BSI, BSI mortality (death within first 30 days after a BSI), BSI caused by the most frequent bacteria, and the impact of known BSI risk factors as mediators.

Results

We documented a first-time BSI for 1,840 (2.9%) participants (51.3% men) during a median follow-up of 14.8 years. Of these, 396 (0.6%) died (56.6% men). Men had 41% higher risk of any first-time BSI (95% confidence interval (CI), 28 to 54%) than women. An estimated 34% of the excess risk of BSI in men was mediated by known BSI risk factors. The hazard ratio (HR) with 95% CI for BSI due to S. aureus was 2.09 (1.28 to 2.54), S. pneumoniae 1.36 (1.05 to 1.76), and E. coli 0.97 (0.84 to 1.13) in men vs women. BSI related mortality was higher in men compared to women with HR 1.87 (1.53 to 2.28).

Conclusions

This large population-based study show that men have higher risk of BSI than women. One-third of this effect was mediated by known risk factors for BSI. This raises important questions regarding sex specific approaches to reduce the burden of BSI.
Infection inhibiting effect of RT-PCR testing-isolation in COVID-19 - a case study of Hiroshima and Fukuoka in Japan -
Authors: Maki Kazuo
Published: August 2021

A simple method of estimating the effect of reverse transcription polymerase chain reaction (RT-PCR) testing-isolation on the restraint of infection of COVID-19 is proposed. The effect is expressed as the ratio χ of the reproductive number to that in the case that no isolation measure would be taken. The method was applied in the case of the third infection wave (from December, 2020 to February, 2021) of Hiroshima and Fukuoka in Japan. The ratio χ was estimated to be 0.78 to 0.84 and 0.86 to 0.9 in Hiroshima and Fukuoka, respectively. It is also shown that the reduction of χ by 0.07 would have reduced at least 50% of total infected patients during the third infection wave in Fukuoka.
Uncovering the gastrointestinal passage, intestinal epithelial cellular uptake and AGO2 loading of milk miRNAs in neonates using xenomiRs as tracers
Authors: Weil Patrick Philipp , Reincke Susanna , Hirsch Christian Alexander , Giachero Federica , Aydin Malik , Scholz Jonas , Jönsson Franziska , Hagedorn Claudia , Nguyen Duc Ninh , Thymann Thomas , Pembaur Anton , Orth Valerie , Wünsche Victoria , Jiang Ping-Ping , Wirth Stefan , Jenke Andreas C. W. , Sangild Per Torp , Kreppel Florian , Postberg Jan
Published: August 2021

Background

Human breast milk has a high microRNA (miRNA) content. It remains unknown whether and how milk miRNAs might affect intestinal gene regulation and homeostasis of the developing microbiome after initiation of enteral nutrition. However, this requires that relevant milk miRNA amounts survive gastrointestinal passage, are taken up by cells, and become available to the RNA interference (RNAi) machinery. It seems important to dissect the fate of these miRNAs after oral ingestion and gastrointestinal passage.

Objective

Our goal was to analyze the potential transmissibility of milk miRNAs via the gastrointestinal system in neonate humans and a porcine modelin vivoto contribute to the discussion whether milk miRNAs could influence gene regulation in neonates and thus might vertically transmit developmental relevant signals.

Design

We performed cross-species profiling of miRNAs via deep-sequencing and utilized dietary xenobiotic taxon-specific milk miRNA (xenomiRs) as tracers in human and porcine neonates, followed by functional studies in primary human fetal intestinal epithelial cells (HIEC-6) using Ad5-mediated miRNA-gene transfer.

Results

Mammals share many milk miRNAs yet exhibit taxon-specific miRNA fingerprints. We traced bovine-specific miRNAs from formula-nutrition in human preterm stool and 9 days after onset of enteral feeding in intestinal cells of preterm piglets. Thereafter, several xenomiRs accumulated in the intestinal cells. Moreover, few hours after introducing enteral feeding in preterm piglets with supplemented reporter miRNAs (cel-miR-39-5p/-3p), we observed their enrichment in blood serum and in AGO2-immunocomplexes from intestinal biopsies.

Conclusions

Milk-derived miRNAs survived gastrointestinal passage in human and porcine neonates. Bovine-specific miRNAs accumulated in intestinal cells of preterm piglets after enteral feeding with bovine colostrum/formula. In piglets, colostrum supplementation with cel-miR-39-5p/-3p resulted in increased blood levels of cel-miR-39-3p and argonaute RISC catalytic component 2 (AGO2) loading in intestinal cells. This suggests the possibility of vertical transmission of miRNA signaling from milk through the neonatal digestive tract.
Loss of full-length dystrophin expression results in major cell-autonomous abnormalities in proliferating myoblasts
Authors: Gosselin Maxime R. F. , Mournetas Virginie , Borczyk Malgorzata , Verma Suraj , Occhipinti Annalisa , Róg Justyna , Bozycki Lukasz , Korostynski Michal , Robson Samuel C. , Angione Claudio , Pinset Christian , Górecki Dariusz C.
Published: August 2021

Duchenne muscular dystrophy (DMD) affects myofibers and muscle stem cells (SC), causing progressive muscle degeneration and repair defects. It was not known whether dystrophic myoblasts—the effector cells of muscle growth and regeneration—are affected. Using a combination of transcriptomic, molecular, functional analyses, and genome-scale metabolic modelling, we demonstrate, for the first time, convergent cell-autonomous abnormalities in primary mouse and human dystrophic myoblasts. In Dmdmdxmouse myoblasts lacking full-length dystrophin transcripts, the expression of 170 other genes was significantly altered. Myod1 (p=2.9e-21) and key muscle genes controlled by MyoD (Myog, Mymk, Mymx, epigenetic regulators, ECM interactors, calcium signalling and fibrosis genes) were significantly downregulated. Gene ontology enrichment analysis indicated significant alterations in genes involved in muscle development and function. These transcriptomic abnormalities translated into functional alterations such as increased proliferation (p=3.0e-3), reduced chemotaxis towards both sera-rich (p=3.8e-2) and cytokine-containing medium (p=1.0e-2), and significantly accelerated differentiation in 3D organotypic cultures. These altered myoblast functions are essential for muscle regeneration. The defects were caused by the loss of expression of full-length dystrophin, as strikingly similar and not exacerbated alterations were also observed in dystrophin-nullDmdmdx-βgeomyoblasts. Corresponding abnormalities were identified in an established dystrophic mouse muscle (SC5) cell line and human DMD primary myoblasts, confirming universal, cross-species and cell-autonomous nature of these defects. The genome-scale metabolic analysis in human DMD myoblasts indicated significant alteration in the rate of glycolysis/gluconeogenesis (log2FC = 4.8), leukotriene metabolism (log2FC = 4.754), mitochondrial beta-oxidation of branched-chain, odd-chain, and di-unsaturated fatty acids (n-6) (log2FC = -1.187, log2FC = -0.8295 and log2FC = -0.655). These results demonstrate the disease continuum: DMD defects in satellite cells cause myoblast dysfunctions affecting muscle regeneration, which is essential to counteract myofiber loss. Contrary to the established belief, our data demonstrate that typical DMD alterations occur in myoblasts, making these cells a novel therapeutic target for the treatment of this lethal disease.
Innate and adaptive immunity to transfused allogenic red blood cells in mice requires MyD88
Authors: Soldatenko Arielle , Hoyt Laura R. , Xu Lan , Calabro Samuele , Lewis Steven M. , Gallman Antonia E. , Hudson Krystalyn E. , Stowell Sean R. , Luckey Chance J. , Zimring James C. , Liu Dong , Santhanakrishnan Manjula , Hendrickson Jeanne E. , Eisenbarth Stephanie C.
Published: August 2021

Red blood cell (RBC) transfusion therapy is essential for the survival of patients with hematological disorders such as sickle cell anemia. A potentially fatal complication of transfusion is development of non-ABO alloantibodies to polymorphic RBC antigens, yet mechanisms of alloantibody formation remain unclear. Human and mouse RBCs acquire a “storage lesion” prior to transfusion, which in mice contributes to immunogenicity. We previously reported that mouse splenic dendritic cells (DCs) are required for RBC alloimmunization and are activated by sterile and leukoreduced mouse RBCs after storage. Yet how syngeneic RBCs activate innate immune pathways to induce DC activation is unknown. We now show that DC activation to transfused RBCs occurs regardless of alloantigen presence, suggesting that RBC damage induced during storage triggers innate immune receptors. We discovered an unexpected dependence of RBC alloimmunization on the Toll-like receptor (TLR) signaling adaptor molecule MyD88. TLRs are a class of pattern recognition receptors (PRRs) that regulate DC activation and signal through two adaptor molecules, MyD88 and TRIF. We show that the inflammatory cytokine response, DC activation, and the subsequent alloantibody response to transfused syngeneic RBCs require MyD88 but not TRIF, suggesting a restricted set of PRRs are responsible for sensing RBCs and triggering alloimmunization.
Infection increases activity via Toll dependent and independent mechanisms in Drosophila melanogaster
Authors: Vincent Crystal M. , Beckwith Esteban J. , Pearson William H. , Kierdorf Katrin , Gilestro Giorgio , Dionne Marc S.
Published: August 2021

Host behavioural changes are among the most apparent effects of infection. ‘Sickness behaviour’ can involve a variety of symptoms, including anorexia, depression, and changed activity levels. Here we use a real-time tracking and behavioural profiling platform to show that, in Drosophila melanogaster, many systemic bacterial infections cause significant increases in physical activity, and that the extent of this activity increase is a predictor of survival time in several lethal infections. Using various bacteria and D. melanogaster immune and activity mutants, we show that increased activity is driven by at least two different mechanisms. Increased activity after infection with Micrococcus luteus, a Gram-positive bacterium rapidly cleared by the immune response, strictly requires the Toll ligand spätzle and Toll-pathway activity in the fat body and the brain. In contrast, increased activity after infection with Francisella novicida, a Gram-negative bacterium that cannot be cleared by the immune response, is entirely independent of either spätzle or the parallel IMD pathway. The existence of multiple signalling mechanisms by which bacterial infections drive increases in physical activity implies that this effect may be an important aspect of the host response.
Differential proteomic analysis of laser-microdissected penetration glands of avian schistosome cercariae with a focus on proteins involved in host invasion
Authors: Vondráček Oldřich , Mikeš Libor , Talacko Pavel , Leontovyč Roman , Bulantová Jana , Horák Petr
Published: August 2021

Schistosome invasive stages, cercariae, leave intermediate snail hosts, penetrate the skin of definitive hosts, and transform to schistosomula migrating to final localization. During invasion, cercariae employ histolytic and other bioactive products of specialized holocrine secretory cells – postacetabular (PA) and circumacetabular (CA) penetration glands. Although several studies attempted to characterize protein composition of the in vitro induced gland secretions in Schistosoma mansoni and Schistosoma japonicum, the results were inconsistent and dependent on the method of sample collection and processing. Products of both gland types mixed during their secretion did not allow localization of identified proteins to a particular gland. Here we compared proteomes of separately isolated cercarial gland cells of the avian schistosome Trichobilharzia szidati employing laser-assisted microdissection and shotgun LC-MS/MS, thus obtaining the largest dataset so far concerning the representation and localization of cercarial penetration gland proteins. We optimized the methods of sample processing with cercarial bodies (heads) first. Alizarin-pre-stained, chemically non-fixed samples provided optimal results of MS analyses, and enabled distinguishing PA and CA glands for microdissection. Using 7.5 × 106 μm3 sample volume per gland replicate, we identified 3347 peptides assigned to 792 proteins, from which 461 occurred in at least 2 of 3 replicates in either gland type (PA = 455, 40 exclusives; CA = 421, 6 exclusives; 60 proteins differed significantly in their abundance between the glands). Peptidases of 5 catalytic types accounted for ca. 8 % and 6 % of reliably identified proteins in PA and CA glands, respectively. Invadolysin, nardilysin, cathepsins B2 and L3, and elastase 2b orthologs were the major gland endopeptidases. Two cystatins and a serpin were highly abundant peptidase inhibitors in the glands. CA glands were rich in venom allergen-like proteins. The assembled total cercarial body proteome included 1631 identified proteins and revealed additional interesting factors possibly related to tissue invasion.

Highlights

Proteomes of two penetration gland types in schistosome cercariae greatly differ

Postacetabular glands possess 40 unique proteins and are abundant in hydrolases

Circumacetabular glands posses 6 unique proteins and are rich in VAL proteins

Peptidases make up 8 % of postacetabular and 6 % of circumacetabular gland proteins

Cercarial elastase is unique to circumacetabular glands of Trichobilharzia szidati

Note: Supplementary data associated with this article All supplementary data files can be accessed from the following link: http://www.helminthology.cz/supplementary_files.html
Metformin preconditioning protects against myocardial stunning and preserves mitochondrial dynamics and protein translation in a mouse model of cardiac arrest
Authors: Rutledge Cody A. , Lagranha Claudia , Chiba Takuto , Redding Kevin , Stolz Donna B. , Goetzman Eric , Sims-Lucas Sunder , Kaufman Brett A.
Published: August 2021

Cardiac arrest (CA) causes high mortality due to multi-system organ damage attributable to ischemia-reperfusion injury. Recent work in our group found that among diabetic patients who experienced cardiac arrest, those taking metformin had less evidence of cardiac and renal damage after cardiac arrest when compared to those not taking metformin. To investigate the potential for metformin to impact cardiac arrest outcomes, the current study investigates metformin interventions on cardiac and renal outcomes in a non-diabetic CA mouse model. We found that two weeks of metformin pretreatment protects against reduced ejection fraction and reduces kidney ischemia-reperfusion injury at 24 hours post-arrest. This cardiac and renal protection depends on AMPK signaling, as demonstrated by outcomes in mice pretreated with the AMPK activator AICAR or metformin plus the AMPK inhibitor compound C.

At this 24-hour time point, gene expression analysis showed that metformin pretreatment caused changes supporting autophagy, antioxidant response, and protein translation. Further investigation found associated improvements in mitochondrial structure and markers of autophagy. We also found that markers of protein nitrosylation between sham and arrest were not significantly different and thus unlikely to be a driver of gene expression differences. Notably, Western analysis indicated that protein synthesis was preserved in arrest hearts of animals pretreated with metformin. The AMPK activation-mediated protection of protein synthesis was also demonstrated in a hypoxia/reoxygenation cell culture model. Despite the positive impacts of pretreatment in vivo and in vitro, metformin did not preserve ejection fraction when deployed at resuscitation. Taken together, we propose that metformin’s in vivo cardiac preservation occurs through AMPK activation, requires adaptation before arrest, and is associated with preserved protein translation.

New and Noteworthy

We leveraged a mouse model of cardiac arrest to study whether metformin pretreatment could protect cardiac function after arrest. We find that AMPK activity is crucial to this protection and characterize several pathways associated with this response. Signaling nodes with strong association may be precise targets to promote cardiac function in ischemia/reperfusion injury or in cardiac stunning.
Using AlphaFold for Rapid and Accurate Fixed Backbone Protein Design
Authors: Moffat Lewis , Greener Joe G. , Jones David T.
Published: August 2021

Abstract

The prediction of protein structure and the design of novel protein sequences and structures have long been intertwined. The recently released AlphaFold has heralded a new generation of accurate protein structure prediction, but the extent to which this affects protein design stands yet unexplored. Here we develop a rapid and effective approach for fixed backbone computational protein design, leveraging the predictive power of AlphaFold. For several designs we demonstrate that not only are the AlphaFold predicted structures in agreement with the desired backbones, but they are also supported by the structure predictions of other supervised methods as well asab initiofolding. These results suggest that AlphaFold, and methods like it, are able to facilitate the development of a new range of novel and accurate protein design methodologies.
Characterizing stochastic cell cycle dynamics in exponential growth
Authors: Huang Dean , Lo Teresa , Merrikh Houra , Wiggins Paul A.
Published: August 2021

Two powerful and complementary experimental approaches are commonly used to study the cell cycle and cell biology: One class of experiments characterizes the statistics (or demographics) of an unsynchronized exponentially-growing population, while the other captures cell cycle dynamics, either by time-lapse imaging of full cell cycles or in bulk experiments on synchronized populations. In this paper, we study the subtle relationship between observations in these two distinct experimental approaches. We begin with an existing model: a single-cell deterministic description of cell cycle dynamics where cell states (i.e. periods or phases) have precise lifetimes. We then generalize this description to a stochastic model in which the states have stochastic lifetimes, as described by arbitrary probability distribution functions. Our analyses of the demographics of an exponential culture reveal a simple and exact correspondence between the deterministic and stochastic models: The corresponding state lifetimes in the deterministic model are equal to the exponential mean of the lifetimes in the stochastic model. An important implication is therefore that the demographics of an exponential culture will be well-fit by a deterministic model even if the state timing is stochastic. Although we explore the implications of the models in the context of the Escherichia coli cell cycle, we expect both the models as well as the significance of the exponential-mean lifetimes to find many applications in the quantitative analysis of cell cycle dynamics in other biological systems.
Enterohaemorrhagic E. coli utilizes an AND-OR logic gate to regulate expression of an outer membrane haem receptor
Authors: Sy Brandon M. , Tree Jai J.
Published: August 2021

To sense the transition from environment to host, bacteria use a range of environmental cues to control expression of virulence genes. Iron is tightly sequestered in host tissues and in the human pathogen enterohaemorrhagic E. coli (EHEC) iron-limitation induces transcription of the outermembrane haem transporter encoded by chuAS. ChuA expression is post-transcriptionally activated at 37°C by a FourU RNA thermometer ensuring that the haem receptor is only expressed under low iron, high temperature conditions that indicate the host. Here we demonstrate that expression of chuA is also independently regulated by the cAMP-responsive sRNA CyaR and transcriptional terminator Rho. These results indicate that chuAS expression is regulated at the transcription initiation, transcript elongation, and translational level. The natural dependence of these processes creates a hierarchy of regulatory AND and OR logic gates that integrate information about the local environment. We show that the logic of the chuA regulatory circuit is activated under conditions that satisfy low iron AND (low glucose OR high temperature). We speculate that additional sensing of a gluconeogenic environment allows further precision in determining when EHEC is at the gastrointestinal epithelium of the host. With previous studies, it appears that the chuAS transcript is controlled by eight regulatory inputs that control expression through six different transcriptional and post-transcriptional mechanisms. The results highlight the ability of regulatory sRNAs to integrate multiple environmental signals into a conditional hierarchy of signal input.
Enterotoxigenic Escherichia coli display a distinct growth phase before entry into stationary phase with shifts in tryptophan- fucose- and putrescine metabolism and degradation of neurotransmitter precursors
Authors: Joffré Enrique , Xiao Xue , Correia Mário S. P. , Nookaew Intawat , Sasse Samantha , Globisch Daniel , Zhu Baoli , Sjöling Åsa
Published: August 2021

Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea in children and adults in endemic areas. Gene regulation of ETEC during growth in vitro and in vivo needs to be further evaluated, and here we describe the full transcriptome and metabolome of ETEC during growth from mid-logarithmic growth to stationary phase in rich medium (LB medium). We identified specific genes and pathways subjected to rapid transient alterations in gene expression and metabolite production during the transition between logarithmic to stationary growth. The transient phase during late exponential growth is different from the subsequent induction of stationary phase-induced genes, including stress and survival responses as described earlier. The transient phase was characterized by the repression of genes and metabolites involved in organic substance transport. Genes involved in fucose and putrescine metabolism were upregulated, and genes involved in iron transport were repressed. Expression of toxins and colonization factors were not changed, suggesting retained virulence. Metabolomic analyses showed that the transient phase was characterized by a drop of intracellular amino acids, e.g., L-tyrosine, L-tryptophan, L-phenylalanine, L-leucine, and L-glutamic acid, followed by increased levels at induction of stationary phase. A pathway enrichment analysis of the entire transcriptome and metabolome showed activation of pathways involved in the degradation of neurotransmitters aminobutyrate (GABA) and precursors of 5-hydroxytryptamine (serotonin). This work provides a comprehensive framework for further studies on transcriptional and metabolic regulation in pathogenic E. coli.

Importance

We show that E. coli, exemplified by the pathogenic subspecies enterotoxigenic E. coli (ETEC), undergoes a stepwise transcriptional and metabolic transition into the stationary phase. At a specific entry point, E. coli induces activation and repression of specific pathways. This leads to a rapid decrease of intracellular levels of L-tyrosine, L-tryptophan, L-phenylalanine, L-leucine, and L-glutamic acid due to metabolism into secondary compounds. The resulting metabolic activity leads to an intense but short peak of indole production, suggesting that this is the previously described “indole peak,” rapid decrease of intermediate molecules of bacterial neurotransmitters, increased putrescine and fucose uptake, increased glutathione levels, and decreased iron uptake. This specific transient shift in gene expression and metabolomics is short-lived and disappears when bacteria enter the stationary phase. We suggest it mainly prepares bacteria for ceased growth, but the pathways involved suggest that this transient phase substantially influences survival and virulence.
The ultrafast snap of a finger is mediated by skin friction
Authors: Acharya Raghav , Challita Elio J. , Ilton Mark , Bhamla M. Saad
Published: August 2021

The snap of a finger has been used as a form of communication and music for millennia across human cultures. However, a systematic analysis of the dynamics of this rapid motion has not yet been performed. Using high-speed imaging and force sensors, we analyze the dynamics of the finger snap. Our analysis reveals the central role of skin friction in mediating the snap dynamics by acting as a latch to control the resulting high velocities. We evaluate the role of this frictional latch experimentally, by covering the thumb and middle finger with different materials to produce different friction coefficients and varying compressibility. In doing so, we reveal that the compressible, frictional latch of the finger pads likely operate in a regime optimally tuned for both friction and compression. We also develop a soft, compressible friction-based latch-mediated spring actuated (LaMSA) model to further elucidate the key role of friction and how it interacts with a compressible latch. Our mathematical model reveals that friction plays a dual role in the finger snap, both aiding in force loading and energy storage while hindering energy release. Our work reveals how friction between surfaces can be harnessed as a tunable latch system and provide design insight towards the frictional complexity in many robotics and ultra-fast energy-release structures.
Systematic investigation of the link between enzyme catalysis and cold adaptation
Authors: Stark Catherine D. , Bautista-Leung Teanna , Siegfried Joanna , Herschlag Daniel
Published: August 2021

Cold temperature is prevalent across the biosphere and slows the rates of chemical reactions. Increased catalysis has been predicted to be a general adaptive trait of enzymes to reduced temperature, and this expectation has informed physical models for enzyme catalysis and influenced bioprospecting strategies. To broadly test rate as an adaptive trait to cold, we paired kinetic constants of 2223 enzyme reactions with their organism’s optimal growth temperature (TGrowth) and analyzed trends of rate as a function of TGrowth. These data do not support a prevalent increase in rate in cold adaptation. In the model enzyme ketosteroid isomerase (KSI), there was prior evidence for temperature adaptation from a change in an active site residue that results in a tradeoff between activity and stability. Here, we found that little of the overall rate variation for 20 KSI variants was accounted for by TGrowth. In contrast, and consistent with prior expectations, we observed a correlation between stability and TGrowth across 433 proteins. These results suggest that temperature exerts a weaker selection pressure on enzyme rate than stability and that evolutionary forces other than temperature are responsible for the majority of enzymatic rate variation.
Next generation SARM1 knockout and epitope tagged CRISPR-Cas9-generated isogenic mice reveal that SARM1 does not participate in regulating nuclear transcription, despite confirmation of protein expression in macrophages
Authors: Doran Ciara G. , Sugisawa Ryoichi , Carty Michael , Roche Fiona , Fergus Claire , Hokamp Karsten , Kelly Vincent P. , Bowie Andrew G
Published: August 2021

SARM1 is an ancient and highly conserved TIR-domain containing protein, with a diverse range of proposed roles in both innate immunity and neuronal death and degeneration. Murine SARM1 has been reported to regulate the transcription of specific chemokines in both neurons and macrophages, however the extent and mechanism by which SARM1 contributes to transcription regulation remains to be fully understood. Here, using RNA sequencing we identify differential gene expression in bone marrow-derived macrophages (BMDM) from C57BL/6 congenic 129 ES cell-derived Sarm1-/- mice compared to wild type (WT). However, we show that passenger genes which are derived from the 129 donor strain of mice flank the Sarm1 locus, confounding interpretation of results, since many of the identified differentially regulated genes come from the region containing passenger genes. To re-examine the transcriptional role of SARM1 in the absence of such passenger genes, we generated three different Sarm1-/- mice using CRISPR/Cas9 technology. Vincristine treatment of ex vivo cultured post-natal neurons from these mice confirmed SARM1’s previously identified key function as an executor of axon degeneration. However, using these mice, we show that the absence of SARM1 has no impact on transcription of genes previously shown to be altered in macrophages or in the brainstem. To gain further insight into SARM1 function, we generated and characterized a mouse expressing epitope-tagged SARM1, as it has been difficult to date to confirm which cells and tissues express SARM1 protein. In these mice we see high SARM1 protein expression in the brain and brainstem, and lower but detectable levels in macrophages. Overall, the generation of these next generation SARM1 knockout and epitope-tagged mice has clarified that SARM1 is expressed in mouse macrophages but has no general role in transcriptional regulation in these cells, and has provided important new animal models to further explore SARM1 function.
Standard metabolic rate does not associate with age-at-maturity genotype in juvenile Atlantic salmon
Authors: Åsheim Eirik R. , Prokkola Jenni M. , Morozov Sergey , Aykanat Tutku , Primmer Craig R
Published: August 2021

Atlantic salmon (Salmo salar) is a species with diverse life-history strategies, to which the timing of maturation contributes considerably. Recently, the genome region including the genevgll3has gained attention as a locus with a large effect on salmon maturation timing, and recent studies on thevgll3locus in salmon have indicated that its effect might be mediated through body condition and accumulation of adipose tissue. However, the cellular and physiological pathways leading fromvgll3genotype to phenotype are still unknown. Standard metabolic rate is a potentially important trait for resource acquisition and assimilation and we hypothesized that this trait, being a proxy for the maintenance energy expenditure of an individual, could be an important link in the pathway fromvgll3genotype to maturation-timing phenotype. As a first step to studying links betweenvgll3and the metabolic phenotype of Atlantic salmon, we measured the standard metabolic rate of 150 first year Atlantic salmon juveniles of both sexes, originating from 14 different families with either late maturing or early maturingvgll3genotypes. No significant difference in mass-adjusted standard metabolic rate was detected between individuals with differentvgll3genotypes, indicating that juvenile salmon of differentvgll3genotypes have similar maintenance energy requirements in the experimental conditions used and that the effects ofvgll3on body condition and maturation are not strongly related to maintenance energy expenditure in either sex at this life stage.

Summary statement

We show thatvgll3, a gene known to have significant effects on Atlantic salmon (Salmo salar)life-history strategy, does not associate with standard metabolic rate in salmon juveniles.