bluuebunny/crossref_metadata_2025 huggingface dataset:
Determining the microbial species content in tissue from Alzheimer’s and Parkinson’s Disease patients
Authors: Leitao Rodrigo , Wan Iam Ut , Fisher Matthew C. , Rhodes Johanna
Published: October 2023

The aetiology of Alzheimer’s disease (AD) and Parkinson’s Disease (PD) are unknown and tend to manifest at a later stage in life; even though these diseases have different pathogenic mechanisms, they are both characterized by neuroinflammation in the brain. Links between bacterial and viral infection and AD/PD has been suggested in several studies, however, few have attempted to establish a link between fungal infection and AD/PD. In this study we develop and describe a nanopore-based sequencing approach to characterise the presence or absence of fungi in both human brain tissue and cerebrospinal fluid (CSF). This approach detects fungal DNA in human brain and CSF samples even at low levels, whereas our quantitative polymerase chain reaction (qPCR) assay (FungiQuant) was unable to detect fungal DNA in the same samples. Comparison against kit-controls showed ubiquitous low-level fungal contamination that we observed in healthy human brains and CSF as well AD/PD brains and CSF. We use this technique to demonstrate the presence of fungal DNA in healthy human brains as well as AD/PD brains, withAlternaria spp.,Colletotrichum graminicola, andFilobasidium floriformeas the most prominent species. In addition, antibiotic resistantPseudomonas spp. was identified within the brain of an AD patient. Our method will be broadly applicable to investigating potential links between microbial infection and AD/PD.
Nuclear Pyruvate Dehydrogenase Complex Regulates Histone Acetylation and Transcriptional Regulation in the Ethylene Response
Authors: Shao Zhengyao , Bian Liangqiao , Ahmadi Shyon K. , Daniel Tyler J. , Belmonte Miguel A. , Burns Jackson G. , Kotla Prashanth , Bi Yang , Shen Zhouxin , Xu Shou-Ling , Wang Zhi-Yong , Briggs Steven P. , Qiao Hong
Published: October 2023

Ethylene plays its essential roles in plant development, growth, and defense responses by controlling the transcriptional reprograming, in which EIN2-C-directed regulation of histone acetylation is the first key-step for chromatin to perceive ethylene signaling. But how the nuclear acetyl coenzyme A (acetyl CoA) is produced to ensure the ethylene-mediated histone acetylation is unknown. Here we report that ethylene triggers the accumulation of the pyruvate dehydrogenase complex (PDC) in the nucleus to synthesize nuclear acetyl CoA to regulate ethylene response. PDC is identified as an EIN2-C nuclear partner, and ethylene triggers its nuclear accumulation. Mutations in PDC lead to an ethylene-hyposensitivity that results from the reduction of histone acetylation and transcription activation. Enzymatically active nuclear PDC synthesize nuclear acetyl CoA for EIN2-C-directed histone acetylation and transcription regulation. These findings uncover a mechanism by which PDC-EIN2 converges the mitochondrial enzyme mediated nuclear acetyl CoA synthesis with epigenetic and transcriptional regulation for plant hormone response.
Diatom pyrenoids are encased in a protein shell that enables efficient CO2fixation
Authors: Shimakawa Ginga , Demulder Manon , Flori Serena , Kawamoto Akihiro , Tsuji Yoshinori , Nawaly Hermanus , Tanaka Atsuko , Tohda Rei , Ota Tadayoshi , Matsui Hiroaki , Morishima Natsumi , Okubo Ryosuke , Wietrzynski Wojciech , Lamm Lorenz , Righetto Ricardo D. , Uwizeye Clarisse , Gallet Benoit , Jouneau Pierre-Henri , Gerle Christoph , Kurisu Genji , Finazzi Giovanni , Engel Benjamin D. , Matsuda Yusuke
Published: October 2023

Pyrenoids are subcompartments of algal chloroplasts that concentrate Rubisco enzymes and their CO2substrate, thereby increasing the efficiency of carbon fixation. Diatoms perform up to 20% of global CO2fixation, but their pyrenoids remain poorly characterized at a molecular level. Here, we usedin vivophoto-crosslinking to catalogue components of diatom pyrenoids and identified a pyrenoid shell (PyShell) protein, which we localized to the pyrenoid periphery of both the pennate diatom,Pheaodactylum tricornutum, and the centric diatom,Thalassiosira pseudonana.In situcryo-electron tomography (cryo-ET) revealed that the pyrenoids of both diatom species are encased in a lattice-like protein sheath. Disruption of PyShell expression inT. pseudonanaresulted in the absence of this protein sheath, altered pyrenoid morphology, and a high-CO2requiring phenotype, with impaired growth and reduced carbon fixation efficiency under standard atmospheric conditions. Pyrenoids in mutant cells were fragmented and lacked the thylakoid membranes that normally traverse the Rubisco matrix, demonstrating how the PyShell plays a guiding role in establishing pyrenoid architecture. Recombinant PyShell proteins self-assembled into helical tubes, enabling us to determine a 3.0 Å-resolution PyShell structure. We then fit thisin vitrostructure into anin situsubtomogram average of the pyrenoid’s protein sheath, yielding a putative atomic model of the PyShell within diatom cells. The structure and function of the diatom PyShell provides a new molecular view of how CO2is assimilated in the ocean, a crucial biome that is on the front lines of climate change.
Cytoplasmic Viscosity is a Potential Biomarker for Metastatic Breast Cancer Cells
Authors: Dessard Marie , Manneville Jean-Baptiste , Berret Jean-François
Published: October 2023

Abstract

Cellular microrheology has shown that cancer cells with high metastatic potential are softer compared to non-tumorigenic normal cells. These findings rely on measuring the apparent Young modulus of whole cells using primarily atomic force microscopy. The present study aims to explore whether alternative mechanical parameters have discriminating features with regard to metastatic potential. Magnetic rotational spectroscopy (MRS) is employed in the examination of mammary epithelial cell lines: MCF-7 and MDA-MB-231, representing low and high metastatic potential, alongside normal-like MCF-10A cells. MRS utilizes active micron-sized magnetic wires in a rotating magnetic field to measure the viscosity and elastic modulus of the cytoplasm. All three cell lines display viscoelastic behavior, with cytoplasmic viscosities ranging from 10-70 Pa s and elastic moduli from 30-80 Pa. It is found that the tumorigenic MCF-7 and MDA-MB-231 cells are softer than the MCF-10A cells, with a twofold decrease in elastic modulus. To differentiate cells with low and high malignancy however, viscosity emerges as the more discriminating parameter, as MCF-7 exhibits a 5 times higher viscosity as compared to MDA-MB-231. These findings highlight the sensitivity of cytoplasmic viscosity to metastatic potential, suggesting its potential utility as a mechanical marker for malignant cancer cells.

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How predictability and individual alpha frequency shape memory: insights from an event-related potential investigation
Authors: Jano Sophie , Chatburn Alex , Cross Zachariah , Schlesewsky Matthias , Bornkessel-Schlesewsky Ina
Published: October 2023

Prediction and memory are strongly intertwined, with predictions relying on memory retrieval, whilst also influencing memory encoding. However, it is unclear how predictability influences explicit memory performance, and how individual neural factors may modulate this relationship. The current study sought to investigate the effect of predictability on memory processing with an analysis of the N400 event-related potential in a context extending beyond language. Participants (N= 48, females = 33) completed a study-test paradigm where they first viewed predictable and unpredictable four-item ‘ABCD’ sequences of outdoor scene images, whilst their brain activity was recorded using electroencephalography (EEG). Subsequently, their memory for the images was tested, and N400 patterns during learning were compared with memory outcomes. Behavioural results revealed better memory for images in predictable sequences in contrast to unpredictable sequences. Memory was also strongest for predictable images in the ‘B’ position, suggesting that when processing longer sequences, the brain may prioritise the data deemed most informative. Strikingly, greater N400 amplitudes during learning were associated with enhanced memory at test for individuals with low versus high individual alpha frequencies (IAFs). In light of the relationship between the N400 and stimulus predictability, this finding may imply that predictive processing differs between individuals to influence the extent of memory encoding. Finally, exploratory analyses provided evidence for a later positivity that was predictive of subsequent memory performance. Ultimately, the results highlight the complex and interconnected relationship between predictive processing and memory, whilst shedding light on the accumulation of predictions across longer sequences.
Sodiummyo-inositol cotransporter-1, SMIT1, promotes cardiac hypertrophy and fibrosis in pressure overloaded mouse hearts
Authors: Marino Alice , Cumps Julien , Guilbert Laura , Baufays Claire , Ginion Audrey , Ferté Laura , Battault Sylvain , Ambroise Jerome , Bearzatto Bertrand , Zuurbier Coert J. , Lezoualch Frank , Pestiaux Camille , Pyka Grzegorz , Kerckhofs Greet , Tyteca Donatienne , Bouzin Caroline , Bertrand Luc , Horman Sandrine , Beauloye Christophe
Published: October 2023

Background

Sodiummyo-inositol cotransporter-1 (SMIT1) belongs to the sodium-glucose cotransporter (SGLT) family. SMIT1 is expressed in cardiac cells, including fibroblasts and cardiomyocytes. However, the function of SMIT1 in the heart remains unknown.

Methods

We used a model of pressure overload induced by transverse aortic constriction in wild type (WT) mice and mice lacking SMIT1 (Smit1-/-), combined with echocardiography, immunoblot and staining, contrast-enhanced microfocus computed tomography, and RNA-sequencing to evaluate the contribution of SMIT1 in cardiac hypertrophy, fibrosis and function. In addition, we used primary cultures of adult mouse and neonatal rat cardiomyocytes to define the molecular pathways affected by SMIT1.

Results

We found that aortic banding fails to induce systolic dysfunction, cardiac hypertrophy and fibrosis inSmit1-/-mice, in contrast to WT controls. Deletion of SMIT1 reduces cardiacO-GlcNAcylation and maintains basal levels of Carabin following hemodynamic stress. In the absence of SMIT1, Carabin inhibits calcineurin/NFAT and Ras/ERK1/2 pathways, putting a brake on transcriptional reprogramming and further development of cardiac hypertrophy.In vitro, we showed that the lack of SMIT1 mitigates phenylephrine-induced hypertrophy and calcium increase in isolated cardiomyocytes.

Conclusions

This work establishes SMIT1 as a key driver of hypertrophy, suggesting that pharmacological inhibition of this SGLT member can serve as a potential strategy to prevent or treat pathological hypertrophy and heart failure.

Abstract Figure

Graphical abstract.

Model of the role of SMIT1 in the development of cardiac hypertrophy.

We found that SMIT1 modulates intracellular calcium levels, downregulates Carabin and increases OGT expression, to promote pathological cardiac hypertrophy and heart failure development.
Prefrontal activity sharpens spatial sensitivity of extrastriate neurons
Authors: Vanegas M. Isabel , Akbarian Amir , Clark Kelsey L. , Nesse William H. , Noudoost Behrad
Published: October 2023

Prefrontal cortex is known to exert its control over representation of visual signals in extrastriate areas such as V4. Frontal Eye Field (FEF) is suggested to be the proxy for the prefrontal control of visual signals. However, it is not known which aspects of sensory representation within extrastriate areas are under the influence of FEF activity. We employed a causal manipulation to examine how FEF activity contributes to spatial sensitivity of extrastriate neurons. Finding FEF and V4 areas with overlapping response field (RF) in two macaque monkeys, we recorded V4 responses before and after inactivation of the overlapping FEF. We assessed spatial sensitivity of V4 neurons in terms of their response gain, RF spread, coding capacity, and spatial discriminability. Unexpectedly, we found that in the absence of FEF activity, spontaneous and visually-evoked activity of V4 neurons both increase and their RFs enlarge. However, assessing the spatial sensitivity within V4, we found that these changes were associated with a reduction in the ability of V4 neurons to represent spatial information: After FEF inactivation, V4 neurons showed a reduced response gain and a decrease in their spatial discriminability and coding capacity. These results show the necessity of FEF activity for shaping spatial responses of extrastriate neurons and indicates the importance of FEF inputs in sharpening the sensitivity of V4 responses.
In praise of fossil fuel subsidies (for cooking)‡
Authors: Gould Carlos F. , Bailis Rob , Balakrishnan Kalpana , Burke Marshall , Espinoza Sebastián , Mehta Sumi , Schlesinger Samuel B. , Suarez-Lopez José R. , Pillarisetti Ajay
Published: October 2023

Households that burn biomass in inefficient open fires – a practice that results in $1.6 trillion in global damages from health impacts and climate-altering emissions yearly – are often unable to access cleaner alternatives, like gas, which is widely available but unaffordable, or electricity, which is unattainable for many due to insufficient supply and reliability of electricity services. Governments are often reluctant to make gas affordable. We argue that condemnation of all fossil fuel subsidies is short-sighted and does not adequately consider subsidizing gas for cooking as a potential strategy to improve public health and reduce greenhouse gas emissions.
Measures of population immunity can predict the dominant clade of influenza A (H3N2) in the 2017-2018 season and reveal age-associated differences in susceptibility and antibody-binding specificity
Authors: Kim Kangchon , Vieira Marcos C. , Gouma Sigrid , Weirick Madison E. , Hensley Scott E. , Cobey Sarah
Published: October 2023

Background

For antigenically variable pathogens such as influenza, strain fitness is partly determined by the relative availability of hosts susceptible to infection with that strain compared to others. Antibodies to the hemagglutinin (HA) and neuraminidase (NA) confer substantial protection against influenza infection. We asked if a cross-sectional antibody-derived estimate of population susceptibility to different clades of influenza A (H3N2) could predict the success of clades in the following season.

Methods

We collected sera from 483 healthy individuals aged 1 to 90 years in the summer of 2017 and analyzed neutralizing responses to the HA and NA of representative strains using Focus Reduction Neutralization Tests (FNRT) and Enzyme-Linked Lectin Assays (ELLA). We estimated relative population-average and age-specific susceptibilities to circulating viral clades and compared those estimates to changes in clade frequencies in the following 2017-18 season.

Results

The clade to which neutralizing antibody titers were lowest, indicating greater population susceptibility, dominated the next season. Titer correlations between viral strains varied by age, suggesting age-associated differences in epitope targeting driven by shared past exposures. Yet substantial unexplained variation remains within age groups.

Conclusions

This study indicates how representative measures of population immunity might improve evolutionary forecasts and inform selective pressures on influenza.
Urinary high-risk HPV DNA detection to enhance cervical cancer screening in developing countries
Authors: Intan Novia Syari , Utama Revata , Wulandari Dewi , Wisdharilla Reiva , Khanza Shafira Mutia , Ramadhan Muhammad Rifki , Widyahening Indah Suci , Nurainy Neni , Sari Rini Mulia , Andrijono
Published: October 2023

Objectives: To increase cervical cancer screening capacity and participation, we evaluated the performance of the newly developed hrHPV ReadyMix qPCR Kit for detecting high-risk Human Papillomavirus (HPV) in urine samples while simultaneously genotyping HPV16, HPV18, and HPV52. Methods: 876 samples were used to assess the performance of hrHPV ReadyMix qPCR Kit in detecting high-risk HPV in standard cervical swab sample compared to the Roche cobas 6800 HPV. The high-risk HPV detection in urine was compared to the corresponding paired cervical swab. Results: The sensitivity of HPV detection in cervical swabs using hrHPV ReadyMix qPCR Kit reached 96.55% and the specificity reached 99.87%. Despite higher Ct values, urine samples demonstrated 80.88% sensitivity and 100.00% specificity compared to cervical swabs. Our method enables population-based high-risk HPV analysis with a 6.62% HPV prevalence from cervical swabs and 6.28% from urine samples. Furthermore, urine samples using the hrHPV ReadyMix qPCR Kit showed comparable HPV type distribution and the ability to genotype HPV16 and HPV18, to Roche the cobas 6800 HPV. Conclusions: Self-collected urine samples offer a 98.48% diagnostic accuracy for detecting high-risk HPV infection. This study highlights the hrHPV ReadyMix qPCR Kit's potential in enhancing cervical cancer screening, offering valuable insights for future interventions.
Mapping the landscape: A protocol of a jurisdictional scan of self-identified learning health systems
Authors: Vanderhout Shelley , Bird Marissa , Giannarakos Antonia , Whitmore Carly
Published: October 2023

Background

There is a growing movement to implement learning health systems (LHS), in which real-time evidence, informatics, patient-provider partnerships and experiences, and organizational culture are aligned to support improvements in care. However, what constitutes a LHS varies based on context and capacity, hindering standardization, scale-up, and knowledge sharing. Further, LHS often use “usual care” as the benchmark for comparing new approaches to care, but disentangling usual care from multifarious care modalities found across settings is challenging. To advance robust LHS, a comprehensive overview of existing LHS including strengths and opportunities for growth is needed.

Objectives

To scope and identify international existing LHS to: 1) inform the global landscape of LHS, highlight common strengths, and identify opportunities for growth or improvement; and 2) identify common characteristics, emphases, assumptions, or challenges described in establishing counterfactuals in LHS.

Methods

A jurisdictional scan will be conducted according to modified PRISMA guidelines. LHS will be identified through a search of peer-reviewed and grey literature using Ovid Medline, Ebsco CINAHL, Ovid Embase, Clarivate Web of Science, and PubMed Non-Medline databases and the web along with informal discussions with peer LHS experts. Self-identified LHS will be included if they are described in sufficient detail, either in literature or during informal discussions, according to ≥4 of 10 criteria (core functionalities, analytics, use of evidence, co-design/implementation, evaluation, change management/governance structures, data sharing, knowledge sharing, training/capacity building, equity, sustainability) in an existing framework to characterize LHS. Search results will be screened, extracted, and analyzed to inform two descriptive reviews pertaining to our two main objectives. Data will be extracted according to a pre-specified extraction form and summarized descriptively.

Implications

This research will characterize the current landscape of worldwide LHS and provide a foundation for promoting knowledge and resource sharing, identifying next steps for the growth, improvement, and evaluation of LHS.
Comparative Organ Disease Burden and Sequelae of Influenza and SARS-CoV-2 Infection: An Observational Study Using Real-World Data
Authors: Bartha Istvan , Maher Cyrus , Lavrenko Victor , Boundy Keith , Kinter Elizabeth , Yeh Wendy , Corti Davide , Telenti Amalio
Published: October 2023

Infections with SARS-CoV-2 and influenza are associated with acute and post-acute complications and sequelae of many organ systems (i.e., disease burden). It is important to understand the global disease burden that associates with and follows acute infection in order to establish preventive and therapeutic strategies and to reduce the use of health resources and improve patient health outcomes. To address these questions, we utilized the National Covid Cohort Collaborative, which is an integrated and harmonized data repository of electronic health record data in the USA. From this database, we included in analysis 346,648 eligible SARS-CoV-2-infected patients, 78,086 eligible influenza infected patients, and 146,635 uninfected controls. We describe the disease burden that extends over 2-3 months following infection, and we quantify the reduction of disease burden by treatment. We identify a burden of disease following medically attended influenza that is comparable to that of medically attended SARS-CoV-2 infection. However, in contrast to SARS-CoV-2, influenza acute infection and disease burden are not responsive to antiviral treatment and thus remain as an unmet medical need. Focusing therapeutic strategies solely on the short-term management of acute infection may also underestimate the extended health benefits of antiviral treatment.
Lifetime exposure to violence and early cardiometabolic risk factors in a healthy Swedish cohort
Authors: Lynch Rebekka , Aspelund Thor , Fang Fang , Bergstedt Jacob , Hauksdóttir Arna , Arnberg Filip K. , Hrafnkelsdóttir Þórdís Jóna , Pedersen Nancy L. , Valdimarsdóttir Unnur
Published: October 2023

Introduction

Violence exposure has been associated with cardiovascular disease. Less is known about underlying mechanisms, including early cardiometabolic risk factors, and possible sex differences of such associations.

Methods

We used data from the Swedish LifeGene study on 23,215 males and females, aged 18-50 years. At baseline (2009-1016) participants answered the Life Stressor Checklist-Revised alongside questions on medical diagnoses of hypertension, diabetes, dyslipidemia and smoking history. At a clinical visit, blood pressure, BMI, glycated hemoglobin (HbA1c), total cholesterol, ApoB/ApoA1 ratio, and high-sensitivity C-Reactive Protein (hs-CRP) were measured. Modified Poisson and linear regression were used to test the association between violence and cardiometabolic risk factors.

Results

At mean age 33±8 years, lifetime exposure to violence was reported by 23% of females and 15% of males. Those exposed to violence were more likely to smoke (PR 1.86, CI: 1.66–2.07) and report a diagnosis of hypertension (PR 1.39, CI: 1.18-1.64). While no differences were observed in measured systolic blood pressure (B -0.34, CI: -0.70, 0.02), HbA1c (B 0.06, CI: - 0.08, 0.20) or total cholesterol (B -0.01, CI: -0.04, 0.02), both males and females exposed to violence had higher BMI (B 0.51, CI: 0.39–0.63) and hs-CRP (B 0.11, CI: 0.06–0.16), after adjustment. Violence in childhood, as opposed to adulthood, and exposure to both sexual and physical violence, as opposed to either type, was more strongly associated with hs-CRP and BMI.

Discussion

In a young healthy Swedish sample, lifetime exposure to violence was associated with some but not all early cardiometabolic risk factors among both males and females.
Synthetic Peptide Nucleic Acids in Action:In VivoInterference of thegroELGene from Pea Aphid EndosymbiontBuchnera aphidicola
Authors: Tan Kathrine Xin Yee , Shigenobu Shuji
Published: October 2023

The unculturable nature of intracellular obligate symbionts presents a significant challenge for elucidating gene functionality, necessitating the development of gene manipulation techniques. One of the best-studied obligate symbioses is that between aphids and the bacterial endosymbiontBuchnera aphidicola.Given the extensive genome reduction observed inBuchnera, the remaining genes are crucial for understanding the host-symbiont relationship, but a lack of tools for manipulating gene function in the endosymbiont has significantly impeded the exploration of the molecular mechanisms underlying this mutualism. In this study, we introduced a novel gene manipulation technique employing synthetic single-stranded peptide nucleic acids (PNAs). We targeted the criticalBuchnera groELusing specially designed antisense PNAs conjugated to an arginine-rich cell-penetrating peptide (CPP). Within 24 h of PNA administration via microinjection, we observed a significant reduction ingroELexpression andBuchneracell count. Notably, the interference ofgroELled to profound morphological malformations inBuchnera, indicative of impaired cellular integrity. The gene knockdown technique developed in this study, involving the microinjection of CPP-conjugated antisense PNAs, provides a potent approach forin vivogene manipulation of unculturable intracellular symbionts, offering valuable insights into their biology and interactions with hosts.
Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin
Authors: Venetz Jessica , Żygadłowska Olga M. , Dotsios Nicky , Wallenius Anna J. , van Helmond Niels A.G.M. , Lenstra Wytze K. , Klomp Robin , Slomp Caroline P. , Jetten Mike S.M. , Veraart Annelies J.
Published: October 2023

In the water column of coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter. This filter can counteract high benthic methane fluxes and thereby lower methane emissions to the atmosphere. Recent metagenomic studies revealed that the metabolism of the MOB in the filter is versatile, and could quickly respond to changing oxygen concentrations. Changes in oxygen availability in coastal basins are largely driven by seasonal stratification and mixing. However, it is still unclear how well the methane biofilter functions throughout the seasons, and how this relates to MOB community composition. Here, we determined water column methane and oxygen depth profiles and the methanotrophic community structure, methane oxidation potential, and methane fluxes of the Scharendijke basin in marine Lake Grevelingen between March and October 2021. In this period, the methane filter mainly consisted of three MOB belonging toMethylomonadaceae. Although in low relative abundance, the methanotrophic community was present in the mixed water column in March and had increased to 9 % by July in the stratified water column, with a distinct vertical niche partitioning in the redoxcline. The methane and oxygen gradients were vertically decoupled in summer upon the formation of a suboxic zone. Surprisingly, this did not affect the vertical distribution or potential methane oxidation of MOB. Moreover, water-air fluxes remained below 0.6 mmol m-2day-1. Our findings suggest active methane removal by MOB in virtually anoxic water. Weakening of the stratification in September resulted in higher diffusive methane fluxes to the atmosphere (up to 1.6 mmol m-2day-1). This was likely due to a faster supply of methane, but also a reduction of methane oxidation. Thus, despite the rapid adaptation and versatile genomic potential of the MOB community, seasonal water column dynamics significantly influence methane removal efficiency.
A Layered Microcircuit Model of Somatosensory Cortex with Three Interneuron Types and Cell-Type-Specific Short-Term Plasticity
Authors: Jiang Han-Jia , Qi Guanxiao , Duarte Renato , Feldmeyer Dirk , van Albada Sacha J
Published: October 2023

Three major types of GABAergic interneurons, parvalbumin- (PV), somatostatin- (SOM) and vasoactive intestinal peptide-expressing (VIP) cells, play critical but distinct roles in the cortical microcircuitry. Their specific electrophysiology and connectivity shape their inhibitory functions. To study the network dynamics and signal processing specific to these cell types in the cerebral cortex, we developed a multi-layer model incorporating biologically realistic interneuron parameters from rodent somatosensory cortex. The model is fitted toin vivodata on cell-type-specific population firing rates. With a protocol of cell-type-specific stimulation, network responses when activating different neuron types are examined. The model reproduces the experimentally observed inhibitory effects of PV and SOM cells and disinhibitory effect of VIP cells on excitatory cells. We further create a version of the model incorporating cell-type-specific short-term synaptic plasticity (STP). While the ongoing activity with and without STP is similar, STP modulates the responses of Exc, SOM, and VIP cells to cell-type-specific stimulation, presumably by changing the dominant inhibitory pathways. With slight adjustments, the model also reproduces sensory responses of specific interneuron types recordedin vivo. Our model provides predictions on network dynamics involving cell-type-specific short-term plasticity and can serve to explore the computational roles of inhibitory interneurons in sensory functions.
Assessing Lanthanide-Dependent Methanol Dehydrogenase Activity: The Assay Matters
Authors: Phi Manh Tri , Singer Helena , Zäh Felix , Haisch Christoph , Schneider Sabine , den Camp Huub J.M. Op , Daumann Lena J.
Published: October 2023

Artificial dye-coupled assays have been widely adopted as a rapid and convenient method to assess the activity of methanol dehydrogenases (MDH). Lanthanide(Ln)-dependent XoxF-MDHs from methanotrophs and methylotrophs are able to incorporate different lanthanides (Lns) in their active site. The artificial dye-coupled assay showed that the earlier Lns exhibit a higher enzyme activity than the late Lns. Although this assay is widely used, there are limitations. It is not unusual that a pH of 9 is required and that activators like ammonium have to be added to the assay mixture which do not reflect the conditions inside the cell. Moreover, different Ln-MDH variants are not obtained by the direct isolation from the cells grown with the respective Ln, but by metal titration of the Ln in a partial-apo-MDH or by incubation of an apo-MDH with the Ln. Herein, we report the cultivation of Ln-dependent methanotrophMethylacidiphilum fumariolicumSolV with nine different Lns, the isolation of the respective MDH and the assessment of the enzyme activity using the artificial dye-coupled assay. We compare these results with an adapted protein-coupled assay using the physiological partner and electron acceptor cytochromecGJ(cytcGJ) instead of artificial dyes. We demonstrate that, depending on the assay, two distinct trends are observed among the Ln series. The specific activity of La-, Ce- and Pr-MDH, as measured by the protein-coupled assay, exceeds the specific enzyme activity measured by the dye-coupled assay. This suggests that the early Lns also have a positive effect on the interaction between XoxF-MDH and its cytcGJthereby increasing functional efficiency.
Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP
Authors: Yi Soon , Singh Shashi S. , Rozen-Gagnon Kathryn , Luna Joseph M.
Published: October 2023

RNA binding proteins (RBPs) are essential for RNA metabolism and profoundly impact health and disease. The subcellular organization of RBP interaction networks with target RNAs remains largely unexplored. Here, we develop colocalization CLIP, a method that combines CrossLinking and ImmunoPrecipitation (CLIP) with proximity labeling, to explore in-depth the subcellular RNA interactions of the well-studied RNA-binding protein HuR. Using this method, we uncover HuR’s dynamic and location-specific interactions with RNA, revealing alterations in sequence preferences and interactions in the nucleus, cytosol, or stress granule compartments. We uncover HuR’s unique binding preferences within stress granules during arsenite stress, illuminating intricate interactions that conventional methodologies cannot capture. Overall, coCLIP provides a powerful method for revealing RBP:RNA interactions based on localization and lays the foundation for an advanced understanding of RBP models that incorporate subcellular location as a critical determinant of their functions.
Expression of Filaments of theGeobacterExtracellular Cytochrome OmcS inShewanella oneidensis
Authors: Lin Tong , Ding Wenqi , Zhang Danni , Yang Yun , Li Feng , Xu Dake , Lovley Derek R. , Song Hao
Published: October 2023

The physiological role ofGeobacter sulfurreducensextracellular cytochrome filaments is a matter of debate and the development of proposed electronic device applications of cytochrome filaments awaits methods for large-scale cytochrome nanowire production. Functional studies inGeobacter sulfurreducensare stymied by the broad diversity of redox-active proteins on the outer cell surface and the redundancy and plasticity of extracellular electron transport routes.G. sulfurreducensis a poor chassis for producing cytochrome nanowires for electronics because of its slow, anaerobic growth. Here we report that filaments of theG. sulfurreducenscytochrome OmcS can be heterologously expressed inShewanella oneidensis. Multiple lines of evidence demonstrated that a strain ofS. oneidensis, expressing theG. sulfurreducensOmcS gene on a plasmid, localized OmcS on the outer cell surface. Atomic force microscopy revealed filaments with the unique morphology of OmcS filaments emanating from cells. Electron transfer to OmcS appeared to require a functional outer-membrane porin-cytochrome conduit. The results suggest thatS. oneidensis, which grows rapidly to high culture densities under aerobic conditions, may be a suitable for development of a chassis for producing cytochrome nanowires for electronics applications and may also be good model microbe for elucidating cytochrome filament function in anaerobic extracellular electron transfer.
Mutations upstream fromsdaCandmalTinEscherichia coliuncover a complex interplay between the cAMP receptor protein and different sigma factors
Authors: Frendorf Pernille Ott , Heyde Sophia A. H. , Nørholm Morten H. H.
Published: October 2023

InEscherichia coli, one of the best understood microorganisms, much can still be learned about the basic interactions between transcription factors and promoters, particularly in the stationary phase. When a cAMP-deficientcyamutant is supplied with maltose as the main carbon source, mutations develop upstream from the two genesmalTandsdaC. Here, we explore the regulation of the two promoters, using fluorescence-based genetic reporters in combination with both spontaneously evolved and systematically engineeredcis-acting mutations. We show that in thecyamutant, regulation ofmalTandsdaCevolves toward cAMP-independence and increased expression in stationary phase. Furthermore, we show that the location of the cAMP receptor protein (Crp) binding site upstream ofmalTis important for alternative sigma factor usage. This provides new insights into the architecture of bacterial promoters and the global interplay between Crp and sigma factors in different growth phases.
Ultrasound-mediated drug diffusion, uptake, and cytotoxicity in glioblastoma 3D tumour sphere model
Authors: Wanigasekara Janith , Mondala Julie Rose Mae , Cullen Patrick J. , Tiwari Brijesh , Curtin James F.
Published: October 2023

A myriad of biological effects can be stimulated by the ultrasound (US) for the treatment of cancer. The objective of our research was to investigate the effect of ultrasound alone and in combination with the chemotherapeutic drugs such as doxorubicin (DOX) and temozolomide (TMZ) on human glioblastoma (GBM) and the human epidermoid carcinoma cancer 2D and 3D cell cultures. Results indicated that the US 96-probe device could induce tumour sphere cytotoxicity in a dosage- and time-dependent manner, with multiple treatments augmenting this cytotoxic effect. With enhanced cytotoxicity, US decreased tumour sphere growth metabolic activity, disrupted spheroid integrity, and heightened the occurrence of DNA double strand breaks, resulting in damage to tumour spheres and an inability to rebuild tumour spheres after multiple US treatments. The combination of US and TMZ / DOX enhanced the efficiency of treatment for GBM and epidermoid carcinoma by enhancing induced cytotoxicity in 3D tumour spheres compared to 2D monolayer cells, and also by increasing the incubation time, which is the most crucial way to differentiate between the effectiveness of drug treatment with and without US. In conclusion, our data demonstrate that US enhances drug diffusion, uptake, and cytotoxicity using 3D spheroid models when compared with 2D cultures. It also demonstrates the significance of 3D cell culture models in drug delivery and discovery research.

Graphical Abstract
Identification of visible and near-infrared signature peaks for arboviruses andPlasmodium
Authors: Goh Brendon , Soares Magalhães Ricardo J. , Ciocchetta Silvia , Liu Wenjun , Sikulu-Lord Maggy T.
Published: October 2023

Arbovirus and malaria infections affect more than half of the world’s population causing major financial and physical burden. Current diagnostic tools such as microscopy, molecular and serological techniques are technically demanding, costly, or time consuming. Near-infrared spectroscopy has recently been demonstrated as a potential diagnostic tool for malaria and arbovirus and as a screening tool for disease vectors. However, pathogen specific infrared peaks that allow detection of these infections are yet to be described. In this study, we identified unique NIRS peaks from existing laboratory strains of four major arboviruses including Barmah Forest virus (BFV), Dengue virus (DENV), Ross River virus (RRV), Sindbis virus (SINV) andPlasmodium falciparum. Secondly, to determine the diagnostic ability of these peaks, we developed machine learning algorithms using Artificial Neural network (ANN) to differentiate arboviruses from media in which they are grown. Signature peaks for BFV were identified within the visible region at 410, 430, 562 and 588nm and the NIR region at, 946, 958, 1130, 1154 and 1780 nm. DENV related peaks were seen at 410nm within the visible region and 1130 nm within the NIR region. Signature peaks for RRV were observed within the visible region at 410 and 430 nm and within the NIR region at 1130 and 1780 nm, while SINV had a prominent peak at 410 nm within the visible region. Peaks at 514, 528, 547, 561, 582, and 595nm and peaks at 1388, 1432, 1681, 1700, 1721, 1882, 1905, 2245, 2278, 2300 nm were unique forP. falciparum. NIRS predictive sensitivity defined as the ability to predict an arbovirus as an infection was 90% (n = 20) for BFV, 100% (n =10) for RRV and 97.5% (n= 40) for DENV, while infection specificity defined as the ability to predict media as not-infected was 100% (n= 10). Our findings indicate that spectral signatures obtained by NIRS are potential biomarkers for diagnosis arboviruses and malaria.

Author summary

More than half of the world is at risk of contracting either malaria or arboviral infections. In resource limited settings, timely detection of these infections and the ability to screen thousands of people in a day using affordable tools is key to preventing their spread and unprecedented outbreaks. This emphasizes the need to develop portable, rapid, and easy to use diagnostic and surveillance tools. The near-infrared spectroscopy technique has recently been shown to be a potential tool for the diagnosis and surveillance of both malaria and arboviral infections. However, signature spectral biomarkers for these infections remain to be described. This study has identified several spectral biomarkers for DEN, RRV, BVF, SIN arboviruses andP. falciparum parasites. These biomarkers will assist the future assessment of this technique as a diagnostic and or surveillance tool for these infections in the field.
Mechanistic models for West Nile Virus transmission: A systematic review of features, aims, and parameterisation
Authors: de Wit Mariken , Dimas Martins Afonso , Delecroix Clara , Heesterbeek Hans , ten Bosch Quirine
Published: October 2023

Mathematical models within the Ross-Macdonald framework increasingly play a role in our understanding of vector-borne disease dynamics and as tools for assessing scenarios to respond to emerging threats. These threats are typically characterised by a high degree of heterogeneity, introducing a range of possible complexities in models and challenges to maintain the link with empirical evidence.

We systematically identified and analysed a total of 67 published papers presenting compartmental West Nile Virus (WNV) models that use parameter values derived from empirical studies. Using a set of fifteen criteria, we measured the dissimilarity compared to the Ross–Macdonald framework. We also retrieved the purpose and type of models and traced the empirical sources of their parameters.

Our review highlights the increasing refinements in WNV models. Models for prediction included the highest number of refinements. We found uneven distributions of refinements and of evidence for parameter values. We identified several challenges in parameterising such increasingly complex models. For parameters common to most models, we also synthesise the empirical evidence for their values and ranges. The study highlights the potential to improve the quality of WNV models and their applicability for policy by establishing closer collaboration between mathematical modelling and empirical work.
Immune Epitopes of SARS-CoV-2 Spike Protein and Considerations for Universal Vaccine Development
Authors: Magazine Nicholas , Zhang Tianyi , Bungwon Anang D. , McGee Michael C. , Wu Yingying , Veggiani Gianluca , Huang Weishan
Published: October 2023

Despite the success of global vaccination programs in slowing the spread of COVID-19, these efforts have been hindered by the emergence of new SARS-CoV-2 strains capable of evading prior immunity. The mutation and evolution of SARS-CoV-2 have created a demand for persistent efforts in vaccine development. SARS-CoV-2 Spike protein has been the primary target for COVID-19 vaccine development, but it is also the hotspot of mutations directly involved in host susceptibility and immune evasion. Our ability to predict emerging mutants and select conserved epitopes is critical for the development of a broadly neutralizing therapy or a universal vaccine. In this article, we review the general paradigm of immune responses to COVID-19 vaccines, highlighting the immunological epitopes of Spike protein that are likely associated with eliciting protective immunity resulting from vaccination. Specifically, we analyze the structural and evolutionary characteristics of the SARS-CoV-2 Spike protein related to immune activation and function via the toll-like receptors (TLRs), B cells, and T cells. We aim to provide a comprehensive analysis of immune epitopes of Spike protein, thereby contributing to the development of new strategies for broad neutralization or universal vaccination.
Designer Fat Cells: Adipogenic Differentiation of CRISPR-Cas9 Genome-Engineered Induced Pluripotent Stem Cells
Authors: Ely E. V. , Kapinski A. T. , Paradi S. G. , Tang R. , Guilak F. , Collins K. H.
Published: October 2023

Adipose tissue is an active endocrine organ that can signal bidirectionally to many tissues and organ systems in the body. With obesity, adipose tissue is a source of low-level inflammation that contributes to various co-morbidities and damage to downstream effector tissues. The ability to synthesize genetically engineered adipose tissue could have critical applications in studying adipokine signaling and the use of adipose tissue for novel therapeutic strategies. This study aimed to develop a method for non-viral adipogenic differentiation of genome-edited murine induced pluripotent stem cells (iPSCs) and to test the ability of such cells to engraft in micein vivo. Designer adipocytes were created from iPSCs, which can be readily genetically engineered using CRISPR-Cas9 to knock out or insert individual genes of interest. As a model system for adipocyte-based drug delivery, an existing iPSC cell line that transcribes interleukin 1 receptor antagonist under the endogenous macrophage chemoattractant protein-1 promoter was tested for adipogenic capabilities under these same differentiation conditions. To understand the role of various adipocyte subtypes and their impact on health and disease, an efficient method was devised for inducing browning and whitening of IPSC-derived adipocytes in culture. Finally, to study the downstream effects of designer adipocytesin vivo, we transplanted the designer adipocytes into fat-free lipodystrophic mice as a model system for studying adipose signaling in different models of disease or repair. This novel translational tissue engineering and regenerative medicine platform provides an innovative approach to studying the role of adipose interorgan communication in various conditions.
Viral genomic features predictorthopoxvirusreservoir hosts
Authors: Tseng Katie K. , Koehler Heather , Becker Daniel J. , Gibb Rory , Carlson Colin J. , del Pilar Fernandez Maria , Seifert Stephanie N.
Published: October 2023

Orthopoxviruses (OPVs), including the causative agents of smallpox and mpox have led to devastating outbreaks in human populations worldwide. However, the discontinuation of smallpox vaccination, which also provides cross-protection against related OPVs, has diminished global immunity to OPVs more broadly. We apply machine learning models incorporating both host ecological and viral genomic features to predict likely reservoirs of OPVs. We demonstrate that incorporating viral genomic features in addition to host ecological traits enhanced the accuracy of potential OPV host predictions, highlighting the importance of host-virus molecular interactions in predicting potential host species. We identify hotspots for geographic regions rich with potential OPV hosts in parts of southeast Asia, equatorial Africa, and the Amazon, revealing high overlap between regions predicted to have a high number of potential OPV host species and those with the lowest smallpox vaccination coverage, indicating a heightened risk for the emergence or establishment of zoonotic OPVs. Our findings can be used to target wildlife surveillance, particularly related to concerns about mpox establishment beyond its historical range.