bluuebunny/crossref_metadata_2025 huggingface dataset:
Hippocampal grading provides higher Alzheimer’s Disease prediction accuracy than hippocampal volume
Authors: Morrison Cassandra , Dadar Mahsa , Shafiee Neda , Collins D. Louis ,   Alzheimer’s Disease Neuroimaging Initiative
Published: July 2022

Background

Finding an early biomarker of Alzheimer’s disease (AD) is essential to develop and implement early treatments. Much research has focused on using hippocampal volume to measure neurodegeneration in aging and Alzheimer’s disease (AD). However, a new method to measure hippocampal change, known as hippocampal grading, has shown enhanced predictive power in older adults. It is unknown whether this method can capture hippocampal changes at each progressive stage of AD better than hippocampal volume. The goal of this study was to determine if hippocampal grading is more strongly associated with group differences between normal controls (NC), early MCI (eMCI), late (lMCI), and AD than hippocampal volume.

Methods

Data from 1666 Alzheimer’s Disease Neuroimaging Initiative older adults with baseline MRI scans were included in the first set of analyses (513 normal controls NC, 269 eMCI, 556 lMCI, and 328 AD). Sub-analyses were also completed using only those that were amyloid positive (N=834; 179 NC, 148 eMCI, 298 lMCI, and 209 AD). We compared seven different classification techniques to classify participants into their correct cohort using 10-fold cross-validation. The following classifiers were applied: support vector machines, decision trees, k-nearest neighbors, error-correcting output codes, binary Gaussian kernel, binary linear, and random forest. These multiple classifiers enable comparison to other research and examination of the most suitable classifier for Scoring by Nonlocal Image Patch Estimator (SNIPE) grading, SNIPE volume, and Freesurfer volume. This model was then validated in the Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing (AIBL).

Results

SNIPE grading provided the highest classification accuracy over SNIPE volume and Freesurfer volume for all classifications in both the full sample and amyloid positive sample. When classifying NC from AD, SNIPE grading provided an accuracy of 89% for the full sample and 87% for the amyloid positive group. Much lower accuracies of 65% and 46% were obtained when using Freesurfer in the full sample and amyloid positive sample, respectively. Similar accuracies were obtained in the AIBL validation cohort for SNIPE grading (NC vs AD: 90% classification accuracy).

Conclusion

These findings suggest that SNIPE grading offers increased prediction accuracy compared to both SNIPE volume and Freesurfer volume. SNIPE grading offers promise as a means to classify between people with and without AD. Future research is needed to determine the predictive power of grading at detecting conversion to MCI and AD in amyloid positive cognitively normal older adults (i.e., early in the AD continuum).

Key points

HC grading may better classify different disease cohorts than HC volume

Higher prediction accuracy was obtained for HC grading than HC volume

HC grading offers promise as a method to detect declines in aging and Alzheimer’s
Brief intensive social gaze training normalizes functional brain connectivity in boys with fragile X syndrome
Authors: Saggar Manish , Bruno Jennifer L. , Hall Scott S.
Published: July 2022

Boys with fragile X syndrome (FXS), the leading known genetic cause of autism spectrum disorder (ASD), demonstrate significant impairments in social gaze and associated weaknesses in communication, social interaction, and other areas of adaptive functioning. Little is known, however, concerning the impact of behavioral treatments for these behaviors on functional brain connectivity in this population. As part of a larger study, boys with FXS (mean age 13.23 +/- 2.31 years) and comparison boys with ASD (mean age 12.15 +/- 2.76 years) received resting-state magnetic resonance imaging scans prior to and following social gaze training administered by a trained behavior therapist in our laboratory. Network-agnostic connectome-based predictive modeling (CPM) of pre-treatment RSFC data revealed a set of positive (FXS > ASD) and negative (FXS < ASD) edges that differentiated the groups significantly and consistently across all folds of cross-validation. Following administration of the brief training, the FXS and ASD groups demonstrated normalization of connectivity differences. The divergence in the spatial pattern of normalization response, based on functional connectivity differences pre-treatment, suggests a unique pattern of response to treatment in the FXS and ASD groups. These results support using connectome-based predictive modeling as an outcome measure in clinical trials.
Impact of neuropsychiatric symptoms on limbic structures in age-related cognitive decline
Authors: Lucas Ronat , Van-Tien Hoang , Alexandru Hanganu ,   the ADNI
Published: July 2022

Objectives

Neuropsychiatric symptoms (NPS) are known to increase the risk of cognitive decline in aging. Several studies have investigated the brain substrates of these symptoms, reporting a broad involvement of the limbic regions.

Participants

Using the Alzheimer’s Disease Neuroimaging Initiative database, we investigated 223 participants with normal cognition, 367 with mild cognitive impairment (MCI) and 175 with Alzheimer’s disease (AD).

Measurements

Neuropsychiatric symptoms were assessed with the Neuropsychiatric Inventory and MRIs were processed with FreeSurfer. We used a general linear model (FreeSurfer) and multivariate analysis of covariance (IBM SPSS software) to establish the associations between the severity of neuropsychiatric symptoms and morphometry in cortical and subcortical structures in each clinical group.

Results

The results outlined significant associations between cortical and subcortical structures and neuropsychiatric symptoms. In cognitively normal participants, only a positive association between nighttime behaviors and bilateral caudate nuclei volumes was found. In patients with MCI, agitation, depression, apathy and nighttime behaviors were respectively negatively associated with (i) left precentral and inferior frontal and inferior parietal volumes; (ii) left fusiform volume and area; (iii) right precentral thickness, left frontopolar area and bilateral ventral diencephalon volumes; (iv) right lingual thickness, whereas depression and nighttime behaviors were also respectively positively associated with right ventral diencephalon volume; and left temporal volume and area. In patients with Alzheimer’s disease, broader association were outlined between NPS severity and cortical structures notably agitation, apathy, irritability and nighttime behaviors outlined respectively positive associations with : (i) volumes in the right temporal regions and with surface area in the frontal region; (ii) the cortical thickness of the right pericalcarine region; (iii) volumes in the frontal, temporal and parietal regions; (iv) volume of the right cuneus region; whereas depression and apathy were also respectively negatively associated with the cortical thickness of the left parietal superior region; and cortical volume and area of the parietal regions.

Conclusions

These results showed that NPS have broad association patterns with associative brain structures and few associations with limbic structures. These associations were also dependent on the clinical stage of cognitive impairment.
Chronic fatigue, depression and anxiety symptoms in Long COVID are strongly predicted by neuroimmune and neuro-oxidative pathways which are caused by the inflammation during acute infection
Authors: Al-Hakeim Hussein Kadhem , Al-Rubaye Haneen Tahseen , Almulla Abbas F. , Al-Hadrawi Dhurgham Shihab , Maes Michael
Published: July 2022

Background

Long-term coronavirus disease 2019 (Long COVID) is associated with physio-somatic (chronic fatigue syndrome and somatic symptoms) and affective (depression and anxiety) symptoms. The severity of the Long COVID physio-affective phenome is largely predicted by peak body temperature (BT) and lowered oxygen saturation (SpO2) during the acute infectious phase. This study aims to delineate whether the association of BT and SpO2 during the acute phase and the Long COVID physio-affective phenome is mediated by neurotoxicity (NT) resulting from activated immune-inflammatory and oxidative stress pathways.

Methods

We recruited 86 patients with Long COVID (3-4 months after the acute phase) and 39 healthy controls and assessed serum C-reactive protein (CRP), caspase-1, interleukin (IL)-1β, IL-18, IL-10, myeloperoxidase (MPO), advanced oxidation protein products (AOPP), total antioxidant capacity (TAC), and calcium (Ca), as well as peak BT and SpO2 during the acute phase.

Results

Cluster analysis revealed that a significant part (34.9%) of Long COVID patients (n=30) show a highly elevated NT index computed based on IL-1β, IL-18, Caspase-1, CRP, MPO and AOPP. Partial Least Squares analysis showed that 61.6% of the variance in the physio-affective phenome of Long COVID is explained by the NT index, lowered Ca, peak BT/SpO2 in the acute phase, and prior vaccinations with Astra-Zeneca or Pfizer. The most important predictors of the physio-affective phenome are Ca, CRP, IL-1β, AOPP and MPO.

Conclusion

The infectious-immune-inflammatory core of acute COVID-19 strongly predicts the development of physio-affective symptoms 3-4 months later, and these effects are partly mediated by neuro-immune and neuro-oxidative pathways.
RT-LAMP-CRISPR-Cas13a technology as a promising diagnostic tool for the SARS-CoV-2 virus
Authors: Ortiz-Cartagena Concha , Fernández-García Laura , Blasco Lucia , Pacios Olga , Bleriot Inés , López María , Cantón Rafael , Tomás María
Published: July 2022

At the end of 2019, the new coronavirus, SARS-CoV-2, began a pandemic that persists to date and which has caused more than 6.2 million deaths. In the last couple of years, researchers have made great efforts to develop a diagnostic technique that maintains high levels of sensitivity and specificity, since an accurate and early diagnosis is required to minimize the prevalence of SARS-CoV-2 infection. In this context, CRISPR-Cas systems are proposed as promising tools for development in diagnostic techniques due to their high specificity, highlighting that Cas13 endonuclease discriminates single nucleotide changes and displays a collateral activity against single stranded RNA molecules. With the aim of improve the sensitivity of the diagnosis, this technology is usually combined with isothermal pre-amplification reactions (SHERLOCK, DETECTR). Basing on this, we have developed an RT-LAMP-CRISPR-Cas13a for SARS-CoV-2 virus detection in nasopharyngeal samples without using RNA extraction kit that exhibited 100 % specificity and 83 % sensitivity, as well as a positive predictive value of 100 % and a negative predictive value of 100%, 81%, 79.1% and 66.7 % in <20 Ct, 20-30 Ct, >30 Ct and total Ct values, respectively.

Importance

During Covid19 crisis has driven the development innovative molecular diagnose including the CRISPR-Cas technology. This work we have performed a protocol working with RNA-extraction kit free samples, places RT-LAMP-CRISPR-Cas13a technology at the top of rapid and specific diagnostic methods for COVID19 due to the high levels of specificity (100%), sensitivity (83%), PPV (100%) and NPV (81% in high loads viral) obtained in clinical samples.
Enhanced hippocampal LTP but typical NMDA receptor and AMPA receptor function in a novel rat model of CDKL5 deficiency disorder
Authors: de Oliveira L Simões , O’Leary HE , Nawaz S. , Loureiro R , Davenport EC , Baxter P. , Dando OR , Perkins E. , Booker SA , Hardingham GE , Cousin MA , Chattarji S , Benke TA , Wyllie DJA , Kind PC
Published: July 2022

Mutations in the X-linked gene cyclin-dependent kinase-like 5 (CDKL5) cause a severe neurological disorder characterised by early-onset epileptic seizures, autism and intellectual disability (ID). Impaired hippocampal function has been implicated in other models of monogenic forms of autism spectrum disorders and ID and is often linked to epilepsy and behavioural abnormalities. Many individuals with CDKL5 deficiency disorder (CDD) have null mutations and complete loss of CDKL5 protein, therefore in the current study we used a novel Cdkl5 KO rat model to elucidate the impact of CDKL5 loss on cellular excitability and synaptic function of CA1 pyramidal cells (PCs). We hypothesised abnormal pre and/or post synaptic function underlie the enhanced LTP we observe in the hippocampus of Cdkl5 KO rats. We tested this hypothesis using a combination of extracellular and whole-cell electrophysiological recordings, biochemistry, and histology. We show that NMDA receptor function and subunit expression are unaltered throughout development, and Ca2+ permeable AMPA receptor mediated currents are unchanged in Cdkl5 KO rats. We observe reduced mEPSC frequency accompanied by increased spine density in basal dendrites of CA1 PCs, however we find no evidence supporting an increase in silent synapses when assessed using a minimal stimulation protocol in slices. Additionally, we found no change in paired-pulse ratio, consistent with normal release probability in Cdkl5 KO rats and supported by typical expression of pre-synaptic proteins in synaptosome preparations. Together these data indicate a role for CDKL5 in hippocampal synaptic function and raise the possibility that altered intracellular signalling rather than synaptic deficits might contribute to the altered plasticity.
Human genetic adaptation related to cellular zinc homeostasis
Authors: Roca-Umbert Ana , Garcia-Calleja Jorge , Vogel-González Marina , Fierro-Villegas Alejandro , Ill-Raga Gerard , Herrera-Fernández Víctor , Bosnjak Anja , Muntané Gerard , Gutiérrez Esteban , Campelo Felix , Vicente Rubén , Bosch Elena
Published: July 2022

SLC30A9encodes a ubiquitously zinc transporter (ZnT9) and has been consistently suggested as a candidate for positive selection in humans. However, no direct adaptive molecular phenotype has been demonstrated. Our results provide evidence for directional selection operating in two major complementary haplotypes in Africa and East Asia. These haplotypes are associated with differential gene expression but also differ in the Met50Val substitution (rs1047626) in ZnT9, which we show is found in homozygosis in the Denisovan genome and displays accompanying signatures suggestive of archaic introgression. Although we found no significant differences in systemic zinc content between individuals with different rs1047626 genotypes, we demonstrate that the expression of the derived isoform (ZnT9 50Val) in HEK293 cells shows a gain of function when compared with the ancestral (ZnT9 50Met) variant. Notably, the ZnT9 50Val variant was found associated with differences in zinc handling by the mitochondria and endoplasmic reticulum, with an impact on mitochondrial metabolism. Given the essential role of the mitochondria in skeletal muscle and since the derived allele at rs1047626 is known to be associated with greater susceptibility to several neuropsychiatric traits, we propose that adaptation to cold may have driven this selection event, while also impacting predisposition to neuropsychiatric disorders in modern humans.

Author Summary

Contrasting continental signatures of positive natural selection have been previously found in the humanSLC30A9gene encoding the protein ZnT9, which transports zinc across cell membranes. Here we investigate the genetic variants that have been targeted by natural selection in the surrounding region of this gene and which molecular and whole-body changes may have brought about. We found that two majorSLC30A9variant combinations (haplotypes) that are extremely frequent in Africa and East Asia, respectively, are expressed differentially. These two haplotypes also differ at one site that creates an amino acid difference at ZnT9; the version most often found outside Africa avoiding zinc overload in the endoplasmic reticulum and mitochondria and directly influencing mitochondrial activity. Moreover, we found that this substitution, which is known to be associated with greater susceptibility to several neuropsychiatric disorders, is present in the Denisova and displays accompanying patterns of variation that could be suggestive of adaptive introgression. Since mitochondria play an important role in skeletal muscle energy metabolism, we speculate that adaptation to cold may have driven this selection event outside Africa, while also impacting predisposition to neuropsychiatric disorders in modern humans.
Structural Modeling of Peptide Toxin - Ion Channel Interactions using RosettaDock
Authors: Mateos Diego Lopez , Yarov-Yarovoy Vladimir
Published: July 2022

Voltage-gated ion channels play essential physiological roles in action potential generation and propagation. Peptidic toxins from animal venoms target ion channels and provide useful scaffolds for the rational design of novel channel modulators with enhanced potency and subtype selectivity. Despite recent progress in obtaining experimental structures of peptide toxin – ion channel complexes, structural determination of peptide toxins bound to ion channels in physiologically important states remains challenging. Here we describe an application of RosettaDock approach to structural modeling of peptide toxins interactions with ion channels. We tested this approach on 10 structures of peptide toxinion channel complexes and demonstrated that it can sample near-native structures in all tested cases. Our approach will be useful for improving understanding of the molecular mechanism of natural peptide toxin modulation of ion channel gating and for the structural modeling of novel peptide-based ion channel modulators.
The Structural Flexibility of MAD1 Facilitates the Assembly of the Mitotic Checkpoint Complex
Authors: Chen Chu , Piano Valentina , Alex Amal , Han Simon J. Y. , In ’t Veld Pim J Huis , Roy Babhrubahan , Musacchio Andrea , Joglekar Ajit P.
Published: July 2022

The spindle assembly checkpoint (SAC) safeguards the genome during cell division by generating an effector molecule known as the Mitotic Checkpoint Complex (MCC). The MCC comprises two subcomplexes, and during its assembly, formation of the CDC20:MAD2 subcomplex is the rate-limiting step. Recent studies show that the rate of CDC20:MAD2 formation is significantly accelerated by the cooperative binding of CDC20 to SAC proteins MAD1 and BUB1. However, the molecular basis for this acceleration is not fully understood. Here, we demonstrate that the structural flexibility of MAD1 at a conserved hinge near the C-terminus is essential for catalytic MCC assembly. This MAD1 hinge enables the MAD1:MAD2 complex to assume a folded conformation in vivo. Importantly, truncating the hinge reduces the rate of MCC assembly in vitro and SAC signaling in vivo. Conversely, mutations that preserve hinge flexibility retain SAC signaling, indicating that the structural flexibility of the hinge, rather than a specific amino acid sequence, is important for SAC signaling. We summarize these observations in a “knitting” model that explains how the folded conformation of MAD1:MAD2 promotes CDC20:MAD2 assembly.
Model of neural induction in the ascidian embryo
Authors: Bettoni Rossana , Hudson Clare , Yasuo Hitoyoshi , de Buyl Sophie , Dupont Geneviève
Published: July 2022

How cell specification can be controlled in a reproducible manner is a fundamental question in development biology. In ascidians, a group of marine invertebrate chordates, geometry plays a key role in achieving this control. Here, we use mathematical modeling to demonstrate that geometry dictates the neural-epidermal cell fate choice in the 32-cell stage ascidian embryo by a two-step process involving first the modulation of ERK signaling and second, the expression of the neural marker gene,Otx. The model describes signal transduction by the ERK pathway that is stimulated by FGF and repressed by ephrin, and ERK-mediated control ofOtxgene expression, which involves both an activator and an inhibitor of transcription. Considering the measured area of cell surface contacts with FGF- or ephrin-expressing cells as inputs, the solutions of the model reproduce the experimental observations about ERK activation andOtxexpression in the different cells under normal and perturbed conditions. Sensitivity analyses and computations of Hill coefficients allow to quantify the robustness of the specification mechanism controlled by cell surface area and to identify the respective role played by each signaling input. Simulations also predict in which conditions the dual control of gene expression by an activator and an inhibitor that are both under the control of ERK can induce a robust ON/OFF control of neural fate induction.

Author summary

The development of a single cell zygote into a multicellular embryo occurs thanks to the combination of cell division and cell specification. The latter process corresponds to the progressive acquisition by the embryonic cells of their final physiological and functional characteristics, which rely on well-defined signaling-controlled genetic programs. The origin of the great robustness of cell specification remains poorly understood. Here, we address this question in the framework of the embryonic neural fate induction in ascidians, which are marine invertebrates. At the 32-cells stage, four cells identified by their precise location in the embryo adopt neural fate. On the basis of experimental observations, we develop a mathematical model that predicts that the choice between the neural or epidermal fate is controlled by the cell surface areas of the cells in contact with two antagonistic signals, FGF and ephrin. Our findings provide a computational confirmation of the major role played by the geometry of the embryo in controlling cell lineage acquisition during ascidian development.
Pro-apoptotic and anti-invasive properties underscore the tumor suppressing impact of myoglobin on subset of human breast cancer cells
Authors: Aboouf Mostafa A. , Armbruster Julia , Thiersch Markus , Guscetti Franco , Kristiansen Glen , Schraml Peter , Bicker Anne , Petry Ruben , Hankeln Thomas , Gassmann Max , Gorr Thomas A.
Published: July 2022

Expression of myoglobin (MB), well known as the oxygen storage and transport protein of myocytes, is a novel hallmark of the luminal subtype in breast cancer patients and correlates with better prognosis. The mechanisms by which MB impacts mammary tumorigenesis are hitherto unclear. We aimed to unravel this role, by using CRISPR/Cas9 technology to generate MB-deficient clones of MCF7 and SKBR3 breast cancer cell lines and subsequently characterize them by transcriptomics plus molecular and functional analyses. As main findings, loss of MB, at normoxia, upregulated the expression of cell cyclins and increased cell survival while it prevented apoptosis in MCF7 cells. Also, MB-deficient cells were less sensitive to doxorubicin but not ionizing radiation. Under hypoxia, loss of MB enhanced partial epithelial to mesenchymal transition, thus augmenting the migratory and invasive cell behavior. Notably, in human invasive mammary ductal carcinoma tissues, MB and apoptotic marker levels were positively correlated. In addition, MB protein expression in invasive ductal carcinomas was associated with a positive prognostic value, independent of the known tumor suppressor p53. In conclusion, we provide multiple lines of evidence that endogenous MB in cancer cells by itself exerts novel tumor-suppressive roles through which it can reduce cancer malignancy.
Small cytosolic dsDNAs repress cGAS activation and induce autophagy
Authors: Liu Yao , Chen Xiao , Zhao Yuemei , Wang Xingyue , Chen Lina , Wang Weiyun , Zhong Shouhui , Hu Meizhen , Dai Zhizheng , Jiang Jiayu , Cheng Xiaoxiao , Zuo Jiwei , Liu Hui , Ma Di , Wang Xin , Ji Hongyu , Hu Shanshan , Luo Yu-Wei , Huang Ai-Long , Tang Kai-Fu
Published: July 2022

Cyclic GMP-AMP (cGAMP) synthase (cGAS), a major cytosolic DNA sensor, activates innate immune responses by producing cGAMP, which activates stimulator of interferon genes (STING)1. Cytosolic DNA induces autophagy in a cGAS-dependent manner to avoid persistent immune stimulation. Although dsDNAs < 20 bp can bind to cGAS, robust cGAS activation requires dsDNAs > 45 bp 2-4. However, whether cytosolic dsDNAs < 45 bp exist in mammalian cells remains unclear. Here, we identified a class of small cytosolic DNAs (scDNAs) of ∼20–40 bp in human and mouse cell lines. scDNAs competed with herring testis DNA (HT-DNA, ∼200–1500 bp) for binding to cGAS, and repressing HT-DNA-induced cGAS activation and the associated interferon β (IFNβ) production. Moreover, scDNAs promoted cGAS and Beclin-1 interaction, triggering the release of Rubicon, a negative regulator of phosphatidylinositol 3-kinase class III (PI3KC3)5,6, from the Beclin-1–PI3KC3 complex, activating PI3KC3 and inducing autophagy. DNA damage decreased and autophagy inducers increased scDNA levels. scDNA transfection or autophagy induction attenuated DNA damage-induced cGAS-STING activation and IFNβ expression. Thus, scDNAs acted as molecular brakes of cGAS activation, preventing excessive inflammatory cytokine production following DNA damage. Our findings lay foundations for understanding the physiological and pathological functions of scDNAs.
Cyclin D1-Cdk4 regulates neuronal activity through phosphorylation of GABAA receptors
Authors: Pedraza Neus , Monserrat Ma Ventura , Ferrezuelo Francisco , Torres-Rosell Jordi , Colomina Neus , Soto David , Esteban Jose A , Miguez Fede , Egea Joaquim , Gari Eloi
Published: July 2022

Cyclin D1 (Ccnd1)-Cdk4 complexes drive cell cycle progression through phosphorylation of pRb. Interestingly, Ccnd1 moves to the cytoplasm at the onset of differentiation in neuronal precursors. However, the cytoplasmic functions and targets of Ccnd1 in post-mitotic neurons are unknown. Here we identify the α4 subunit of gamma-aminobutyric acid (GABA) type A receptors (GABAARs) as an interactor and target of Ccnd1-Cdk4. Ccnd1 binds to an intracellular loop in α4 and, together with Cdk4, phosphorylates the α4 subunit at threonine 423 and serine 431. These modifications increase the activity of α4-containing GABAARs, measured in whole-cell patch-clamp recordings, and upregulate its surface levels. In agreement with this role of Ccnd1-Cdk4 in neuronal signaling, inhibition of Cdk4 decreases synaptic and extrasynaptic currents in the hippocampus of newborn rats. Moreover, CCND1 knockout mice display an altered pattern of dendritic spines, according to α4 functions in synaptic pruning. Overall, our findings molecularly link Ccnd1-Cdk4 to GABAARs activity in the central nervous system and highlight a novel role for this G1 cyclin in neuronal signaling.
Phospholipids Diffusion on the Surface of Model Lipid Droplets
Authors: Asfia Shima , Seemann Ralf , Fleury Jean-Baptiste
Published: July 2022

Lipid droplets (LD) are organelles localized in the membrane of the Endoplasmic Reticulum (ER) that play an important role in metabolic functions. They consist of a core of neutral lipids surrounded by a monolayer of phosphoplipids and proteins resembling an oil-in-water emulsion droplet. Many studies have focused on the biophysical properties of these LDs. However, despite numerous efforts, we are lacking information on the mobility of phospholipids on the LDs surface, although they may play a key role in the protein distribution. In this article, we developed a microfluidic setup that allows the formation of a triolein-buffer interface decorated with a phospholipid monolayer. Using this setup, we measured the motility of phospholipid molecules by performing Fluo-rescent Recovery After Photobleaching (FRAP) experiments for different lipidic compositions. The results of the FRAP measurements reveal that the motility of phospholipids is controlled by the monolayer packing decorating the interface.
LipIDens: Simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins
Authors: Ansell T. Bertie , Song Wanling , Coupland Claire E. , Carrique Loic , Corey Robin A. , Duncan Anna L. , Cassidy C. Keith , Geurts Maxwell M. G. , Rasmussen Tim , Ward Andrew B. , Siebold Christian , Stansfeld Phillip J. , Sansom Mark S. P.
Published: July 2022

Cryo-electron microscopy (cryo-EM) enables the determination of membrane protein structures in native-like environments. Characterising how membrane proteins interact with the surrounding membrane lipid environment is assisted by resolution of lipid-like densities visible in cryo-EM maps. Nevertheless, establishing the molecular identity of putative lipid and/or detergent densities remains challenging. Here we present LipIDens, a pipeline for molecular dynamics (MD) simulation-assisted interpretation of lipid and lipid-like densities in cryo-EM structures. The pipeline integrates the implementation and analysis of multi-scale MD simulations for identification, ranking and refinement of lipid binding poses which superpose onto cryo-EM map densities. Thus, LipIDens enables direct integration of experimental and computational structural approaches to facilitate the interpretation of lipid-like cryo-EM densities and to reveal the molecular identities of protein-lipid interactions within a bilayer environment. The LipIDens code is open-source and embedded within a notebook format to assist automation and usability.
Fecal virome transfer improves proliferation of commensal gut Akkermansia muciniphila and unexpectedly enhances the fertility rate in laboratory mice
Authors: Sølbeck Rasmussen Torben , Junker Mentzel Caroline M. , Danielsen Malene Refslund , Jakobsen Rasmus Riemer , Fisker Zachariassen Line Sidsel , Castro Mejia Josue Leonardo , Hansen Lars Hestbjerg , Hansen Axel Kornerup , Nielsen Dennis Sandris
Published: July 2022

Probiotics have been suggested as nutritional supplements to improve gastrointestinal health. However, the probiotics marketed today only colonize the densely populated gut to a limited extent. Bacteriophages comprise the majority of viruses in the human gut virome and there are strong indications that they play important roles in shaping the gut microbiome (GM). Here we investigate the use of fecal virome transplantation (FVT) as a mean to alter GM composition to lead the way for persistent colonization of two types of probiotics: Lacticaseibacillus rhamnosus GG (LGG) representing a well-established probiotic and Akkermansia muciniphila (AKM) representing a putative next-generation probiotic. Male and female C57BL/6NTac mice were cohoused in pairs at 4 weeks of age and received the following treatment by oral gavage at week 5 and 6: AKM+FVT, probiotic sham (Pro-sham)+FVT, LGG+Saline, AKM+Saline, and control (Pro-sham+Saline). The FVT originated from donor mice with high relative abundance of A. muciniphila. All animals were terminated at age 9 weeks. The FVT treatment did not increase the relative abundance of the administered LGG or AKM in the recipient mice. Instead FVT significantly (p<0.05) increased the abundance of naturally occurring A. muciniphila compared to the control. This highlights the potential of stimulating the commensal “probiotics” that already are permanent members of the gut. Being co-housed male and female, a fraction of the female mice became pregnant. Unexpectedly, the FVT treated mice were found to have a significantly (p<0.05) higher fertility rate independent of probiotic administration. These preliminary observations urge for follow-up studies investigating GM/fertility interactions.
Noradrenergic signaling in the rodent orbitofrontal cortex is required to update goal-directed actions
Authors: Cerpa Juan-Carlos , Piccin Alessandro , Dehove Margot , Lavigne Marina , Kremer Eric J. , Wolff Mathieu , Parkes Shauna L. , Coutureau Etienne
Published: July 2022

In a constantly changing environment, organisms must track the current relationship between actions and their specific consequences and use this information to guide decision-making. Such goal-directed behavior relies on circuits involving cortical and subcortical structures. Notably, a functional heterogeneity exists within the medial prefrontal, insular, and orbitofrontal cortices (OFC) in rodents. The role of the latter in goal-directed behavior has been debated, but recent data indicate that the ventral and lateral subregions of the OFC are needed to integrate changes in the relationships between actions and their outcomes. Neuromodulatory agents are also crucial components of prefrontal functions and behavioral flexibility might depend upon the noradrenergic modulation of prefrontal cortex. Therefore, we assessed whether noradrenergic innervation of the OFC plays a role in updating action-outcome relationships. We used an identity-based reversal task and found that depletion or chemogenetic silencing of noradrenergic inputs within the OFC rendered rats unable to associate new outcomes with previously acquired actions. Silencing of noradrenergic inputs in the medial prefrontal cortex or depletion of dopaminergic inputs in the OFC did not reproduce this deficit. Together, our results indicate that noradrenergic projections to the OFC are required to update goal-directed actions.

GRAPHICAL ABSTRACT

HIGHLIGHTS

Rats learn initial action-outcome associations in an instrumental task

Noradrenergic depletion in the OFC prevents the encoding and expression of these associations following reversal learning

Dopaminergic depletion in the OFC does not result in behavioral deficits

LC:OFC noradrenergic projections are required to update action-outcome associations

IN BRIEF

Cerpa et al. investigate whether noradrenergic projections from the locus coeruleus (LC) to the orbitofrontal cortex are involved in updating previously established goal-directed actions following environmental change. They find that these LC projections are required to both encode and express reversed action-outcome associations in rats.
A Novel Homeostatic Mechanism Tunes PI(4,5)P2-dependent Signaling at the Plasma Membrane
Authors: Wills Rachel C. , Doyle Colleen P. , Zewe James P. , Pacheco Jonathan , Hansen Scott D. , Hammond Gerald R. V.
Published: July 2022

The lipid molecule phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2) controls all aspects of plasma membrane (PM) function in animal cells, from its selective permeability to the attachment of the cytoskeleton. Although disruption of PI(4,5)P2is associated with a wide range of diseases, it remains unclear how cells sense and maintain PI(4,5)P2levels to support various cell functions. Here, we show that the PIP4K family of enzymes that synthesize PI(4,5)P2via a minor pathway, also function as sensors of tonic PI(4,5)P2levels. PIP4Ks are recruited to the PM by elevated PI(4,5)P2levels, where they inhibit the major PI(4,5)P2-synthesizing PIP5Ks. Perturbation of this simple homeostatic mechanism reveals differential sensitivity of PI(4,5)P2-dependent signaling to elevated PI(4,5)P2levels. These findings reveal that a subset of PI(4,5)P2-driven functions may drive disease associated with disrupted PI(4,5)P2homeostasis.

One-Sentence Summary

The enzyme PIP4K functions as both a sensor and negative regulator of PI(4,5)P2synthesis by the closely related PIP5K enzymes, tuning the activity of numerous membrane functions.
A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer
Authors: Newman Kahlan E. , Tindall Sarah N. , Mader Sophie L. , Khalid Syma , Thomas Gavin H. , van der Woude Marjan W.
Published: July 2022

Acylation of diverse carbohydrates occurs across all domains of life and can be catalysed by proteins with a membrane bound acyltransferase-3 (AT3) domain (PF01757). In bacteria, these proteins are essential in processes including symbiosis, resistance to viruses and antimicrobials, and biosynthesis of antibiotics, yet their structure and mechanism is largely unknown. In this study, evolutionary co-variance analysis was used to build a computational model of the structure of a bacterial O-antigen modifying acetyltransferase, OafB. The resulting structure exhibited a novel fold for the AT3 domain, which molecular dynamics simulations demonstrated is stable in the membrane. The AT3 domain contains 10 transmembrane helices arranged to form a large cytoplasmic cavity lined by residues known to be essential for function. Further molecular dynamics simulations support a model where the acyl-coA donor spans the membrane through accessing a pore created by movement of an important loop capping the inner cavity, enabling OafB to present the acetyl group close to the likely catalytic resides on the extracytoplasmic surface. Limited but important interactions with the fused SGNH domain in OafB are identified and modelling suggests this domain is mobile and can both accept acyl-groups from the AT3 and then reach beyond the membrane to reach acceptor substrates. Together this new general model of AT3 function provides a framework for the development of inhibitors that could abrogate critical functions of bacterial pathogens.
AncientClostridiumDNA and variants of tetanus neurotoxins associated with human archaeological remains
Authors: Hodgins Harold P. , Chen Pengsheng , Lobb Briallen , Wei Xin , Tremblay Benjamin JM , Mansfield Michael J. , Lee Victoria CY , Lee Pyung-Gang , Coffin Jeffrey , Duggan Ana T. , Dolphin Alexis E. , Renaud Gabriel , Dong Min , Doxey Andrew C.
Published: July 2022

The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, through a large-scale metagenomic analysis of archeological samples, we discovered bacterial species related to modern-dayClostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. We assembled draft genomes from 38 distinct human archeological samples spanning five continents and dating to as early as ~4000 BCE. These genomes had varying levels of completeness and a subset of them displayed hallmarks of ancient DNA damage. While 24 fall into knownC. tetaniclades, phylogenetic analysis revealed novelC. tetanilineages, as well as two novelClostridiumspecies (“Clostridiumsp. X and Y”) closely related toC. tetani. Within these genomes, we found 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from a ~6000-year-old Chilean mummy sample and found that it induced tetanus muscle paralysis in mice with potency comparable to modern TeNT. Our work identifies neurotoxigenicC. tetaniin ancient DNA, newClostridiumspecies unique to ancient human samples, and a novel variant of TeNT that can cause disease in mammals.
Pseudomonas aeruginosa transcriptome analysis in a cystic fibrosis lung model reveals metabolic changes accompanying biofilm maturation and increased antibiotic tolerance over time
Authors: Harrington Niamh E. , Allen Freya , Garcia-Maset Ramón , Harrison Freya
Published: July 2022

The opportunistic pathogen Pseudomonas aeruginosa forms biofilm infections in the lungs of people with the genetic condition cystic fibrosis (CF) that can persist for decades. There are numerous P. aeruginosa lifestyle changes associated with chronic biofilm infection cued by the CF lung environment. These include a loss of virulence, metabolic changes, and increased antimicrobial tolerance. We have investigated P. aeruginosa PA14 biofilm infection over 7 d in an ex vivo pig lung (EVPL) model for CF, previously shown to facilitate formation of a clinically-relevant P. aeruginosa biofilm structure with gene expression comparable to human infection. We extracted and sequenced P. aeruginosa RNA from EVPL-associated biofilms 24 h, 48 h, and 7 d after infection, and compared gene expression between sequential time points. We also investigated tolerance to polymyxins across these three time points. Our results indicate that the EVPL model can maintain a P. aeruginosa biofilm population, which exhibits increased antibiotic tolerance, for at least 7 d. Differential expression of antimicrobial resistance-associated genes was not observed, however there was significant upregulation of sulfur metabolism and phenazine biosynthesis-related genes, as well as maintenance of a structured biofilm. These findings provide further insight into the incidence of increased P. aeruginosa antibiotic tolerance during infection of the CF lung, and the gene expression changes that arise as chronic infection establishes.
Activation-pathway transitions in human voltage-gated proton channels revealed by a non-canonical fluorescent amino acid
Authors: Suárez-Delgado Esteban , Orozco-Contreras M. E. , Rangel-Yescas Gisela E. , Islas León D.
Published: July 2022

Voltage-dependent gating of the voltage-gated proton channels (HV1) remains poorly understood, partly because of the difficulty of obtaining direct measurements of voltage sensor movement in the form of gating currents. To circumvent this problem, we have implemented patch-clamp fluorometry in combination with the incorporation of the fluorescent non-canonical amino acid Anap to monitor channel opening and movement of the S4 segment. Simultaneous recording of currents and fluorescence signals allows for direct correlation of these parameters and investigation of their dependence on voltage and the pH gradient (ΔpH). We present data that indicate that Anap incorporated in the S4 helix is quenched by an aromatic residue located in the S2 helix, and that motion of the S4 relative to this quencher is responsible for fluorescence increases upon depolarization. The kinetics of the fluorescence signal reveals the existence of a very slow transition in the deactivation pathway, which seems to be singularly regulated by ΔpH. Our experiments also suggest that the voltage sensor can move after channel opening and that the absolute value of the pH can influence the channel opening step. These results shed light on the complexities of voltage-dependent opening of human HV1 channels.

Significance statement

The activation mechanisms of voltage-gated proton channels (HV1) are not well understood. Here we have combined patch-clamp fluorometry and a fluorescent non-canonical amino acid to uncover transitions in the activation pathway of human HV1 that are modulated by voltage and the pH gradient.
How do firms use cloud computing to transform their organization? Evidence from a global survey
Authors: Bounfour Ahmed , Etienne Jean-Michel , Cheng Xiaolin , Nonnis Alberto
Published: July 2022

Purpose

The paper aims to address the organizational transformation of firms for value creation resulting from cloud computing (CC).

Design/methodology/approach

With reference to the theory of organizational fit, we modeled organizational transformation as a function of five aspects of CC practice: functionality, data management, roles and competences of information technology services, control and organizational culture. The output variable was tested against a set of input variables defined with reference to the technology–organization–environment (TOE) and technology acceptance model (TAM). Based on a sample of 487 companies in seven countries in Europe, Asia, and the United States, the authors distinguished two groups of firms: transformational and hyper transformational.

Findings

The results highlight the key factors that determine whether a firm falls into one of these two groups, and include perceived usefulness and perceived ease of use, complexity and compatibility of CC technology, and adequacy of resources. Top management support and government policy are found to only play a role for the transformational group while, surprisingly, vendor support had no impact for either group.

Originality/value

This research contributes to the literature on the role of digital transformation in value creation and on digitization of firms and organizational design, notably by considering the contribution of CC to the organizational dimension. To the best of the authors’ knowledge, this is the first study to make the link between TOE and TAM models and organizational fit theory, thereby going beyond the general approach to adoption found in information system research.
Is there a long-run relationship between the unemployment insurance and the labor force participation rate in the USA? A nonlinear analysis
Authors: Ahmed Haydory Akbar
Published: July 2022

Purpose

This paper explores the evidence of a long-run co-movement between aggregate unemployment insurance spending and the labor force participation rate in the USA. The unemployment insurance (UI) program tends to expand during an economic downturn and contract during an expansion. UI may incentivize unemployment and may also facilitate better matching in the labor market. Statistical evidence of the presence of a co-movement will thus shed new light on their dynamics.

Design/methodology/approach

This research applies time-series econometric approach using monthly data from 1959:1 to 2020:3 to test threshold cointegration and estimate a threshold vector error-correction (TVEC) model. The estimates from the TVEC model investigating the nature of short-run dynamics.

Findings

The Enders and Siklos (2001) test find evidence of threshold cointegration between the two indicating the presence of long-run co-movement. The estimates from the TVEC model investigating the nature of short-run dynamics find evidence that the growth in aggregate UI spending and the growth in labor force participation rate adjust simultaneously to maintain the long-run co-movement above the threshold in the short run. The author also observes the same short-run dynamics for the growth in aggregate UI spending and the growth in the labor force participation rate for females.

Research limitations/implications

This model is bi-variate by construction and does not address causality.

Practical implications

The author argues that the UI program positively impacts the female labor market outcomes, for example, better matching. This finding may explain the upward trend in the labor force participation rate for females in the USA.

Social implications

The research findings may justify the transfer programs for minority and immigrants.

Originality/value

This is first research that analyzes the UI programs impact on the labor force participation using a macroeconometric approach. To the best of the author's knowledge, this is the first study in this genre.
Board gender diversity, firm performance and corporate financial distress risk: international evidence from tourism industry
Authors: Lee Kin Wai , Thong Tiong Yang
Published: July 2022

Purpose

This paper examines contextual factors that affect the association between board gender diversity and firm performance.

Design/methodology/approach

The authors use a global sample of listed firms in the tourism industry in 30 countries from 2015 to 2020.

Findings

First, firm performance is positively associated with the proportion of female directors on a board. Second, the positive association between firm performance and the proportion of female directors on the board is higher in (1) countries with stronger shareholder rights, (2) countries with stronger securities law regulation stipulating disclosure of board diversity, (3) countries with stronger economic empowerment of women, and (4) during the COVID-19 crisis. Third, corporate financial distress risk is lower in firms with higher proportion of female directors on the board. Fourth, the negative association between corporate financial distress risk and the proportion of female directors on the board is more pronounced in (1) countries with stronger securities law regulations stipulating disclosure of board gender diversity, (2) countries with stronger economic empowerment of women, and (3) during the COVID-19 crisis.

Originality/value

The results indicate that contextual factors (comprising country-level corporate governance structures, economic empowerment of women and economic crisis) can affect the association between board gender diversity and firm performance.