bluuebunny/crossref_metadata_2025 huggingface dataset:
A 27-YEAR-OLD FEMALE WITH MILD BLURRY VISION AND PROLONGED LIGHT ADJUSTMENT IN THE MORNING
Authors: Nanda Tavish , Chin Adam , Rifkin Lana
Published: August 2022

Purpose:

The following case report highlights a rare presentation of chronic myeloid leukemia-associated hyper-viscosity syndrome and provides a brief review of expected findings and treatment outcomes.

Methods:

An otherwise healthy 27-year-old woman presented to the ophthalmology clinic with mild bilateral blurriness (20/20 in both eyes) and prolonged light adaption in the morning for several months. Examination demonstrated severe bilateral venous stasis, white-centered hemorrhages, intraretinal hemorrhage, and peripheral ischemia with diffuse leakage.

Results:

Same-day CBC demonstrated a leukocytosis of >600,000. Subsequent bone marrow biopsy confirmed the 9,22 translocation (Philadelphia chromosome). On further examination, the patient had an enlarged cardiac silhouette, cytopenia, and splenomegaly past the umbilicus, consistent with a severe and life-threatening leukostasis.

Conclusion:

Ocular involvement can occur in acute and chronic leukemia. Five to ten percentage of patients present to an eye physician first, without a known diagnosis. Prompt systemic treatment can result in near-complete reversal of any intraocular injury in most mild-to-moderate cases, as was the case here.
Practice Environment and Workforce Outcomes of Nurse Practitioners in Community Health Centers
Authors: Kueakomoldej Supakorn , Liu Jianfang , Pittman Patricia , Turi Eleanor , Poghosyan Lusine
Published: August 2022

The nurse practitioner (NP) workforce in community health centers (CHCs) increases access to primary care for underserved populations. Working with medically complex patients, high workloads, and low resources in the CHC setting, CHC NPs may be susceptible to poor workforce outcomes. This study uses NP survey data collected from 6 US states to describe and assess the relationship between CHC NP practice environment and burnout, job satisfaction, and turnover intention. CHC NPs rated their practice environments favorably, and more than 89% of CHC NPs reported satisfaction with their job. Better rating of NPs' relationship with CHC administration was associated with improved job satisfaction and decreased turnover intention.
β2-Microglobulin Participates in the Development of Vestibular Schwannoma by Regulating Nuclear Factor-κB
Authors: Jianfei Long , Yu Zhang , Junwei Ren , Xiang Huang , Bin Wang , Ping Zhong
Published: August 2022

Background and Objectives

Vestibular schwannoma (VS), the most common intercranial schwannoma, originates from the sheath of the vestibular nerve. The growth rate of VS varies greatly, with the tumor enlarging gradually, which can compress the peripheral nerve tissue and reveal corresponding symptoms. This study was aimed to elucidate the growth mechanism of VS by analyzing cellular changes at protein, messenger ribonucleic acid (mRNA), and other molecular levels.

Methods

We determined mRNA and protein levels of β2-microglobulin (β2-M) and nuclear factor κB (NF-κB) in tumors of different sizes using the real-time polymerase chain reaction and Western blotting, respectively. The relationship between these factors was verified in VS primary cells cultured in vitro, and the potential role of β2-M and NF-κB in VS growth was elucidated.

Results

In the secretions of freshly isolated tumor tissue cultured for 72 h, the concentration of β2-M was positively correlated with the tumor diameter. Furthermore, tumors with larger diameter showed higher expressions of β2-M and NF-κB at protein and mRNA level. β2-M treatment resulted in elevated protein expression of NF-κB and also its phosphorylated form in vitro.

Conclusion

β2-M may participate in VS growth by regulating NF-κB and act as a key regulatory molecule in VS tumor growth.
Time From Infiltrate on Chest Radiograph to Venovenous Extracorporeal Membrane Oxygenation in COVID-19 Affects Mortality
Authors: Powell Elizabeth K. , Krause Eric , Esposito Emily , Lankford Allison , Levine Andrea , Young Bree Ann C. , Haase Daniel J. , Tabatabai Ali , Taylor Bradley S. , Scalea Thomas M. , Galvagno Samuel M.
Published: August 2022

Venovenous extracorporeal membrane oxygenation (VV ECMO) has been used to treat severe coronavirus disease 2019 (COVID-19) acute respiratory distress syndrome; however, patient selection criteria have evolved throughout the pandemic. In this study, we sought to determine the association of patient mortality with time from positive COVID-19 test and infiltrate on chest radiograph (x-ray) to VV ECMO cannulation. We hypothesized that an increasing duration between a positive COVID-19 test or infiltrates on chest x-ray and cannulation would be associated with increased mortality.

This is a single-center retrospective chart review of COVID-19 VV ECMO patients from March 1, 2020 to July 28, 2021. Unadjusted and adjusted multivariate analyses were performed to assess for mortality differences.

A total of 93 patients were included in our study. Increased time, in days, from infiltrate on chest x-ray to cannulation was associated with increased mortality in both unadjusted (5–9, P = 0.002) and adjusted regression analyses (odds ratio [OR]: 1.49, 95% CI: 1.22–1.81, P < 0.01). Time from positive test to cannulation was not found to be significant between survivors and nonsurvivors (7.5–11, P = 0.06).

Time from infiltrate on chest x-ray to cannulation for VV ECMO should be considered when assessing patient candidacy. Further larger cohort and prospective studies are required.
The relationship between sarcopenia, dysphagia, malnutrition, and frailty: making the case for proactive swallowing exercises to promote healthy aging
Authors: Molfenter Sonja M.
Published: August 2022

Purpose of review

The purpose of this review is to summarize current evidence regarding the relationship between sarcopenia of the swallowing muscles, dysphagia, malnutrition, and frailty in the context of aging. Further, this review will provide preliminary support for proactive swallowing exercises to reverse and/or prevent sarcopenia of the swallowing muscles.

Recent findings

Recent studies lend support to a cyclic relationship between sarcopenia of the swallowing muscles, dysphagia, malnutrition, and frailty. Unfortunately, all studies are limited by their study design and lack instrumental imaging of swallowing function. Research (in the limbs) supports the use of proactive exercises and protein supplementation to reverse sarcopenia, especially in prefrail individuals. This provides a foundation to design and test similar preventive exercises for the swallowing muscles.

As the population is rapidly aging, it is vital to understand how the natural loss of muscle in aging impacts swallowing function and the downstream impact on nutritional and physical function. Prospective, longitudinal research with sophisticated outcome measures are required to fully understand this cycle and provide an opportunity to test methods for interrupting the cycle.
Video Capsule Endoscopy in a Pediatric Patient With Hematemesis While on Ventricular Assist Device Support
Authors: Abbasi Dezfouly Mostafa , Isaac Daniela M. , Buchholz Holger , Pidborochynski Tara , Conway Jennifer
Published: August 2022

We report the first case of video capsule endoscopy usage to diagnose gastrointestinal bleeding in a pediatric patient on a ventricular assist device. The outcomes of this case are consistent with the findings of reports in adult patients, showing no patient complications, no pacemaker or ventricular assist device interactions, and successful identification of a gastrointestinal source of bleeding. Use of video capsule endoscopy in this patient changed the management plan and eliminated the need for further invasive investigations highlighting the potential utility of this diagnostic method in this patient population.
Anterolateral Thigh Free Flap Donor-Site Morbidity: A Retrospective Cohort Study
Authors: Trapero Ana , Pérez-García Alberto , Andresen-Lorca Belen , Heredia-Alcalde Iván
Published: August 2022

The ability to achieve a good functional outcome, quality of life, and patient satisfaction related to the donor site of free flaps is an important factor in flap selection. One of the main advantages of an anterolateral thigh (ALT) free flap is its minimal donor-site morbidity. We conducted a study to analyze healing of ALT flap donor sites based on the type of closure. A total of 65 patients were included in the study. We divided the participants into two cohorts (i.e., primary closure [n = 51] and skin grafting [n = 14]). There were no statistically significant differences between the two cohorts relative to age, gender, or risk factors for wound healing (e.g., tobacco use, obesity, diabetes mellitus, and cardiovascular disease). We found there was a statistically significant difference (p < .05) between the mean donor-site wound healing time in the primary closure group (n = 51; 22.41 days [±9.94]) compared with the skin grafting group (n = 14; 54.57 days [±21.59]). To reduce wound healing time, improve cosmetic results, and increase functional outcomes in patients undergoing ALT free flap, we recommend using primary closure for the donor sites and avoiding skin grafting whenever possible.
Quality Measure Concepts for Inpatient Rehabilitation That Are Best Understood From the Patient’s Perspective
Authors: Deutsch Anne , Neumann Holly , Goldsmith Arielle , Heinemann Allen W. , Ehrlich-Jones Linda
Published: August 2022

Purpose

The aim of this study was to identify inpatient rehabilitation quality-of-care concepts that are best understood from the patient perspective.

Design

We conducted 12 focus groups with 95 former patients, caregivers, and rehabilitation clinicians and asked them to describe high-quality inpatient rehabilitation care.

Methods

We independently reviewed the focus group transcripts and then used an iterative process to identify the quality measure concepts identified by participants.

Results

Based on participants’ comments, we identified 18 quality measure concepts: respect and dignity, clinician communication with patient, clinician communication with family, organizational culture, clinician engagement with patient, clinician engagement with family, rehabilitation goals, staff expertise, responsiveness, patient safety, physical environment, care coordination, discharge planning, patient and family education, peer support, symptom management (pain, anxiety, fatigue, sadness), sleep, and functioning.

Clinical Relevance to the Practice of Rehabilitation Nursing

Rehabilitation nurses should be aware of the quality-of-care issues that are important to patients and their caregivers.

Conclusion

Important patient-reported domains of quality of care include interpersonal relationships, patient and family engagement, care planning and delivery, access to support, and quality of life.
Pediatric Tissue Expansion: Analysis of the National Surgical Quality Improvement Program–Pediatric
Authors: Harrison Lucas M. , Rizvi Imran , Parsa Shyon , Hallac Rami R. , Kane Alex A. , Seaward James R.
Published: August 2022

Introduction:

Tissue expansion (TE) in pediatric surgery provides vascularized tissue to attain functional and esthetic goals in a broad range of reconstructive procedures. Our study evaluates the demographic, operative, and short-term outcomes of TE in pediatric patients utilizing the American College of Surgeons National Surgical Quality Improvement Program-Pediatric (NSQIP-P) database and highlights factors associated with postoperative complications.

Materials and Methods:

Retrospective review of a large multicenter database of 402 pediatric patients that underwent TE within the NSQIP-P database from 2013 to 2020 at freestanding general acute care children’s hospitals, children’s hospitals within a larger hospital, specialty children’s hospitals, or general acute care hospitals with a pediatric wing. Patient demographics, clinical risk factors, operative information, and postoperative outcomes were collected with an odds ratio analysis of risk factors.

Results:

Patients were majority female (55.5%), White (63.2%), and non-Hispanic (67.4%). The minority were born prematurely (11.9%) and had congenital malformations (16.7%). Complications occurred in 5.7%, unplanned readmission in 4.5%, and unplanned operation in 6.5% of patients. Complications lead to readmission in 2.5% and return to the operating room in 3.2% of patients. American Society of Anesthesiology (ASA) score III-IV, congenital malformations, >1-day hospital stay, and pulmonary, neurologic, and hematologic comorbidities were associated with the greatest increase in odds of complication.

Conclusion:

This study utilizes the NSQIP-P to provide a comprehensive multicenter view of pediatric patients undergoing TE. Increased understanding of risk factors for complications allows for guidance in patient selection and helps in achieving favorable surgical outcomes.
Low-MBL producing genotypes playing a role on protection to leprosy and its multibacillary forms in a highly endemic area for leprosy in Brazil
Authors: de Salles Erika M. , Martins Lívia M. , Escocard Rita de C. M. , Forte Bruno V. G. , Maciel Yonnara E. C. , Kipnis Thereza L. , Nahn Edilbert P. , da Silva Wilmar D. , Peixoto-Rangel Alba L.
Published: August 2022

The high frequency ofMBL2mutant alleles found in various human populations suggests that they provide some selective advantage. One of the hypotheses is that MBL deficiency may be protective against intracellular pathogens, includingMycobacterium leprae. In this study, we investigated the role ofMBL2in the susceptibility to leprosy. Single-nucleotide variants (SNV) B (rs1800450) and C (rs1800451) in exon 1 of theMBL2gene and serum MBL concentrations were assessed in 53 patients with leprosy and 68 healthy controls from southeast Brazil by polymerase chain reaction followed by restriction fragment length polymorphism and commercial capture enzyme-linked immunosorbent assay, respectively. The genotyped SNVs were significantly associated with increased protection against leprosy (OR=0.3757, 95% CI=0.1615⍰08740, p=0.0273) and more severe forms, including multibacillary (OR=0.3769, 95% CI=0.1447⍰0.9818, p=0.0493) and lepromatous (OR=0.2423, 95% CI=0.06547⍰0.8968, p=0.0369) leprosy. On the other hand, low-MBL producing genotypes were associated with the protection for leprosy, especially in its more severe forms. Low MBL levels and low MBL producing variants were associated with protection against leprosy and progression to more severe forms of this disease. Moreover, this study highlights MBL as a regulator of immune function in which alterations may affect normal responses to leprosy infection and inflammatory stimuli.
Variations in ERP Data Quality Across Paradigms, Participants, and Scoring Procedures
Authors: Zhang Guanghui , Luck Steven J.
Published: August 2022

Although it is widely accepted that data quality for event-related potential (ERP) components varies considerably across studies and across participants within a study, ERP data quality has not received much systematic analysis. The present study used a recently developed metric of ERP data quality— the standardized measurement error (SME)—to examine how data quality varies across different ERP paradigms, across individual participants, and across different procedures for quantifying amplitude and latency values. The EEG recordings were taken from the ERP CORE, which includes data from 40 neurotypical college students for seven widely studied ERP components: P3b, N170, mismatch negativity, N400, error-related negativity, N2pc, and lateralized readiness potential. Large differences in data quality were observed across the different ERP components, and very large differences in data quality were observed across participants. Data quality also varied depending on the algorithm used to quantify the amplitude and especially the latency of a given ERP component. These results provide an initial set of benchmark values that can be used for comparison with previous and future ERP studies. They also provide useful information for predicting effect sizes and statistical power in future studies, even with different numbers of trials. More broadly, this study provides a general approach that could be used to determine which specific experimental designs, data collection procedures, and data processing algorithms lead to the best data quality.
On the evolution of the plant phytochrome chromophore biosynthesis
Authors: Frascogna Federica , Ledermann Benjamin , Hartmann Jana , Patallo Eugenio Pérez , Zeqiri Fjoralba , Hofmann Eckhard , Frankenberg-Dinkel Nicole
Published: August 2022

Phytochromes are biliprotein photoreceptors present in plants, algae, certain bacteria and fungi. Land plant phytochromes use phytochromobilin (PΦB) as the bilin chromophore. Phytochromes of streptophyte algae, the clade within which land plants evolved, employ phycocyanobilin (PCB), leading to a more blue-shifted absorption spectrum. Both chromophores are synthesized by ferredoxin-dependent bilin reductases (FDBRs) starting from biliverdin IXα (BV). In cyanobacteria and chlorophyta, BV is reduced to PCB by the FDBR phycocyanobilin:ferredoxin oxidoreductase (PcyA), whereas, in land plants, BV is reduced to PФB by phytochromobilin synthase (HY2). However, phylogenetic studies suggested the absence of any ortholog of PcyA in streptophyte algae and the presence of only PФB biosynthesis related genes (HY2). The HY2 of the early diverging streptophyte algaKlebsormidium nitens(formerlyKlebsormidium flaccidum) was already indirectly indicated to be involved in PCB biosynthesis. Here, we overexpressed and purified a His6-tagged variant ofK. nitensHY2 (KflaHY2) inE. coli. Employing anaerobic bilin reductase activity assays and coupled phytochrome assembly assays, we were able to confirm the product and to identify intermediates of the reaction. Site-directed mutagenesis revealed two aspartate residues critical for catalysis. While it was not possible to convert KflaHY2 into a PΦB-producing enzyme by simply exchanging the catalytic pair, the biochemical investigation of two additional members of the HY2 lineage enabled us to define two distinct clades, the PCB-HY2 and the PΦB-HY2 clade. Overall, our study gives insight into the evolution of the HY2 lineage of FDBRs.
Re-evaluating frontopolar and temporoparietal contributions to detection and discrimination confidence
Authors: Mazor Matan , Gong Chudi , Fleming Stephen M.
Published: August 2022

Previously, we identified a subset of regions where the relation between decision confidence and univariate fMRI activity was quadratic, with stronger activation for both high and low compared to intermediate levels of confidence. We further showed that, in a subset of these regions, this quadratic modulation appeared only for confidence in detection decisions about the presence or absence of a stimulus, and not for confidence in discrimination decisions about stimulus identity (Mazor, Friston & Fleming, 2021). Here, in a pre-registered follow-up experiment, we sought to replicate our original findings and identify the origins of putative detection-specific confidence signals by introducing a novel asymmetric-discrimination condition: a discrimination task with the signal-detection properties of a detection task. This task required discriminating two alternatives (two different grating tilts) but was engineered such that the distribution of perceptual evidence was asymmetric, just as in yes/no detection. We successfully replicated the quadratic modulation of subjective confidence in prefrontal, parietal and temporal cortices. However, in contrast to our original report, this quadratic effect was similar in detection and discrimination responses, but stronger in the novel asymmetric-discrimination condition. We interpret our findings as weighing against the detection-specificity of confidence signatures and speculate about possible alternative origins of a quadratic modulation of decision confidence.
Assessment of fish spermatogenesis through high-quality immunofluorescence against fish testicular samples with an antibody set
Authors: Ye Ding , Liu Tao , Li Yongming , Sun Yonghua
Published: August 2022

A complete evaluation of the spermatogenetic status of a fish by accurately identifying different types of spermatogenic cells is useful not only for reproductive studies but also for genetic breeding. For this task, it is required to establish a simple and practical experimental procedure, to obtain repeatable, high-quality imaging data. Here, we have developed antibodies against the zebrafish (Danio rerio) spermatogenesis-related proteins, including Ddx4, Piwil1, Sycp3, and Pcna, and an integrated method for high-quality and high-through output immunofluorescence on testis sections of different fish species. We accurately identified different spermatogenic cells at different stages. Type-A spermatogonia can be identified by the highest expression of Ddx4 and Piwil1 among different spermatogenic cells. Type-B spermatogonia is identified by the second highest expression of Ddx4 and the highest expression of Pcna among different spermatogenic cells. Spermatids can be distinguished from spermatozoa by the expression of Piwil1. The different subtypes of primary spermatocytes (SPC-I) can be identified by co-staining of Sycp3 and Pcna. Leptotene SPC-I show polar expression of both Sycp3 and Pcna at the same side of the nucleus. All the antibodies were tested for practicality in four fish species, Chinese rare minnow (Gobiocypris rarus), common carp (Cyprinus carpio), blunt snout bream (Megalobrama amblycephala), and rice field eel (Monopterus albus). Using this method and the antibody sets, we were able to precisely and accurately evaluate the spermatogenetic status in different fish species.

Highlights

A practical method for high-quality immunofluorescence against fish testicular samples has been developed.

An antibody set of Ddx4, Piwil1, Sycp3 and Pcna have been developed for identification of a variety of spermatogenic cells in different fish species.

Antibodies against zebrafish proteins have been tested in the four fish species, Chinese rare minnow, common carp, blunt snout bream and rice field eel.
Immunosuppressive tocilizumab prevents astrocyte induced neurotoxicity in hiPSC-LRRK2 Parkinson’s disease by targeting receptor interleukin-6
Authors: Pons-Espinal Meritxell , Blasco-Agell Lucas , Fernandez-Carasa Irene , di Domenico Angelique , Richaud Yvonne , Mosquera Jose Luis , Marruecos Laura , Espinosa Lluís , Garrido Alicia , Tolosa Eduardo , Edel Michael J. , Otero Manel Juan , Ferrer Isidre , Raya Angel , Consiglio Antonella
Published: August 2022

Parkinson’s disease (PD) is associated with premature death of dopamine-producing neurons in the brain. Previous studies have shown that astrocytes of PD patients may contribute to neuronal degeneration by mechanisms involving both direct cell-to-cell contact and transfer of soluble molecules. Since it has been proposed that PD patients exhibit an overall pro-inflammatory state, and since astrocytes are key mediators of the inflammation response in the brain, here we sought to address whether astrocyte-mediated inflammatory signaling could contribute to PD neuropathology. For this purpose, we generated astrocytes from induced pluripotent stem cells (iPSCs) representing PD patients and healthy controls. Transcriptomic analyses identified a unique inflammatory gene expression signature in PD astrocytes compared to controls. In particular, the pro-inflammatory cytokine IL-6 was found to be highly expressed and released by PD astrocytes, and to induce toxicity in dopamine neurons. Mechanistically, neuronal cell death was mediated by IL-6 signaling via IL-6 receptor (IL-6R) expressed in human PD neurons, leading to downstream activation of STAT3. Importantly, astrocyte-induced cell death in PD disease midbrain neurons could be prevented by blocking IL6R-mediated signaling using clinically available antibodies. Moreover, examination of postmortem tissue brain of early-stage PD patients uncovered increased numbers of dopamine neurons overexpressing IL-6R and of reactive astrocytes overexpressing IL-6, compared to healthy brains. Our findings highlight the potential role of astrocyte-mediated inflammatory signaling in neuronal loss in PD, and open the way for new therapies based on IL-6 immunomodulation for preventing PD pathogenesis.
Multi-dimensional antibiotic resistance time series reveals the phenotype-based fitness landscape for Escherichia coli
Authors: Iwasawa Junichiro , Maeda Tomoya , Shibai Atsushi , Kotani Hazuki , Kawada Masako , Furusawa Chikara
Published: August 2022

The fitness landscape represents the complex relationship between genotype or phenotype and fitness under a given environment, the structure of which allows the explanation and prediction of evolutionary trajectories. Although previous studies have constructed fitness landscapes based on comprehensively studying the mutations in specific genes, the high dimensionality of genotypic changes prevents us from developing a fitness landscape capable of predicting evolution for the whole cell. Herein, we address this problem by inferring the fitness landscape for antibiotic resistance evolution by quantifying the phenotypic changes, that is, multi-dimensional time-series measurements of the drug resistance profile. Using the time-series data of drug resistance for multiple drugs, we inferred that the fitness landscape underlies the evolution dynamics of resistance. We showed that different peaks of the landscape correspond to different drug resistance mechanisms, thus supporting the validity of the inferred fitness landscape. We further discuss how inferred phenotype-fitness landscapes could contribute to the prediction and control of evolution. This approach bridges the gap between phenotypic/genotypic changes and fitness while contributing to a better understanding of drug resistance evolution.
Carbon oxidation with sacrificial anodes to inhibit O2evolution in membrane-less bioelectrochemical systems for microbial electrosynthesis
Authors: Rohbohm Nils , Sun Tianran , Blasco-Gómez Ramiro , Byrne James M. , Kappler Andreas , Angenent Largus T.
Published: August 2022

Microbial electrosynthesis is an emerging biosynthesis technology that produces value-added chemicals and fuels and, at the same time, reduces the environmental carbon footprint. However, constraints, such as low current densities and high inner resistance, disfavor this technology for industrial-scale purposes. The cathode performance has been strongly improved in recent years, while the anode performance has not been given enough attention despite its importance in closing the electric circuit. For traditional water electrolysis, O2is produced at the anode, which is toxic to the anaerobic autotrophs that engage in microbial electrosynthesis. To overcome O2toxicity in conventional microbial electrosynthesis, the anode and the cathode chamber have been separated by an ion-exchange membrane to avoid contact between the microbes and O2. However, ion-exchange membranes increase the maintenance costs and compromise the production efficiency by introducing an additional internal resistance. Furthermore, O2is inevitably transferred to the catholyte due to diffusion and electro-osmotic fluxes that occur within the membrane. Here, we proved the concept of integrating carbon oxidation with sacrificial anodes and microbes to simultaneously inhibit the O2evolution reaction (OER) and circumvent membrane application, which allows microbial electrosynthesis to proceed in a single chamber. The carbon-based anodes performed carbon oxidation as the alternative reaction to the OER. This enables microbial electrosynthesis to be performed with cell voltages as low as 1.8-2.1 V at 10 A·m-2. We utilizedMethanothermobacter thermautotrophicusΔH in a single-chamber Bioelectrochemical system (BES) with the best performing carbon-based anode (i.e., activated-carbon anode with soluble iron) to achieve a maximum cathode-geometric CH4production rate of 27.3 L·m-2·d-1, which is equal to a volumetric methane production rate of 0.11 L·L-1·d-1in our BES, at a coulombic efficiency of 99.4%. In this study,Methanothermobacter thermautotrophicusΔH was majorly limited by sulfur that inhibited electromethanogenesis. However, this proof-of-concept study allows microbial electrosynthesis to be performed more energy-efficiently and can be immediately utilized for research purposes in microbial electrosynthesis.
Mechanism of Ca2+ transport by ferroportin
Authors: Shen Jiemin , Wilbon Azaan Saalim , Zhou Ming , Pan Yaping
Published: August 2022

Ferroportin (Fpn) is a transporter that releases Fe2+ from cells and is important for iron homeostasis in circulation. Export of Fe2+ by Fpn is coupled to import of H+ to maintain charge balance. Although Ca2+ was shown to modulate Fe2+ transport in Fpn, transport of Ca2+ by Fpn has not been demonstrated. Here we show that human Fpn (HsFpn) mediates Ca2+ transport, and that the Ca2+ transport does not rely on the transport of other ions. We determine the structure of Ca2+-bound HsFpn and identify a single Ca2+ binding site distinct from the Fe2+ binding sites. Further studies validate the Ca2+ binding site and show that Ca2+ transport is inhibited in the presence of Fe2+ but not vice versa. Function of Fpn as a Ca2+ uniporter in the absence of Fe2+ provides a molecular basis for regulations of iron homeostasis by Ca2+.
Chimeric PRMT6 protein produced by an endogenous retrovirus promoter regulates cell fate decision in mouse preimplantation embryos
Authors: Honda Shinnosuke , Hatamura Maho , Kunimoto Yuri , Ikeda Shuntaro , Minami Naojiro
Published: August 2022

Murine endogenous retrovirus with leucine tRNA primer, also known as MERVL, is expressed during zygotic genome activation in mammalian embryos. Here we show that protein arginine N-methyltransferase 6 (Prmt6) forms a chimeric transcript with MT2B2, one of the long terminal repeat sequences of MERVL, and is translated into an elongated chimeric protein (PRMT6MT2B2) whose function differs from that of the canonical PRMT6 protein (PRMT6CAN) in mouse preimplantation embryos. Overexpression of PRMT6CANin fibroblast cells increased asymmetric dimethylation of the third arginine residue of both histone H2A (H2AR3me2a) and histone H4 (H4R3me2a), while overexpression of PRMT6MT2B2increased only H2AR3me2a. In addition, overexpression of PRMT6MT2B2in one blastomere of mouse two-cell embryos promoted cell proliferation and differentiation of the blastomere into epiblast cells at the blastocyst stage, while overexpression of PRMT6CANrepressed cell proliferation. This is the first report of the translation of a chimeric protein (PRMT6MT2B2) in mouse preimplantation embryos. Our results suggest that analyzing chimeric transcripts with MERVL will provide insight into the relationship between zygotic genome activation and subsequent intra- and extra-cellular lineage determination.
Development of two microbial source tracking markers for detection of wastewater-associatedEscherichia coliisolates
Authors: Gomi Ryota , Haramoto Eiji , Wada Hiroyuki , Sugie Yoshinori , Ma Chih-Yu , Raya Sunayana , Malla Bikash , Nishimura Fumitake , Tanaka Hiroaki , Ihara Masaru
Published: August 2022

Escherichia colihas been used as an indicator of fecal pollution in environmental waters. However, its presence in environmental waters does not provide information on the source of water pollution. Identifying the source of water pollution is paramount to be able to effectively reduce contamination. The present study aimed to identifyE. colimicrobial source tracking (MST) markers that can be used to identify domestic wastewater contamination in environmental waters. We first analyzed wastewaterE. coligenomes sequenced by us (n = 50) and RefSeq animalE. coligenomes of fecal origin (n = 82), and identified 144 candidate wastewater-associated marker genes. The sensitivity and specificity of the candidate marker genes were then assessed by screening the genes in 335 RefSeq wastewaterE. coligenomes and 3,318 RefSeq animalE. coligenomes. We finally identified two MST markers, namely W_nqrC and W_clsA_2, which could be used for detection of wastewater-associatedE. coliisolates. These two markers showed higher performance than the previously developed human wastewater-associatedE. colimarkers H8 and H12. When used in combination, W_nqrC and W_clsA_2 showed specificity of 98.9% and sensitivity of 25.7%. PCR assays to detect W_nqrC and W_clsA_2 were also developed and validated. The developed PCR assays are potentially useful for detectingE. coliisolates of wastewater origin in environmental waters, though users should keep in mind that the sensitivity of these markers is not high. Further studies are needed to assess the applicability of the developed markers to a culture-independent approach.
Basins of attraction of microbiome structure and soil ecosystem functions
Authors: Fujita Hiroaki , Yoshida Shigenobu , Suzuki Kenta , Toju Hirokazu
Published: August 2022

Theory predicts that biological communities can have multiple basins of attraction in terms of their species/taxonomic compositions. The presence of such basins of community structure has been examined in classic empirical studies on forest–savanna transitions and those on eutrophication in freshwater lakes. Nonetheless, it remains a major challenge to extend the investigations of multistability to species-rich microbial communities. By targeting soil microbiomes, we infer the stability landscapes of community structure based on the concepts of statistical physics. Our analysis on the compiled dataset involving 11 archaeal, 332 bacterial, and 240 fungal families detected from > 1,500 agroecosystem soil samples suggested that both prokaryotic and fungal community compositions could be classified into several basins of attraction. We also found that the basins differed greatly in their associations with crop disease prevalence in agroecosystems. A further analysis highlighted microbial taxa potentially playing key roles in transitions between basins with different ecosystem-scale functions. The statistical framework commonly applicable to diverse microbial and non-microbial communities will reorganize our understanding of relationship among community structure, stability, and functions.
snPATHO-seq: unlocking the FFPE archives for single nucleus RNA profiling
Authors: Vallejo Andres F , Harvey Kate , Wang Taopeng , Wise Kellie , Butler Lisa M. , Polo Jose , Plummer Jasmine , Swarbrick Alex , Martelotto Luciano G
Published: August 2022

FFPE (formalin-fixed, paraffin-embedded) tissue archives are the largest repository of clinically annotated human specimens. Despite numerous advances in technology, current methods for sequencing of FFPE-fixed single-cells are slow, labour intensive, insufficiently sensitive and have a low resolution, making it difficult to fully exploit their enormous research and clinical potential. Here we introduce single nuclei pathology sequencing (snPATHO-Seq), a sensitive and efficient high-throughput platform to profile the transcriptome of single nuclei extracted from formalin-fixed paraffin-embedded (FFPE) samples. snPATHO-Seq combines an optimised nuclei extraction protocol from archival samples with 10x Genomics probe-based technology targeting the whole transcriptome. We performed direct comparison of the Fixed RNA Profiling (FRP) and established 3’ single cell RNA-Sequencing (scRNA-Seq) workflows through a comprehensive bioinformatics analysis of matched fresh and fixed samples derived from the LNCaP prostate cancer cell line. FRP detected 2.1 times more transcripts in the fixed sample than the 3’ kit did in the fresh sample. Low mitochondrial genes detection using the FRP was translated into 99.9 percent of cells passing the QC filters, compared to 81.6 percent of cells using the v3.1 chemistry. We then optimized snPATHO-Seq and applied it to a human breast cancer metastasis to the liver collected at autopsy and preserved in FFPE, a particularly challenging sample type. Remarkably, at 28,000 reads/cell snPATHO-Seq was able to detect a median of 1850 genes/cell and 3,216 UMI counts/cell. Comparison of snPATHO-Seq with spatial transcriptomics data (10x Genomics Visium FFPE v1) derived from an adjacent section of the same sample revealed a strong correlation, validating the accuracy of the snPATHO-Seq data. Gene expression data from snPATHO-Seq was used to predict cell type composition within each spatial transcriptomic location via deconvolution. Overall, snPATHO-Seq enables high quality and sensitivity snRNA-Seq from preserved tissue samples, unlocking the vast archives of FFPE tissues and thereby allowing extensive retrospective clinical genomic studies.
EnterotoxigenicEscherichia coliheat-labile toxin drives enteropathic changes in small intestinal epithelia
Authors: Sheikh Alaullah , Tumala Brunda , Vickers Tim J. , Martin John C. , Rosa Bruce A. , Sabui Subrata , Basu Supratim , Simoes Rita D. , Mitreva Makedonka , Storer Chad , Tyksen Erik , Head Richard D. , Beatty Wandy , Said Hamid M. , Fleckenstein James M.
Published: August 2022

abstract

EnterotoxigenicE. coli(ETEC), produce heat-labile (LT) and/or heat-stable (ST) enterotoxins, and are a common cause of diarrhea in children of resource-poor regions. ETEC have also been linked repeatedly to poorly understood sequelae including enteropathy, malnutrition, and growth impairment. While the cellular actions of ETEC enterotoxins leading to diarrhea are well-established, their potential contribution to subsequent pathology is unclear. LT stimulates cellular cAMP production to activate protein kinase A (PKA) which phosphorylates cellular ion channels that drive export of salt and water into the intestinal lumen resulting in diarrhea. However, as PKA exhibits broad kinase activity and its activated catalytic subunits modulate transcription of many genes, we interrogated the transcriptional profiles of LT-treated small intestinal epithelia. These studies demonstrated toxin-induced changes in hundreds of genes including those required for biogenesis and function of the brush border, the major site absorption of nutrients, and suppression of a key transcription factors, HNF4 and SMAD4, critical to differentiation of intestinal epithelia. Accordingly, LT treatment of intestinal epithelial cells significantly disrupted the absorptive microvillus architecture and altered transport of essential nutrients. In addition, challenge of neonatal mice with LT-producing ETEC recapitulated the architectural derangement of the brush border while maternal vaccination with LT prevented brush border disruption in ETEC-challenged neonatal mice. Finally, mice repeatedly challenged with toxigenic ETEC exhibited impaired growth recapitulating the multiplicative impact of recurring ETEC infections in children. These findings highlight impacts of ETEC enterotoxins beyond acute diarrheal illness and may inform approaches to mitigate and prevent major sequelae including malnutrition that impact millions of young children.
The fungal expel of 5-fluorocytosine derived fluoropyrimidines mitigates its antifungal activity and generates a cytotoxic environment
Authors: Sastré-Velásquez Luis Enrique , Dallemulle Alex , Kühbacher Alexander , Baldin Clara , Alcazar-Fuoli Laura , Niedrig Anna , Müller Christoph , Gsaller Fabio
Published: August 2022

Invasive aspergillosis remains one of the most devastating fungal diseases and is predominantly linked to infections caused by the opportunistic human mold pathogen Aspergillus fumigatus. Major treatment regimens for the disease comprise the administration of antifungals belonging to the azole, polyene and echinocandin drug class. The prodrug 5-fluorocytosine (5FC), which is the only representative of a fourth class, the nucleobase analogs, shows unsatisfactory in vitro activities and is barely used for the treatment of aspergillosis. The main route of 5FC activation in A. fumigatus comprises its deamination into 5-fluorouracil (5FU) by FcyA, which is followed by Uprt-mediated 5FU phosphoribosylation into 5-fluorouridine monophosphate (5FUMP). In this study, we characterized and examined the role of a metabolic bypass that generates this nucleotide via 5-fluorouridine (5FUR) through uridine phosphorylase and uridine kinase activities. Resistance profiling of mutants lacking distinct pyrimidine salvage activities suggested a minor contribution of the alternative route in 5FUMP formation. We further analyzed the contribution of drug efflux in 5FC tolerance and found that A. fumigatus cells exposed to 5FC reduce intracellular fluoropyrimidine levels through their export into the environment. This release, which was particularly high in mutants lacking Uprt, generates a toxic environment for cytosine deaminase lacking mutants as well as mammalian cells. Employing the broad-spectrum fungal efflux pump inhibitor clorgyline, we demonstrate synergistic properties of this compound in combination with 5FC, 5FU as well as 5FUR.
The Ebola virus VP40 matrix undergoes endosomal disassembly essential for membrane fusion
Authors: Winter Sophie L. , Golani Gonen , Lolicato Fabio , Vallbracht Melina , Thiyagarajah Keerthihan , Ahmed Samy Sid , Lüchtenborg Christian , Fackler Oliver T. , Brügger Britta , Hoenen Thomas , Nickel Walter , Schwarz Ulrich S. , Chlanda Petr
Published: August 2022

Ebola viruses (EBOVs) are filamentous particles, whose shape and stability are determined by the VP40 matrix. Virus entry into host cells occurs via membrane fusion in late endosomes; however, the mechanism of how the remarkably long virions undergo uncoating including virion disassembly and nucleocapsid release into the cytosol, remains unknown. Here, we investigate the structural architecture of EBOVs entering host cells and discover that the VP40 matrix disassembles prior to membrane fusion. We reveal that VP40 disassembly is caused by the weakening of VP40-lipid interactions driven by low endosomal pH that equilibrates passively across the viral envelope without a dedicated ion channel. We further show that viral membrane fusion depends on VP40 matrix integrity, and its disassembly reduces the energy barrier for fusion stalk formation. Thus, pH-driven structural remodeling of the VP40 matrix acts as a molecular switch coupling viral matrix uncoating to membrane fusion during EBOV entry.
JNK signalling regulates self-renewal of proliferative urine-derived renal progenitor cells via inhibition of ferroptosis
Authors: Nguyen Lisa , Westerhoff Michelle , Thewes Leonie , Wruck Wasco , Reichert Andreas S. , Berndt Carsten , Adjaye James
Published: August 2022

With a global increase in chronic kidney disease patients, alternatives to dialysis and organ transplantation are needed. Stem cell-based therapies could be one possibility to treat chronic kidney disease. Here, we used multipotent urine-derived renal progenitor cells (UdRPCs) to study nephrogenesis. UdRPCs treated with the JNK inhibitor-AEG3482, displayed decreased proliferation and downregulated transcription of cell cycle-associated genes as well as the kidney progenitor markers -SIX2, CITED1, and SALL1. In addition, levels of activated SMAD2/3, which is associated with the maintenance of self-renewal in UdRPCs, were decreased. JNK inhibition resulted in less efficient oxidative phosphorylation and more lipid peroxidation via ferroptosis-an iron-dependent non-apoptotic cell death pathway linked to various forms of kidney disease. Our study reveals the importance of JNK signalling in maintaining self-renewal as well as protection against ferroptosis in SIX2-positive UdRPCs. We propose that UdRPCs can be used for modelling ferroptosis-induced kidney diseases.
Rotavirus NSP1 subverts the antiviral OAS-RNase L pathway by inducing RNase L degradation
Authors: Dai Jin , Yi Guanghui , Philip Asha A. , Patton John T.
Published: August 2022

The interferon (IFN)-inducible 2′,5′-oligoadenylate synthetase (OAS) - RNase L pathway plays a critical role in antiviral immunity. Group A rotaviruses, including the simian SA11 strain, inhibit this pathway through two activities: an E3-ligase related activity of NSP1 that degrades proteins necessary for IFN signaling, and a phosphodiesterase (PDE) activity of VP3 that hydrolyzes the RNase L-activator 2′,5′-oligoadenylate. Unexpectedly, we found that a recombinant (r) SA11 double-mutant virus deficient in both activities (rSA11-VP3H797R-NSP1ΔC17) retained the ability to prevent RNase L activation. Mass spectrometry led to the discovery that NSP1 interacts with RNase L in rSA11-infected MA104 cells. This interaction was confirmed through co-pulldown assay of cells transiently expressing NSP1 and RNase L. Immunoblot analysis showed that infection with wild type rSA11 virus, rSA11-VP3H797R-NSP1ΔC17 double-mutant virus, or single mutant forms of the latter virus, all resulted in the depletion of endogenous RNase L. The loss of RNase L was reversed by addition of the neddylation inhibitor MLN4924, but not the proteasome inhibitor MG132. Analysis of additional mutant forms of rSA11 showed that RNase L degradation no longer occurred when either the N-terminal RING domain of NSP1 was mutated or the C-terminal 98 amino acids of NSP1 were deleted. The C-terminal RNase L degradation domain is positioned upstream and is functionally independent of the NSP1 domain necessary for inhibiting IFN expression. Our studies reveal a new role for NSP1 and its E3-ligase related activity as an antagonist of RNase L and uncover a novel virus-mediated strategy of inhibiting the OAS-RNase L pathway.

IMPORTANCE

For productive infection, rotavirus and other RNA viruses must suppress interferon (IFN) signaling and the expression of IFN-stimulated antiviral gene products. Particularly important is inhibiting the interferon (IFN)-inducible 2′,5′-oligoadenylate synthetase (OAS) - RNase L pathway, as activated RNase L can direct the nonspecific degradation of viral and cellular RNAs, thereby blocking viral replication and triggering cell death pathways. In this study, we have discovered that the simian SA11 strain of rotavirus employs a novel strategy of inhibiting the OAS-RNase L pathway. This strategy is mediated by SA11 NSP1, a nonstructural protein that hijacks E3 cullin-RING ligases, causing the ubiquitination and degradation of host proteins essential for IFN induction. Our analysis shows that SA11 NSP1 also recognizes and causes the ubiquitination of RNase L, an activity resulting in depletion of endogenous RNase L. These data raise the possibility of using therapeutics targeting cellular E3 ligases to control rotavirus infections.