bluuebunny/crossref_metadata_2025 huggingface dataset:
The ubiquitin ligase STUB1 suppresses tumorigenesis of renal cell carcinomas through regulating YTHDF1 stability
Authors: Ma Siquan , Sun Yi , Gao Guoyao , Zeng Jin , Chen Ke , Zhao Zhenyu
Published: August 2023

STIP1 homology and U-box protein 1 (STUB1), a key RING family E3 ubiquitin ligase, plays both oncogenic and tumor-suppressive roles in a variety of human cancers. However, the role and mechanism of STUB1 in clear cell renal cell carcinoma (ccRCC) remains poorly defined. Here, we identified YTHDF1 as a novel STUB1 interactor by affinity purification mass spectrometry (AP-MS). STUB1 polyubiquitylates YTHDF1 and promotes YTHDF1 degradation. STUB1 depletion stabilizes YTHDF1 in renal cancer cells. STUB1-knockdown renal cancer cells exhibit increased migration and invasion in YTHDF1 dependent manner. Further study demonstrates that STUB1 knockdown promoted the tumorigenicity of ccRCC in a xenograft model. Clinically, STUB1 expression is down-regulated in ccRCC tissues, and the low expression level of STUB1 was associated with higher tumor stage and poor overall survival in patients with ccRCC. These findings reveal that STUB1 acts as an E3 ubiquitin ligase and promotes degradation of YTHDF1, and STUB1 inhibits the tumorigenicity of ccRCC through ubiquitinating YTHDF1.

Novelty & Impact Statements

STUB1 plays both oncogenic and tumor-suppressive roles in a variety of human cancers. Here, the authors demonstrated that STUB1 acts as a tumor suppressor in ccRCC, and the low expression level of STUB1 was associated with higher tumor stage and poor overall survival in patients with ccRCC. In addition, STUB1-knockdown renal cancer cells exhibit increased migration and invasion in YTHDF1 dependent manner. Mechanistically, STUB1 polyubiquitylates YTHDF1 and promotes YTHDF1 degradation.
Proportionality-based association metrics in count compositional data
Authors: McGregor Kevin , Okaeme Nneka , Khorasaniha Reihane , Veniamin Simona , Jovel Juan , Miller Richard , Mahmood Ramsha , Graham Morag , Bonner Christine , Bernstein Charles N. , Arnold Douglas L. , Bar-Or Amit , Hart Janace , Marrie Ruth Ann , O’Mahony Julia , Yeh E. Ann , Zhao Yinshan , Banwell Brenda , Waubant Emmanuelle , Knox Natalie , Van Domselaar Gary , Zhu Feng , Mirza Ali I. , Tremlett Helen , Armstrong Heather
Published: August 2023

Motivation

Compositional data comprise vectors that describe the constituent parts of a whole. Data arising from various -omics platforms such as 16S and RNA-sequencing are compositional in nature. However, correlations between features on raw counts have no meaningful interpretation. Metrics of proportionality were formulated to address this problem. However, there is an inherent bias that arises when calculating these metrics empirically on count-based measures due to variability in read depths.

Results

We quantify the bias introduced by empirically calculating proportionality-based association metrics in count data. Additionally, we propose a means of estimating these metrics within a logit-normal multinomial model in pursuit of more accurate estimates. The model-based estimates are shown to outperform empirical estimates in simulated data, and are additionally applied to a mouse embryonic stem-cell single-cell sequencing dataset as well as a pediatric-onset multiple sclerosis metagenomic dataset.

Availability and Implementation

An R package is available athttps://CRAN.R-project.org/package=countprop.

Supplementary information

Supplementary data are available at Bioinformatics online.
Allosteric activation of the co-receptor BAK1 by the EFR receptor kinase initiates immune signaling
Authors: Mühlenbeck Henning , Tsutsui Yuko , Lemmon Mark A. , Bender Kyle W. , Zipfel Cyril
Published: August 2023

Transmembrane signaling by plant receptor kinases (RKs) has long been thought to involve reciprocal trans-phosphorylation of their intracellular kinase domains. The fact that many of these are pseudokinase domains, however, suggests that additional mechanisms must govern RK signaling activation. Non-catalytic signaling mechanisms of protein kinase domainshave been described in metazoans, but information is scarce for plants. Recently, a non-catalytic function was reported for the leucine-rich repeat (LRR)-RK subfamily XIIa member EFR (ELONGATION FACTOR TU RECEPTOR) and phosphorylation-dependent conformational changes were proposed to regulate signaling of RKs with non-RD kinase domains. Here, using EFR as a model, we describe a non-catalytic activation mechanism for LRR-RKs with non-RD kinase domains. EFR is an active kinase, but a kinase-dead variant retains the ability to enhance catalytic activity of its co-receptor kinase BAK1/SERK3 (BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1/SOMATIC EMBRYOGENESIS RECEPTOR KINASE 3). Applying hydrogen-deuterium exchange mass spectrometry (HDX-MS) analysis and designing homology-based intragenic suppressor mutations, we provide evidence that the EFR kinase domain must adopt its active conformation in order to activate BAK1 allosterically, likely by supporting αC-helix positioning in BAK1. Our results suggest a conformational toggle model for signaling, in which BAK1 first phosphorylates EFR in the activation loop to stabilize its active conformation, allowing EFR in turn to allosterically activate BAK1.
Genetic and Structural Basis of Colistin Resistance inKlebsiella pneumoniae: Unraveling the Molecular Mechanisms
Authors: Alousi Sahar , Saad Jamal , Panossian Balig , Makhlouf Rita , Al Khoury Charbel , Rahy Kelven , Thoumi Sergio , Araj George F. , Khnayzer Rony , Tokajian Sima
Published: August 2023

Antimicrobial Antimicrobial resistance (AMR), together with extensively drug resistant (XDR), mainly among Gram-negative bacteria, has been on the rise. Colistin (polymyxin E) remains one of the primary available last resorts to treat infections by XDR bacteria with the rapid emergence of global resistance. Since the exact mechanism of bacterial resistance to colistin remains unfolded, this study warranted elucidating the underlying mechanism of colistin resistance and heteroresistance among carbapenem-resistant (CR)Klebsiella pneumoniaeisolates.

Molecular analysis was carried out on the resistant isolates using a genome-wide characterization approach, and MALDI-TOF MS for lipid A. Among the 32 CRK. pneumoniaeisolates, three and seven isolates showed resistance and intermediate resistance, respectively, to colistin. The seven isolates with intermediate resistance exhibited the “skip-well” phenomenon, attributed to the presence of resistant subpopulations. The three isolates with full resistance to colistin showed ions using MALDI-TOF MS at m/z 1840 and 1824 representing bisphosphorylated and hexaacylated lipid A with or without hydroxylation, at position C’-2 of the fatty acyl chain, respectively. Studying the genetic environment ofmgrBlocus revealed the presence of insertion sequences that disrupted themgrBlocus in the three colistin resistant isolates: IS1R and IS903B. Our findings showed that colistin resistance/heteroresistance was inducible with mutations in chromosomal regulatory networks controlling lipid A moiety and IS sequences disrupting themgrBgene leading to elevated MIC values and treatment failure. IS monitoring inK. pneumoniaecould help prevent the spread of colistin resistance and decrease colistin treatment failure.
M4-mediated cholinergic transmission is reduced in parkinsonian mice and its restoration alleviates motor deficits and levodopa-induced dyskinesia
Authors: Nielsen Beatriz E. , Ford Christopher P.
Published: August 2023

The dynamic equilibrium between dopamine (DA) and acetylcholine (ACh) in the dorsal striatum is thought to be essential for motor function, as imbalances in their levels are associated with Parkinson’s disease (PD) and levodopa-induced dyskinesia (LID). While loss of DA leads to enhanced striatal ACh, whether this translates to specific alterations in transmission remains unclear. To address this, we examined how the strength of ACh release and signaling onto direct-pathway medium spiny neurons is altered in parkinsonian mice. Rather than the predicted cholinergic enhancement, we found that the strength of muscarinic M4-receptor mediated transmission was reduced following DA loss, resulting from downregulated receptors and downstream signaling. Despite M4-receptors being thought to mediate anti-kinetic effects, restoring M4-receptor function partially rescued parkinsonian balance and coordination deficits and limited the development of levodopa-induced dyskinetic behaviors, indicating that decreased M4-function contributed to circuit and motor dysfunctions in response to DA loss.
The histidine kinase NahK regulates pyocyanin production through the PQS system
Authors: Mendoza Alicia G. , Guercio Danielle , Smiley Marina K. , Sharma Gaurav K. , Withorn Jason M. , Hudson-Smith Natalie V. , Ndukwe Chika , Dietrich Lars E. P. , Boon Elizabeth M.
Published: August 2023

Many bacterial histidine kinases work in two-component systems that combine into larger multi-kinase networks. NahK is one of the kinases in the GacS Multi-Kinase Network (MKN), which is the MKN that controls biofilm regulation in the opportunistic pathogenPseudomonas aeruginosa (P. aeruginosa). This network has also been associated with regulating many virulence factorsP. aeruginosasecretes to cause disease. However, the individual role of each kinase is unknown. In this study, we identify NahK as a novel regulator of the phenazine pyocyanin (PYO). Deletion ofnahKled to a four-fold increase in PYO production, almost exclusively through upregulation of phenazine operon two (phz2). We determined that this upregulation is due to mis-regulation of allP. aeruginosaquorum sensing systems, with a large upregulation of thePseudomonasquinolone signal (PQS) system and a decrease in production of the acyl-homoserine lactone-producing system,las.In addition, we see differences in expression of quorum sensing inhibitor proteins that align with these changes. Together, this data contributes to understanding how the GacS MKN modulates QS and virulence.

Importance

Pseudomonas aeruginosais a Gram-negative bacterium that establishes biofilms as part of its pathogenicity.P. aeruginosainfections are associated with nosocomial infections. As the prevalence of multi-drug resistantP. aeruginosaincreases, it is essential to understand underlying virulence molecular mechanisms. Histidine kinase NahK is one of several kinases inP. aeruginosaimplicated in biofilm formation and dispersal. Previous work has shown that the nitric oxide sensor, NosP, triggers biofilm dispersal by inhibiting NahK. The data presented here demonstrates that NahK plays additional important roles in theP. aeruginosalifestyle, including regulating bacterial communication mechanisms such as quorum sensing. These effects have larger implications in infection as they affect toxin production and virulence.
Ultra-high density electrodes improve detection, yield, and cell type identification in neuronal recordings
Authors: Ye Zhiwen , Shelton Andrew M , Shaker Jordan R , Boussard Julien M , Colonell Jennifer , Birman Daniel , Manavi Sahar , Chen Susu , Windolf Charlie , Hurwitz Cole , Namima Tomoyuki , Pedraja Frederico , Weiss Shahaf , Raducanu Bogdan , Ness Torbjørn , Jia Xiaoxuan , Mastroberardino Giulia , Rossi L. Federico , Carandini Matteo , Hausser Michael , Einevoll Gaute T , Laurent Gilles , Sawtell Nathaniel B , Bair Wyeth , Pasupathy Anitha , Mora-Lopez Carolina , Dutta Barun , Paninski Liam , Siegle Joshua H , Koch Christof , Olsen Shawn R , Harris Timothy D , Steinmetz Nicholas A
Published: August 2023

To understand the neural basis of behavior, it is essential to sensitively and accurately measure neural activity at single neuron and single spike resolution. Extracellular electrophysiology delivers this, but it has biases in the neurons it detects and it imperfectly resolves their action potentials. To minimize these limitations, we developed a silicon probe with much smaller and denser recording sites than previous designs, called Neuropixels Ultra (NP Ultra). This device samples neuronal activity at ultra-high spatial density (~10 times higher than previous probes) with low noise levels, while trading off recording span. NP Ultra is effectively an implantable voltage-sensing camera that captures a planar image of a neuron's electrical field. We use a spike sorting algorithm optimized for these probes to demonstrate that the yield of visually-responsive neurons in recordings from mouse visual cortex improves up to ~3-fold. We show that NP Ultra can record from small neuronal structures including axons and dendrites. Recordings across multiple brain regions and four species revealed a subset of extracellular action potentials with unexpectedly small spatial spread and axon-like features. We share a large-scale dataset of these brain-wide recordings in mice as a resource for studies of neuronal biophysics. Finally, using ground-truth identification of three major inhibitory cortical cell types, we found that these cell types were discriminable with approximately 75% success, a significant improvement over lower-resolution recordings. NP Ultra improves spike sorting performance, detection of subcellular compartments, and cell type classification to enable more powerful dissection of neural circuit activity during behavior.
The floral development of the allotetraploidCoffea arabicaL. correlates with a small RNA dynamic reprogramming
Authors: Ribeiro Thales Henrique Cherubino , Baldrich Patricia , de Oliveira Raphael Ricon , Fernandes-Brum Christiane Noronha , Mathioni Sandra Marisa , Cardoso Thaís Cunha de Sousa , Gomes Matheus de Souza , Amaral Laurence Rodrigues do , de Oliveira Kellen Kauanne Pimenta , dos Reis Gabriel Lasmar , Meyers Blake C. , Chalfun-Junior Antonio
Published: August 2023

Non-coding and coding RNAs are key regulators of plant growth, development, and stress responses. To investigate the types of transcripts accumulated during the vegetative to reproductive transition and floral development in theCoffea arabicaL., we sequenced small RNA libraries from eight developmental stages, up to anthesis.

We combined this data with messenger RNA and PARE sequencing of two important development stages that marks the transition of an apparent latent to a rapid growth stage. In addition, we took advantage of multiplein silicotools to characterize genomic loci producing small RNAs such as phasiRNAs, miRNAs and tRFs.

Our differential and co-expression analysis showed that some types of small RNAs such as tRNAs, snoRNAs, snRNAs and phasiRNAs preferentially accumulate in a stage- specific manner.

Members of the miR482/miR2118 superfamily and their 21-nucleotide phasiRNAs originating from resistance genes show a robust co-expression pattern that is maintained across all the evaluated developmental stages. Finally, the majority of miRNAs accumulate in a family-stage specific manner, related to modulated hormonal responses and transcription factors expression.

Societal Impact Statement

This research holds potential to benefit millions of coffee-producing families in over 60 countries. We uncovered molecular regulatory mechanisms governing flower development, one of the causes for theCoffea arabica’s uneven ripening. The absence of uniformity in coffee production, spanning from floral induction to branch senescence, has a detrimental impact on the final product’s quality. These insights will inform strategies for controlled coffee maturation, leading to improved, uniform harvests.
Decoding the genomic landscape of chromatin-associated biomolecular condensates
Authors: Yu Zhaowei , Wang Qi , Zhu Guangya , Zhu Jidong , Zhang Yong
Published: August 2023

Biomolecular condensates play a significant role in chromatin activities, primarily by concentrating and compartmentalizing proteins and/or nucleic acids. However, their genomic landscapes and compositions remain largely unexplored due to a lack of dedicated computational tools for systematic identificationin vivo. To address this, we developed CondSigDetector, a computational framework designed to detect condensate-like chromatin-associated protein co-occupancy signatures (CondSigs), to predict genomic loci and component proteins of distinct chromatin-associated biomolecular condensates. Applying this framework to mouse embryonic stem cells (mESC) and human K562 cells enabled us to depict the high-resolution genomic landscape of chromatin-associated biomolecular condensates, and uncover both known and potentially novel biomolecular condensates. Multi-omics analysis and experimental validation further verified the condensation properties of CondSigs. Additionally, our investigation shed light on the impact of chromatin-associated biomolecular condensates on chromatin activities. Collectively, CondSigDetector provides a novel approach to decode the genomic landscape of chromatin-associated condensates, facilitating a deeper understanding of their biological functions and underlying mechanisms in cells.
A fluorescence viewer for rapid molecular assay readout in space and low-resource terrestrial environments
Authors: Misquitta Kristoff , Miller Bess M. , Malecek Kathryn , Gleason Emily , Martin Kathryn , Walesky Chad M. , Foley Kevin , Copeland D. Scott , Saavedra Ezequiel Alvarez , Kraves Sebastian
Published: August 2023

Fluorescence-based assays provide sensitive and adaptable methods for point of care testing, environmental monitoring, studies of protein abundance and activity, and a wide variety of additional applications. Currently, their utility in remote and low-resource environments is limited by the need for technically complicated or expensive instruments to read out fluorescence signal. Here we describe the Genes in Space Fluorescence Viewer (GiS Viewer), a portable, durable viewer for rapid molecular assay readout that can be used to visualize fluorescence in the red and green ranges. The GiS Viewer can be used to visualize any assay run in standard PCR tubes and contains a heating element. Results are visible by eye or can be imaged with a smartphone or tablet for downstream quantification. We demonstrate the capabilities of the GiS Viewer using two case studies – detection of SARS-CoV-2 RNA using RT-LAMP and quantification of drug-induced changes in gene expression via qRT-PCR on Earth and aboard the International Space Station. We show that the GiS Viewer provides a reliable method to visualize fluorescence in space without the need to return samples to Earth and can further be used to assess the results of RT-LAMP and qRT-PCR assays on Earth.
The Risk of Mpox (Monkeypox) Importation and Subsequent Outbreak Potential in Mainland China: A Retrospective Statistical Modelling Study
Authors: Deng Xiaowei , Tian Yuyang , Zou Junyi , Yang Juan , Sun Kaiyuan , Yu Hongjie
Published: August 2023

The 2022 mpox outbreak has spread rapidly across multiple countries in the non-endemic region, mainly among men who have sex with men (MSM), while China only has limited recorded importation and no local outbreak. We constructed probabilistic models to simulate the risk of mpox importation in mainland China, with the help of reported monkeypox cases during this multi-country outbreak and the international air-travel data. And we further evaluated the mpox outbreak potential given that undetected mpox infections were introduced into men who have sex with men, considering different transmissibility, population immunity and population activity. We found that the reduced international air-travel volume and stringent border entry policy decreased about 94% and 69% mpox importations respectively. Once a mpox case is introduced into active MSM population with almost no population immunity, the risk of triggering local transmission is estimated at 42%, and would rise to >95% with over six cases. Our study demonstrates the key role of the reduced international air-travel volume and stringent border entry policy during the COVID-19 pandemic on reducing mpox importations, and the subsequent risk of triggering local outbreaks among MSM.
The Effects of Development Assistance on Sexual and Reproductive Health Services in Low- and Middle-Income Countries: A Cross-Country Panel Data Analysis
Authors: Ekman Björn , Sundewall Jesper , Schmit Jessy
Published: August 2023

Using data on 119 low- and lower-middle income countries from 2002 to 2020, we apply fixed-effects (FE) methods to evaluate the impacts of three different classifications of development assistance on access to three types of sexual and reproductive health (SRH) services: access to skilled birth attendance, prevalence of modern contraceptives, and coverage of antiretroviral therapies against HIV/AIDS. The results suggest that aid has had a small, but positive effect on these outcomes over this period. For example, SRH aid has increased service coverage rates by between 0.190 and 0.628 percentage points. The results also indicate that the effect of aid has improved across the period and is larger in low-income countries compared with lower-middle income countries. The findings also indicate that bilateral aid may be somewhat more effective than other types of aid. Importantly, the results suggest that development assistance is more effective if it reaches a certain share of overall health spending. The findings are robust to a series of sensitivity checks. The results of the study lend support to the continued allocation of aid to low-income countries to support the provision of sexual and reproductive health services. Both providers and recipients of SRH aid would be advised to identify ways to improve the effectiveness of development assistance in this area.
Smoking during pregnancy and its effect on placental weight: A Mendelian randomization study
Authors: Jaitner Annika , Vaudel Marc , Tsaneva-Atanasova Krasimira , Njølstad Pål R. , Jacobsson Bo , Bowden Jack , Johansson Stefan , Freathy Rachel M.
Published: August 2023

Background

The causal relationship between maternal smoking in pregnancy and reduced offspring birth weight is well established and is likely due to impaired placental function. However, observational studies have given conflicting results on the association between smoking and placental weight. We aimed to estimate the causal effect of newly pregnant mothers quitting smoking on their placental weight at the time of delivery.

Methods

We used one-sample Mendelian randomization, drawing data from the Avon Longitudinal Study of Parents and Children (ALSPAC) (up to N = 805) and the Norwegian Mother, Father and Child Cohort Study (MoBa) (up to N = 4475). The analysis was performed in pre-pregnancy smokers only, due to the specific role of the genetic instrument SNP rs1051730 (CHRNA5 – CHRNA3 – CHRNB4) in affecting smoking cessation but not initiation.

Results

Fixed effect meta-analysis showed a 175 g [95%CI: 16, 334] higher placental weight for pre-pregnancy smoking mothers who continued smoking at the beginning of pregnancy, compared with those who stopped smoking. Using the number of cigarettes smoked per day in the first trimester as the exposure, the causal estimate was a 12 g [95%CI: 2,22] higher placental weight per cigarette per day. Results were similar when the smoking exposures were measured at the end of pregnancy. Using the residuals of birth weight regressed on placental weight as the outcome, we showed weak evidence of lower offspring birth weight relative to the placental weight for continuing smoking.

Conclusion

Our results suggest that continued smoking during pregnancy causes higher placental weights.

Key Messages

It is well known that maternal smoking in pregnancy causes a lower birth weight on average, but the relationship between maternal smoking and placental weight is less clear, with observational studies showing conflicting results.

Our Mendelian randomization study suggests that for pre-pregnancy smokers, continuing smoking during pregnancy causes higher placental weight at term than quitting smoking.

Our study also suggests that a greater number of cigarettes smoked per day during pregnancy causes a larger placental weight at term.

A possible explanation for our findings is that the placenta grows larger in mothers who smoke during pregnancy to compensate for the lower oxygen availability, but further work is needed to confirm and further investigate this hypothesis.
Participatory Approaches in Community Health in light of the COVID-19 Pandemic: A Scoping Review Protocol
Authors: Frahsa Annika , Liwanag Harvy Joy , Kobler Cristopher , Ipekci Aziz Mert , Minder Beatrice , Schow Diana
Published: August 2023

Background

Participatory approaches are considered essential to ensure community health in the context of the COVID-19 pandemic. Previous reviews on community participation have explored different aspects of participation in specific contexts, such as public health emergencies, but none has examined participatory approaches both in depth and in breadth across diverse activities during the COVID-19 pandemic and considering diverse communities in all country contexts. This scoping review seeks to: (a) provide an overview of participatory approaches in terms of the features and depth of participation, the breadth of the communities and stakeholders involved, and for what types of activities and interventions in light of the COVID-19 pandemic across all country contexts; (b) explore the challenges and facilitators of participation processes; and (c) analyse to what extent participation impacts community health, including health equity, in the context of a public health emergency.

Methods

We developed this protocol following the latest JBI guidance on scoping reviews. A comprehensive search strategy combining the concepts of participation, community health, and COVID-19 was used to search the databases of Medline/Ovid, Embase.com, Cochrane CENTRAL, Web of Science, APA PsycInfo/Ovid, Global Health/Ovid, ERIC/OvidSP, CINAHL/EBSCOhost, ClinTrials.gov, and the grey literature through Google Scholar. At least two reviewers will perform screening of titles/abstracts and full text using the inclusion and exclusion criteria defined in this protocol. Article characteristics and data on participatory approaches and community health will be charted to provide an overview of the literature, map the variations in participatory approaches and community health, and explore patterns in the links between participation, community health, and the type of activities to address the challenges related to the COVID-19 pandemic.

Discussion

We anticipate that review findings will contribute to advance innovative thinking about community participation and facilitating better application and integration of participatory approaches to ensure community health in a future public health emergency or in building back better fairer in the new normal.
Regulation of Lung Immune Tone by the Gut-Lung Axis via Dietary Fiber, Gut Microbiota, and Short-Chain Fatty Acids
Authors: Maruyama Daisuke , Liao Wen-I , Tian Xiaoli , Bredon Marius , Knapp Johannes , Tat Christine , Doan Thien N. M. , Chassaing Benoit , Bhargava Aditi , Sokol Harry , Prakash Arun
Published: August 2023

Lung immune tone, i.e. the immune state of the lung, can vary between individuals and over a single individual’s lifetime, and its basis and regulation in the context of inflammatory responses to injury is poorly understood. The gut microbiome, through the gut-lung axis, can influence lung injury outcomes but how the diet and microbiota affect lung immune tone is also unclear. We hypothesized that lung immune tone would be influenced by the presence of fiber-fermenting short-chain fatty acid (SCFA)-producing gut bacteria. To test this hypothesis, we conducted a fiber diet intervention study followed by lung injury in mice and profiled gut microbiota using 16S sequencing, metabolomics, and lung immune tone. We also studied germ-free mice to evaluate lung immune tone in the absence of microbiota and performedin vitromechanistic studies on immune tone and metabolic programming of alveolar macrophages exposed to the SCFA propionate (C3). Mice on high-fiber diet were protected from sterile lung injury compared to mice on a fiber-free diet. This protection strongly correlated with lower lung immune tone, elevated propionate levels and enrichment of specific fecal microbiota taxa; conversely, lower levels of SCFAs and an increase in other fatty acid metabolites and bacterial taxa correlated with increased lung immune tone and increased lung injury in the fiber-free group.In vitro, C3 reduced lung alveolar macrophage immune tone (through suppression of IL-1β and IL-18) and metabolically reprogrammed them (switching from glycolysis to oxidative phosphorylation after LPS challenge). Overall, our findings reveal that the gut-lung axis, through dietary fiber intake and enrichment of SCFA-producing gut bacteria, can regulate innate lung immune tone via IL-1β and IL-18 pathways. These results provide a rationale for the therapeutic development of dietary interventions to preserve or enhance specific aspects of host lung immunity.
Structure basis of the phytoplasma effector SAP05 recognition specificities to plant Rpn10 in ubiquitin-independent protein degradation
Authors: Zhang Liying , Du Yunxiang , Zheng Qingyun
Published: August 2023

Recent research reported an effector protein SAP05 secreted by phytoplasma could hijack hostage Rpn10 subunit of proteasome and target degradation of GATA or SPL transcription factors (TFs) without ubiquitin. As a result, plant phenotypes will be reprogrammed to a state suitable for phytoplasma amplification and insect vector propagation which present prolonged growth cycles, witches’ broom-like proliferations of leaves and sterile shoots. We are curious about how could SAP05 target degradation bypassing the ubiquitin pathway and if there is any conserved interaction between different species of SAP05 with AtRpn10. Here, we have determined the crystal structure of the AtRpn10 complex with AY-WB or OY SAP05. Structure alignment revealed similar recognition patterns through sequences of two species SAP05 are poor homologous, which suggested phytoplasma may conduct resemble mode in plant infection. After docking the complex structure to the plant proteasome, we found that SAP05’s location is near the ATPase central pore, which may be close enough to submit substrate with no need for ubiquitin in the degradation process.
Recurrent Neural Network-based Prediction of O-GlcNAcylation Sites in Mammalian Proteins
Authors: Seber Pedro , Braatz Richard D.
Published: August 2023

O-GlcNAcylation has the potential to be an important target for therapeutics, but a motif or an algorithm to reliably predict O-GlcNAcylation sites is not available. In spite of the importance of O-GlcNAcylation, current predictive models are insufficient as they fail to generalize, and many are no longer available. This article constructs MLP and RNN models to predict the presence of O-GlcNAcylation sites based on protein sequences. Multiple different datasets are evaluated separately and assessed in terms of strengths and issues. The models trained in this work achieve considerably better metrics than previously published models, with at least a two-fold increase in F1score relative to previously published models; the specific gains vary depending on the dataset. Within a given dataset, the results are robust to changes in cross-validation and test data as determined by nested validation. The best model achieves an F1score of 36% (more than 3.5-fold greater than the previous best model) and a Matthews Correlation Coefficient of 35% (more than 4.5-fold greater than the previous best model), and, for the F1score, 7.6-fold higher than when not using any model. Shapley values are used to interpret the model ‘s predictions and provide biological insight into O-GlcNAcylation.
HSPA8-mediated stability of the CLPP protein regulates mitochondrial autophagy in cisplatin-resistant ovarian cancer cells
Authors: Kou Xinxin , Yang Xiaoxia , Zhao Zheng , Li Lei
Published: August 2023

Background

Currently, platinum agents remain the mainstay of chemotherapy for ovarian cancer (OC). However, cisplatin (DDP) resistance is a major reason for chemotherapy failure. Thus, it is extremely important to elucidate the mechanism of resistance to DDP.

Methods

We establish 2 DDP-resistant ovarian cancer cell lines and find that caseinolytic protease P (CLPP) is significantly downregulated in the DDP-resistant cell lines when compared to wild-type ovarian cancer cell lines (SK-OV-3 and OVcar3). Next, we investigate the functions of CLPP in the DDP-resistant and wild-type ovarian cancer cells using various assays including cell counting kit-8 assays, western blotting, immunofluorescent staining, and reactive oxygen species (ROS) and apoptosis detection.

Results

Our experiments show that CLPP knockdown significantly increase the half maximal inhibitory concentration (IC50) and mitophagy of wild-type SK-OV-3 and OVcar3 cells, while CLPP overexpression reduces the IC50values and mitophagy of DDP-resistant SK-OV-3 and OVcar3 cells. Next, we perform database predictions and experiments to show that heat shock protein family A member 8 (HSPA8) regulates CLPP protein stability. The dynamic effects of the HSPA8/CLPP axis in the ovarian cancer cells were also examined. HSPA8 increases mitophagy and the IC50values of SK-OV-3 and OVcar3 cells, but inhibits their ROS production and apoptosis. In addition, CLPP partly reverses the effects induced by HSPA8 in the SK-OV-3 and OVcar3 cells.

Conclusions

CLPP increases the DDP resistance of ovarian cancer by inhibiting mitophagy and promoting cellular stress. Meanwhile, HSPA8 promotes the degradation of CLPP protein by inducing its stability.
Beyond microRNAs: Analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation
Authors: Hejret Vaclav , Varadarajan Nandan Mysore , Klimentova Eva , Gresova Katarina , Giassa Ilektra-Chara , Vanacova Stepanka , Alexiou Panagiotis
Published: August 2023

Argonaute proteins are instrumental in regulating RNA stability and translation. AGO2, the major mammalian Argonaute protein, is known to primarily associate with microRNAs, a family of small RNA ‘driver’ sequences, and identifies its targets primarily via a ‘seed’ mediated partial complementarity process Despite numerous studies, a definitive experimental dataset of AGO2 ‘driver’-’target’ interactions remains elusive. Our study employs two experimental methods - AGO2 CLASH and AGO2 eCLIP, to generate thousands of AGO2 target sites verified by chimeric reads. These chimeric reads contain both the AGO2 loaded small RNA ‘driver’ and the target sequence, providing a robust resource for modeling AGO2 binding preferences. Our novel analysis pipeline reveals thousands of AGO2 target sites driven by microRNAs and a significant number of AGO2 ‘drivers’ derived from fragments of other small RNAs such as tRNAs, YRNAs, snoRNAs, rRNAs, and more. We utilize convolutional neural networks to train machine learning models that accurately predict the binding potential for each ‘driver’ class and experimentally validate several interactions. In conclusion, our comprehensive analysis of the AGO2 targetome broadens our understanding of its ‘driver’ repertoire and potential function in development and disease. Moreover, we offer practical bioinformatic tools for future experiments and the prediction of AGO2 targets. All data and code from this study are freely available athttps://github.com/ML-Bioinfo-CEITEC/HybriDetector/

Contact

panagiotis.alexiou@um.edu.mt,stepanka.vanacova@ceitec.muni.cz
Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components
Authors: Duan Changhai , Liu Yang , Liu Ying , Liu Lirui , Cai Mingwei , Zhang Rui , Zeng Qinglu , Koonin Eugene V. , Krupovic Mart , Li Meng
Published: August 2023

Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. The virome of Bathyarchaeia so far has not been characterized. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realmsDuplodnaviriaandAdnaviria, and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family ‘Fuxiviridae’ harbor an atypical type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family ‘Chiyouviridae’ encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibition of host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.
Diversity in Notch ligand-receptor signaling interactions
Authors: Kuintzle Rachael , Santat Leah A. , Elowitz Michael B.
Published: August 2023

The Notch signaling pathway uses families of ligands and receptors to transmit signals to nearby cells. These components are expressed in diverse combinations in different cell types, interact in a many-to-many fashion, both within the same cell (in cis) and between cells (in trans), and their interactions are modulated by Fringe glycosyltransferases. A fundamental question is how the strength of Notch signaling depends on which pathway components are expressed, at what levels, and in which cells. Here, we used a quantitative, bottom-up, cell-based approach to systematically characterize trans-activation, cis-inhibition, and cis-activation signaling efficiencies across a range of ligand and Fringe expression levels in two mammalian cell types. Each ligand (Dll1, Dll4, Jag1, and Jag2) and receptor variant (Notch1 and Notch2) analyzed here exhibited a unique profile of interactions, Fringe-dependence, and signaling outcomes. All four ligands were able to bind receptors in cis and in trans, and all ligands trans-activated both receptors, although Jag1-Notch1 signaling was substantially weaker than other ligand-receptor combinations. Cis-interactions were predominantly inhibitory, with the exception of the Dll1-and Dll4-Notch2 pairs, which exhibited cis-activation stronger than trans-activation. Lfng strengthened Delta-mediated trans-activation and weakened Jagged-mediated trans-activation for both receptors. Finally, cis-ligands showed diverse cis-inhibition strengths, which depended on the identity of the trans-ligand as well as the receptor. The map of receptor-ligand-Fringe interaction outcomes revealed here should help guide rational perturbation and control of the Notch pathway.
AKT2 Loss Impairs BRAF-Mutant Melanoma Metastasis
Authors: McRee Siobhan K. , Bayer Abraham L. , Pietruska Jodie , Tsichlis Philip N. , Hinds Philip W.
Published: August 2023

Despite recent advances in treatment, melanoma remains the deadliest form of skin cancer, due to its highly metastatic nature. Melanomas harboring oncogenic BRAFV600Emutations combined with PTEN loss exhibit unrestrained PI3K/AKT signaling and increased invasiveness. However, the contribution of different AKT isoforms to melanoma initiation, progression, and metastasis has not been comprehensively explored, and questions remain whether individual isoforms play distinct or redundant roles in each step. We investigate the contribution of individual AKT isoforms to melanoma initiation using a novel mouse model of AKT isoform-specific loss in a murine melanoma model, and investigate tumor progression, maintenance, and metastasis among a panel of human metastatic melanoma cell lines using AKT-isoform specific knockdown studies. We elucidate that AKT2 is dispensable for primary tumor formation but promotes migration and invasionin vitroand metastatic seedingin vivo, while AKT1 is uniquely important for melanoma initiation and cell proliferation. We propose a mechanism whereby inhibition of AKT2 impairs glycolysis and reduces an EMT-related gene expression signature in PTEN-null BRAF-mutant human melanoma cells to limit metastatic spread. Our data suggest that elucidation of AKT2-specific functions in metastasis could inform therapeutic strategies to improve treatment options for melanoma patients.

Graphical Abstract
ATP energy-independently modulates the folding equilibrium of ALS-causing C71G-hPFN1
Authors: Kang Jian , Lim Liangzhong , Song Jianxing
Published: August 2023

C71G is the most aggregation-prone and toxic mutant of 140-residue human profin-1 (hPFN1) that causes familial ALS by gain of toxicity, but its underlying mechanisms still remain unknown. C71G-hPFN1 exists in an equilibrium between folded and unfolded states, whose dynamic/thermodynamic properties and modulation are not yet defined. Here, we utilized NMR to quantify the populations to be 55.2% and 44.8% respectively for folded and unfolded states exchanging at 11.7 Hz. Intriguingly, even the folded state of C71G-hPFN1 has increased ps-ns flexibility and reduced thermodynamic stability, thus rationalizing its high aggregation-proneness. Strikingly, C71G-hPFN1 provides a unique model to unambiguously visualize the effects of ATP and 11 related molecules on its folding equilibrium by NMR. Unexpectedly, ATP completely converted C71G-hPFN1 into the folded state at 1:2, which is physiologically relevant in most living cells. By contrast, TMAO, a well-known protein-folding inducer, showed no detectable conversion even at 1:2000. Surprisingly, the inducing capacity of ATP comes from its triphosphate group, but free triphosphate strongly triggered aggregation. The inducing capacity was determined to rank as: ATP = ATPP = PPP > ADP = AMP-PNP = AMP-PCP = PP, while AMP, Adenosine, P and NaCl showed no detectable capacity. Mechanistically, ATP and triphosphate appear to enhance the intrinsic folding capacity encoded by the sequence. Therefore, by joining Adenosine and triphosphate ATP appears to integrate three abilities: inducing folding, inhibiting aggregation and increasing stability. Our study provide a mechanism for the finding that some single-cell organisms still use polyphosphates as primordial chaperones. Moreover, ATP continue to play foundational roles in modern cells, shedding light on the longstanding enigma of the age-related onset of FALS, which coincides with the ageing-dependent reductions in ATP concentrations.
Observing Mechanosensitive Channels in Action in Living Bacteria
Authors: Sharifian Gh. Mohammad , Wilhelm Michael J. , Dai Hai-Lung
Published: August 2023

Mechanosensitive (MS) channels act to protect the cytoplasmic membrane (CM) of living cells from environmental changes in osmolarity. In this report, we demonstrate the use of time-resolved second-harmonic light scattering (SHS) as a means of experimentally observing the relative state (open vs. closed) of MS channels in living bacteria suspended in different buffer solutions. Specifically, the state of the MS channels was selectively controlled by changing the composition of the suspension medium, inducing either a transient or persistent osmotic shock. SHS was then used to monitor transport of the SHG-active cation, malachite green (MG) across the bacterial CM. When MS channels were forced open, MG cations were able to cross the CM at a rate at least two orders of magnitude faster compared to when the MS channels were closed. These observations were corroborated using both numerical model simulations and complementary fluorescence experiments, in which the propensity for the CM impermeant cation, propidium to stain cells was shown to be contingent upon the relative state of the MS channels (i.e., cells with open MS channels fluoresced red, cells with closed MS channels did not). Application of time-resolved SHS to experimentally distinguish MS channels opened via osmotic shock vs. chemical activation, as well as a general comparison to the patch-clamp method is discussed.
Overexpression and nonsynonymous mutations of UDP-glycosyltransferases potentially associated with pyrethroid resistance inAnopheles funestus
Authors: Al-Yazeedi Talal , Muhammad Abdullahi , Irving Helen , Ahn Seung-Joon , Hearn Jack , Wondji Charles S.
Published: August 2023

UDP-glycosyltransferases (UGTs) constitute a superfamily of enzymes that play a vital role in the biotransformation of diverse hydrophobic substrates into more hydrophilic products, thereby facilitating their excretion from the cell through transporters. The significance of UGTs in conferring insecticide resistance has been emphasized in various insect species. In this study, we characterisedAnopheles funestusUGT genes genome-wide and explored their evolution and association with pyrethroid resistance. We combined genome-wide association of pooled-template sequencing (GWAS-PoolSeq) with the transcriptomic profile of pyrethroid-resistantAn. funestuspopulations, and deep targeted sequencing of UGTs from 80 individual mosquitoes collected in Malawi, Uganda, Cameroon and the two laboratory colonies (FANG and FUMOZ) to investigate the role of UGTs in pyrethroid resistance. We identified common overexpression of UGT310B2 (AFUN000679) in the resistant laboratory colony (FUMOZ) and resistant field populations from Malawi, Cameroon and Uganda. Significant gene-wiseFstdifferentiation between the resistant and putatively susceptible populations was observed for UGT301C2 and UGT302A3 in Malawi, as well as UGT306C2 in Uganda. Furthermore, the gene-wise Tajimas D density curves of the sequenced regions provided insights into genome-wide processes elucidating population structures withinAn. funestuspopulations from these three countries, supporting previous observations. Additionally, we identified significantly differentiated nonsynonymous mutations within UGT genes, which may potentially contribute to pyrethroid resistance. The identified role ofAn. funestusUGT genes in pyrethroid resistance has direct implications for current vector control strategies, management approaches, and the prediction of potential cross-resistance to other insecticides that can be directly detoxified by UGTs.
Digital transformation in family-owned winery SMEs: an exploratory analysis in the South-Italian context
Authors: Costa Alessandra , Presenza Angelo , Abbate Tindara
Published: August 2023

Purpose

This work aims to offer a better understanding of the inevitable challenges related to the digital transformation in the family-owned low-tech SMEs, examining the role assumed by familiness in this specific context. To this end, it examines the main factors that influence the adoption and implementation of digital technologies in the family-owned low-tech SMEs.

Design/methodology/approach

The study uses a multiple case studies approach, by investigating the case of family-owned low-tech SMEs operating in the winery sector and located in the South-Italy area.

Findings

Based on the empirical evidence, findings show how familiness influence the digital transformation of family-owned SMEs and highlight three main factors – individual, process and organization – relevant for the introduction and use of digital technologies in the productive and innovative activities of these organizations.

Originality/value

This paper fills the research gap existing in the literature on the family business. Firstly, it focuses on the digital transformation phenomenon and underlines how familiness, within family-owned low-tech SMEs, can differently influence the firm's innovation processes primarly based on the use of digital technologies oriented to enable business improvements. Then, it identifies diverse dimensions that can act as “barriers” or “facilitators” for adopting advanced digital technologies within the organizations here examined.