bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional genomics analysis identifies impairment of HNF1B function as a cause of Mayer-Rokitansky-Küster-Hauser syndrome
Authors: Thomson Ella , Tran Minh , Robevska Gorjana , Ayers Katie , Bhaskaran Prarthna Gopalakrishnan , Haan Eric , Cereghini Silvia , Vash-Margita Alla , Margetts Miranda , Hensley Alison , Nguyen Quan , Sinclair Andrew , Koopman Peter , Pelosi Emanuele
Published: April 2022

Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is a congenital condition characterized by aplasia or hypoplasia of the uterus and vagina in women with a typical 46,XX karyotype. This condition can occur as type I when isolated or as type II when associated with extragenital anomalies including kidney and skeletal abnormalities. The genetic basis of MRKH syndrome remains unexplained and several candidate genes have been proposed to play a role in its etiology, including HNF1B, LHX1, and WNT4. Here, we conducted a genomic analysis of 13 women affected by MRKH syndrome, resulting in the identification of candidate genes, including several novel candidates. We focused on HNF1B for further investigation due to its known association with, but unknown etiological role in, MRKH syndrome. We ablated Hnf1b specifically in the epithelium of the Müllerian ducts in mice, and found that this caused hypoplastic development of both the epithelial and stromal compartments of the uterus, as well as kidney anomalies, closely mirroring the MRKH type II phenotype. Using single-cell RNA sequencing of uterine tissue in the Hnf1b-ablated embryos, we analyzed the molecules and pathways downstream of Hnf1b, revealing a dysregulation of processes associated with cell proliferation, migration, and differentiation. Thus, we establish that loss of Hnf1b function leads to an MRKH phenotype, and generate the first mouse model of MRKH syndrome type II. Our results support the diagnostic value of HNF1B in clinical genetic testing for MRKH syndrome, and shed new light on the genetic causes of this poorly understood condition in women’s reproductive health.
Systematic Replication Enables Normalization of High-throughput Imaging Assays
Authors: Hunt Gregory J. , Dane Mark A. , Korkola James E. , Heiser Laura M. , Gagnon-Bartsch Johann A.
Published: April 2022

Motivation

High-throughput fluorescent microscopy is a popular class of techniques for studying tissues and cells through automated imaging and feature extraction of hundreds to thousands of samples. Like other high-throughput assays, these approaches can suffer from unwanted noise and technical artifacts that obscure the biological signal. In this work we consider how an experimental design incorporating multiple levels of replication enables removal of technical artifacts from such image-based platforms.

Results

We develop a general approach to remove technical artifacts from high-throughput image data that leverages an experimental design with multiple levels of replication. To illustrate the methods we consider microenvironment microarrays (MEMAs), a high-throughput platform designed to study cellular responses to microenvironmental perturbations. In application on MEMAs, our approach removes unwanted spatial artifacts and thereby enhances the biological signal. This approach has broad applicability to diverse biological assays.

Availability

Raw data is on synapse (syn2862345), analysis code is on github (gjhunt/mema norm), a Docker image is available on dockerhub (gjhunt/memanorm). online.
Nicotinamide riboside improves muscle mitochondrial biogenesis, satellite cell differentiation and gut microbiota composition in a twin study
Authors: Lapatto Helena , Kuusela Minna , Heikkinen Aino , Muniandy Maheswary , van der Kolk Birgitta W. , Gopalakrishnan Swetha , Sandvik Martin , Schmidt Mark S. , Heinonen Sini , Saari Sina , Pöllänen Noora , Kuula Juho , Hakkarainen Antti , Tampio Janne , Saarinen Tuure , Taskinen Marja-Riitta , Lundbom Nina , Groop Per-Henrik , Tiirola Marja , Katajisto Pekka , Lehtonen Marko , Brenner Charles , Kaprio Jaakko , Pekkala Satu , Ollikainen Miina , Pietiläinen Kirsi H. , Pirinen Eija
Published: April 2022

NAD+ precursor nicotinamide riboside (NR) has emerged as a promising compound to improve obesity-associated mitochondrial dysfunction and metabolic syndrome in mice. However, most short-term clinical trials conducted so far have failed to report positive outcomes. Therefore, we aimed to determine whether long-term NR supplementation boosts mitochondrial biogenesis and metabolic health in humans. Twins from 22 BMI-discordant monozygotic pairs were supplemented with an escalating dose of NR (250-1000 mg/day) for 5 months (clinicaltrials.gov entry NCT03951285). NR improved blood and tissue NAD+ metabolism, muscle mitochondrial number, myoblast differentiation and gut microbiota composition independent of BMI. NR also showed a capacity to modulate epigenetic control of gene expression in muscle and adipose tissue. However, NR did not ameliorate adiposity or metabolic health. Overall, our results suggest that NR acts as a potent modifier of NAD+ metabolism, muscle mitochondrial biogenesis and stem cell function, gut microbiota, and DNA methylation in humans irrespective of BMI.
Gestational Early-Time Restricted Feeding Results in Sex-Specific Glucose Intolerance in Adult Male Mice
Authors: Mulcahy Molly C. , Habbal Noura El , Snyder Detrick , Redd JeAnna R. , Sun Haijing , Gregg Brigid E. , Bridges Dave
Published: April 2022

The timing of food intake is a novel dietary component that can impact health. Time-restricted feeding (TRF), a form of intermittent fasting, manipulates food timing. During pregnancy, one may experience disruptions to food intake for diverse reasons (e.g. nausea and vomiting of pregnancy, food insecurity, desire to manage gestational weight gain, disordered eating behaviors, changes in taste and food preferences, etc) and therefore may experience periods of intentional or unintentional fasting similar to TRF protocols. Because interest in TRF is gaining popularity and feeding may be interrupted in those who are pregnant, it is important to understand the long-term effects of TRF during pregnancy on the resultant offspring. Using a mouse model, we tested the effects of gestational exposure to early TRF (eTRF) over the life course of both male and female offspring. Offspring body composition was similar between experimental groups in both males and females from weaning (day 21) to adulthood (day 70), with minor increases in food intake in eTRF females and improved glucose tolerance in males. After 10 weeks of high fat, high sucrose diet feeding, male eTRF offspring were more sensitive to insulin but developed glucose intolerance with impaired insulin secretion. As such, gestational eTRF causes sex-specific deleterious effects on glucose homeostasis after chronic high fat, high sucrose diet feeding in male offspring. Further studies are needed to determine the effect gestational eTRF has on the male pancreas as well as to elucidate the mechanisms that protect females from this metabolic dysfunction.
A fast machine-learning-guided primer design pipeline for selective whole genome amplification
Authors: Yu Jane A. , Oppler Zachary J. , Mitchell Matthew W. , Song Yun S. , Brisson Dustin
Published: April 2022

Addressing many of the major outstanding questions in the fields of microbial evolution and pathogenesis will require analyses of populations of microbial genomes. Although population genomic studies provide the analytical resolution to investigate evolutionary and mechanistic processes at fine spatial and temporal scales – precisely the scales at which these processes occur – microbial population genomic research is currently hindered by the practicalities of obtaining sufficient quantities of the relatively pure microbial genomic DNA necessary for next-generation sequencing. Here we present swga2.0, an optimized and parallelized pipeline to design selective whole genome amplification (SWGA) primer sets. Unlike previous methods, swga2.0 incorporates active and machine learning methods to evaluate the amplification efficacy of individual primers and primer sets. Additionally, swga2.0 optimizes primer set search and evaluate strategies, including parallelization at each stage of the pipeline, to dramatically decrease program runtime from weeks to minutes. Here we describe the swga2.0 pipeline, including the empirical data used to identify primer and primer set characteristics, that improve amplification performance. Additionally, we evaluated the novel swga2.0 pipeline by designing primers sets that successfully amplify Prevotella melaninogenica, an important component of the lung microbiome in cystic fibrosis patients, from samples dominated by human DNA.
Age-related changes of deep-brain neurophysiological activity
Authors: Hinault T. , Baillet S. , Courtney SM.
Published: April 2022

Cognitive decline with age is associated with brain atrophy and reduced brain activations, but the underlying neurophysiological mechanisms are unclear, especially in deeper brain structures primarily affected by healthy aging or neurodegenerative processes. Here, we characterize time-resolved, resting-state magnetoencephalography activity of the hippocampus and subcortical brain regions in a large cohort of healthy young and older volunteers from the Cam-CAN open repository. The data show age-related changes in both rhythmic and arrhythmic signal strength and temporal variability in multiple deeper brain regions, including the hippocampus, striatum, and thalamus. We observe a slowing of neural activity in deeper brain regions, which echoes previous reports of cortical slowing. We also report reduced occipito-parietal alpha peak associated with increased theta-band activity and signal variability in the hippocampus, an effect that may reflect compensatory processes as theta activity and variability were more strongly expressed when cognitive performances are preserved. Overall, this study advances the understanding of the biological nature of inter-individual variability in aging. The data provide new insight of how hippocampus and subcortical neurophysiological activity evolve with biological age, and highlight frequency-specific effects associated with cognitive decline vs. cognitive maintenance.
The distribution of the Lansing Effect across animal species
Authors: Ivimey-Cook Edward , Shorr Sarema , Moorad Jacob
Published: April 2022

Maternal senescence is a reduction in individual performance associated with an increase in its mother’s age at conception. When manifested on adult lifespan, this is known as the ‘Lansing Effect’. Single-species studies report both maternal age-related increases and decreases in adult lifespan, but no comprehensive review of the literature has yet determined if the Lansing Effect is a widespread phenomenon. To address this knowledge gap, we performed a meta-analysis of maternal aging rates taken from all available published studies. We recovered 74 estimates from 20 studies representing 14 species. All studies taken together suggest a propensity for a Lansing Effect with an estimated average effect of maternal age on adult lifespan of between -22% to -17% (the lifespan response to an increase in maternal age expressed in the same time units), depending upon our specific choice of model. We failed to find a significant effect of animal class or insect order, but given the oversampling of insect species in the published literature and the paucity of vertebrate studies, we infer that only rotifers and insects demonstrate a tendency for expressing the phenomenon.
Rac rather than Rho drives the early transcriptional response to extracellular matrix stiffness and mediates repression of ATF3
Authors: Dang Irène , Bae Yongho , Brazzo Joseph A. , Assoian Richard K
Published: April 2022

The Rho family GTPases, Rac and Rho, play critical roles in transmitting mechanical information contained within the extracellular matrix (ECM) to the cell. Rac and Rho have well described roles in regulating stiffness-dependent actin remodeling, proliferation and motility. However, much less is known about the relative roles of these GTPases in stiffness-dependent transcription, particularly at the genome-wide level. Here, we selectively inhibited Rac and Rho in mouse embryonic fibroblasts cultured on deformable substrata and used RNA sequencing to elucidate and compare the contribution of these GTPases to the early transcriptional response to ECM stiffness. Surprisingly, we found that Rac activation is almost exclusively responsible for the initial transcriptional response to ECM stiffness. We also identified Activating Transcription Factor 3 (ATF3) as a major target of stiffness/Rac signaling and show that ATF3 repression by ECM stiffness connects the stiffness-dependent activation of Rac to the induction of cyclin D1.
Tackling RecalcitrantPseudomonas aeruginosaInfections In Critical Illness via Anti-virulence Monotherapy
Authors: Singh Vijay K. , Almpani Marianna , Maura Damien , Kitao Tomoe , Ferrari Livia , Fontana Stefano , Bergamini Gabriella , Calcaterra Elisa , Pignaffo Chiara , Negri Michele , de Oliveira Pereira Thays , Skinner Frances , Gkikas Manos , Andreotti Danielle , Felici Antonio , Déziel Eric , Lépine Francois , Rahme Laurence G.
Published: April 2022

Intestinal barrier derangement allows intestinal bacteria and their products to translocate to the systemic circulation.Pseudomonas aeruginosa(PA) superimposed infection in critically ill patients increases gut permeability and leads to gut-driven sepsis.PAinfections are challenging due to multi-drug resistance (MDR), biofilms, and/or antibiotic tolerance. Inhibition of the quorum-sensing transcriptional regulator MvfR(PqsR) is a desirable anti-PAstrategy as MvfR controls multiple acute and chronic virulence functions. Here we show that MvfR promotes intestinal permeability and report novel potent anti-MvfR compounds, the N-Aryl Malonamides (NAMs) resulting from extensive structure-activity-relationship studies and thorough assessment of the inhibition of MvfR-controlled virulence functions. This novel class of anti-virulence non-native ligand-based agents has a half-maximal inhibitory concentration in the nanomolar range and strong target engagement. Using a NAM lead in monotherapy protects murine intestinal barrier function, abolishes MvfR-regulated small molecules, ameliorates bacterial dissemination, and lowers inflammatory cytokines. This study demonstrates the importance of MvfR inPA-driven intestinal permeability. It underscores the utility of anti-MvfR agents in maintaining gut mucosal integrity, which should be part of any successful strategy to prevent/treatPAinfections and associated gut-derived sepsis in critical illness settings. NAMs provide for the development of crucial preventive/therapeutic monotherapy options against untreatable MDRPAinfections.
Receptor-like kinases FER and SRK mediate Lotus japonicus freezing tolerance and climate adaptation
Authors: Mustamin Yusdar , Akyol Turgut Yigit , Gordon Max , Manggabarani Andi Madihah , Isomura Yoshiko , Kawamura Yasuko , Bamba Masaru , Williams Cranos , Andersen Stig Uggerhøj , Sato Shusei
Published: April 2022

Many plant species have succeeded in colonizing a wide range of diverse climates through local adaptation, but the underlying molecular genetics remain obscure. We previously found that winter survival was a direct target of selection during colonization of Japan by the perennial legume Lotus japonicus and identified associated candidate genes. Here, we show that two of these, the FERONIA-receptor like kinase (LjFER) and a novel S-receptor-like kinase (LjSRK) are required for non-acclimated freezing tolerance and show haplotype-dependent cold-responsive expression. Our work demonstrates that recruiting a conserved growth regulator, FER, and a novel receptor-like kinase, SRK, into the set of cold-responsive genes has contributed to freezing tolerance and local climate adaptation in L. japonicus, offering new functional genetic insight into perennial herb evolution.
miRNA408 and its encoded peptide, miPEP408, regulate arsenic stress response in Arabidopsis
Authors: Kumar Ravi Shankar , Sinha Hiteshwari , Datta Tapasya , Asif Mehar Hasan , Trivedi Prabodh Kumar
Published: April 2022

MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in regulating various developmental and biological processes. The expression of miRNAs is differentially modulated in response to various stresses. Based on the recent findings, it has been shown that some of the pri-miRNAs encode small regulatory peptides, microRNA-encoded peptides (miPEP). miPEPs are reported to regulate the growth and development of plants by modulating corresponding miRNA expression; however, the role of these peptides in different stresses has not been explored yet. Here, we reported that pri-miR408 encodes a small peptide, miPEP408, that regulates the expression of miR408, its targets, and associated phenotype in Arabidopsis. Plants overexpressing miR408 showed severe sensitivity under low sulphur (LS), Arsenite As(III) and LS+As(III) stress, while miR408 mutant developed through the CRISPR/Cas9 approach showed tolerance. Transgenic lines showed phenotypic alteration and modulation in the expression of genes involved in the sulphur reduction pathway and affect sulphate and glutathione accumulation. Similar to miR408 overexpressing lines, the exogenous application of synthetic miPEP408 or miPEP408 overexpression led to sensitivity in plants under LS, As(III) and combined LS+As(III) stress compared to control. This study suggests the involvement of miR408 and miPEP408 in heavy metal and nutrient deficiency responses.

One-sentence summary

miR408 and peptide encoded by miR408, miPEP408, regulate arsenic stress and low sulphur responses in Arabidopsis.
The localization of PHRAGMOPLAST ORIENTING KINESIN1 at the division site depends on two microtubule binding proteins TANGLED1 and AUXIN-INDUCED-IN-ROOT-CULTURES9 in Arabidopsis
Authors: Mills Alison M. , Morris Victoria H. , Rasmussen Carolyn G
Published: April 2022

Proper plant growth and development requires spatial coordination of cell divisions. Two unrelated microtubule-binding proteins, TANGLED1 (TAN1) and AUXIN-INDUCED-IN-ROOT-CULTURES9 (AIR9), are together required for normal growth and division-plane orientation in Arabidopsis. tan1 air9 double mutants have synthetic growth and division-plane orientation defects while single mutants lack obvious defects. Here we show that the division-site localized protein, PHRAGMOPLAST-ORIENTING-KINESIN1 (POK1), was aberrantly lost from the division site during metaphase and telophase in tan1 air9 mutants. Since TAN1 and POK1 interact via the first 132 amino acids of TAN1 (TAN11-132), we assessed its localization and function in the tan1 air9 double mutant. TAN11-132 rescued tan1 air9 mutant phenotypes and localized to the division site in telophase. However, replacing six amino-acid residues within TAN11-132 that disrupts POK1-TAN1 interaction in the yeast-two-hybrid system caused loss of both rescue and division-site localization of TAN11-132 in tan1 air9 mutants. Full-length TAN1 with the same alanine substitutions had defects in phragmoplast guidance and reduced TAN1 and POK1 localization at the division site but rescued most tan1 air9 mutant phenotypes. Together, these data suggest that TAN1 and AIR9 are required for POK1 localization, and yet unknown proteins may stabilize TAN1-POK1 interactions.

One sentence summary

Specific amino acids within TAN1 are required for its correct localization and function partially through interaction with POK1; both TAN1 and AIR9 mediate POK1 division site localization.
A toolbox for systematic discovery of stable and transient protein interactors in baker’s yeast
Authors: Fenech Emma J. , Cohen Nir , Kupervaser Meital , Gazi Zohar , Schuldiner Maya
Published: April 2022

Identification of both stable and transient interactions is essential for understanding protein function and regulation. While assessing stable interactions is more straightforward, capturing transient ones is challenging. In recent years, sophisticated tools have emerged to improve transient interactor discovery, with many harnessing the power of evolved biotin ligases for proximity labelling. However, biotinylation-based methods have lagged behind in the model eukaryote, Saccharomyces cerevisiae, possibly due to the presence of several abundant, endogenously biotinylated proteins. In this study, we optimised robust biotin- ligation methodologies in yeast and increased their sensitivity by creating a bespoke technique for downregulating endogenous biotinylation which we term ABOLISH (Auxin- induced BiOtin LIgase diminiSHing). We used the endoplasmic reticulum insertase complex (EMC) to demonstrate our approaches and uncover new substrates. To make these tools available for systematic probing of both stable and transient interactions, we generated five full-genome collections of strains in which every yeast protein is tagged with each of the tested biotinylation machineries; some on the background of the ABOLISH system. This comprehensive toolkit enables functional interactomics of the entire yeast proteome.
Two types of human TCR differentially regulate reactivity to self and non-self antigens
Authors: Trofimov Assya , Brouillard Philippe , Larouche Jean-David , Séguin Jonathan , Laverdure Jean-Philippe , Brasey Ann , Ehx Gregory , Roy Denis-Claude , Busque Lambert , Lachance Silvy , Lemieux Sébastien , Perreault Claude
Published: April 2022

Based on analyses of TCR sequences from over 1,000 individuals, we report that the TCR repertoire is composed of two ontogenically and functionally distinct types of TCRs. Their production is regulated by variations in thymic output and terminal deoxynucleotidyl transferase (TDT) activity. Neonatal TCRs derived from TDT-negative progenitors persist throughout life, are highly shared among subjects, and are polyreactive to self and microbial antigens. Thus, >50% of cord blood TCRs are responsive to SARS-CoV2 and other common pathogens. TDT- dependent TCRs present distinct structural features and are less shared among subjects. TDT- dependent TCRs are produced in maximal numbers during infancy when thymic output and TDT activity reach a summit, are more abundant in subjects with AIRE mutations, and seem to play a dominant role in graft-versus-host disease. Factors decreasing thymic output (age, male sex) negatively impact TCR diversity. Males compensate for their lower repertoire diversity via hyperexpansion of selected TCR clonotypes.
Ligand Binding Prediction using Protein Structure Graphs and Residual Graph Attention Networks
Authors: Pandey Mohit , Radaeva Mariia , Mslati Hazem , Garland Olivia , Fernandez Michael , Ester Martin , Cherkasov Artem
Published: April 2022

Motivation

Computational prediction of ligand-target interactions is a crucial part of modern drug discovery as it helps to bypass high costs and labor demands of in vitro and in vivo screening. As the wealth of bioactivity data accumulates, it provides opportunities for the development of deep learning (DL) models with increasing predictive powers. Conventionally, such models were either limited to the use of very simplified representations of proteins or ineffective voxelization of their 3D structures. Herein, we present the development of the PSG-BAR (Protein Structure Graph –Binding Affinity Regression) approach that utilizes 3D structural information of the proteins along with 2D graph representations of ligands. The method also introduces attention scores to selectively weight protein regions that are most important for ligand binding.

Results

The developed approach demonstrates the state-of-the-art performance on several binding affinity benchmarking datasets. The attention-based pooling of protein graphs enables identification of surface residues as critical residues for protein-ligand binding. Finally, we validate our model predictions against an experimental assay on a viral main protease (Mpro)– the hallmark target of SARS-CoV-2 coronavirus.

Availability

The code for PSG-BAR is made available athttps://github.com/diamondspark/PSG-BAR

Contact

acherkasov@prostatecentre.com
Integrated Genomics Approaches Identify Transcriptional Mediators and Epigenetic Responses to Afghan Desert Particulate Matter in Small Airway Epithelial Cells
Authors: Gupta Arnav , Sasse Sarah K. , Berman Reena , Gruca Margaret A. , Dowell Robin D. , Chu Hong Wei , Downey Gregory P. , Gerber Anthony N.
Published: April 2022

Military Deployment to Southwest Asia and Afghanistan and exposure to toxic airborne particulates has been associated with an increased risk of developing respiratory disease, collectively termed deployment-related respiratory diseases (DRRD). Our knowledge about how particulates mediate respiratory disease is limited, precluding the appropriate recognition or management. Central to this limitation is the lack of understanding of how exposures translate into dysregulated cell identity with dysregulated transcriptional programs. The small airway epithelium is involved in both the pathobiology of DRRD and fine particulate matter deposition. To characterize small airway epithelial cell epigenetic and transcriptional responses to Afghan desert particulate matter (APM) and investigate the functional interactions of transcription factors that mediate these responses, we applied two genomics assays, the assay for transposase accessible chromatin with sequencing (ATAC-seq) and Precision Run-on sequencing (PRO-seq). We identified activity changes in a series of transcriptional pathways as candidate regulators of susceptibility to subsequent insults, including signal-dependent pathways, such as loss of cytochrome P450 or P53/P63, and lineage-determining transcription factors, such as GRHL2 loss or TEAD3 activation. We further demonstrated that TEAD3 activation was unique to APM exposure despite similar inflammatory responses when compared with wood smoke particle exposure and that P53/P63 program loss was uniquely positioned at the intersection of signal-dependent and lineage-determining transcriptional programs. Our results establish the utility of an integrated genomics approach in characterizing responses to exposures and identify genomic targets for the advanced investigation of the pathogenesis of DRRD.
Humanization and Expression of IgG and IgM Antibodies in Plants as Potential Diagnostic Reagents for Valley Fever
Authors: Jugler Collin , Grill Francisca J. , Grys Thomas E. , Lake Douglas F. , Chen Qiang
Published: April 2022

Monoclonal antibodies (mAbs) are important proteins used in many life science applications, from diagnostics to therapeutics. High demand for mAbs for different applications urges the development of rapid and reliable recombinant production platforms. Plants provide a quick and inexpensive system for producing recombinant mAbs. Moreover, when paired with an established platform for mAb discovery, plants can easily be tailored to produce mAbs of different isotypes against the same target. Here, we demonstrate that a hybridoma-generated mouse mAb against chitinase 1 (CTS1), an antigen fromCoccidioidesspp., can be biologically engineered for use with serologic diagnostic test kits for coccidioidomycosis (Valley Fever) using plant expression. The original mouse IgG was modified and recombinantly produced in plants as IgG and IgM isotypes with human kappa, gamma, and mu constant regions. The two mAb isotypes produced in plants were shown to maintain target antigen recognition to CTS1 using similar reagents as the Food and Drug Administration (FDA)-approved Valley Fever diagnostic kits. As none of the currently approved kits provide antibody dilution controls, humanization of antibodies that bind to CTS1, a major component of the diagnostic antigen preparation, may provide a solution to the lack of consistently reactive antibody controls for Valley Fever diagnosis. Furthermore, our work provides a foundation for reproducible and consistent production of recombinant mAbs engineered to have a specific isotype for use in diagnostic assays.
Conserved FimK truncation coincides with increased expression of type 3 fimbriae and cultured bladder epithelial cell association in Klebsiella quasipneumoniae
Authors: Venkitapathi Sundharamani , Wijesundara Yalini H. , Herbert Fabian C. , Gassensmith Jeremiah J. , Zimmern Philippe E. , De Nisco Nicole J.
Published: April 2022

Klebsiella spp. commonly cause both uncomplicated urinary tract infection (UTI) and recurrent UTI (rUTI). Klebsiella quasipneumoniae, a relatively newly defined species of Klebsiella, has been shown to be metabolically distinct from Klebsiella pneumoniae, but its urovirulence mechanisms have not been defined. K. pneumoniae uses both type 1 and type 3 fimbriae to attach to host epithelial cells. The type 1 fimbrial operon is well-conserved between Escherichia coli and K. pneumoniae with the exception of fimK, which is unique to Klebsiella spp. FimK contains an N-terminal DNA binding domain and a C-terminal phosphodiesterase (PDE) domain that has been hypothesized to cross-regulate type 3 fimbriae expression via modulation of cellular levels of cyclic di-GMP. Here, we find that a conserved premature stop codon in K. quasipneumoniae fimK results in truncation of the C-terminal PDE domain and that the bladder epithelial cell association and invasion of uropathogenic K. quasipneumoniae strain KqPF9 is dependent on type 3 but not type 1 fimbriae. Further, we show that basal expression of both type 1 and type 3 fimbrial operons as well as bladder epithelial cell association is elevated in KqPF9 relative to uropathogenic K. pneumoniae TOP52 and that complementation of KqPF9ΔfimK with the TOP52 fimK allele reduced type 3 fimbrial expression and bladder epithelial cell attachment. Taken together these data suggest that the C-terminal PDE of FimK can modulate type 3 fimbrial expression in K. pneumoniae and its absence in K. quasipneumoniae may lead to a loss of type 3 fimbrial cross-regulation.

Importance

K. quasipneumoniae is often indicated as the cause of many opportunistic infections including urinary tract infection (UTI), which affects >50% of women worldwide. However, virulence mechanisms of K. quasipneumoniae remain uninvestigated. Prior to this work, K. quasipneumoniae and K. pneumoniae had only been distinguished phenotypically by metabolic differences. This work contributes to the understanding of K. quasipneumoniae virulence phenotypes by evaluating the contribution of type 1 and type 3 fimbriae, which are critical colonization factors encoded by all Klebsiella spp., to K. quasipneumoniae bladder epithelial cell attachment. We identify clear phenotypic differences in both bladder epithelial cell attachment between uropathogenic K. pneumoniae and K. quasipneumoniae. Importantly, we find that a structural difference in the fimbrial regulatory gene fimK may contribute to differential co-regulation of type 1 and type 3 fimbriae between the two Klebsiella species.
Heterogeneous Receptor Expression Underlies Non-uniform Peptidergic Modulation of Olfaction inDrosophila
Authors: Sizemore Tyler R. , Jonaitis Julius , Dacks Andrew M.
Published: April 2022

Sensory systems are dynamically adjusted according to the animal’s ongoing needs by neuromodulators, such as neuropeptides. Although many neuropeptides are often widely-distributed throughout sensory networks, it is unclear whether such neuropeptides uniformly modulate network activity. Here, we leverage the numerically tractable primary olfactory center ofDrosophila(the antennal lobe, AL) to resolve whether one such widely-distributed neuropeptide (myoinhibitory peptide, MIP) uniformly modulates AL processing. We find that despite being uniformly distributed across the AL, MIP decreases olfactory input to some glomeruli, while simultaneously increasing olfactory input to other glomeruli. We reveal that a heterogeneous ensemble of local interneurons (LNs) are the sole source of MIP within the AL. Through high-resolution connectomic analyses, as well asin vivophysiology, we find that the non-uniform effects of MIP are not likely due to MIPergic LN intrinsic properties (e.g., synaptic inputs/outputs, odor-evoked responses, etc.). Instead, we show that differential expression of the inhibitory MIP receptor (sex peptide receptor, SPR) across glomeruli allows MIP to act on distinct intraglomerular substrates, thus enabling differential modulation of olfactory input. Our findings demonstrate how even a seemingly simple case of modulation (i.e., a single neuropeptide acting through a single receptor) can have complex consequences on network processing by acting non-uniformly within different components of the overall network.
Prolonged exposure to insulin causes epigenetic alteration leading to insulin resistance
Authors: Bano Shehnaz , More Shyam , Mongad Dattatray S. , Khalique Abdul , Dhotre Dhiraj P. , Bhat Manoj K. , Seshadri Vasudevan
Published: April 2022

Glucose homeostasis is maintained by insulin. It has been observed that hyperinsulinemia precedes insulin resistance and Type 2 diabetes. Insulin resistance is caused by multiple factors including genetic and diet. The molecular mechanism underlying insulin resistance (IR) is not completely understood. Using Glut4 and insulin receptor-expressing CHO cells we had previously shown that prolonged exposure of these cells to insulin in the absence of high levels of glucose led to insulin resistance in the cells. In the present study, we have shown that the underlying cause for the impaired GLUT4 trafficking is the defective PI3K/AKT pathway. This insulin resistance is likely due to epigenetic alterations as it is stable and can be maintained for several generations even when insulin is not provided, and epigenetic modifiers can reverse the insulin resistance. We extended these studies to liver cell line (BRL-3A) and show that these cells also develop impaired insulin signaling upon exposure to insulin in the absence of high levels of glucose. Transcriptomic analysis of the insulin-sensitive and -resistance cells uncover altered signaling networks involved in chromatin remodelling, Rho GTPases, and ubiquitination. Pathway analysis reveals the role of demethylase Kdm5b and lysine methyltransferase (Kmt2a and Kmt2e) in the development of insulin resistance. It is also observed that trimethylation of histone H3 at lysine 4 (H3K4me3) is increased in insulin resistance cellular models. We further showed that mice injected with low doses of insulin when fasting develop insulin resistance with impaired glucose tolerance and increased HOMA-IR index. Altogether, these findings suggest dysregulated synthesis of insulin in the absence of glucose stimulus could lead to epigenetic alterations that may lead to insulin resistance.

Summary Statement

Insulin stimulation in the absence of glucose leads to insulin resistance. We have developed a cell and mouse model of insulin resistance in this study to characterise the molecular signalling involved in insulin resistance and early onset of type 2 diabetes. The transcriptomic analysis provides new insights on epi-transcriptomic regulation in insulin resistance.
Nanoparticle coatings for controlled release of quercetin from an angioplasty balloon
Authors: Craciun Ioana , Astete Carlos E. , Boldor Dorin , Jennings Merilyn H. , Gorman Jake D. , Sabliov Cristina M. , Dugas Tammy R.
Published: April 2022

Peripheral artery disease (PAD) is a systemic vascular disease of the legs that results in a blockage of blood flow from the heart to the lower extremities. Now one of the most common causes of mortality in the U.S., the first line of therapy for PAD is to mechanically open the blockages using balloon angioplasty. Coating the balloons with antiproliferative agents can potentially reduce vessel re-narrowing, or restenosis after surgical intervention, but current drug-coated balloons releasing chemotherapy agents like paclitaxel have in some cases shown increased mortality long-term. Our aim was to design a novel drug-coated balloon using a polymeric nanodelivery system for a sustained release of polyphenols that reduce restenosis but with reduced toxicity compared to chemotherapy agents. Poly (lactic-co-glycolic acid) (PLGA) nanoparticles with entrapped quercetin, a dimethoxy quercetin (rhamnazin), as well as quercetin conjugated to PLGA, were developed. Balloon catheters were coated with polymeric nanoparticles using an ultrasonic method, and nanoparticle characteristics, drug loading, coating uniformity and drug release were determined. The adhesion of nanoparticles to vascular smooth muscle cells and the antiproliferative effect of nano-delivered polyphenols were also assessed. Of the nanoparticle systems tested, those with covalently attached quercetin provided the most sustained release over a 6-day period. Although these particles adhered to cells to a smaller extent compared to other nanoparticle formulations, their attachment was resistant to washing. These particles also exhibited the greatest anti-proliferative effect. In addition, their attachment was not altered when the cells were grown in calcifying conditions, and in PAD tissue calcification is typically a condition that impedes drug delivery. Moreover, the ultrasonic coating method generated a uniform balloon coating. The polymeric nanoparticle system with covalently attached quercetin developed herein is thus proposed as a promising platform to reduce restenosis post-angioplasty.
Variation in fine scale recombination rate in temperature-evolved Drosophila melanogaster populations in response to selection
Authors: Winbush Ari , Singh Nadia D.
Published: April 2022

Meiotic recombination plays a critical evolutionary role in maintaining fitness in response to selective pressures due to changing environments. Variation in recombination rate has been observed amongst and between species and populations and within genomes across numerous taxa. Studies have demonstrated a link between changes in recombination rate and selection but the extent to which fine scale recombination rate varies between evolved populations during the evolutionary period in response to selection is under active research. Here we utilize a set of three temperature-evolved Drosophila melanogaster populations that were shown to have diverged in several phenotypes including recombination rate based on the temperature regime in which they evolved. Using whole genome sequencing data of these populations, we generated fine scale recombination maps of the three populations. We compare recombination rates and patterns among the three populations and show that they have diverged at fine scales but are conserved at broader scales. We further demonstrate a correlation between recombination rates and genomic variation in the three populations and observe variation in putative warm-spots between the populations with these enhanced areas and associated genes overlapping areas previously shown to have diverged in the three populations due to selection. These data support the existence of recombination modifiers in these populations which are subject to selection during evolutionary change.
Pubertal Development Underlies Optimization of Inhibitory Control Through Specialization of Ventrolateral Prefrontal Cortex
Authors: Ravindranath Orma , Calabro Finnegan J. , Foran William , Luna Beatriz
Published: April 2022

Inhibitory control improves into young adulthood after specialization of relevant brain systems during adolescence. However, the biological mechanisms supporting this unique transition are not well understood. Given that adolescence is defined by pubertal maturation, we examined relative contributions of chronological age and pubertal maturation to inhibitory control development. 105 8-19-year-olds completed 1-5 longitudinal visits (227 visits total) in which pubertal development was assessed via self-reported Tanner stage and inhibitory control was assessed with an in-scanner antisaccade task. As expected, percent and latency of correct antisaccade responses improved with age and pubertal stage. When controlling for pubertal stage, chronological age was distinctly associated with correct response rate. In contrast, pubertal stage was uniquely associated with antisaccade latency even when controlling for age. Chronological age was associated with fMRI task activation in several regions including the right dorsolateral prefrontal cortex, while puberty was associated with right ventrolateral prefrontal cortex (VLPFC) activation. Furthermore, task-related connectivity between VLPFC and cingulate was associated with both pubertal stage and response latency. These results suggest that while age-related developmental processes may support maturation of brain systems underlying the ability to inhibit a response, puberty may play a larger role in the effectiveness of generating cognitive control responses.
3D-printed equipment to decouple (powder) X-ray diffraction sample preparation and measurement
Authors: Fuß Friederike , Rieckert Max , Steinhauer Simon , Liesegang Moritz , Thiele Günther
Published: April 2022

An alternative storage method to separate sample preparation from single-crystal and powder X-ray diffraction measurements at home source diffractometers is described. For single crystals, a setup is presented which allows storage of preselected crystals under cryogenic and ambient temperatures. For powders, a disposable sample holder is introduced. The method is suitable for the storage of air- and moisture-sensitive samples. Equipment made of biodegradable polylactic acid is produced by 3D printing and can be adapted to individual needs. As 3D printers are widely available at research institutions nowadays, models of the presented equipment are provided for the reader to allow easy reproduction.
Innovation as a driver of SMME performance in South Africa: a quantile regression approach
Authors: Matekenya Weliswa , Moyo Clement
Published: April 2022

Purpose

Innovation is regarded as a crucial determinant of growth and development in South Africa, and small, medium and micro enterprises (SMMEs) have been earmarked as instruments for the achievement of the socio-economic goals and innovation as set out in the National Development Plan. The purpose of this study is to investigate the effect of innovation on SMME performance in South Africa.

Design/methodology/approach

The empirical analysis was conducted using the quantile regression technique to examine the effect of innovation on the performance of firms at different sales levels. Data from the World Bank's enterprise survey was used for the analysis.

Findings

The results of the empirical analysis showed that R & D expenditures have a positive and significant effect on performance for firms with higher sales (high growth or larger firms). There is evidence that the introduction of new products/services promotes performance for low growth/ smaller firms.

Practical implications

The empirical results imply that innovation is crucial for SMMEs’ development and growth. However, smaller/low growth firms are not able to spend on R & D due to a lack of funds which could be the reason for their low survival rate. More support needs to be provided to smaller firms with lower sales growth, given the large financial outlay required for R & D expenditures. Despite the lack of funding for R & D expenditure, smaller firms are encouraged to introduce new products and methods of production that do not require major financial outlays.

Originality/value

There is scant empirical evidence on the impact of innovation on firm performance in South Africa. Most studies investigate the challenges faced by SMMEs and the different types of innovation approaches used by firms. Furthermore, the study employs the quantile regression approach which highlights the effect of innovation on firms of different sizes.
Exploring effects of message framing on supportive behaviors toward environmental corporate social responsibility
Authors: Kim Young , Chon Myoung-Gi
Published: April 2022

Purpose

The purpose of this study was to shed light on how effective environmental corporate social responsibility (CSR) communication can be achieved through persuasive communication strategies using message framing.

Design/methodology/approach

This study conducted an online experimental study with a 2 (narrative: narrative or non-narrative) × 2 (framing: gain or loss) between-subjects design.

Findings

The findings showed that environmental CSR communication using narrative framing messages is most effective in creating strong CSR associations between a company and the environmental CSR domain and sharing the company's CSR information on supportive communication and advocating for the environmental campaign.

Originality/value

This study highlights the importance of a company's environmental CSR communication efforts using the right message format (narrative style) to increase its persuasive sequence from CSR evaluation to supportive behaviors, contributing to theoretical development in the research of environmental CSR communication. This study suggests that environmental CSR campaign managers should first formalize the company's environmental responsiveness by clearly establishing policies and practicing CSR performance that could result in a strong CSR association before asking their target publics to engage in pro-environmental activities.
Covid-19 and intentions to study abroad: evidence from overseas university applications to the UK
Authors: Di Pietro Giorgio
Published: April 2022

Purpose

The purpose of this study is to investigate how Covid-19 impacted overseas students’ decision to apply for an undergraduate degree at UK universities.

Design/methodology/approach

This study compares the number of university applications from overseas students in summer and autumn 2020 with those in the period 2011–2019. Multivariate analysis techniques are used.

Findings

The results show that the pandemic has led to a drop in university applications from foreign students by 11–14%. Such decline has been driven by a reduction in the number of applicants from high-income countries as opposed to those from middle-lower income countries. Two explanations may account for this finding. First, students from affluent countries, compared to those from poorer countries, may be more likely to find a good alternative to the UK where to carry out their studies (including their home country). Second, the option of deferring study abroad plans due to the pandemic may be more affordable for applicants from high-income countries.

Originality/value

While understanding how Covid-19 has impacted international student mobility is an emerging issue in the literature, not only are there few studies providing evidence on this, but these are based on qualitative analysis. This paper uses quantitative methods that allow to separate the effect of Covid-19 from that associated with other factors affecting the flow of international students.