bluuebunny/crossref_metadata_2025 huggingface dataset:
NBTI attenuates neuroinflammation and apoptosis partly by ENT1/NLRP3/Bcl2 pathway after subarachnoid hemorrhage in rats
Authors: Chen Xiaowei , Luo Xiaocheng , Hu Hang , Xu Qianghua
Published: October 2021

Objectives

Neuroinflammation and apoptosis are two key factors contributing to early brain injury (EBI) after subarachnoid hemorrhage (SAH) and are strongly associated with a poor prognosis. Recently, equilibrative nucleoside transporter 1 (ENT1) was emerged to accelerate the severity of inflammation and cell apoptosis in several nervous system diseases, including cerebral ischemia, neurodegeneration and epilepsy. However, no study has yet elaborated the expression levels and effects of ENT1 in EBI after SAH.

Methods

Sprague–Dawley rats were subjected to SAH by endovascular perforation. Nitrobenzylthioinosine (NBTI) was intranasally administered at 0.5 h after SAH. The protein expression levels of ENT1, NLRP3, Bcl2, Bax, ACS, Caspase-1, IL-1 were detected by western blot. The modified Garcia score and beam balance score were employed to evaluate the neurologic function of rats following SAH. In addition, hematoxylin-eosin, fluoro-jade C and TdT-mediated dUTP nick-end labeling staining were then used to evaluate brain tissue damage and neuronal apoptosis.

Results

Analysis indicated that endogenous levels of ENT1 were significantly upregulated at 24-hour post-SAH, accompanied by NLRP3 inflammasome activation and Bcl2 decline. The administration of NBTI, an inhibitor of ENT1, at a dose of 15 mg/kg, ameliorated neurologic deficits and morphologic lesions at both 24 and 72 h after SAH. Moreover, ENT1 inhibition efficiently mitigated neuronal degeneration and cell apoptosis. In addition, NBTI at 15 mg/kg observably increased Bcl2 content and decreased Bax level. Furthermore, suppression of ENT1 notably reduced the expression levels of NLRP3, apoptosis associated speck like protein containing CARD, caspase-1 and IL-1β.

Conclusions

NBTI relieved SAH-induced EBI partly through ENT1/NLRP3/Bcl2 pathway.
Characterization of a pESI-like plasmid and analysis of multidrug-resistant Salmonella enterica Infantis isolates in England and Wales
Authors: Lee Winnie W. Y. , Mattock Jennifer , Greig David R. , Langridge Gemma C. , Baker David , Bloomfield Samuel , Mather Alison E. , Wain John R. , Edwards Andrew M. , Hartman Hassan , Dallman Timothy J. , Chattaway Marie A. , Nair Satheesh
Published: October 2021

Salmonella enterica

serovar Infantis is the fifth most common

Salmonella

serovar isolated in England and Wales. Epidemiological, genotyping and antimicrobial-resistance data for

S

.

enterica

Infantis isolates were used to analyse English and Welsh demographics over a 5 year period. Travel cases associated with

S

.

enterica

Infantis were mainly from Asia, followed by cases from Europe and North America. Since 2000, increasing numbers of

S

.

enterica

Infantis had multidrug resistance determinants harboured on a large plasmid termed ‘plasmid of emerging

S

.

enterica

Infantis’ (pESI). Between 2013 and 2018, 42

S

.

enterica

Infantis isolates were isolated from humans and food that harboured resistance determinants to multiple antimicrobial classes present on a pESI-like plasmid, including extended-spectrum β-lactamases (ESBLs; bla
CTX-M-65). Nanopore sequencing of an ESBL-producing human

S

.

enterica

Infantis isolate indicated the presence of two regions on an IncFIB pESI-like plasmid harbouring multiple resistance genes. Phylogenetic analysis of the English and Welsh

S

.

enterica

Infantis population indicated that the majority of multidrug-resistant isolates harbouring the pESI-like plasmid belonged to a single clade maintained within the population. The bla
CTX-M-65 ESBL isolates first isolated in 2013 comprise a lineage within this clade, which was mainly associated with South America. Our data, therefore, show the emergence of a stable resistant clone that has been in circulation for some time in the human population in England and Wales, highlighting the necessity of monitoring resistance in this serovar.
Genetic evidence supports the development of SLC26A9 targeting therapies for the treatment of lung disease
Authors: Gong Jiafen , He Gengming , Wang Cheng , Bartlett Claire , Panjwani Naim , Mastromatteo Scott , Lin Fan , Keenan Katherine , Avolio Julie , Halevy Anat , Shaw Michelle , Esmaeili Mohsen , Côté-Maurais Guillaume , Adam Damien , Bégin Stéphanie , Bjornson Candice , Chilvers Mark , Reisman Joe , Price April , Parkins Michael , Van Wylick Richard , Berthiaume Yves , Bilodeau Lara , Mateos-Corral Dimas , Hughes Daniel , Smith Mary J. , Morrison Nancy , Brusky Janna , Tullis Elizabeth , Stephenson Anne L. , Quon Bradley S. , Wilcox Pearce , Leung Winnie M. , Solomon Melinda , Sun Lei , Brochiero Emmanuelle , Moraes Theo J. , Gonska Tanja , Ratjen Felix , Rommens Johanna M. , Strug Lisa J.
Published: October 2021

Background

Over 400 variants in the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) are CF-causing. CFTR modulators target variants to improve lung function, but marked variability in response exists and current therapies do not address all CF-causing variants highlighting unmet needs. Alternative epithelial ion channel/transporters such as SLC26A9 could compensate for CFTR dysfunction, providing therapeutic targets that may benefit all individuals with CF.

Method

We investigate the relationship between rs7512462, a marker ofSLC26A9activity, and lung function pre- and post-treatment with CFTR modulators in Canadian and US CF cohorts, in the general population, and in those with chronic obstructive pulmonary disease (COPD).

Results

Rs7512462 CC genotype is associated with greater lung function in CF individuals with minimal function variants (for which there are currently no approved therapies; p=0.008); and for gating (p=0.033) and p.Phe508del/ p.Phe508del (p=0.006) genotypes upon treatment with CFTR modulators. In parallel, human nasal epithelia with CC and p.Phe508del/p.Phe508del after Ussing chamber analysis of a combination of approved and experimental modulator treatments show greater CFTR function (p=0.0022). Beyond CF, rs7512462 is associated with lung function in a meta-analysis of the UK Biobank and Spirometa Consortium (min p=2.74×0-44) and provides p=0.0891 in an analysis of COPD case-control status in the UK Biobank defined by spirometry.

Conclusion

These findings support SLC26A9 as a therapeutic target to improve lung function for all people with CF and in individuals with other obstructive lung diseases.
High risk of SARS-CoV-2 infection among frontline healthcare workers in Northeast Brazil: a respondent-driven sampling approach
Authors: Albuquerque Maria de Fátima Pessoa Militão de , de Souza Wayner Vieira , Montarroyos Ulisses Ramos , Pereira Cresio Romeu , Braga Cynthia , de Araújo Thália Velho Barreto , de Alencar Ximenes Ricardo Arraes , de Barros Miranda-Filho Demócrito , Szwarcwald Célia Landmann , de Souza Junior Paulo Roberto Borges , do Nascimento Xavier Morgana , de Morais Clarice Neuenschwander Lins , de Albuquerque Gabriela Diniz Militao , Bresani Salvi Cristiane C. , de Araújo Mariz Carolline , de Siqueira Filha Noêmia Teixeira , Galindo Jadson Mendonça , de França Neto Cláudio Luiz , Barbosa Jessyka Mary Vasconcelos , de Sousa Mascena Veras Maria Amelia , Lima Luana Nepomuceno Gondim Costa , Cruz Luciane Nascimento , Kendall Carl , Kerr Ligia Regina Franco Sansigolo , Martelli Celina Maria Turchi
Published: October 2021

Introduction

The disparities in the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among frontline health care workers (HCWs) and the unique work circumstances are poorly documented for low-and middle-income countries.

Methods

We assessed the frequency of SARS-CoV-2 infection, personal protective equipment (PPE) shortages, PPE use, and accidents involving biological material among HCWs in the Recife metropolitan area, Northeast Brazil. Using respondent driven sampling, we included HCWs attending suspected or confirmed COVID-19 patients from May 2020 to February 2021.

Results

We analyzed 1,525 HCWs (527 physicians, 471 registered nurses, 263 nursing assistants/technicians, and 264 physical therapists). Women predominated in all categories (81.1%). Nurses were older and had more comorbidities (hypertension and overweight/obesity) than the other HCWs. The overall prevalence of SARS-CoV-2 infection was 61.8% after adjustment for the cluster random effect, weighted by network, and reference population size. The independent risk factors for a positive RT-PCR test were being a nursing assistant (OR adjusted: 2.56), not always using all recommended PPE in routine practice (ORadj: 2.15), and reporting a splash of biological fluid/respiratory secretion in the eyes (ORadj: 3.37).

Conclusions

The high risk of infection among HCWs reflects PPE shortages and younger, possibly less experienced, frontline HCWs. There were disparities in the risk of SARS-CoV-2 infection among HCWs, with nursing assistants being the most vulnerable, possibly due to their longer and frequent contact with COVID-19 patients.
A novel framework based on deep learning and ANOVA feature selection method for diagnosis of COVID-19 cases from chest X-ray Images
Authors: Nasiri Hamid , Alavi Seyyed Ali
Published: October 2021

The new coronavirus (known as COVID-19) was first identified in Wuhan and quickly spread worldwide, wreaking havoc on the economy and people’s everyday lives. Fever, cough, sore throat, headache, exhaustion, muscular aches, and difficulty breathing are all typical symptoms of COVID-19. A reliable detection technique is needed to identify affected individuals and care for them in the early stages of COVID-19 and reduce the virus’s transmission. The most accessible method for COVID-19 identification is RT-PCR; however, due to its time commitment and false-negative results, alternative options must be sought. Indeed, compared to RT-PCR, chest CT scans and chest X-ray images provide superior results. Because of the scarcity and high cost of CT scan equipment, X-ray images are preferable for screening. In this paper, a pre-trained network, DenseNet169, was employed to extract features from X-ray images. Features were chosen by a feature selection method (ANOVA) to reduce computations and time complexity while overcoming the curse of dimensionality to improve predictive accuracy. Finally, selected features were classified by XGBoost. The ChestX-ray8 dataset, which was employed to train and evaluate the proposed method. This method reached 98.72% accuracy for two-class classification (COVID-19, healthy) and 92% accuracy for three-class classification (COVID-19, healthy, pneumonia).
Explainable Transformer-Based Neural Network for the Prediction of Survival Outcomes in Non-Small Cell Lung Cancer (NSCLC)
Authors: Kipkogei Elly , Arango Argoty Gustavo Alonso , Kagiampakis Ioannis , Patra Arijit , Jacob Etai
Published: October 2021

In this paper, we introduce the “Clinical Transformer” - a recasting of the widely used transformer architecture as a method for precision medicine to model relations between molecular and clinical measurements, and the survival of cancer patients. Although the emergence of immunotherapy offers a new hope for cancer patients with dramatic and durable responses having been reported, only a subset of patients demonstrate benefit. Such treatments do not directly target the tumor but recruit the patient’s immune system to fight the disease. Therefore, the response to therapy is more complicated to understand as it is affected by the patient’s physical condition, immune system fitness and the tumor. As in text, where the semantics of a word is dependent on the context of the sentence it belongs to, in immuno-therapy a biomarker may have limited meaning if measured independent of other clinical or molecular features. Hence, we hypothesize that the transformer-inspired model may potentially enable effective modelling of the semantics of different biomarkers with respect to patients’ survival time. Herein, we demonstrate that this approach can offer an attractive alternative to the survival models utilized in current practices as follows: (1) We formulate an embedding strategy applied to molecular and clinical data obtained from the patients. (2) We propose a customized objective function to predict patient survival. (3) We show the applicability of our proposed method to bioinformatics and precision medicine. Applying the clinical transformer to several immuno-oncology clinical studies, we demonstrate how the clinical transformer outperforms other linear and non-linear methods used in current practice for survival prediction. We also show that when initializing the weights of a domain-specific transformer by the weights of a cross-domain transformer, we further improve the predictions. Lastly, we show how the attention mechanism successfully captures some of the known biology behind these therapies.
Predictive value of circulating NMR metabolic biomarkers for type 2 diabetes risk in the UK Biobank study
Authors: Bragg Fiona , Trichia Eirini , Aguilar-Ramirez Diego , Bešević Jelena , Lewington Sarah , Emberson Jonathan
Published: October 2021

Background

Effective targeted prevention of type 2 diabetes (T2D) depends on accurate prediction of disease risk. We assessed the role of metabolomic profiling in improving T2D risk prediction beyond conventional risk factors.

Methods

NMR-metabolomic profiling was undertaken on baseline plasma samples in 65,684 UK Biobank participants without diabetes and not taking lipid-lowering medication. Cox regression yielded adjusted hazard ratios for the associations of 143 individual metabolic biomarkers (including lipids, lipoproteins, fatty acids, amino acids, ketone bodies and other low molecular weight metabolic biomarkers) and 11 metabolic biomarker principal components (PCs) (accounting for 90% of total variance in individual biomarkers) with incident T2D. These 11 PCs were added to established models for T2D risk prediction, and measures of risk discrimination (c-statistic) and reclassification (continuous net reclassification improvement [NRI], integrated discrimination index [IDI]) were assessed.

Findings

During median 11.9 (IQR 11.1-12.6) years’ follow-up, 1719 participants developed T2D. After accounting for multiple testing, 118 metabolic biomarkers showed independent associations with T2D risk (false discovery rate controlled p<0.05), of which 103 persisted after additional adjustment for HbA1c. Overall, 10 metabolic biomarker PCs were independently associated with T2D. Addition of PCs to the established risk prediction model (including age, sex, parental history of diabetes, body mass index and HbA1c) improved T2D risk prediction as assessed by the c-statistic (increased from 0.802 [95% CI 0.791-0.812] to 0.830 [0.822-0.841]), continuous NRI (0.44 [0.38-0.49]), and relative (15.0% [10.5%-20.4%]) and absolute (1.5 [1.0-1.9]) IDI.

Interpretation

When added to conventional risk factors, circulating NMR-based metabolic biomarkers enhanced T2D risk prediction.

Funding

BHF, MRC, CRUK
Multi-parameter optical imaging of immune cell activity in chimeric antigen receptor T-cell and checkpoint blockade therapies
Authors: Xie Jinghang , Rami Fadi El , Zhou Kaixiang , Simonetta Federico , Chen Zixin , Zheng Xianchuang , Chen Min , Balakrishnan Preethi B. , Dai Sheng-Yao , Murty Surya , Alam Israt S. , Baker Jeanette , Negrin Robert S. , Gambhir Sanjiv S. , Rao Jianghong
Published: October 2021

Longitudinal multimodal imaging presents unique opportunities for noninvasive surveillance and prediction of treatment response to cancer immunotherapy. In this work we first designed a novel granzyme B activated self-assembly small molecule, G-SNAT, for quantitative assessment of cytotoxic T lymphocyte mediated cancer cell killingin vivo. In lymphoma tumor bearing mice, the retention of cyanine 5 labeled G-SNAT-Cy5 was shown to be highly correlated to CAR T-cell mediated granzyme B release and tumor eradication. In colorectal tumor-bearing transgenic mice, expressing firefly luciferase in hematopoietic cells, and which received combination treatment of anti-PD-1 and anti-CTLA-4, longitudinal bioluminescence and fluorescence imaging revealed the dynamics of immune cell expansion, trafficking, tumor infiltration, and cytotoxic activity which predicted therapeutic outcome before tumor shrinkage was evident. These results support further development of G-SNAT for imaging early immune response to checkpoint blockade and CAR T-cell therapy in patients and highlight the utility of multimodality imaging for improved mechanistic insights into cancer immunotherapy.
Ubiquitin Proteasome Pathway annotation in Diaphorina citri can reveal potential targets for RNAi based pest management
Authors: Tank Will , Shippy Teresa , Thate Amanda , Massimino Crissy , Hosmani Prashant S , Flores-Gonzalez Mirella , Mueller Lukas A , Hunter Wayne B , Brown Susan J , Delia Tom , Saha Surya
Published: October 2021

Ubiquitination is an ATP-dependent process that targets proteins for degradation by the proteasome. In this study, we annotated 15 genes from the ubiquitin-proteasome pathway in the Asian citrus psyllid, Diaphorina citri. This psyllid vector has come to prominence in the last decade due to its role in the transmission of the devastating bacterial pathogen, Candidatus Liberibacter asiaticus (CLas). Infection of citrus crops by this pathogen causes Huanglongbing (HLB or citrus greening disease) and results in the eventual death of citrus trees. The identification and correct annotation of these genes in D. citri will be useful for functional genomic studies that aid in the development of RNAi-based management strategies aimed at reducing the spread of HLB. Investigating the effects of CLas infection on the expression of ubiquitin-proteasome pathway genes may provide new information regarding the role that these genes play in the acquisition and transmission of CLas by D. citri.
Fast adaptation of cooperative channels engenders Hopf bifurcations in auditory hair cells
Authors: Gianoli Francesco , Hogan Brenna , Dilly Émilien , Risler Thomas , Kozlov Andrei S.
Published: October 2021

Since the pioneering work of Thomas Gold published in 1948, it has been known that we owe our sensitive sense of hearing to a process in the inner ear that can amplify incident sounds on a cycle-by-cycle basis. Termed the active process, it uses energy to counteract the viscous dissipation associated with sound-evoked vibrations of the ear’s mechanotransduction apparatus. Despite its importance, the mechanism of the active process and the proximate source of energy that powers it have remained elusive—especially at the high frequencies characteristic of mammalian hearing. This is partly due to our insufficient understanding of the mechanotransduction process in hair cells, the sensory receptors and amplifiers of the inner ear. It has previously been proposed that a cyclical binding of Ca2+ ions to individual mechanotransduction channels could power the active process. That model, however, relied on tailored reaction rates that structurally forced the direction of the cycle. Here, we ground our study on our previous model of hair-cell mechanotransduction, which relied on the cooperative gating of pairs of channels, and incorporate into it the cyclical binding of Ca2+ ions. With a single binding site per channel and reaction rates drawn from thermodynamic principles, our model shows that hair cells behave as nonlinear oscillators that exhibit Hopf bifurcations, dynamical instabilities long understood to be signatures of the active process. Using realistic parameter values, we find bifurcations at frequencies in the kilohertz range with physiological Ca2+ concentrations. In contrast to the myosin-based mechanism, responsible for low-frequency relaxation oscillations in the vestibular hair cells of amphibians, the current model relies on the electrochemical gradient of Ca2+ as the only energy source for the active process and on the relative motion of cooperative channels within the stereociliary membrane as the single mechanical driver. Equipped with these two mechanisms, a hair bundle proves capable of operating at frequencies in the kilohertz range, characteristic of mammalian hearing.

SIGNIFICANCE

How the inner ear amplifies incident sounds at audible frequencies of several kilohertz is a key question that has remained unanswered despite decades of research into several candidate mechanisms. Here, we model the behavior of hair cells, the sensory receptors of the inner ear, and show that they can undergo oscillatory instabilities called Hopf bifurcations due to the effect of Ca2+ on the cooperative opening and closing of mechanotransduction ion channels. Close to the bifurcation point, a hair cell behaves as a nonlinear oscillator that can amplify its input on a cycle-by-cycle basis. We find that our proposed mechanism can operate in the kilohertz range.
The R346K Mutation in the Mu Variant of SARS-CoV-2 Alter the Interactions with Monoclonal Antibodies from Class 2: A Free Energy of Perturbation Study
Authors: Fratev Filip
Published: October 2021

The Mu variant of SARS-CoV-2 has been recently classified as a variant of interest (VOI) by the world health organization (WHO) but limited data are available at the moment. In particular, a special attention was given to the R346K mutation located in the receptor binding domain (RBD). In the current study we performed Free energy of perturbation (FEP) calculations to elucidate it possible impact on a set of neutralizing monoclonal antibodies (mAbs) which have been shown to be strong inhibitors of the most other known COVID-19 variants. Our results show that R346K affects the class 2 antibodies but its effect is not so significant (0.66 kcal/mol); i.e. reduces the binding with RBD about 3 times. An identical value was calculated also in the presence of both class 1 and class 2 antibodies (BD-812/836). Further, a similar reduction in the binding (0.4 kcal/mol) was obtained for BD-821/771 pair of mAbs. For comparison, the addition of K417N mutation, present in the newly registered Mu variant in July 2021 in UK, affected the class 1 mAbs by 1.29 kcal/mol reducing stronger the binding by about 10 times. Thus, the resistance effect of R346K mutation in the Mu variant is possible but not so significant and is due to the additional decrease of antibody neutralization based on the reduced binding of class 2 antibodies.
Prion-like α-synuclein pathology in the brains of infants: Krabbe disease as a novel seed-competent α-synucleinopathy
Authors: Hatton Christopher , Ghanem Simona S. , Koss David J. , Abdi Ilham Y. , Gibbons Elizabeth , Guerreiro Rita , Bras Jose ,   International DLB Genetics Consortium, Walker Lauren , Gelpi Ellen , Heywood Wendy , Outeiro Tiago F. , Attems Johannes , McFarland Bobby , Forsyth Rob , El-Agnaf Omar M. , Erskine Daniel
Published: October 2021

Krabbe disease (KD) is an infantile neurodegenerative disorder resulting from pathogenic variants in the GALC gene which causes accumulation of the toxic sphingolipid psychosine. GALC variants are associated with increased risk of Lewy body diseases (LBD), an umbrella term for age-associated neurodegenerative diseases in which the protein α-synuclein aggregates into Lewy bodies. To explore whether α-synuclein in KD has pathological similarities to that in LBD, we compared post-mortem KD tissue to that of infant control cases and identified alterations to α-synuclein localisation and expression of modifications associated with LBD. To determine whether α-synuclein in KD displayed pathogenic properties associated with LBD we evaluated its seeding capacity using the real-time quaking-induced conversion assay. Strikingly, seeded aggregation of α-synuclein resulted in the formation of fibrillar aggregates similar to those observed in LBD, confirming the prion-like capacity of KD-derived α-synuclein. These observations constitute the first report of prion-like α-synuclein in the brain tissue of infants and challenge the putative view that α-synuclein pathology is merely an age-associated phenomenon, instead suggesting it can result from alterations to biological processes such as sphingolipid homeostasis. Our findings have important implications for understanding the mechanisms underlying Lewy body formation in LBD.
The Nup2 meiotic-autonomous region relieves autoinhibition of Nup60 to promote progression of meiosis and sporulation in Saccharomyces cerevisiae
Authors: Komachi Kelly , Burgess Sean M.
Published: October 2021

During meiosis, chromosomes undergo dramatic changes in structural organization, nuclear positioning, and motion. Although the nuclear pore complex has been shown to affect genome organization and function in vegetative cells, its role in meiotic chromosome dynamics has remained largely unexplored. Recent work in the budding yeast Saccharomyces cerevisiae demonstrated that the mobile nucleoporin Nup2 is required for normal progression through meiosis I prophase and sporulation in strains where telomere-led chromosome movement has been compromised. The meiotic autonomous region (MAR), a short fragment of Nup2 responsible for its role in meiosis, was shown to localize to the nuclear envelope via Nup60 and to bind to meiotic chromosomes. To understand the relative contribution these two activities have on MAR function, we first carried out a screen for MAR mutants defective in sporulation and found that all the mutations disrupt interaction with both Nup60 and meiotic chromosomes. Moreover, nup60 mutants phenocopy nup2 mutants, exhibiting similar nuclear division kinetics, sporulation efficiencies, and genetic interactions with mutations that affect the telomere bouquet. Although full-length Nup60 requires Nup2 for function, removal of Nup60’s C-terminus allows Nup60 to bind meiotic chromosomes and promote sporulation without Nup2. In contrast, binding of the MAR to meiotic chromosomes is completely dependent on Nup60. Our findings uncover an inhibitory function for the Nup60 C-terminus and suggest that Nup60 mediates recruitment of meiotic chromosomes to the nuclear envelope, while Nup2 plays a secondary role counteracting Nup60’s autoinhibition.
AMPK mediates early activation of the unfolded protein response through a positive feedback loop in palmitate-treated muscle cells
Authors: Gong Jing , Wang Lu , Tao Wuchen , Liu Zonghan , Pang Xiangsheng , Li Wenjiong , Liu Yaxuan , Chen Xiaoping , Zhang Peng
Published: October 2021

Activation of the unfolded protein response (UPR) is closely associated with the pathogenesis of many metabolic diseases including obesity and type 2 diabetes. There is increasing evidence for the interdependence of the UPR and metabolic signaling pathways. The AMP-activated protein kinase (AMPK) signaling pathway controls energy balance in eukaryotes. The aim of this study was to investigate the possible interaction between AMPK signaling and the UPR in muscle cells exposed to a saturated fatty acid, as well as the underlying mechanism. The UPR was induced in C2C12 myotubes by treatment with palmitate along with activation of AMPK signaling. Inhibiting the AMPK pathway with compound C attenuated palmitate-induced UPR activation, while inhibiting the UPR with taurourdodeoxycholic acid alleviated palmitate-induced AMPK activation, suggesting a positive feedback loop between the UPR and AMPK. Additionally, 5-amino-1-β-D-ribofuranosylimidazole-4-carboxamide, an AMPK agonist, caused a dose- and time-dependent upregulation of genes related to the UPR, including activating transcription factor (ATF)4, binding immunoglobulin protein (BIP), and growth arrest and DNA damage-inducible protein (GADD)34. These results provide the first evidence for the involvement of AMPK signaling in the early activation of the UPR induced by saturated fatty acid in skeletal muscle, and suggest that physiologic or pharmacologic activation of the AMPK pathway (ie, by exercise or metformin, respectively) can promote skeletal muscle health and function and thus improve quality of life for individuals with metabolic disorder due to a high-fat diet or obesity.
Membrane permeability differentiation at the lipid divide
Authors: Łapińska Urszula , Glover Georgina , Kahveci Zehra , Irwin Nicholas A. T. , Milner David S. , Tourte Maxime , Albers Sonja-Verena , Santoro Alyson E. , Richards Thomas A. , Pagliara Stefano
Published: October 2021

One of the deepest branches in the tree of life separates the Archaea from the Bacteria. These prokaryotic groups have distinct cellular systems including fundamentally different phospholipid membrane bilayers. This dichotomy has been termed the lipid divide and possibly bestows different biophysical and biochemical characteristics on each cell type. Classic experiments suggest that bacterial membranes (formed from lipids extracted fromEscherichia colifor example) show permeability to key metabolites comparable to archaeal membranes (formed from lipids extracted fromHalobacterium salinarum), yet systematic analyses based on direct measurements of membrane permeability are absent. Here we develop a new approach for assessing the membrane permeability of ~10 μm unilamellar vesicles, consisting of an aqueous medium enclosed by a single lipid bilayer. Comparing the permeability of eighteen metabolites demonstrates that diether glycerol-1-phosphate lipids with methyl branches, often the most abundant membrane lipids of known archaea, are permeable to a wide range of compounds useful for core metabolic networks, including amino acids, sugars, and nucleobases. Permeability is significantly lower in diester glycerol-3-phosphate lipids without methyl branches, the common building block of bacterial membranes. To identify the membrane characteristics that determine permeability we use this experimental platform to test a variety of lipid forms bearing a diversity of intermediate characteristics. We found that increased membrane permeability is dependent on both the methyl branches present on the archaeal phospholipid tails and the ether bond between the tails and the head group. These permeability differences must have had profound effects on the cell physiology and proteome evolution of early prokaryotic forms. To explore this further, we compare the abundance and distribution of transmembrane transporter-encoding protein families present on genomes sampled from across the prokaryotic tree of life. Archaea have a reduced repertoire of transporter gene families, consistent with increased membrane permeation. These results demonstrate that the lipid divide demarcates a clear difference in permeability function with implications for understanding some of the earliest transitions in cell evolution.
Early evolution of beetles regulated by the end-Permian deforestation
Authors: Zhao Xianye , Yu Yilun , Clapham Matthew E. , Yan Evgeny , Chen Jun , Jarzembowski Edmund A. , Zhao Xiangdong , Wang Bo
Published: October 2021

The end-Permian mass extinction (EPME) led to a severe terrestrial ecosystem collapse. However, the ecological response of insects—the most diverse group of organisms on Earth—to the EPME remains poorly understood. Here, we analyse beetle evolutionary history based on taxonomic diversity, morphological disparity, phylogeny, and ecological shifts from the Early Permian to Middle Triassic, using a comprehensive new data set. Permian beetles were dominated by xylophagous stem groups with a high diversity and disparity, which probably played an underappreciated role in the Permian carbon cycle. Our suite of analyses shows that Permian xylophagous beetles suffered a severe extinction during the EPME largely due to the collapse of forest ecosystems, resulting in an Early Triassic gap of xylophagous beetles. New xylophagous beetles appeared widely in the early Middle Triassic, which is consistent with the restoration of forest ecosystems. Our results highlight the ecological significance of insects in deep-time terrestrial ecosystems.
Predicting Individual Traits from Unperformed Tasks
Authors: Gal Shachar , Tik Niv , Bernstein-Eliav Michal , Tavor Ido
Published: October 2021

Relating individual differences in cognitive traits to brain functional organization is a long-lasting challenge for the neuroscience community. Individual intelligence scores were previously predicted from whole-brain connectivity patterns, extracted from functional magnetic resonance imaging (fMRI) data acquired at rest. Recently, it was shown that task-induced brain activation maps outperform these resting-state connectivity patterns in predicting individual intelligence, suggesting that a cognitively demanding environment improves prediction of cognitive abilities. Here, we use data from the Human Connectome Project to predict task-induced brain activation maps from resting-state fMRI, and proceed to use these predicted activity maps to further predict individual differences in a variety of traits. While models based on original task activation maps remain the most accurate, models based on predicted maps significantly outperformed those based on the resting-state connectome. Thus, we provide a promising approach for the evaluation of measures of human behavior from brain activation maps, that could be used without having participants actually perform the tasks.
A multi-omics approach identifies pancreatic cancer cell extracellular vesicles as mediators of the unfolded protein response in normal pancreatic epithelial cells
Authors: Hinzman Charles P. , Bansal Shivani , Li Yaoxiang , Iliuk Anton , Girgis Michael , Singh Baldev , Herremans Kelly M. , Trevino Jose G. , Singh Vijay K. , Banerjee Partha P. , Cheema Amrita K.
Published: October 2021

Although cancer-derived extracellular vesicles (cEVs) are thought to play a pivotal role in promoting cancer progression events, their precise effect on neighboring normal cells is unknown. In this study, we investigated the impact of pancreatic cancer ductal adenocarcinoma (PDAC) derived EVs on recipient non-tumorigenic pancreatic normal epithelial cells upon internalization. We show that PDAC cEVs increase the proliferation and invasive capability of treated normal cells. We further demonstrate that cEVs induce endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) in treated normal pancreatic epithelial cells within 24 hours. Subsequently, these cells release several inflammatory cytokines. Leveraging a layered multi-omics approach, we analyzed EV cargo from a panel of 6 PDAC and 2 normal pancreas cell lines, using multiple EV isolation methods. We found that cEVs were enriched for an array of biomolecules which can induce or regulate ER stress and the UPR, including palmitic acid, sphingomyelins, metabolic regulators of tRNA charging and proteins which regulate trafficking and degradation. We further show that palmitic acid, at doses relevant to those found in cEVs, is sufficient to induce ER stress in normal pancreas cells. These results suggest that cEV cargo packaging may be designed to disseminate proliferative and invasive characteristics upon internalization by distant recipient normal cells, hitherto unreported. This study is among the first to highlight a major role for PDAC cEVs to induce stress in treated normal pancreas cells that may modulate a systemic response leading to altered phenotypes. For the first time, our study implicates cEV transported palmitic acid as a potential driver in this process. These findings highlight the importance of EVs in mediating disease etiology and open potential areas of investigation toward understanding the role of cEV lipids in promoting cell transformation in the surrounding microenvironment.
Creatine transporter deficient rat model show motor dysfunction, cerebellar alterations and muscle creatine deficiency without muscle atrophy
Authors: Duran-Trio Lara , Fernandes-Pires Gabriella , Grosse Jocelyn , Soro-Arnaiz Ines , Roux-Petronelli Clothilde , Binz Pierre-Alain , De Bock Katrien , Cudalbu Cristina , Sandi Carmen , Braissant Olivier
Published: October 2021

Creatine (Cr) is a nitrogenous organic acid and plays roles as fast phosphate energy buffer to replenish ATP, osmolyte, antioxidant, neuromodulator, and as a compound with anabolic and ergogenic properties in muscle. Cr is taken from the diet or endogenously synthetized by the enzymes AGAT and GAMT, and specifically taken up by the transporter SLC6A8. Loss-of-function mutations in the genes encoding for the enzymes or the transporter cause Cerebral Creatine Deficiency Syndromes (CCDS). CCDS are characterized by brain Cr deficiency, intellectual disability with severe speech delay, behavioral troubles, epilepsy and motor dysfunction. Among CCDS, the X-linked Cr transporter deficiency (CTD) is the most prevalent with no efficient treatment so far. Different animal models of CTD show reduced brain Cr levels, cognitive deficiencies and together they cover other traits similar to those of patients. However, motor function was poorly explored in CTD models and some controversies in the phenotype exist in comparison with CTD patients. Our recently described Slc6a8Y389C knock-in (KI) rat model of CTD showed mild impaired motor function, morphological alterations in cerebellum, reduced muscular mass, Cr deficiency and increased guanidinoacetate content in muscle, although no consistent signs of muscle atrophy. Our results indicate that such motor dysfunction co-occurred with both nervous and muscle dysfunction, suggesting that muscle strength and performance as well as neuronal connectivity might be affected by this Cr deficiency in muscle and brain.
Phylogenomic analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving the diversifications, with insights into the complex biogeographic history in the Northern Hemisphere
Authors: Liu Bin-Bin , Ren Chen , Kwak Myounghai , Hodel Richard G.J. , Xu Chao , He Jian , Zhou Wen-Bin , Huang Chien-Hsun , Ma Hong , Qian Guan-Ze , Hong De-Yuan , Wen Jun
Published: October 2021

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, hundreds of single-copy nuclear (SCN) genes (785) and complete plastomes (75) were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, it was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event best explains the cytonuclear discordance that occurred in the Eocene in western North America. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. We detected one deep hybridization event (Malus doumeri) involving the ancestor of pome-bearing species and Docynia delavayi, and one recent hybridization event (Malus coronaria) between M. sieversii and a combined clade of M. ioensis and M. angustifolia. Furthermore, our historical biogeographic analysis combining living and fossil species supported a widespread East Asian-western North American origin of Malus s.l., followed by a series of extinction events in the Eocene in northern East Aisa and western North America. This study provides a valuable evolutionary framework for the breeding and crop improvement of apples and their close relatives.
gcFront: a tool for determining a Pareto front of growth-coupled cell factory designs
Authors: Legon Laurence , Corre Christophe , Bates Declan G. , Mannan Ahmad A.
Published: October 2021

Motivation

A widely applicable strategy to create cell factories is to knock out (KO) genes or reactions to redirect cell metabolism so that chemical synthesis is made obligatory when the cell grows at its maximum rate. Synthesis is thus growth-coupled, and the stronger the coupling the more deleterious any impediments in synthesis are to cell growth, making high producer phenotypes evolutionarily robust. Additionally, we desire that these strains grow and synthesise at high rates. Genome-scale metabolic models can be used to explore and identify KOs that growth-couple synthesis, but these are rare in an immense design space, making the search difficult and slow.

Results

To address this multi-objective optimization problem, we developed a software tool named gcFront - using a genetic algorithm it explores KOs that maximise cell growth, product synthesis, and coupling strength. Moreover, our measure of coupling strength facilitates the search so that gcFront not only finds a growth coupled design in minutes but also outputs many alternative Pareto optimal designs from a single run - granting users flexibility in selecting designs to take to the lab.

Availability and Implementation

gcFront, with documentation and a workable tutorial, is freely available at GitHub: https://github.com/lLegon/gcFront, the repository of which is archived at Zenodo, DOI: 10.5281/zenodo.6338595 (Legon et al., 2022).

Supplementary Information

Supplementary notes and data files are available at Bioinformatics online.
AUG-3387, a Human-Derived Monoclonal Antibody Neutralizes SARS-CoV-2 Variants and Reduces Viral Load from Therapeutic Treatment of Hamsters In Vivo
Authors: Emig Christopher J. , Mena Marco A. , Henry Steven J. , Vitug Adela , Ventura Christian John , Fox Douglas , Nguyenla Xammy Huu , Xu Haiyue , Moon Chaeho , Sahakijjpijarn Sawittree , Kuehl Philip J. , Revelli David , Cui Zengrong , Williams Robert O. , Christensen Dale J.
Published: October 2021

Infections from the SARS-CoV-2 virus have killed over 4.6 million people since it began spreading through human populations in late 2019. In order to develop a therapeutic or prophylactic antibody to help mitigate the effects of the pandemic, a human monoclonal antibody (mAb) that binds to the SARS-CoV-2 spike protein was isolated from a convalescent patient following recovery from COVID-19 disease. This mAb, designated AUG-3387, demonstrates a high affinity for the spike protein of the original viral strains and all variants tested to date. In vitro pseudovirus neutralization and SARS-CoV-2 neutralization activity has been demonstrated in vitro. In addition, a dry powder formulation has been prepared using a Thin-Film Freezing (TFF) process that exhibited a fine particle fraction (FPF) of 50.95 ± 7.69% and a mass median aerodynamic diameter (MMAD) and geometric standard deviation (GSD) of 3.74 ± 0.73 µm and 2.73 ± 0.20, respectively. The dry powder is suitable for delivery directly to the lungs of infected patients using a dry powder inhaler device. Importantly, AUG-3387, administered as a liquid by intraperitoneal injection or the dry powder formulation delivered intratracheally into Syrian hamsters 24 hours after intranasal SARS-CoV-2 infection, demonstrated a dose-dependent reduction in the lung viral load of the virus. These data suggest that AUG-3387 formulated as a dry powder demonstrates potential to treat COVID-19.
Vht hydrogenase is required for hydrogen cycling during nitrogen fixation by the non-hydrogenotrophic methanogen Methanosarcina acetivorans
Authors: Hoerr Jadelyn M. , Dhamad Ahmed E. , Deere Thomas M. , Chanderban Melissa , Lessner Daniel J.
Published: October 2021

Methanosarcina acetivorans is the primary model to understand the physiology of methanogens that do not use hydrogenase to consume or produce hydrogen (H2) during methanogenesis. The genome of M. acetivorans encodes putative methanophenazine-reducing hydrogenases (Vht and Vhx), F420-reducing hydrogenase (Frh), and hydrogenase maturation machinery (Hyp), yet cells lack significant hydrogenase activity under all growth conditions tested to date. Thus, the importance of hydrogenase to the physiology of M. acetivorans has remained a mystery. M. acetivorans can fix dinitrogen (N2) using nitrogenase that is documented in bacteria to produce H2 during the reduction of N2 to ammonia. Therefore, we hypothesized that M. acetivorans uses hydrogenase to recycle H2 produced by nitrogenase during N2 fixation. Results demonstrate that hydrogenase expression and activity is higher in N2-grown cells compared to cells grown with fixed nitrogen (NH4Cl). To test the importance of each hydrogenase and the maturation machinery, the CRISPRi-dCas9 system was used to generate separate M. acetivorans strains where transcription of the vht, frh, vhx, or hyp operons is repressed. Repression of vhx and frh does not alter growth with either NH4Cl or N2 and has no effect on H2 metabolism. However, repression of vht or hyp results in impaired growth with N2 but not NH4Cl. Importantly, H2 produced endogenously by nitrogenase is detected in the headspace of culture tubes containing the vht or hyp repression strains. Overall, the results reveal that Vht hydrogenase recycles H2 produced by nitrogenase that is required for optimal growth of M. acetivorans during N2 fixation.

IMPORTANCE

The metabolism of M. acetivorans and closely related Methanosarcinales is thought to not involve H2. Here we show for the first time M. acetivorans is capable of H2 cycling like hydrogenotrophic Methanosarcinales (e.g., Methanosarcina barkeri). However, unlike M. barkeri hydrogenase activity and H2 cycling is tightly regulated in M. acetivorans and is only utilized during N2 fixation to consume H2 production endogenously by nitrogenase. The in vivo production of H2 by nitrogenase during N2 reduction is also demonstrated for the first time in a methanogen. Overall, the results provide new insight into the evolution and diversity of methanogen metabolism and new details about methanogen nitrogenase that could be leveraged for practical applications, such as nitrogenase-dependent production of H2 as a biofuel.
Investigating the Role of Chromatin Remodeler FOXA1 in Ferroptotic Cell Death
Authors: Logie Emilie , Maes Louis , Van Meenen Joris , De Rijk Peter , Strazisar Mojca , Joris Geert , Cuypers Bart , Laukens Kris , Berghe Wim Vanden
Published: October 2021

Ferroptosis is a lipid peroxidation-dependent mechanism of regulated cell death known to suppress tumor proliferation and progression. Although several genetic and protein hallmarks have been identified in ferroptotic cell death, it remains challenging to fully characterize ferroptosis signaling pathways and to find suitable biomarkers. Moreover, changes taking place in the epigenome of ferroptotic cells remain poorly studied. In this context, we aimed to investigate the role of chromatin remodeler forkhead box protein A1 (FOXA1) in RSL3-treated multiple myeloma cells because, similar to ferroptosis, this transcription factor has been associated with changes in the lipid metabolism, DNA damage, and epithelial-to-mesenchymal transition (EMT). RNA sequencing and Western blot analysis revealed that FOXA1 expression is consistently upregulated upon ferroptosis induction in different in vitro and in vivo disease models. In silico motif analysis and transcription factor enrichment analysis further suggested that ferroptosis-mediated FOXA1 expression is orchestrated by specificity protein 1 (Sp1), a transcription factor known to be influenced by lipid peroxidation. Remarkably, FOXA1 upregulation in ferroptotic myeloma cells did not alter hormone signaling or EMT, two key downstream signaling pathways of FOXA1. CUT&RUN genome-wide transcriptional binding site profiling showed that GPX4-inhibition by RSL3 triggered loss of binding of FOXA1 to pericentromeric regions in multiple myeloma cells, suggesting that this transcription factor is possibly involved in genomic instability, DNA damage, or cellular senescence under ferroptotic conditions.

Abstract Figure