bluuebunny/crossref_metadata_2025 huggingface dataset:
Mother-Infant Gut Viruses and their Bacterial Hosts: Transmission Patterns and Dynamics during Pregnancy and Early Life
Authors: Garmaeva Sanzhima , Sinha Trishla , Gulyaeva Anastasia , Kuzub Nataliia , Spreckels Johanne E , Andreu-Sánchez Sergio , Gacesa Ranko , Vila Arnau Vich , Brushett Siobhan , Kruk Marloes ,   Lifelines NEXT cohort study, Dekens Jackie , Sikkema Jan , Kuipers Folkert , Shkoporov Andrey , Hill Colin , Scherjon Sicco , Wijmenga Cisca , Fu Jingyuan , Kurilshikov Alexander , Zhernakova Alexandra
Published: August 2023

Early development of the gut ecosystem is crucial for lifelong health. While infant gut bacterial communities have been studied extensively, the infant gut virome remains under-explored. We longitudinally assessed the composition of gut viruses and their bacterial hosts in 322 total metagenomes and 205 metaviromes from 30 mothers during and after pregnancy and from their 32 infants during their first year of life. While the maternal gut virome composition remained stable during late pregnancy and after birth, the infant gut virome was dynamic in the first year of life and contained a higher abundance of active temperate phages compared to the maternal gut viromes. The infant gut virome composition was also influenced by infant feeding mode and place of delivery. Lastly, we provide evidence of viral-bacterial strains co-transmission from mothers to infants, demonstrating that infants acquire some of their virome from their mother’s gut.

Highlights

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Longitudinal characterisation of the gut microbiome and virome in 30 mothers during pregnancy, at birth and 3 months after birth and in 32 infants from birth across the first year of life.

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The maternal gut bacteriome changes from the first to the second trimester and then remains stable through birth and the first 3 months after birth.

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The maternal gut virome remains stable during late pregnancy, birth and the first 3 months after birth.

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The infant gut virome is highly dynamic during the first year of life and is shaped by infant feeding mode and place of delivery.

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The infant gut harbours more temperate bacteriophages than the maternal gut, but their relative abundance decreases with increasing infant age.

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Gut viral strains and their bacterial host strains are co-transmitted from mothers to their infants.

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Gut viral strains are transferred from mother to infant around birth directly or via transfer of their bacterial hosts followed by the induction of prophages.
Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data
Authors: Zhang Junpeng , Liu Lin , Wei Xuemei , Zhao Chunwen , Luo Yanbi , Li Jiuyong , Le Thuc Duy
Published: August 2023

RNA-sequencing technology provides an effective tool for understanding miRNA regulation in complex human diseases, including cancers. A large number of computational methods have been developed to make use of bulk and single-cell RNA-sequencing data to identify miRNA regulations at the resolution of multiple samples (i.e. group of cells or tissues). However, due to the heterogeneity of individual samples, there is a strong need to infer miRNA regulation specific to individual samples to uncover miRNA regulation at single-sample resolution level. Here, we develop a framework, Scan, for scanningsample-specific miRNA regulation. Since a single network inference method or strategy cannot perform well for all types of new data, Scan incorporates 27 network inference methods and two strategies to infer tissue-specific or cell-specific miRNA regulation from bulk or single-cell RNA-sequencing data. Results on bulk and single-cell RNA-sequencing data demonstrate the effectiveness of Scan in inferring sample-specific miRNA regulation. Moreover, we have found that incorporating priori information of miRNA targets can improve the accuracy of miRNA target prediction. In addition, Scan can contribute to the clustering cells/tissues and construction of cell/tissue correlation networks. Finally, the comparison results have shown that the performance of network inference methods is likely to be data-specific, and selecting optimal network inference methods is required for more accurate prediction of miRNA targets. We have made Scan freely available to the public to help infer sample-specific miRNA regulation for new data, benchmark new network inference methods and deepen the understanding of miRNA regulation at the resolution of individual samples.
On the comparison between pre- and post-surgery nasal anatomies via computational fluid dynamics
Authors: Segalerba Eric , Dini Ciacci Gabriele , Quadrio Maurizio , Pralits Jan O.
Published: August 2023

Nasal breathing difficulties (NBD) are widespread and difficult to diagnose; the failure rate of their surgical corrections is high. Computational Fluid Dynamics (CFD) enables diagnosis of NBD and surgery planning, by comparing a pre-operative (pre-op) situation with the outcome of virtual surgery (post-op). An equivalent comparison is involved when considering distinct anatomies in the search for the functionally normal nose. Currently, this comparison is carried out in more than one way, under the implicit assumption that results are unchanged, which reflects our limited understanding of the driver of the respiratory function. The study describes how to set up a meaningful comparison. A pre-op anatomy, derived via segmentation from a CT scan, is compared with a post-op anatomy obtained via virtual surgery. State-of-the-art numerical simulations for a steady inspiration carry out the comparison under three types of global constraints, derived from the field of turbulent flow control: a constant pressure drop (CPG) between external ambient and throat, a constant flow rate (CFR) through the airways and a constant power input (CPI) from the lungs can be enforced. A significant difference in the quantities of interest is observed depending on the type of comparison. Global quantities (flow rate, pressure drop, nasal resistance) as well as local ones are affected. The type of flow forcing affects the outcome of the comparison between pre-op and post-op anatomies. Among the three available options, we argue that CPG is the least adequate. Arguments favouring either CFR or CPI are presented.
Genomic analysis of fruit size and shape traits in apple: unveiling candidate genes through GWAS analysis
Authors: Dujak Christian , Aranzana Maria José
Published: August 2023

Genomic tools facilitate the efficient selection of improved genetic materials with within a breeding program. In this work, we focused on two apple fruit quality traits: shape and size. We utilized data from 11 fruit morphology parameters gathered across three years of harvest from 355 genotypes of the Apple REFPOP collection, which serves as a representative sample of the genetic variability present in European cultivated apples. The data was then employed for genome-wide association analysis (GWAS) using the FarmCPU and the BLINK models. The analysis identified 59 SNPs associated with fruit size and shape traits (35 with FarmCPU and 45 with BLINK) responsible for 71 QTNs. These QTNs were distributed across all chromosomes except for chromosome10 and 15. Thirty-four QTNs, identified by 27 SNPs, were related for size traits and thirty-seven QTNs, identified by 26 SNPs, were related to shape attributes. The definition of the haploblocks containing the most relevant SNPs served to propose candidate genes, among them the genes of the ovate family protein MdOFP17 and MdOFP4 which were in a 9.7kb haploblock on chromosome 11. RNA-seq data revealed low or null expression of these genes in the oblong cultivar ‘Skovfoged” and higher expression in the flat ‘Grand’mere’. In conclusion, this comprehensive GWAS analysis of the Apple REFPOP collection has revealed promising genetic markers and candidate genes associated with apple fruit shape and size attributes, providing valuable insights that could enhance the efficiency of future breeding programs.
Mechanics of biomimetic free-standing lipid membranes: Insights on lipid chemistry and bilayer elasticity
Authors: Griffo Alessandra , Sparn Carola , Lolicato Fabio , Nolle Friederike , Khangholi Navid , Seemann Ralf , Fleury Jean-Baptiste , Brinkmann Martin , Nickel Walter , Hähl Hendrik
Published: August 2023

The creation of free-standing lipid membranes has been so far of remarkable interest to investigate processes occurring in the cell membrane since its unsupported part enables studies in which it is important to maintain cell-like physicochemical properties of the lipid bilayer, that nonetheless depend on its molecular composition. In this study, we prepare pore-spanning membranes that mimic the composition of plasma membranes and perform force spectroscopy indentation measurements to unravel mechanistic insights depending on lipid composition. We show that this approach is highly effective for studying the mechanical properties of such membranes. Furthermore, we identify a direct influence of cholesterol and sphingomyelin on the elasticity of the bilayer and adhesion between the two leaflets. Eventually, we explore the possibilities of imaging in the unsupported membrane regions. For this purpose, we investigate the adsorption and movement of a peripheral protein, the fibroblast growth factor 2, on the complex membrane.
Epigenetic mediated functional reprogramming of immune cells leads to HBsAg seroconversion in Hepatitis B Virus Reactivation patients
Authors: Sevak Jayesh Kumar , Islam Mojahidul , Verma Gayantika , Saxena Anoushka , Preedia Babu E , Parveen Shahana , Jindal Ankur , Sharma Manoj Kumar , Ramakrishna Gayatri , Sarin Shiv Kumar , Trehanpati Nirupama
Published: August 2023

Background

Hepatitis B virus (HBV) modulates epigenetic landscape by epigenetic regulators. HBsAg seroconversion is possible with immune activation, therefore we aimed to investigate epigenetic modulation in HBV reactivation (rHBV) for viral clearance and seroconversion.

Methods

Sixteen retrospectively collected rHBV patients [Seroconverters (SC, n=7, HBsAg loss and anti-HBs>10 IU/ml), non- seroconverters (NSC, n=9)], chronic hepatitis B treatment naïve (nCHBV, n=7) patients and healthy controls (HC, n=7) were included in this study. Genome methylation, gene expression, plasma-cytokines, and immune cell profiling was analysed by Reduced Representation Bisulfite Sequencing (RRBS), QRT-PCR, multiplex-cytokine-bead array and flow-cytometry.

Results

rHBV patients having high HBV DNA and ALT showed epigenetic remodellers; KDM2B, NCOR2 and GATA6, immune and metabolic genes; TGF-β, IL-6, IRF8, RPTOR, HK3 significantly (p<0.05) hypomethylated at specific CpG islands compared to nCHBV. TOX was hypomethylated in nCHBV suggesting immune-exhaustion. At-baseline, seroconverters showed hypomethylation of KDM2B, COX19, IRF8, TLR5 and hypermethylation of LAG3 compared to non-seroconverters. Further, in seroconverters at week-24, IL17RA, IFN-γ, TGF-β, and STAT5B (p<0.05) were additionally hypomethylated at specific CpG islands suggesting immune activation. Cytokine-bead analysis revealed increased IL-6 (p=0.009) and decreased LAG3 plasma levels (p=0.01) also imply on significantly differentiated HBV specific CD8, Tfh and Th1/17 cells in seroconverters at baseline and week-24. However, both nCHBV and non-seroconverters had consistent hypomethylation of LAG3 and TOX, which leads to immune exhaustion.

Conclusion

In rHBV, seroconversion is driven by position specific CpG islands methylation in epigenetic remodellers, immune and metabolic genes. Immune metabolic reprograming is reflected by Th1/17 differentiation, extensive interleukin production for HBsAg seroconversion.

Graphical Abstract

Lay summary

Epigenetic landscape in nCHBV depicts exhaustion and immune dysfunction. Out of many hypermethylated CpG islands of nCHBV, few become hypomethylated in rHBV and drives immune and metabolic reprogramming. This study provides insights into the cellular and molecular basis of epigenomic programs that regulate the differentiation and activation of immune cells leading to viral clearance and seroconversion. Targeting epigenetic mechanism could be promising strategy for the treatment of nCHBV and non-seroconverters.
Ubiquitin-driven protein condensation initiates clathrin-mediated endocytosis
Authors: Yuan Feng , Gollapudi Sadhana , Day Kasey J. , Ashby Grant , Sangani Arjun , Malady Brandon T. , Wang Liping , Lafer Eileen M. , Huibregtse Jon M. , Stachowiak Jeanne C.
Published: August 2023

Clathrin-mediated endocytosis is an essential cellular pathway that enables signaling and recycling of transmembrane proteins and lipids. During endocytosis, dozens of cytosolic proteins come together at the plasma membrane, assembling into a highly interconnected network that drives endocytic vesicle biogenesis. Recently, multiple groups have reported that early endocytic proteins form flexible condensates, which provide a platform for efficient assembly of endocytic vesicles. Given the importance of this network in the dynamics of endocytosis, how might cells regulate its stability? Many receptors and endocytic proteins are ubiquitylated, while early endocytic proteins such as Eps15 contain ubiquitin-interacting motifs. Therefore, we examined the influence of ubiquitin on the stability of the early endocytic protein network. In vitro, we found that recruitment of small amounts of polyubiquitin dramatically increased the stability of Eps15 condensates, suggesting that ubiquitylation could nucleate endocytic assemblies. In live cell imaging experiments, a version of Eps15 that lacked the ubiquitin-interacting motif failed to rescue defects in endocytic initiation created by Eps15 knockout. Furthermore, fusion of Eps15 to a deubiquitylase enzyme destabilized nascent endocytic sites within minutes. In both in vitro and live cell settings, dynamic exchange of Eps15 proteins, a hallmark of liquid-like systems, was modulated by Eps15-Ub interactions. These results collectively suggest that ubiquitylation drives assembly of the flexible protein network responsible for catalyzing endocytic events. More broadly, this work illustrates a biophysical mechanism by which ubiquitylated transmembrane proteins at the plasma membrane could regulate the efficiency of endocytic recycling.

Significance Statement

The assembly of proteins into dynamic, liquid-like condensates is an emerging principle of cellular organization. During clathrin-mediated endocytosis, a liquid-like protein network catalyzes vesicle assembly. How do cells regulate these assemblies? Here we show that ubiquitin and endocytic proteins form a dynamic, mutually-reinforcing protein network in vitro and in live cells. To probe the impact of ubiquitylation on the dynamics of endocytosis, we engineered opto-genetic control over recruitment of proteins to nascent endocytic sites. While recruitment of wildtype proteins promoted endocytosis, recruitment of deubiquitylases, enzymes capable of removing ubiquitin, resulted in disassembly of endocytic sites within minutes. These results illustrate that ubiquitylation can regulate the fate of endocytic structures, elucidating a functional connection between protein condensates, endocytosis, and ubiquitin signaling.
Multi-omics Analysis of Aging Liver Reveals Changes in Endoplasmic Stress and Degradation Pathways in Female Nonhuman Primates
Authors: Puppala Sobha , Chan Jeannie , Zimmerman Kip D. , Hamid Zeeshan , Ampong Isaac , Huber Hillary F. , Li Ge , Jadhav Avinash Y. L. , Li Cun , Nathanielsz Peter W. , Olivier Michael , Cox Laura A.
Published: August 2023

The liver is critical for functions that support metabolism, immunity, digestion, detoxification, and vitamin storage. Aging is associated with severity and poor prognosis of various liver diseases such as nonalcoholic fatty liver disease (NAFLD). Previous studies have used multi-omic approaches to study liver diseases or to examine the effects of aging on the liver. However, to date, no studies have used an integrated omics approach to investigate aging-associated molecular changes in the livers of healthy female nonhuman primates. The goal of this study was to identify molecular changes associated with healthy aging in the livers of female baboons (Papiosp., n=35) by integrating multiple omics data types (transcriptomics, proteomics, metabolomics) from samples across the adult age span. To integrate omics data, we performed unbiased weighted gene co-expression network analysis (WGCNA), and the results revealed 3 modules containing 3,149 genes and 33 proteins were positively correlated with age, and 2 modules containing 37 genes and 216 proteins were negatively correlated with age. Pathway enrichment analysis showed that unfolded protein response (UPR) and endoplasmic reticulum (ER) stress were positively associated with age, whereas xenobiotic metabolism and melatonin and serotonin degradation pathways were negatively associated with age. The findings of our study suggest that UPR and a reduction in reactive oxygen species generated from serotonin degradation could protect the liver from oxidative stress during the aging process in healthy female baboons.
Human Saliva Modifies Growth, Biofilm Architecture and Competitive Behaviors of Oral Streptococci
Authors: Choi Allen , Dong Kevin , Williams Emily , Pia Lindsey , Batagower Jordan , Bending Paige , Shin Iris , Peters Daniel I. , Kaspar Justin R.
Published: August 2023

The bacteria within supragingival biofilms participate in complex exchanges with other microbes inhabiting the same niche. One example are the mutans group streptococci (Streptococcus mutans), implicated in the development of tooth decay, and other health-associated commensal streptococci species. Previously, our group transcriptomically characterized intermicrobial interactions betweenS. mutansand several species of oral bacteria. However, these experiments were carried out in a medium that was absent of human saliva. To better mimic their natural environment, we first evaluated how inclusion of saliva affected growth and biofilm formation of eight streptococci species individually, and found saliva to positively benefit growth rates while negatively influencing biomass accumulation and altering spatial arrangement. These results carried over during evaluation of 29 saliva-derived isolates of various species. Surprisingly, we also found that addition of saliva increased the competitive behaviors ofS. mutansin coculture competitions against commensal streptococci that led to increases in biofilm microcolony volumes. Through transcriptomically characterizing mono- and cocultures ofS. mutansandStreptococcus oraliswith and without saliva, we determined that each species developed a nutritional niche under mixed-species growth, withS. mutansupregulating carbohydrate uptake and utilization pathways whileS. oralisupregulated genome features related to peptide uptake and glycan foraging.S. mutansalso upregulated genes involved in oxidative stress tolerance, particularly manganese uptake, which we could artificially manipulate by supplementing in manganese to give it an advantage over its opponent. Our report highlights observable changes in microbial behaviors via leveraging environmental- and host-supplied resources over their competitors.
Spatiotemporally distinct responses to mechanical forces shape the developing seed ofArabidopsis
Authors: Bauer Amélie , Bied Camille , Delattre Adrien , Ingram Gwyneth , Golz John F. , Landrein Benoit
Published: August 2023

Organ morphogenesis depends on mechanical interactions between cells and tissues. These interactions generate forces that can be sensed by cells and affect key cellular processes. However, how mechanical forces contribute, together with biochemical signals, to the shaping of complex organs is still unclear. We address this question using the seed ofArabidopsis asa model system. We show that seeds first experience a phase of high anisotropic growth that is dependent on the response of cortical microtubule (CMT) to forces, which guide cellulose deposition according to shape-driven stresses in the outermost layer of the seed coat. However, at later stages of development, we show that seed growth is isotropic and depend on the properties of an inner layer of the seed coat that stiffens its walls in response to tension but has isotropic material properties. Finally, we show that the transition from anisotropic to isotropic growth is due to dampening of CMT responses to shape-driven stresses. Altogether, our work support that spatiotemporally distinct mechanical responses control the shape of developing seeds inArabidopsis.
Plasma Growth Hormone Pulses Induce Male-biased Pulsatile Chromatin Opening and Epigenetic Regulation in Adult Mouse Liver
Authors: Rampersaud Andy , Connerney Jeannette , Waxman David J.
Published: August 2023

Sex-differences in plasma growth hormone (GH) profiles, pulsatile in males and persistent in females, regulate sex differences in hepatic STAT5 activation linked to sex differences in gene expression and liver disease susceptibility, but little is understood about the fundamental underlying, GH pattern-dependent regulatory mechanisms. Here, DNase hypersensitivity site (DHS) analysis of liver chromatin accessibility in a cohort of 18 individual male mice established that the endogenous male rhythm of plasma GH pulse-stimulated liver STAT5 activation induces dynamic, repeated cycles of chromatin opening and closing at several thousand liver DHS and comprises a novel mechanism conferring male bias to liver chromatin accessibility. Strikingly, a single physiological replacement dose of GH given to hypophysectomized male mice restored, within 30 min, liver STAT5 activity and chromatin accessibility at 83% of the pituitary hormone-dependent dynamic male-biased DHS. Sex-dependent transcription factor binding patterns and chromatin state analysis identified key genomic and epigenetic features distinguishing this dynamic, STAT5-driven mechanism of male-biased chromatin opening from a second GH-dependent mechanism operative at static male-biased DHS, which are constitutively open in male liver. Dynamic but not static male-biased DHS adopt a bivalent-like epigenetic state in female liver, as do static female-biased DHS in male liver, albeit using distinct repressive histone marks in each sex, namely, H3K27me3 at female-biased DHS in male liver, and H3K9me3 at male-biased DHS in female liver. Moreover, sex-biased H3K36me3 marks are uniquely enriched at static sex-biased DHS, which may serve to keep these sex-dependent hepatocyte enhancers free of H3K27me3 repressive marks and thus constitutively open. Pulsatile chromatin opening stimulated by endogenous, physiological hormone pulses is thus one of two distinct GH-determined mechanisms for establishing widespread sex differences in hepatic chromatin accessibility and epigenetic regulation, both closely linked to sex-biased gene transcription and the sexual dimorphism of liver function.
DENND6A couples Arl8b to a Rab34/RILP/dynein complex regulating retrograde lysosomal trafficking and autophagy
Authors: Kumar Rahul , Francis Vincent , Khan Maleeha , Aguila Adriana , Kulasekaran Gopinath , McPherson Peter S.
Published: August 2023

Lysosomes help maintain cellular proteostasis, and defects in lysosomal positioning and function lead to diseases including neurodegenerative disorders. The spatiotemporal distribution of lysosomes is regulated by small GTPases, including Rabs, which are activated by guanine nucleotide exchange factors (GEFs). DENN domain–bearing proteins are the largest family of Rab GEFs. Using a cell-based assay, we screened the DENN domain protein family member DENND6A for potential GEF activity toward all 60 Rabs and identified 20 potential DENND6A substrates, including Rab34. Here, we demonstrate that DENND6A activates Rab34, which recruits a RILP/dynein complex to the lysosomes, promoting lysosomal retrograde trafficking from the cell periphery to the minus ends of microtubules. Further, we identify DENND6A as an effector of Arl8b, a major regulatory GTPase on lysosomes. Initially known for promoting anterograde transport of lysosomes, Arl8b also facilitates lysosomal retrograde transport. We demonstrate that Arl8b recruits DENND6A to peripheral lysosomes to activate Rab34 and initiate retrograde transport, regulating nutrient-dependent lysosomal juxtanuclear repositioning and loss of DENND6A impairs autophagic flux. Our findings support a model whereby Arl8b/DENND6A/Rab34-dependent lysosomal retrograde trafficking controls autophagy.
Serotonin therapies for opioid-induced dysphagia and respiratory depression: sex differences in a rat electromyography model
Authors: Frazure Michael , Morimoto In , Fielder Nathan , Mellen Nicholas , Iceman Kimberly , Pitts Teresa
Published: August 2023

Opioids are well-known to cause respiratory depression, but despite clinical evidence of dysphagia, the effects of opioids on swallow excitability and motor pattern are unknown. We sought to test the effects of the clinically-relevant opioid buprenorphine on pharyngeal swallow and respiratory drive in male and female rats. We also evaluated utility of serotonin 5-HT1A agonists (8-OH-DPAT and buspirone) to improve swallowing and breathing outcomes following buprenorphine administration. Experiments were performed on 44 freely breathing Sprague Dawley rats anesthetized with sodium pentobarbital. Bipolar fine wire electrodes were inserted into the mylohyoid, thyroarytenoid, posterior cricoarytenoid, thyropharyngeus and diaphragm muscles to measure electromyographic (EMG) activity of swallowing and breathing behaviors. We evaluated the hypotheses that swallow varies by stimulus, opioids depress swallow and breathing, and that 5-HT1A agonists improve these depressions. Our results largely confirmed the hypotheses: 1) Swallow-related muscle activity was larger during swallows elicited by oral water infusion plus esophageal distension than by either stimulus alone. 2) Buprenorphine depressed swallow in both sexes, but most significantly in females. 3) Female animals were more susceptible to buprenorphine-induced respiratory arrest. 4) 8-OH-DPAT rescued breathing following buprenorphine-induced respiratory arrest, and pre-treatment with the partial 5-HT1A agonist buspirone prevented buprenorphine-induced respiratory arrest in female animals. 5) 8-OH-DPAT enhanced swallow-related mylohyoid drive, but did not restore excitability of the swallow pattern generator following total suppression by buprenorphine. Our results highlight sex-specific and behavior-specific effects of buprenorphine and provide pre-clinical evidence of a 5HT1A agonist for the treatment of respiratory depression and dysphagia.
A suppressor screenin C. elegansidentifies a multi-protein interaction interface that stabilizes the synaptonemal complex
Authors: Kursel Lisa E. , Martinez Jesus E. Aguayo , Rog Ofer
Published: August 2023

Successful chromosome segregation into gametes depends on tightly-regulated interactions between the parental chromosomes. During meiosis, chromosomes are aligned end-to-end by an interface called the synaptonemal complex, which also regulates exchanges between them. However, despite the functional and ultrastructural conservation of this essential interface, how protein-protein interactions within the synaptonemal complex regulate chromosomal interactions remains poorly understood. Here we describe a novel interaction interface in theC. eleganssynaptonemal complex, comprised of short segments of three proteins, SYP-1, SYP-3 and SYP-4. We identified the interface through a saturated suppressor screen of a mutant that destabilizes the synaptonemal complex. The specificity and tight distribution of suppressors point to a charge-based interface that promotes interactions between synaptonemal complex subunits and, in turn, allows intimate interactions between chromosomes. Our work highlights the power of genetic studies to illuminate the mechanisms that underly meiotic chromosome interactions.

Significance Statement

Gamete production requires tightly regulated interactions between the parental chromosomes, which co-align and exchange information. These events are mediated by the synaptonemal complex – a thread-like structure that assembles between the parental chromosomes. The molecular interactions that underly synaptonemal complex assembly remain poorly understood due to rapid sequence divergence and challenges in biochemical reconstitution. Here we identify a novel three-component interface in the nematode synaptonemal complex. Destabilization and subsequent restoration of this interface link the integrity of the synaptonemal complex with chromosome alignment and regulation of exchanges. Beyond mechanistic understanding of chromosomal interactions, our work provides a blueprint for genetic probing of large cellular assemblies that are refractory to structural analysis and sheds light on the forces that shape their evolution.
Analysis ofPseudomonas aeruginosatranscription in anex vivocystic fibrosis sputum model identifies metal restriction as a gene expression stimulus
Authors: Neff Samuel L. , Doing Georgia , Reiter Taylor , Hampton Thomas H. , Greene Casey S. , Hogan Deborah A.
Published: August 2023

ChronicPseudomonas aeruginosalung infections are a distinctive feature of cystic fibrosis (CF) pathology, that challenge adults with CF even with the advent of highly effective modulator therapies. CharacterizingP. aeruginosatranscription in the CF lung and identifying factors that drive gene expression could yield novel strategies to eradicate infection or otherwise improve outcomes. To complement publishedP. aeruginosagene expression studies in laboratory culture models designed to model the CF lung environment, we employed an ex vivo sputum model in which laboratory strain PAO1 was incubated in sputum from different CF donors. As part of the analysis, we compared PAO1 gene expression in this “spike-in” sputum model to that forP. aeruginosagrown in artificial sputum medium (ASM). Analyses focused on genes that were differentially expressed between sputum and ASM and genes that were most highly expressed in sputum. We present a new approach that used sets of genes with correlated expression, identified by the gene expression analysis tool eADAGE, to analyze the differential activity of pathways inP. aeruginosagrown in CF sputum from different individuals. A key characteristic ofP. aeruginosagrown in expectorated CF sputum was related to zinc and iron acquisition, but this signal varied by donor sputum. In addition, a significant correlation betweenP. aeruginosaexpression of the H1-type VI secretion system and corrector use by the sputum donor was observed. These methods may be broadly useful in looking for variable signals across clinical samples.

Importance

Identifying the gene expression programs used byPseudomonas aeruginosato colonize the lungs of people with cystic fibrosis (CF) will illuminate new therapeutic strategies. To capture these transcriptional programs, we cultured the commonP. aeruginosalaboratory strain PAO1 in expectorated sputum from CF patient donors. Through bioinformatics analysis, we defined sets of genes that are more transcriptionally active in real CF sputum compared to artificial sputum media (ASM). Many of the most differentially active gene sets contained genes related to metal acquisition, suggesting that these gene sets play an active role in scavenging for metals in the CF lung environment which is inadequately represented in ASM. Future studies ofP. aeruginosatranscription in CF may benefit from the use of an expectorated sputum model or modified forms of ASM supplemented with metals.
A bacterial expression cloning screen reveals tardigrade single-stranded DNA-binding proteins as potent desicco-protectants
Authors: Hibshman Jonathan D. , Clark-Hachtel Courtney M. , Bloom Kerry S. , Goldstein Bob
Published: August 2023

Tardigrades are known for their ability to survive remarkable extremes, but relatively little is known about the molecular underpinnings that allow for their extraordinary stress tolerance. We devised an expression cloning approach to screen for novel protectants from desiccation-tolerant tardigrades. We expressed cDNA libraries from the tardigradesHypsibius exemplarisandRamazzottius varieornatusinE. coliand subjected the bacteria to desiccation. Sequencing the populations of surviving bacteria revealed enrichment of mitochondrial single-stranded DNA-binding proteins (mtSSBs) from both tardigrade species. Expression of mtSSBs in bacteria improved desiccation survival to similar levels as some of the best protectants known to date. The DNA-binding activity of the oligonucleotide/oligosaccharide binding (OB) fold domain of mtSSB was necessary and sufficient to improve desiccation tolerance. By comparing the efficacy of mtSSBs from multiple organisms, we provide evidence that desicco-protection is a conserved feature of mtSSBs. More broadly, any OB-fold containing protein may act similarly to promote desiccation tolerance, likely by coating ssDNA to limit damage during desiccation. These results identify single-stranded DNA-binding activity as a potent contributor to extreme desiccation tolerance.
Pharmacologic Targeting of PDIA1 Inhibits NLRP3 Inflammasome Assembly and Activation
Authors: Rosarda Jessica D. , Stanton Caroline R. , Chen Emily B. , Bollong Michael J. , Wiseman R. Luke
Published: August 2023

The NLRP3 inflammasome is a cytosolic protein complex that regulates innate immune signaling in response to diverse pathogenic insults through the proteolytic processing and secretion of pro-inflammatory cytokines such as IL-1β. Hyperactivation of NLRP3 inflammasome signaling is implicated in the onset and pathogenesis of numerous diseases, motivating the discovery of new strategies to suppress NLRP3 inflammasome activity. We sought to define the potential for the proteostasis regulator AA147 to inhibit the assembly and activation of the NLRP3 inflammasome. AA147 is a pro-drug that is metabolically converted to a reactive metabolite at the endoplasmic reticulum (ER) membrane to covalently modify ER-localized proteins such as protein disulfide isomerases (PDIs). We show that AA147 inhibits NLRP3 inflammasome activity in monocytes and monocyte-derived macrophages through a mechanism involving impaired assembly of the active inflammasome complex. This inhibition is mediated through AA147-dependent covalent modification of PDIA1. Genetic depletion or treatment with other highly selective PDIA1 inhibitors similarly blocks NLRP3 inflammasome assembly and activation. Our results identify PDIA1 as a potential therapeutic target to mitigate NLRP3 inflammasome-mediated pro-inflammatory signaling implicated in etiologically diverse diseases.
Incidence and Clinical Parameters of HIV-1 Paradoxical and Unmasking Immune Reconstitution Syndrome in Antiretroviral Naïve Pregnant Women attending selected facilities in Kenya
Authors: Muthuka K. John , Nyamai M. Everlyn , Kelly J. Oluoch , Charles Maibvise , Nabaweesi Rosemary
Published: August 2023

Background

Following ART initiation, a spectrum of HIV-associated immune reconstitution inflammatory syndrome (IRIS), as opportunistic infections occurs, presenting as either paradoxical or unmasking IRIS. There are benefits of ART for maternal health and prevention of perinatal transmission, however, some risks may be possible with IRIS. The study sought to estimate the incidence, compare survival times to, and investigate the baseline clinical predictors of HIV-1 paradoxical and unmasking IRIS as well as identify the homogeneity defined by combinations of specific covariates in Art Naïve Pregnant Women.

Methods

A prospective, active records observational study [P609/08/-2018-E] was conducted among ART-naive pregnant women attending antenatal care unit (ANCu) from Kenyatta National andMbagathiHospitals in Kenya. Participants enrolled were between the ages of 20 - 49 years with a clear documentation of HIV status and, an independent review committee adjudicated IRIS diagnosis. Associations between baseline pre-ART characteristics, biomarkers, and IRIS diagnosis were assessed with Cox models. Decision-tree analysis was finally performed to identify homogeneity defined by combinations of specific parameters.

Results

Of the initial total 532 women, (24.8%) (n=133) participants experienced IRIS by the 12thweek post ART initiation, 27.3 % (n= 36) and 72.7% (n = 96) paradoxical and unmasking respectively. Maternal Basal Metabolic Index (MBMI) of (25 -29.9) significantly predicted unmasking IRIS [(β)=0.907, Wald test (β^) = 6.550, (HR = 2.478, 95% C.I 1.237 – 4.965, P = 0.010] same case to gravidity of above 5 [(β)=0.743, P = 0.338] while that of 2-3 predicted paradoxical IRIS [(β)= - 0.542, P = 0.037. WHO-HIV clinical stage 1 and 2 showed a link towards paradoxical IRIS, [(β)=- 0.111 and (β)= - 0.276 (P < 0.05)], clinical stage 4 with unmasking IRIS [(β)= 0.047, HR = 1.048, P = 0.941]. CD4 count > 500 cells/mm3skewed towards unmasking IRIS diagnosis [(β)= 0.192, HR = 1.211, P = 0.416], while RNA-HIV viral loads > 50 copies/ml towards paradoxical IRIS [(β)= - 0.199, HR = 0.820, P = 0.360. On decision tree analysis, 76% (P = 0.729) of ART naïve pregnant women aged 20-29 and 40-49 years of age presented with unmasking IRIS and a gravidity of 4-5 and 1 predicted 88% (P = 0.045) unmasking IRIS as compared to that of 2-3 62 % (P = 0.045).

Conclusion

Unmasking IRIS was the common type of IRIS post-ART initiation. Maternal BMI and RNA-HIV viral loads level predicted paradoxical IRIS while the baseline CD4 count and WHO-HIV clinical infection stage 1 and 4 were associated with unmasking IRIS. Gravidities of 1 and 4 – 5 predicted unmasking IRIS.
Comprehensive and quantitative analysis of intracellular structure polarization at the apical–basal axis in elongatingArabidopsiszygotes
Authors: Hiromoto Yukiko , Minamino Naoki , Kikuchi Suzuka , Kimata Yusuke , Matsumoto Hikari , Nakagawa Sakumi , Ueda Minako , Higaki Takumi
Published: August 2023

A comprehensive and quantitative evaluation of multiple intracellular structures or proteins is a promising approach to provide a deeper understanding of and new insights into cellular polarity. In this study, we developed an image analysis pipeline to obtain intensity profiles of fluorescent probes along the apical–basal axis in elongatingArabidopsis thalianazygotes based on two-photon live-cell imaging data. This technique showed the intracellular distribution of actin filaments, mitochondria, microtubules, and vacuolar membranes along the apical–basal axis in elongating zygotes from the onset of cell elongation to just before asymmetric cell division. Hierarchical cluster analysis of the quantitative data on intracellular distribution revealed that the zygote may be compartmentalized into two parts, with a boundary located 43.6% from the cell tip, immediately after fertilization. To explore the biological significance of this compartmentalization, we examined the positions of the asymmetric cell divisions from the dataset used in this distribution analysis. We found that the cell division plane was reproducibly inserted 20.5% from the cell tip. This position corresponded well with the midpoint of the compartmentalized apical region, suggesting a potential relationship between the zygote compartmentalization, which begins with cell elongation, and the position of the asymmetric cell division.
WWP2 MEDIATES THE METABOLIC REPROGRAMMING OF RENAL MYOFIBROBLASTS TO PROMOTE KIDNEY FIBROSIS
Authors: Chen Huimei , You Ran , Guo Jing , Zhou Wei , Chew Gabriel , Devapragash Nithya , Loh Jui Zhi , Gesualdo Loreto , Li Yanwei , Jiang Yuteng , Tan Elisabeth Li Sa , Chen Shuang , Pontrelli Paola , Pesce Francesco , Behmoaras Jacques , Zhang Aihua , Petretto Enrico
Published: August 2023

Renal fibrosis is a common pathological endpoint in chronic kidney disease (CKD) that is challenging to reverse. Although myofibroblasts are mainly responsible for the accumulation of a fibrillar collagen-rich extracellular matrix (ECM) in fibrotic kidney, recent studies have unveiled their diversity in terms of proliferative and fibrotic characteristics. This diversity could be linked with the existence of different metabolic states, and myofibroblast metabolic reprogramming may contribute to the pathogenesis and progression of renal fibrosis. Here, we reveal an unexpected role of the E3 ubiquitin-protein ligase WWP2 in the metabolic reprogramming of myofibroblasts during renal fibrosis. The tubulointerstitial expression of WWP2 contributes to the progression of fibrosis in CKD patients, and in pre-clinical murine models of CKD. WWP2 deficiency increases fatty acid oxidation and activates the pentose phosphate pathway, boosting mitochondrial respiration at the expense of glycolysis. This concurrently promotes myofibroblast proliferation and halts pro-fibrotic activation, reducing the severity of kidney fibrosis. Mechanistically, WWP2 suppresses the transcription of PGC-1α, a metabolic mediator shaping myofibroblast fibrotic response. Pharmacological interventions targeting PGC-1α reverse the effects of WWP2 on fibrotic myofibroblasts. These findings demonstrate the influence of WWP2 on essential metabolic pathways involved in fibrogenesis, uncovering the WWP2-PGC-1α axis that orchestrates the metabolic reprogramming of myofibroblasts during renal fibrosis. Our study presents a potential novel target for therapeutic intervention in the treatment of chronic kidney disease.

Graphical abstract

Highlights

WWP2 expression is elevated in the tubulointerstitium of fibrotic kidneys and contributes to CKD pathogenesis and progression.

WWP2 uncouples the pro-fibrotic activation and cell proliferation in renal myofibroblasts.

WWP2 controls mitochondrial respiration in renal myofibroblasts through the metabolic regulator PGC-1α

Myofibroblast metabolic reprogramming mediates the effect of WWP2 on fibrotic myofibroblasts.
An analysis of British Michelin-starred restaurants: guests' online reviews
Authors: Saydam Mehmet Bahri , Altun Özlem
Published: August 2023

Purpose

This study aims to explore the perspectives of patrons and the underlying factors influencing luxury consumption in British Michelin-starred restaurants. While numerous studies have investigated consumers' purchase behavior of luxury items, there is limited research focusing on the utilization of premium restaurant services. Additionally, the hospitality literature has rarely addressed the emergence of discreet luxury consumption. Therefore, this research aims to examine the experiences of British Michelin-starred restaurants by incorporating online reviews from some of the most renowned establishments in the country. The initial objective of this study was to identify the predominant themes within British Michelin-starred restaurant experiences. Furthermore, the authors sought to analyze whether these main themes varied across different market segments based on guest types.

Design/methodology/approach

Using text mining tools, the authors analyzed a sample of 4,393 online reviews. Qualitative data analysis was conducted using the Leximancer program, which identified the dominant themes. Additionally, the authors performed an analysis to identify the major narratives associated with different types of guests.

Findings

The results of this analysis demonstrate that guests express a high level of satisfaction with their experiences at British Michelin-starred restaurants. The dominant themes within the narratives include food, wine, restaurant, time, reservation and innovation. It is important to note that these narratives vary depending on the type of guest.

Originality/value

Previous studies have highlighted the importance of market segmentation in Michelin-starred restaurants. This research addresses this need by specifically categorizing British Michelin-starred restaurants based on traveler type and the main concerns of their customers. The extensive data the authors collected and the authors' approach to utilizing guests' testimonials instead of traditional surveys contribute significantly to the field of academia and restaurant management.
Understanding the characteristics of work that foster workplace well-being in an apprenticeship programme and their effects on apprentices' employability. Exploring the gender moderation effect
Authors: Ullibarriarana-Garate Ainhoa , Agirre-Aramburu Izaskun , Mesonero-De Miguel Mikel
Published: August 2023

Purpose

This study seeks to show whether workplace experience (WE) in an apprenticeship programme affects the duration of joblessness amongst recent university graduates and to determine the antecedents that support a workplace well-being experience during an apprenticeship programme. Additionally, the research introduces the moderating effect of gender in order better to understand under what circumstances apprenticeship reduces the time taken to find employment.

Design/methodology/approach

The research proposes PLS equation modelling constructed with a sample of 129 students from the Business Administration and Management degree at Mondragon University.

Findings

The research finds that social support and job demand are key features of work that should be addressed to ensure a workplace well-being experience in an apprenticeship programme. In addition, a workplace well-being experience during apprenticeship reduced the time taken by students to access their first job. This means that job training in a company helps students get their first job, but it is not the primary factor. The study also shows that men who had workplace well-being experience in an apprenticeship programme take less time to find their first job.

Originality/value

The study proposes an exclusive analysis of apprenticeship programmes in higher education systems from the perspective of workplace well-being experience, based on the DCS model. This research also adds to the literature on apprenticeship by providing evidence that a positive experience of work during an apprenticeship programme facilitates undergraduate students in securing employment. Furthermore, this paper confirms that workplace well-being experiences in apprenticeship programmes constitute a valid tool for tackling youth unemployment, and finds that it is more efficient amongst males than females.
Cultural dimensions as key aspects to change and improve school performance: a qualitative study in the Brazilian public schools
Authors: Oliveira Pedro Henrique de , Almada Santos Fernando César , Paschoalotto Marco Antônio Catussi , Delmônico Diego Valério de Godoy , Terence Ana Cláudia Fernandes
Published: August 2023

Purpose

Despite the school organizational culture broad literature, there is still a gap on culture and educational management, mainly in the public environment. To fill out this space, this article wants to point out the cultural factors that creates school management change in the Brazilian public school context.

Design/methodology/approach

The sample is a polar multi-case approach with two high performance and two low performance Brazilian schools. The authors conducted 12 interviews, three each school, with school principal, pedagogical coordinator and administrative officer. To analyze the data, the authors applied synthetic analysis to identify the cultural factors and your conduciveness to change in schools.

Findings

The results point out organizational culture as low understood in public municipal schools. These results also indicate the cultural dimensions power distance, uncertainty avoidance, individualism, masculinity, long-term orientation and indulgence as influencers of school management. Therefore, organizational culture is a factor to change and improve performance in public school management.

Research limitations/implications

Despite the low comprehensiveness by the school managers, the authors pointed out the importance of the cultural factors, such as power distance, uncertainty avoidance, individualism, masculinity, long-term orientation and indulgence, in the school management. Future research could assess quantitatively the cultural factors presented here.

Social implications

The paper provides cultural aspects in the school environment that should be considered in the school management improvement process and school principals’ actions.

Originality/value

The results fulfil the gap of organizational culture and school management in the public sector studies, by pointing out cultural factors of change in the school environment.