bluuebunny/crossref_metadata_2025 huggingface dataset:
The Business Case for Addressing Burnout in Frontline Leaders
Authors: Lyle-Edrosolo Giancarlo
Published: December 2022

In 2019, the National Academy of Sciences, Engineering, and Medicine identified clinician burnout as a major problem that required immediate action because of its threat to both health care worker safety and patient safety. Unfortunately, the rise of COVID-19 in 2020 with no signs of a clear ending (as of the summer of 2022) has compounded this problem. Consequently, much focus has been placed by many to address clinician burnout and help alleviate this major threat to safety. Unfortunately, compared with clinician burnout, articles and resources to address frontline leader (FL) burnout are fewer. FLs are key to supporting teams and are integral to their success. They also execute and operationalize organizational strategic plans to ensure patient safety at the point of care. The burnout issue with bedside clinicians is a big issue, a fractured fault line in our health care system. However, without addressing the well-being of FLs, this fault line becomes a chasm. The column shares background from the American Organization for Nursling Leadership longitudinal studies and other pertinent research. It also provides examples of practices across the nation of how nurse executives are supporting their teams and promoting leader support and well-being.
Innovation and Evidence-Based Decision-Making
Authors: Clemmons-Brown Connie A.
Published: December 2022

Merger and acquisition activities in health care are increasing in both the number and cumulative value of transactions in recent years, creating new and dynamic pressures on health care systems and current operating environments. These industry shifts, coupled with crises such as the COVID-19 global pandemic, create opportunities for innovation to increase capacity, improve productivity, achieve economies of scale, and positively impact health care quality, safety, access, and cost. However, neither consolidation nor innovation in and of themselves will yield sustainable clinical best practices nor achieve the desired quality, financial, efficiency, retention, or engagement outcomes. This article describes the approach used by one system-level Doctor of Nursing Practice prepared nurse executive to leverage evidence-based decision-making to guide, lead, and support the innovation needed to address first-year new graduate nurse turnover in a multistate not-for-profit health care system.
Hot Gloved Finger Sign in Endobronchial Metastasis From Hepatocellular Carcinoma on FDG PET/CT
Authors: Zhang Jun , Dong Aisheng , Wang Yang
Published: December 2022

Endobronchial metastasis from hepatocellular carcinoma is exceedingly rare. We describe FDG PET/CT findings in a case with isolated endobronchial metastasis from hepatocellular carcinoma 13 years after hepatectomy. The endobronchial metastasis appeared as hypermetabolic branching tubular opacities, producing a hot gloved finger sign on FDG PET/CT. This case indicates that the hot gloved finger sign may be suggestive of extensive endobronchial growing of a malignant condition but not endobronchial mucoid plug.
Unilateral Reduction of 18F-FDG Accumulation in Brown Adipose Tissue by Sympathectomy for Hyperhidrosis
Authors: Shirakawa Chigusa , Koyasu Sho , Takada Masahiro , Toi Masakazu , Nakamoto Yuji
Published: December 2022

A 30-year-old woman with left breast cancer underwent 18F-FDG PET/CT for staging. Intense FDG uptake was observed in the primary lesion, as well as on the left side of the neck to the supraclavicular fossa and left paravertebral region. History taking revealed that she had undergone a right thoracic sympathectomy for hyperhidrosis, which resulted in attenuated FDG uptake in the right-sided brown adipose tissue (BAT). With another examination keeping adequate warming, the accumulation of BAT was reduced and a diagnosis of cT1N1M0 was made. Unilateral sympathetic blockade can cause asymmetric FDG accumulation in BAT, which interferes with interpretation in tumors.
Solitary Scapular Metastasis as the First Presentation of Prostate Adenocarcinoma Identified on 99mTc-MDP SPECT/CT
Authors: Liu Wei , Zheng Xiao-Zuo , Dong Zi-Qian , Huang Jian-Min , Xie Peng
Published: December 2022

Metastases of prostate carcinoma in the skeleton are usually multiple. Solitary metastasis in appendicular skeleton is extremely rare. We present bone scan findings of solitary scapular metastasis from prostate adenocarcinoma as the initial presentation of his malignancy in a 62-year-old man. The99mTc-MDP SPECT/CT demonstrated intense activity in the coracoid process of left scapula, whereas the tracer uptakes in other bones were not typical of metastases. The subsequent pathological results of the punctured left scapula confirmed as metastasis from prostate adenocarcinoma.
Optimal Measurement Sites of Coronary-Computed Tomography Angiography-derived Fractional Flow Reserve
Authors: Chen Yan Chun , Zhou Fan , Wang Yi Ning , Zhang Jia Yin , Yu Meng Meng , Hou Yang , Xu Peng Peng , Zhang Xiao Lei , Xue Yi , Zheng Min Wen , Zhang Bo , Zhang Dai Min , Hu Xiu Hua , Xu Lei , Liu Hui , Lu Guang Ming , Tang Chun Xiang , Zhang Long Jiang
Published: December 2022

Objectives:

To investigate the optimal measurement site of coronary-computed tomography angiography-derived fractional flow reserve (FFRCT) for the assessment of coronary artery disease (CAD) in the whole clinical routine practice.

Materials and Methods:

This retrospective multicenter study included 396 CAD patients who underwent coronary-computed tomography angiography, FFRCT, and invasive FFR. FFRCT was measured at 1 cm (FFRCT-1 cm), 2 cm (FFRCT-2 cm), 3 cm (FFRCT-3 cm), and 4 cm (FFRCT-4 cm) distal to coronary stenosis, respectively. FFRCT and invasive FFR ≤0.80 were defined as lesion-specific ischemia. The diagnostic performance of FFRCT to detect ischemia was obtained using invasive FFR as the reference standard. Reduced invasive coronary angiography rate and revascularization efficiency were calculated. After a median follow-up of 35 months in 267 patients for major adverse cardiovascular events (MACE), Cox hazard proportional models were performed with FFRCT values at each measurement site.

Results:

For discriminating lesion-specific ischemia, the areas under the curve of FFRCT-1 cm (0.91) as well as FFRCT-2 cm (0.91) were higher than those of FFRCT-3 cm (0.89) and FFRCT-4 cm (0.88), respectively (all P<0.05). The higher reduced invasive coronary angiography rate (81.6%) was found at FFRCT-1 cm than FFRCT-2 cm (81.6% vs. 62.6%, P<0.05). Revascularization efficiency did not differ between FFRCT-1 cm and FFRCT-2 cm (80.8% vs. 65.5%, P=0.019). In 12.4% (33/267) MACE occurred and only values of FFRCT-2 cm were independently predictive of MACE (hazard ratio: 0.957 [95% CI: 0.925-0.989]; P=0.010).

Conclusions:

This study indicates FFRCT-2 cm is the optimal measurement site with superior diagnostic performance and independent prognostic role.
Myocardial Work Measurement With Functional Capacity Evaluation in Primary Systemic Hypertension Patients
Authors: Ran Hong , Ma Xiao-wu , Wan Lin-lin , Ren Jun-yi , Zhang Jian-xin , Zhang Ping-yang , Schneider Matthias
Published: December 2022

Objective:

Noninvasive measurement of myocardial work (MW) incorporates left ventricular (LV) pressure, and, therefore, allows correction of global longitudinal strain for changing afterload conditions. We sought to investigate MW as a tool to detect early signs of LV dysfunction in primary systemic hypertension patients, particularly with different predictive indices.

Methods and Results:

None left ventricular hypertrophy (NLVH) and left ventricular hypertrophy (LVH) patients established were all primary systemic hypertension with preserved ejection fraction. Forty in NLVH and forty in LVH according to left ventricular end-diastolic mass index (LVEDmassI) were prospectively enrolled. The following indices of MW were assessed: global work index, global constructive work, global wasted work (GWW), and global work efficiency (GWE). Both global work index (P=0.348) and global constructive work (P=0.225) were increased in NLVH and decreased in LVH, and GWW (P<0.001) was increased significantly in NLVH and increased more in LVH, while GWE (P<0.001) was decreased significantly in NLVH and decreased more in LVH. The clinical utility of GWW (95% CI: 0.802-0.951) and GWE (95% CI: 0.811-0.950) were verified by receiver-operating characteristic curve analysis showing larger net benefits as evaluated with LVH and control comparisons. In multivariate linear regression analysis, 4-dimenaional LVEDmassI was independently associated with GWE (P=0.018) in systemic hypertension patients. Assessment of intraobserver and interobserver variability in the MW echocardiographic data documented good interclass correlation coefficients (all >0.85).

Conclusion:

GWW and GWE derived from MW are more accurate, sensitive, and reproducible predictors to detect early LV dysfunction in primary systemic hypertension patients, especially in distinguishing the potential functional abnormality of NLVH and LVH, even though the ejection fraction is preserved.
SEVERE CORONAVIRUS DISEASE 2019: FROM PATHOGENESIS TO THERAPY
Authors: Cavaillon Jean-Marc , Artigas Antonio , Barratt-Due Andreas , Giamarellos-Bourboulis Evangelos J. , Gómez Hernando , Hayem Gilles , Vlaar Alexander P. J. , Wiersinga W. Joost
Published: December 2022

The COVID-19 pandemic has been a challenge to propose efficient therapies. Because severe SARS-CoV2 infection is a viral sepsis eventually followed by an immunological autoinflammatory phenomenon, many approaches have been inspired by the previous attempts made in bacterial sepsis, while specific antiviral strategies (use of interferon or specific drugs) have been additionally investigated. We summarize our current thinking on the use of SARS-CoV-2 antivirals, corticosteroids, anti–IL-1, anti-IL-6, anti-C5a, as well as stem cell therapy in severe COVID-19. Patient stratification and appropriate time window will be important to be defined to guide successful treatment.
A rare case of neonatal meningoencephalitis from Paenibacillus thiaminolyticus
Authors: Smallcomb Laura S. , Dixon Terry C. , Azad Kamran N. , Marvin Whitney E.
Published: December 2022

Paenibacillus

infections can be life threatening and are being reported with increasing incidence. There are only a few case reports of infections and are mainly described in patients who are immunocompromised, injection drug users, or those with prosthetic devices. Due to improved testing and identification, it appears that these infections may not be as rare as once perceived. We present a case of a 16-day-old term neonate who presented with status epilepticus and was found to have

Paenibacillus thiaminolyticus

meningoencephalitis. The patient was successfully treated with a combination of ampicillin and ceftazidime then meropenem. To our knowledge, this is the first reported case of an infant in the United States who survived this serious invasive infection. We also present an option for therapy given the difficulty treating invasive intracranial infections.
Case report: isolation of Hydrogenophaga from septic blood culture following near-death drowning in lakewater
Authors: Feichtinger Stuart , Lazar Angela A. , Luebbe Megan A. , Accola Molly A. , Jung-Hynes Brittney D. , Anderson Patti J. , Koglin Kelly M. , Schliesman Karen S. , Ehlenbach William , Smith Jeannina , Chen Derrick J. , Rehrauer William M. , Bailey Adam L.
Published: December 2022

A patient suffered a non-fatal wet drowning in a freshwater lake and developed bacteremia several days later. Blood culture grew a Gram-negative rod that could not be identified by MALDI-TOF MS. 16S ribosomal RNA sequencing of the isolate identified the microbe as Hydrogenophaga laconesensis––an environmental microbe commonly found in freshwater. The recovery of multiple pathogenic microorganisms (although not Hydrogenophaga laconesensis) from culture of respiratory specimens prompted the initiation of antibiotic therapy with cefepime and, later, vancomycin. The patient’s clinical course gradually improved over the course of two weeks and she was ultimately discharged home with minimal sequelae. To our knowledge, this is the first evidence of human infection with bacteria in the Hydrogenophaga genus. Hydrogenophaga may be considered in cases of freshwater near-drowning, and MALDI-TOF MS databases should be updated to include Hydrogenophaga laconesensis.
Invasive terrestrial invertebrate detection in water and soil using a targeted eDNA approach
Authors: Villacorta-Rath Cecilia , Lach Lori , Andrade-Rodriguez Natalia , Burrows Damien , Gleeson Dianne , Trujillo-González Alejandro
Published: December 2022

Terrestrial invasive invertebrates can rapidly colonize new areas, causing detrimental effects on biodiversity, economy, and lifestyle. Targeted environmental DNA (eDNA) methods could constitute an early detection tool given their sensitivity to small numbers of individuals.

We hypothesized that terrestrial runoff would transport eDNA from the land into adjacent water bodies and used the invasive yellow crazy ant (Anoplolepis gracilipes) as a model species to test this hypothesis. We collected water samples from four waterbodies adjacent to infestations following rainfall events for eDNA analysis. We also collected soil samples from areas of known infestations and tested five eDNA extraction methods to determine their efficiency to extract eDNA from soil.

Water samples resulted in positive yellow crazy ant eDNA amplification (20–100% field replicates across all sites), even at one site located 300 m away from where ants had been detected visually. Soil samples resulted in a high percentage of false negatives when sampled from ant transit areas than from nest entrances.

Unpurified DNA extracts from soil also resulted in false negative detections, and only after applying a purification step of DNA extracts, we detected yellow crazy ant eDNA in 40–100% of field replicates across all methods and sites.

This is the first study to empirically show that eDNA from a terrestrial invertebrate can be successfully isolated and amplified from adjacent or downstream waterbodies. Our results indicate that eDNA has the potential to be a useful method for detecting terrestrial invertebrates from soil and water.
Hexokinase 2 localizes to the nucleus in response to glucose limitation but does not regulate gene expression
Authors: Lesko Mitchell A. , Chandrashekarappa Dakshayini G. , Jordahl Eric M. , Oppenheimer Katherine G. , Bowman Ray Wesley , Shang Chaowei , Durrant Jacob , Schmidt Martin C. , O’Donnell Allyson F.
Published: December 2022

Glucose is the preferred carbon source for most eukaryotes, and the first step in its metabolism is phosphorylation to glucose-6-phosphate. This reaction is catalyzed by a family of enzymes called either hexokinases or glucokinases depending on their substrate specificity. The yeastSaccharomyces cerevisiaeencodes three such enzymes, Hxk1, Hxk2 and Glk1. In yeast and mammals, some isoforms of this enzyme are found in the nucleus, suggesting a possible moonlighting function beyond glucose phosphorylation. In contrast to mammalian hexokinases, the yeast Hxk2 enzyme has been proposed to shuttle into the nucleus in glucose replete conditions where it reportedly moonlights as part of a glucose-repressive transcriptional complex. To achieve this role in glucose repression, Hxk2 reportedly binds the Mig1 transcriptional repressor, is dephosphorylated at serine 15 in its N-terminus, and requires an N-terminal nuclear localization sequence (NLS).

In this study, we use high-resolution, quantitative, fluorescent microscopy of live cells to determine the conditions, residues, and regulatory proteins required for Hxk2 nuclear localization. In direct contradiction to previous yeast studies, our quantitative imaging demonstrates that Hxk2 is largely excluded from the nucleus under glucose replete conditions but is retained in the nucleus under glucose limiting conditions. Our data show that the Hxk2 N-terminus does not contain an NLS but instead comprises sequences necessary for nuclear exclusion and multimerization regulation. Amino acid substitutions of the phosphorylated residue, serine 15, disrupt Hxk2 dimerization but have no effect on its glucose-regulated nuclear localization. Substitution of alanine at the nearby residue, lysine 13, affects both dimerization and maintenance of nuclear exclusion under glucose replete conditions. Modeling and simulation provide insight into the molecular mechanisms of this regulation. In marked contrast to earlier studies, we find that the transcriptional repressor Mig1 and the protein kinase Snf1 have little effect on Hxk2 localization. Instead, the protein kinase Tda1 is a key regulator of Hxk2 localization.

Finally, RNAseq analyses of the yeast transcriptome further dispel the idea that Hxk2 moonlights as a transcriptional repressor, demonstrating that Hxk2 has a negligible role in transcriptional regulation in both glucose replete and limiting conditions. Taken together, our studies provide a paradigm shift for the conditions, residues, and regulators controlling Hxk2 dimerization and nuclear localization. Based on our data, the nuclear translocation of Hxk2 in yeast occurs in glucose starvation conditions, a finding that aligns well with the nuclear regulation of mammalian orthologs of this enzyme. Our findings lay the foundation for future studies of Hxk2 nuclear activity.
Antibody Affinity Maturation to SARS-CoV-2 Omicron Variants in a Teachers Cohort
Authors: James-Pemberton Philip H. , Kohli Shivali , Westlake Aaron C. , Antill Alex , Olkhov Rouslan V. , Shaw Andrew M.
Published: December 2022

In summer of 2022, a cohort of 28 staff members were recruited from a UK primary school setting. The prevalent variants at the time were Omicron BA.1.159, BA.4/5 and BA.2: 61% of the cohort reported a lateral flow confirmed positive test for SARS-CoV-2 infection in late 2021 or 2022. A fully quantitative antibody screen for concentration and affinity was performed for spike protein variants Wuhan, Alpha, Beta, Gamma, Delta and Omicron BA.1, BA.2.75, BA.2.12.1, BA.4 and BA.5 and a pH dependent affinity was derived from disruption of the epitope-paratope complex at pH 3.2. The cohort showed a Universal positive immunity endotype, U(+), incidence of 78% (95% CI 60% - 88%) with good antibody concentrations to all ten variants; the incidence drops to 25% (95% CI 13% - 43%) when the affinity spectrum is measured. The antibody affinity profiles for each Omicron variant were all significantly better than Alpha, Beta, Gamma and Delta reflecting exposure to the antigens; we surmise either from the booster vaccines or continual contact with the virus, presenting in the school children either asymptomatically or symptomatically. Significant antibody affinity maturation was seen to the spike protein in all prevalent variants of SARS-CoV-2. Antibody concentrations were waning compared to the post-booster vaccine response. Using our hypothesised 3.4 mg/L nasal mucosal protection threshold, we postulate 46% of the cohort required boosting within 60 days and 66% within 120 days. We propose a smart boosting programme around the constant-exposure teacher cohort and parents of children could reduce community transmission.
Arabidopsis hydathodes are sites of intense auxin metabolism and nutrient scavenging
Authors: Routaboul Jean-Marc , Bellenot Caroline , Clément Gilles , Citerne Sylvie , Remblière Céline , Charvin Magali , Franke Lars , Chiarenza Serge , Vasselon Damien , Jardinaud Marie-Françoise , Carrère Sébastien , Nussaume Laurent , Laufs Patrick , Leonhardt Nathalie , Navarro Lionel , Schattat Martin , Noël Laurent D.
Published: December 2022

Hydathodes are small organs located on the leaf margins of all vascular plants. They release excess xylem sap through guttation when stomata are closed or when the humidity level is high. Many promoter analyses have suggested other hydathode functions in metabolite transport and auxin metabolism, but experimental demonstration is still lacking. Here, we compared the transcriptomic and metabolomic features of mature Arabidopsis hydathodes to the leaf blade. 1460 differentially-expressed genes were identified revealing that genes related to auxin metabolism, transport, stress, DNA, plant cell wall, RNA or wax were on average more expressed in hydathodes. On the other hand, genes involved in glucosinolate metabolism, sulfation pathway, metal handling or photosynthesis were downregulated in hydathodes. In hydathodes, there are an increased expression of auxin transcriptional regulators and biosynthetic genes, a lower expression of auxin transport genes and a differential expression of genes related to its vacuolar storage that is consistent with increased contents of free and conjugated auxin. We also found that ca. 78% of the total content of 52 xylem sap metabolites were removed from guttation fluid at the hydathode level. Using reverse genetics, we showed that the capture of nitrate and phosphate in the guttation fluid relies on theNRT2.1andPHT1;4transporters, respectively. Thus, hydathodes absorb a significant part of xylem sap nutrients, limiting the loss of valuable chemicals during guttation. Our transcriptomic and metabolomic analyses reveal an organ with its own transcriptomic and physiological identity and highlight hydathode biological processes that may impact the whole plant.

One sentence summary

Transcriptome and physiological analysis of mature and healthy hydathodes of Arabidopsis demonstrates that those organs are sites of intense auxin metabolism and nutrient scavenging
Investigating the origin of subtelomeric and centromeric AT-rich elements inAspergillus flavus
Authors: Lustig Arthur J.
Published: December 2022

An in silico study ofAspergillus flavusgenome stability uncovered significant variations in both coding and non-coding regions. The non-coding insertions uniformly consisted of AT-rich sequences that are evolutionarily maintained, albeit distributed at widely different sites in an array ofA. flavusstrains. A survey of ≥ 2kb AT-rich elements (AT ≥ 70%; ATEs) uncovered three classes. The first class is composed of homologous insertions at ectopic, non-allelic sites that contain homology to transposable elements (TEs). Strains differed significantly in frequency, position, and TE type, but displayed a common enrichment in subtelomeric regions. The TEs were heavily mutated, with patterns consistent with the ancestral activity of repeat-induced point mutations (RIP). The second class consists of ∼100 kb regions at each centromere. Centromeric ATEs and TE clusters within these centromeres display a high level of sequence identity between strains. The third class consists of a conserved set of novel subtelomeric ATE repeats which lack discernible TEs and, unlike TEs, display a constant polarity relative to the telomere. Members of one of these classes are derivatives of a progenitor ATE that is predicted to have undergone extensive homologous recombination during evolution. These studies suggest that transposition and RIP are forces in the evolution of subtelomeric and centromeric structure and function.
Metabolomic comparison usingStreptomycesspp. as a factory of secondary metabolites
Authors: Flores Clavo Rene , Kelyene Pereira Alana , Ruiz Quiñones Nataly , Henrique Costa Jonas , Pacheco Fill Taícia , Fantinatti Garboggini Fabiana
Published: December 2022

Understanding extremophiles and their usefulness in biotechnology involves studying their habitat, physiology and biochemical adaptations, as well as their ability to produce biocatalysts, in environments that are still poorly explored. In northwestern Peru, which has saline lagoons of marine origin Pacific Ocean, the other site is from the coast of Brazil of the Atlantic Ocean. Both environments are considered extreme. The objective of the present work was to compare two different strains isolated from these extreme environments at the metabolic level using molecular network methodology through the Global Natural Products Molecular Social Network (GNPS). In our study, the MS/MS spectra from the network were compared with GNPS spectral libraries, where the metabolites were annotated. Differences were observed in the molecular network presented in the two strains ofStreptomycesspp. coming from these two different environments. Within the an-notated compounds from marine bacteria, the metabolites characterized forStreptomycessp. B-81 from Peruvian marshes were lobophorins A (1) and H (2), as well as divergolides A (3), B (4) and C (5).Streptomycessp. 796.1 produced different compounds, such as glucopiericidin A (6) and dehy-dro-piericidin A1a (7). The search for new metabolites in underexplored environments may therefore reveal new metabolites with potential application in different areas of biotechnology.
GEMC1 and MCIDAS interactions with SWI/SNF complexes regulate the multiciliated cell-specific transcriptional program
Authors: Lewis Michael , Terre Berta , Knobel Philip A. , Cheng Tao , Lu Hao , Attolini Camille Stephan-Otto , Smak Jordann , Coyaud Etienne , Garcia-Cao Isabel , Querol Jessica , Gil-Gomez Gabriel , Piergiovanni Gabrielle , Costanzo Vincenzo , Peiró Sandra , Raught Brian , Zhao Haotian , Salvatella Xavier , Roy Sudipto , Mahjoub Moe , Stracker Travis H.
Published: December 2022

Multiciliated cells (MCCs) project dozens to hundreds of motile cilia from their apical surface to promote the movement of fluids or gametes in the mammalian brain, airway or reproductive organs. Differentiation of MCCs requires the sequential action of the Geminin family transcriptional activators, GEMC1 and MCIDAS, that both interact with E2F4/5-DP1. How these factors activate transcription and the extent to which they play redundant functions remains poorly understood. Here, we demonstrate that the transcriptional targets and proximal proteomes of GEMC1 and MCIDAS are highly similar. However, we identified distinct interactions with SWI/SNF subcomplexes; GEMC1 interacts primarily with the ARID1A containing BAF complex while MCIDAS interacts primarily with BRD9 containing ncBAF complexes. Treatment with a BRD9 inhibitor impaired MCIDAS-mediated activation of several target genes and compromised the MCC differentiation program in multiple cell based models. Our data suggest that the differential engagement of distinct SWI/SNF subcomplexes by GEMC1 and MCIDAS is required for MCC-specific transcriptional regulation and mediated by their distinct C-terminal domains.
Cell coupling compensates for changes in single-cell Her6 dynamics and provides phenotypic robustness
Authors: Doostdar Parnian , Hawley Joshua , Marinopoulou Elli , Lea Robert , Biga Veronica , Papalopulu Nancy , Rodriguez Ximena Soto
Published: December 2022

her6is a zebrafish ortholog ofHes1, known for its role in maintaining neural progenitors during neural development. Here, we characterise the population-level effect of altering Her6 protein expression dynamics at the single-cell level in the embryonic zebrafish telencephalon. Using an endogenousHer6:Venusreporter and 4D single-cell tracking, we show that Her6 oscillates in neural telencephalic progenitors and that fusion of a protein destabilisation domain (PEST) to Her6:Venus alters its expression dynamics causing most cells to downregulate Her6 prematurely. However, in PEST mutants, a higher proportion of cells exhibit Her6 oscillations and while expression is reduced in most cells, some cells express Her6 at wild-type levels resulting in increased heterogeneity of Her6 expression in the population. Despite the profound differences in the single-cell Her6 dynamics, differentiation markers do not exhibit major differences early on, while an increase in differentiation is observed at later developmental stages (vglut2a, gad1andgad2). At the same time, at late stage the overall size of the telencephalon remains the same. Computational modelling that simulates changes in Her6 protein stability reveals that the increase in population Her6 expression heterogeneity is an emergent property of finely tuned Notch signalling coupling between single cells. Our study suggests that such cell coupling provides a compensation strategy whereby a normal phenotype is maintained while single-cell dynamics are abnormal, although the limit of this compensation is reached at late developmental stages. We conclude that in the neural progenitor population, cell coupling controls Her6 expression heterogeneity and in doing so, it provides phenotypic robustness when individual cells lose Her6 expression prematurely.
ExpressUrself: A spatial model for predicting recombinant expression from mRNA sequence
Authors: Dunne Michael P. , Caceres-Delpiano Javier
Published: December 2022

Maximising the yield of recombinantly expressed proteins is a critical part of any protein engineering pipeline. In most cases, the expression of a given protein can be tuned by adjusting its DNA coding sequence, however finding coding sequences that optimise expression is a nontrivial task. The 3-dimensional structure of mRNA is known to strongly influence the expression levels of proteins, due to its effect on the efficiency of ribosome attachment. While correlations between mRNA structure and expression are well established, no model to date has succeeded in effectively utilising this information to accurately predict expression levels. Here we present ExpressUrself, a model designed to capture spatial characteristics of the sequence surrounding the start codon of an mRNA transcript, and intended to be used for optimising protein expression. The model is trained and tested on a large data set of variant DNA sequences and is able to predict the expression of previously unseen transcripts to a high degree of accuracy.
Dynamically regulated transcription factors are encoded by highly unstable mRNAs in theDrosophilalarval brain
Authors: Thompson Mary Kay , Ceccarelli Arianna , Ish-Horowicz David , Davis Ilan
Published: December 2022

The level of each RNA species depends on the balance between its rates of production and decay. Although previous studies have measured RNA decay across the genome in tissue culture and single-celled organisms, few experiments have been performed in intact complex tissues and organs. It is therefore unclear whether the determinants of RNA decay found in cultured cells are preserved in an intact tissue, and whether they differ between neighboring cell types and are regulated during development. To address these questions, we measured RNA synthesis and decay rates genome wide via metabolic labeling of whole culturedDrosophilalarval brains using 4-thiouridine. Our analysis revealed that decay rates span a range of more than 100-fold, and that RNA stability is linked to gene function, with mRNAs encoding transcription factors being much less stable than mRNAs involved in core metabolic functions. Surprisingly, among transcription factor mRNAs there was a clear demarcation between more widely used transcription factors and those that are expressed only transiently during development. mRNAs encoding transient transcription factors are among the least stable in the brain. These mRNAs are characterized by epigenetic silencing in most cell types, as shown by their enrichment with the histone modification H3K27me3. Our data suggests the presence of an mRNA destabilizing mechanism targeted to these transiently expressed transcription factors to allow their levels to be regulated rapidly with high precision. Our study also demonstrates a general method for measuring mRNA transcription and decay rates in intact organs or tissues, offering insights into the role of mRNA stability in the regulation of complex developmental programs.
Novel Complete Methanogenic Pathways in Longitudinal Genomic Study of Monogastric Age-Associated Archaea
Authors: Feehan Brandi , Ran Qinghong , Dorman Victoria , Rumback Kourtney , Pogranichniy Sophia , Ward Kaitlyn , Goodband Robert , Niederwerder Megan C , Lee Sonny T M
Published: December 2022

Background

Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focussing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea detection and methanogenic functions while assessing global and host distribution of our novel archaeal metagenome assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, and MAG taxonomic assignment and functional annotation.

Results

We generated 1,130 non-redundant MAGs with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: ordersMethanomassiliicoccales(5) andMethanobacteriales(3); generaUBA71(3),Methanomethylophilus(1),MX-02(1), andMethanobrevibacter(3). We recovered the first US swineMethanobrevibacter UBA71 sp006954425andMethanobrevibacter gottschalkiiMAGs. TheMethanobacterialesMAGs were identified primarily during the young, preweaned host whereasMethanomassiliicoccalesprimarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in monogastric archaea which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further our understanding of microbiome development and functions.
Activation loop phosphorylation tunes conformational dynamics underlying Pyk2 tyrosine kinase activation
Authors: Palhano Zanela TM , Woudenberg A , Romero Bello KG , Underbakke ES
Published: December 2022

Pyk2 is a multidomain non-receptor tyrosine kinase that undergoes a multistage activation mechanism. Activation is instigated by conformational rearrangements relieving autoinhibitory FERM domain interactions. The kinase autophosphorylates a central linker residue to recruit Src kinase. Pyk2 and Src mutually phosphorylate activation loops to confer full activation. While the mechanisms of autoinhibition are established, the conformational dynamics associated with autophosphorylation and Src recruitment remain unclear. We employ hydrogen/deuterium exchange mass spectrometry (HDX-MS) and kinase activity profiling to map the conformational dynamics associated with substrate binding and Src-mediated activation loop phosphorylation. Nucleotide engagement stabilizes the autoinhibitory interface, while phosphorylation deprotects both FERM and kinase regulatory surfaces. Phosphorylation organizes active site motifs linking catalytic loop with activation segment. Dynamics of the activation segment anchor propagate to EF/G-helices to prevent reversion of the autoinhibitory FERM interaction. We employ targeted mutagenesis to dissect how phosphorylation-induced conformational rearrangements elevate kinase activity above the basal autophosphorylation rate.
A decrease in fatty acid synthesis rescues cells with limited peptidoglycan synthesis capacity
Authors: Willdigg Jessica R. , Patel Yesha , Helmann John D.
Published: December 2022

Proper synthesis and maintenance of a multilayered cell envelope is critical for bacterial fitness. However, whether mechanisms exist to coordinate synthesis of the membrane and peptidoglycan layers is unclear. InBacillus subtilis, synthesis of peptidoglycan (PG) during cell elongation is mediated by an elongasome complex acting in concert with class A PBPs (aPBPs). We previously described mutant strains limited in their capacity for PG synthesis due to a loss of aPBPs and an inability to compensate by upregulation of elongasome function. Growth of these PG-limited cells can be restored by suppressor mutations predicted to decrease membrane synthesis. One suppressor mutation leads to an altered function repressor, FapR*, that functions as a super-repressor and leads to decreased transcription of fatty acid synthesis (FAS) genes. Consistent with fatty acid limitation mitigating cell wall synthesis defects, inhibition of FAS by cerulenin also restored growth of PG-limited cells. Moreover, cerulenin can counteract the inhibitory effect of β-lactams in some strains. These results imply that limiting PG synthesis results in impaired growth, in part, due to an imbalance of PG and cell membrane synthesis and thatB. subtilislacks a robust physiological mechanism to reduce membrane synthesis when PG synthesis is impaired.

Importance

Understanding how a bacterium coordinates cell envelope synthesis is essential to fully appreciate how bacteria grow, divide, and resist cell envelope stresses such as β-lactam antibiotics. Balanced synthesis of the peptidoglycan cell wall and the cell membrane is critical for cells to maintain shape, turgor pressure and resist external cell envelope threats. UsingBacillus subtilis, we show that cells deficient in peptidoglycan synthesis can be rescued by compensatory mutations that decrease the synthesis of fatty acids. Further, we show that inhibiting fatty acid synthesis with cerulenin is sufficient to restore growth of cells deficient in peptidoglycan synthesis. Understanding the coordination of cell wall and membrane synthesis may provide insights relevant to antimicrobial treatment.
Low Dimensional Chaotic Attractors in Daily Hospital Occupancy from COVID-19 in the USA and Canada
Authors: Gonçalves Carlos Pedro
Published: December 2022

Epidemiological application of chaos theory methods have uncovered the existence of chaotic markers in SARS-CoV-2’s epidemiological data, including low dimensional attractors with positive Lyapunov exponents, and evidence markers of a dynamics that is close to the onset of chaos for different regions. We expand on these previous works, performing a comparative study of United States of America (USA) and Canada’s COVID-19 daily hospital occupancy cases, applying a combination of chaos theory, machine learning and topological data analysis methods. Both countries show markers of low dimensional chaos for the COVID-19 hospitalization data, with a high predictability for adaptive artificial intelligence systems exploiting the recurrence structure of these attractors, with more than 95%R2scores for up to 42 days ahead prediction. The evidence is favorable to the USA’s hospitalizations being closer to the onset of chaos and more predictable than Canada, the reasons for this higher predictability are accounted for by using topological data analysis methods.
Non-targeted metabolomics identifies erythronate accumulation in cancer cells
Authors: Zhang Jie , Keibler Mark A. , Dong Wentao , Ghelfi Jenny , Cordes Thekla , Kanashova Tamara , Pailot Arnaud , Linster Carole , Dittmar Gunnar , Metallo Christian M. , Lautenschlaeger Tim , Hiller Karsten , Stephanopoulos Gregory
Published: December 2022

Using a non-targeted isotope-assisted metabolomics approach, we identified erythronate as a metabolite that accumulates in several human cancer cell lines. Erythronate has been reported to be a detoxification product derived from off-target glycolytic metabolism. We provide data supporting a possible alternative route to erythronate production involving the dephosphorylation of the pentose phosphate pathway intermediate erythrose-4-phosphate to form erythrose, followed by the oxidation of erythrose by an aldehyde dehydrogenase. Finally, we detected increased erythronate concentrations in tumors relative to adjacent normal tissues from lung cancer patients. These findings suggest the accumulation of erythronate to be an example of metabolic reprogramming in cancer cells, raising the possibility that elevated level of erythronate may serve as a biomarker of certain types of cancer.
Conformational dynamics of cohesin/Scc2 loading complex are regulated by Smc3 acetylation and ATP binding
Authors: Kaushik Aditi , Than Thane , Petela Naomi J , Voulgaris Menelaos , Percival Charlotte , Daniels Peter , Rafferty John B , Nasmyth Kim A , Hu Bin
Published: December 2022

The ring-shaped cohesin complex is the key player in sister chromatid cohesion, DNA repair, and gene transcription. The loading of cohesin to chromosomes requires the loader Scc2 and is regulated by ATP. This process is also hindered by Smc3 acetylation. However, the molecular mechanism underlying this inhibition remains mysterious. Here we identify a novel configuration of Scc2 with pre-engaged cohesin and reveal dynamic conformations of the cohesin/Scc2 complex in the loading reaction. We demonstrate that Smc3 acetylation blocks the association of Scc2 with pre-engaged cohesin by impairing the interaction of Scc2 with Smc3’s head. Lastly, we show that ATP binding induces the cohesin/Scc2 complex to clamp DNA by promoting the interaction between Scc2 and Smc3 coiled coil. Our results illuminate a dynamic reconfiguration of the cohesin/Scc2 complex during loading and indicate how Smc3 acetylation and ATP regulate this process.
Elevated plasma and urinary erythritol is a biomarker of excess simple carbohydrate intake in mice
Authors: Ortiz Semira R. , Field Martha S.
Published: December 2022

Background

Elevated serum erythritol is a predictive biomarker of diabetes and cardiovascular incidence and complications. Erythritol is synthesized endogenously from glucose, but little is known regarding the origin of elevated circulating erythritolin vivo.

Objective

In vitroevidence indicates that intracellular erythritol is elevated by high-glucose cell culture conditions and that final step of erythritol synthesis is catalyzed by the enzymes SORD and ADH1. The purpose of this study was to determine if dietary intake and/or diet-induced obesity (DIO) affect erythritol synthesis in mice, and if this relationship is modified by loss of the enzymes SORD or ADH1.

Methods

First, 8-week-old, maleSord+/+,Sord-/-,Adh1+/+, andAdh1-/-mice were fed either low-fat diet (LFD) with 10% fat-derived calories or DIO high-fat diet (HFD) with 60% fat-derived calories for 8 weeks. Plasma and tissue erythritol were measured using GC-MS. Second, wild-type 8-week-old C57BL/6J mice were fed LFD or HFD with plain drinking water or 30% sucrose water for 8 weeks. Blood glucose and plasma and urinary erythritol were measured in non-fasted and fasted samples. Tissue erythritol was measured following sacrifice. Finally,Sord+/+andSord-/-mice were fed LFD with 30% sucrose water for two weeks, then non-fasted plasma, urine, and tissue erythritol were quantified.

Results

Plasma and tissue erythritol were not impacted by loss ofSordorAdh1on LFD or HFD. In wild-type mice, consumption of 30% sucrose water significantly elevated plasma and urinary erythritol on both LFD and HFD compared to plain water.Sordgenotype did not affect plasma or urinary erythritol in response to sucrose feeding, butSord-/-mice had reduced kidney erythritol content compared to wildtype littermates in response to sucrose.

Conclusions

Sucrose intake, not high-fat diet, elevates erythritol synthesis and excretion in mice. Loss of ADH1 or SORD does not significantly impact erythritol levels in mice.
A novel type of monocytic leukemia stem cell revealed by the clinical use of venetoclax-based therapy
Authors: Pei Shanshan , Gillen Austin E , Shelton Ian T , Stevens Brett M , Gasparetto Maura , Engel Krysta , Staggs Sarah , Wang Yanan , Showers William , Inguva Anagha , Amaya Maria L , Minhajuddin Mohammad , Winters Amanda , Patel Sweta B , Tolison Hunter , Krug Anna , Young Tracy N , Schowinsky Jeffrey , McMahon Christine , Smith Clayton A , Pollyea Daniel A , Jordan Craig T
Published: December 2022

The BCL-2 inhibitor venetoclax has recently emerged as an important component of acute myeloid leukemia (AML) therapy. Notably, use of this agent has revealed a previously unrecognized form of pathogenesis characterized by monocytic disease progression. We demonstrate that this form of disease arises from a fundamentally different type of leukemia stem cell (LSC), which we designate as monocytic LSC (m-LSC), that is developmentally and clinically distinct from the more well-described primitive LSC (p-LSC). The m-LSC is distinguished by a unique immunophenotype (CD34-, CD4+, CD11b-, CD14-, CD36-), unique transcriptional state, reliance on purine/pyrimidine metabolism, and selective sensitivity to cladribine. Critically, in some instances m-LSC and p-LSC subtypes can co-reside in the same AML patient and simultaneously contribute to overall tumor complexity. Thus, our findings demonstrate that LSC heterogeneity has direct clinical significance and highlights the need to distinguish and target m-LSCs as a means to improve clinical outcomes with venetoclax-based regimens.

Statement of Significance

These studies identify and characterize a new type of human acute myeloid leukemia stem cell (LSC) that is responsible for monocytic disease progression in acute myeloid leukemia (AML) patients treated with venetoclax-based regimens. Our studies describe the phenotype, molecular properties, and drug sensitivities of this unique LSC subclass.
Coordinated Regulation of Cdc42ep1, Actin, and Septin Filaments during Neural Crest Cell Migration
Authors: Kho Mary , Hladyshau Siarhei , Tsygankov Denis , Nie Shuyi
Published: December 2022

The septin cytoskeleton has been demonstrated to interact with other cytoskeletal components to regulate various cellular processes, including cell migration. However, the mechanisms of how septin regulates cell migration are not fully understood. In this study, we use the highly migratory neural crest cells of frog embryos to examine the role of septin filaments in cell migration. We found that septin filaments are required for proper migration of neural crest cells by controlling both the speed and the direction of cell migration. We further determined that septin filaments regulate these features of cell migration by interacting with actin stress fibers. In neural crest cells, septin filaments co-align with actin stress fibers, and the loss of septin filaments leads to impaired stability and contractility of actin stress fibers. In addition, we showed that a partial loss of septin filaments leads to drastic changes in the orientations of newly formed actin stress fibers, suggesting that septin filaments help maintain the persistent orientation of actin stress fibers during directed cell migration. Lastly, our study revealed that these activities of septin filaments depend on Cdc42ep1, which co-localizes with septin filaments in the center of neural crest cells. Cdc42ep1 interacts with septin filaments in a reciprocal manner, with septin filaments recruiting Cdc42ep1 to the cell center and Cdc42ep1 supporting the formation of septin filaments.