bluuebunny/crossref_metadata_2025 huggingface dataset:
Is the hydrogen of the 2’-hydroxyl group of HENMT1 aSchrödinger’shydrogen?
Authors: Kaldis Philipp , Zhao Li Na
Published: May 2023

piRNAs are important in protecting germline integrity. 3’-terminal 2’-O-methylation is essential for piRNA maturation and to protect it from degradation. HENMT1 carries out the 2’-O-methylation, which is of key importance for piRNA stability and functionality. However, neither the structure nor the catalytic mechanism of HENMT1 have been studied. We have constructed a catalytic-competent HENMT1 complex using computational approaches, in which Mg2+is primarily coordinated by four evolutionary conserved residues, and is further auxiliary coordinated by the 3’-O and 2’-O on the 3’-terminal nucleotide of the piRNA. Our study suggests that metal has limited effects on substrate and cofactor binding but is essential for catalysis. The reaction consists of deprotonation of the 2’-OH to 2’-O and methyl transfer from SAM to the 2’-O. The methyl transfer is spontaneous and fast. Our in-depth analysis suggests that the 2’-OH may be deprotonated before entering the active site or it may be partially deprotonated at the active site by His800 and Asp859, which are in a special alignment that facilitates the proton transfer out of the active site. Furthermore, we have developed a detailed potential reaction scenario and our study indicates that HEN1 is Mg2+utilizing but is not a Mg2+dependent enzyme.
Evidence for the cardiodepressive effects of the plasticizer di-2-ethylhexylphthalate (DEHP)
Authors: Swift Luther M. , Roberts Anysja , Pressman Jenna , Guerrelli Devon , Allen Samuel , Haq Kazi T. , Reisz Julie A , D’Alessandro Angelo , Posnack Nikki Gillum
Published: May 2023

Di-2-ethylhexylphthalate (DEHP) is commonly used in the manufacturing of plastic materials, including intravenous bags, blood storage bags, and medical-grade tubing. DEHP can leach from plastic medical products, which can result in inadvertent patient exposure. DEHP concentrations were measured in red blood cell (RBC) units stored between 7-42 days (23-119 μg/mL). Using these concentrations as a guide, Langendorff-perfused rat heart preparations were acutely exposed to DEHP. Sinus activity remained stable with lower doses of DEHP (25-50 μg/mL), but sinus rate declined by 43% and sinus node recovery time prolonged by 56.5% following 30-minute exposure to 100 μg/ml DEHP. DEHP exposure also exerted a negative dromotropic response, as indicated by a 69.4% longer PR interval, 108.5% longer Wenckebach cycle length, and increased incidence of atrioventricular uncoupling. Pretreatment with doxycycline partially rescued the effects of DEHP on sinus activity, but did not ameliorate the effects on atrioventricular conduction. DEHP exposure also prolonged the ventricular action potential and effective refractory period, but had no measurable effect on intracellular calcium transient duration. Follow-up studies using hiPSC-CM confirmed that DEHP slows electrical conduction in a time (15 min – 3 hours) and dose-dependent manner (10-100 μg/mL). Previous studies have suggested that phthalate toxicity is specifically attributed to metabolites of DEHP, including mono-2-ethylhexyl phthalate (MEHP). This study demonstrates that DEHP exposure also contributes to cardiac dysfunction in a dose- and time-dependent manner. Future work is warranted to investigate the impact of DEHP (and its metabolites) on human health, with special consideration for clinical procedures that employ plastic materials.
Dissecting endocytic mechanisms reveals new molecular targets to enhance sodium iodide symporter activity with clinical relevance to radioiodide therapy
Authors: Read Martin L. , Brookes Katie , Zha Ling , Manivannan Selvambigai , Kim Jana , Kocbiyik Merve , Fletcher Alice , Gorvin Caroline M. , Firth George , Fruhwirth Gilbert O. , Nicola Juan P. , Jhiang Sissy , Ringel Matthew D. , Campbell Moray J. , Sunassee Kavitha , Blower Philip J. , Boelaert Kristien , Nieto Hannah R. , Smith Vicki E. , McCabe Christopher J.
Published: May 2023

The sodium/iodide symporter (NIS) frequently shows diminished plasma membrane (PM) targeting in differentiated thyroid cancer (DTC), resulting in suboptimal radioiodide (RAI) treatment and poor prognosis. The mechanisms which govern the endocytosis of NIS away from the PM are ill-defined. Here, we challenged the hypothesis that new mechanistic understanding of NIS endocytosis would facilitate prediction of patient outcomes and enable specific drug modulation of RAI uptake in vivo. Through mutagenesis, NanoBiT interaction assays, cell surface biotinylation assays, RAI uptake and NanoBRET, we identify an acidic dipeptide within the NIS C-terminus which mediates binding to the σ2 subunit of the Adaptor Protein 2 (AP2) heterotetramer. We discovered that the FDA-approved drug chloroquine modulates NIS accumulation at the PM in a functional manner that is AP2 dependent. In vivo, chloroquine treatment of BALB/c mice significantly enhanced thyroidal uptake of99mTc pertechnetate in combination with the histone deacetylase (HDAC) inhibitor SAHA, accompanied by increased thyroidal NIS mRNA. Bioinformatic analyses validated the clinical relevance of AP2 genes with disease-free survival in RAI-treated DTC, enabling construction of an AP2 gene-related risk score classifier for predicting recurrence. We propose that NIS internalisation is orchestrated by the interaction of a C-terminal diacidic motif with AP2σ2, together with the proto-oncogene PBF acting via AP2μ2. Given that NIS internalisation was specifically druggable in vivo, our data provide new translatable potential for improving RAI therapy using FDA-approved drugs in patients with aggressive thyroid cancer.

We delineate the role of endocytic genes in regulating NIS activity at the plasma membrane and highlight the potential for systemic targeting of endocytosis to enhance radioiodine effectiveness in radioiodine-refractory cancer cells.
Optipyzer: A fast and flexible multi-species codon optimization server
Authors: LeRoy Nathan , Roleck Caleigh
Published: May 2023

Codon optimization is a commonly used tool in many fields of scientific research to optimize the expression profile of recombinant proteins in a target organism. It seeks to swap synonymous codons in a recombinant gene to reflect the specific codon usage bias of the expression system. While many tools for codon optimization exist, they cannot optimize a single gene for expression in multiple species and are typically limited in their ability to process large sets of genes. Additionally, these tools often only provide a single interface for running optimizations, making them incompatible with existing bioinformatics tools and pipelines. To address these shortcomings we created Optipyzer: an online codon optimization web server with an accompanying web interface and Python package for multi-species codon optimizations. Optipyzer was designed to be fast, flexible, and extensible - providing numerous interfaces for query submission. We believe that Optipyzer can be a powerful tool for the modern biologist by seamlessly integrating into any workflow. The main web interface can be accessed athttps://optipyzer.com.
Pose prediction accuracy in ligand docking to RNA
Authors: Agarwal Rupesh , Rajeshwar T. Rajitha , Smith Jeremy C.
Published: May 2023

Structure-based virtual high-throughput screening is used in early-stage drug discovery. Over the years, docking protocols and scoring functions for protein-ligand complexes have evolved to improve accuracy in the computation of binding strengths and poses. In the last decade, RNA has also emerged as a target class for new small molecule drugs. However, most ligand docking programs have been validated and tested for proteins and not RNA. Here, we test the docking power (pose prediction accuracy) of three state-of-the-art docking protocols on ∼173 RNA-small molecule crystal structures. The programs are AutoDock4 (AD4) and AutoDock Vina (Vina), which were designed for protein targets, and rDock, which was designed for both protein and nucleic acid targets. AD4 performed relatively poorly. For RNA targets for which a crystal structure of a bound ligand is available, and the goal is to identify new molecules for the same pocket, rDock performs slightly better than Vina. However, in the more common type of early-stage drug discovery setting, in which no structure of a ligand:target complex is known, rDock performed similar to Vina, with a low success rate of ∼27 %. Vina was found to bias for ligands with certain physicochemical properties whereas rDock performs similarly for all ligand properties. Thus, for projects where no ligand:protein structure already exists, Vina and rDock are both applicable. However, the relatively poor performance of all methods relative to protein target docking illustrates a need for further methods refinement.
Acute resistance exercise induces mitophagy and mitophagomes on subsarcolemmal clefts in human skeletal muscle: Focus on BNIP3L/NIX40 as a mitophagy flux marker
Authors: Díaz-Castro F. , Tuñón-Suárez M. , Quezada N. , Rivera P. , Cancino J. , Zbinden-Foncea H. , Morselli E. , Castro-Sepúlveda M.
Published: May 2023

Objective

Mitochondrial dynamics and quality control in skeletal muscle are central to healthy metabolism. Resistance exercise is a recognized tool for improving skeletal muscle function; however, its effect on mitochondria is still not fully understood. We investigated the impact of resistance exercise on mitochondrial morphology and mitophagy in human skeletal muscle.

Methods

Eight healthy men performed resistance exercise on one leg, and muscle biopsies were subsequently obtained from the resting leg (Rest) and the exercised leg (Ex) to measure protein abundance and mitochondrial morphology. Additionally, muscle biopsies were obtained from twelve healthy men, and the abundance of BNIP3L protein was correlated with muscle cell and whole body health markers.

Results

Ex increased p-Drp1 and decreased MFN2, Parkin, and BNIP3L protein levels. Electron microscopy indicated an increase in mitochondrial circularity, cristae abnormality, and mitophagosome structures in Ex, with a marked increase in subsarcolemmal mitophagosomes. We also identified mitophagosomes outside the muscle. Experiments in human myotubes showed a severe decrease in BNIP3L protein in response to CCCP-induced mitochondrial damage with and without bafilomycin. A positive correlation was found between BNIP3L and exercise RQ, HOMA index, while a negative correlation was found with mitophagosomes abundance and VO2max.

Conclusion

Our study describes the effect of resistance exercise on mitochondrial dynamics and mitophagy in skeletal muscle, demonstrating induction of mitochondrial fission and mitophagy in the exercised leg. Moreover, we propose BNIP3L as a potential regulator and marker of mitophagy flux.
ATP-Gated Potassium Channels Contribute to Ketogenic Diet-Mediated Analgesia in Mice
Authors: Enders Jonathan D. , Thomas Sarah , Lynch Paige , Jack Jarrid , Ryals Janelle M. , Puchalska Patrycja , Crawford Peter , Wright Douglas E.
Published: May 2023

Chronic pain is a substantial health burden and options for treating chronic pain remain minimally effective. Ketogenic diets are emerging as well-tolerated, effective therapeutic strategies in preclinical models of chronic pain, especially diabetic neuropathy. We tested whether a ketogenic diet is antinociceptive through ketone oxidation and related activation of ATP-gated potassium (KATP) channels in mice. We demonstrate that consumption of a ketogenic diet for one week reduced evoked nocifensive behaviors (licking, biting, lifting) following intraplantar injection of different noxious stimuli (methylglyoxal, cinnamaldehyde, capsaicin, or Yoda1) in mice. A ketogenic diet also decreased the expression of p-ERK, an indicator of neuronal activation in the spinal cord, following peripheral administration of these stimuli. Using a genetic mouse model with deficient ketone oxidation in peripheral sensory neurons, we demonstrate that protection against methylglyoxal-induced nociception by a ketogenic diet partially depends on ketone oxidation by peripheral neurons. Injection of tolbutamide, a KATPchannel antagonist, prevented ketogenic diet-mediated antinociception following intraplantar capsaicin injection. Tolbutamide also restored the expression of spinal activation markers in ketogenic diet-fed, capsaicin-injected mice. Moreover, activation of KATPchannels with the KATPchannel agonist diazoxide reduced pain-like behaviors in capsaicin-injected, chow-fed mice, similar to the effects observed with a ketogenic diet. Diazoxide also reduced the number of p-ERK+cells in capsaicin-injected mice. These data support a mechanism that includes neuronal ketone oxidation and activation of KATPchannels to provide ketogenic diet-related analgesia. This study also identifies KATPchannels as a new target to mimic the antinociceptive effects of a ketogenic diet.
Structural and Functional Characterization of the Aorta in Hypertrophic Obstructive Cardiomyopathy
Authors: Ibrahim AM. , Latif N. , Roshdy M. , Sarathchandra P. , Hosny M. , Elsawy A. , Hekal S. , Attia A. , Elmozy W. , Elaithy A. , Elguindy A. , Afifi A. , Aguib Y. , Yacoub M.
Published: May 2023

Background and aims

Changes in the phenotype and genotype in Hypertrophic Obstructive Cardiomyopathy (HOCM) are thought to involve the myocardium as well as extracardiac tissues. The extent and significance of extra-myocardial changes has not been adequately studied. We here describe the structural and functional changes in the ascending aorta of HOCM patients.

Methods

Changes in the aortic wall were studied in a cohort of 102 consecutive HOCM patients undergoing myectomy, and 10 normal controls. Biopsies were examined histologically, immunohistochemically and by electron microscopy. Changes in protein expression were quantified using morphometry and western blotting. Pulse wave velocity (PWV) was measured using Cardiac Magnetic Resonance (CMR), in 86 HCM patients compared to 166 age-matched normal controls.

Results

In HCM, the number of medial lamellar units (MLU) was significantly decreased, associated with an increase in the interlamellar distance and a preserved thickness of the aortic wall, as compared to controls. Electron microscopy showed an altered lamellar structure with disorientation of elastin fibers from the circumferential direction. There was an altered composition and orientation of smooth muscle cells. In addition, there was a significant decrease in alpha-smooth muscle actin, smooth muscle myosin, smooth muscle 22 and integrin beta1, and a significant increase in calponin and caspase3. Fibulins 1, 2 and 5, had a reduced expression in HOCM aortic biopsies. Functionally, PWV was significantly higher in HOCM patients compared to healthy controls.

Conclusion

In HOCM patients, specific molecular and structural changes in the composition and organisation of the arterial wall have been identified. This was associated with increased stiffness of the arterial wall.

Translational Perspective

This study sheds light for the first time on the altered lamellar organization in the aorta of Hypertrophic Obstructive Cardiomyopathy (HOCM), in addition to the Smooth muscle cells and Extracellular Matrix abnormalities, to explain the increased wall stiffness associated with patients clinical phenotype. The data provide insights on extra-myocardial targets that can have potential value for risk stratification and personalized therapeutics for HOCM patients.
A pilot clinical study to estimate intracranial pressure utilising cerebral photoplethysmograms in traumatic brain injury patients
Authors: Roldan Maria , Abay Tomas Ysehak , Uff Christopher , Kyriacou Panayiotis A.
Published: May 2023

Objective

In this research a non-invasive ICP optical sensor has been developed and evaluated in a clinical pilot study. The technology is based on infrared light interrogating brain tissue, including photodetectors used to detect the backscattered light, which is modulated by vascular pulsations in the brain vascular tissue. The hypothesis underpinning this research is based on the expected changes in the extramural arterial pressure affecting the morphology of the recorded optical signals (photoplethysmograms (PPGs)), therefore analysis of the acquired signals using a bespoke algorithm could enable the calculation of the intracranial pressure non-invasively (nICP).

Methods

This pilot study is the first evaluation of the nICP probe in patients in whom the gold standard comparator of invasive ICP was available. nICP monitoring was performed for up to 48 hours in each of the 40 patients undergoing invasive ICP monitoring as part of their prescribed medical treatment. The quality of the recorded PPG signals was analysed, and time-based features were extracted off-line. Data from all ICP levels were randomly allocated into two groups to train (80%) and test (20%) a machine learning algorithm. A Bland Altman analysis and ROC curve were calculated to evaluate the accuracy of the estimated nICP value compared to the gold standard of synchronously acquired invasive ICP data.

Results

The successful acquisition of cerebral PPG signals from TBI patients for the subsequent extraction of morphological features allowed the generation of a bagging tree model to estimate ICP non-invasively. The non-invasive estimation of ICP was achieved with 95% limits of agreement of 3.8 mmHg and a negligible bias. Furthermore, the model achieved a good correlation coefficient of 82.54% compared to standard clinical invasive ICP monitoring. Finally, the ROC curve analysis showed good diagnostic capability with a sensitivity of 80% and specificity of 89%.

Conclusion

Clinical evaluation of this novel optical nICP sensor demonstrated for the first time that it could estimate ICP non-invasively to an acceptable and clinically useful accuracy and paves the way for further technology optimisation and larger clinical studies.
Interhelical E@g-N@aInteractions Modulate Coiled Coil Stability within aDe NovoSet of Orthogonal Peptide Heterodimers
Authors: Perez Anthony R. , Lee Yumie , Colvin Michael E. , Merg Andrea D.
Published: May 2023

The designability of orthogonal coiled coil (CC) dimers, which draw on well-established design rules, plays a pivotal role in fueling the development of CCs as synthetically versatile assembly-directing motifs for the fabrication of bionanomaterials. Here, we aim to expand the synthetic CC toolkit through establishing a “minimalistic” set of orthogonal,de novoCC peptides that comprise 3.5 heptads in length and a single buried Asn to prescribe dimer formation. The designed sequences display excellent partner fidelity, confirmed via circular dichroism (CD) spectroscopy, and are corroboratedin silicousing molecular dynamics (MD) simulation. Detailed analysis of the MD conformational data highlights the importance of interhelical E@g-N@ainteractions in coordinating an extensive 6-residue hydrogen bonding network that “locks” the interchain Asn-Asn’ contact in place. The enhanced stability imparted to the Asn-Asn’ bond elicits an increase in thermal stability of CCs up to ∼15°C and accounts for significant differences in stability within the collection of similarly designed orthogonal CC pairs. The presented work underlines the utility of MD simulation as a tool for constructingde novo, orthogonal CCs, and presents an alternative handle for modulating the stability of orthogonal CCs via tuning the number of interhelical E@g-N@acontacts. Expansion of CC design rules is a key ingredient for guiding the design and assembly of more complex, intricate CC-based architectures for tackling a variety of challenges within the fields of nanomedicine and bionanotechnology.
Functional and metagenomic level diversities of human gut symbiont-derived glycolipids
Authors: Yoo Ji-Sun , Goh Byoungsook , Heo Kyoo , Jung Da-Jung , Zheng Wen , Lee ChangWon C. , Geva-Zatorsky Naama , Wu Meng , Park Seung Bum , Kasper Dennis L. , Oh Sungwhan F.
Published: May 2023

Bioactive metabolites produced by symbiotic microbiota causally impact host health and disease, nonetheless, incomplete functional annotation of genes as well as complexities and dynamic nature of microbiota make understanding species-level contribution in production and actions difficult. Alpha-galactosylceramides produced byBacteroides fragilis(BfaGC) are one of the first modulators of colonic immune development, but biosynthetic pathways and the significance of the single species in the symbiont community still remained elusive.

To address these questions at the microbiota level, we have investigated the lipidomic profiles of prominent gut symbionts and the metagenome-level landscape of responsible gene signatures in the human gut. We first elucidated the chemical diversity of sphingolipid biosynthesis pathways of major bacterial species. In addition to commonly shared ceramide backbone synthases showing two distinct intermediates, alpha-galactosyltransferase (agcT), the necessary and sufficient component for BfaGC production and host colonic type I natural killer T (NKT) cell regulation byB. fragilis,was characterized by forward-genetics based targeted metabolomic screenings. Phylogenetic analysis of agcT in human gut symbionts revealed that only a few ceramide producers have agcT and hence can produce aGCs, on the other hand, structurally conserved homologues of agcT are widely distributed among species lacking ceramides. Among them, alpha-glucosyl-diacylglycerol(aGlcDAG)-producing glycosyltransferases with conserved GT4-GT1 domains are one of the most prominent homologs in gut microbiota, represented byEnterococcus bgsB. Of interest, aGlcDAGs produced by bgsB can antagonize BfaGC-mediated activation of NKT cells, showing the opposite, lipid structure-specific actions to regulate host immune responses. Further metagenomic analysis of multiple human cohorts uncovered that theagcTgene signature is almost exclusively contributed byB. fragilis, regardless of age, geographical and health status, where thebgsBsignature is contributed by >100 species, of which abundance of individual microbes is highly variable. Our results collectively showcase the diversities of gut microbiota producing biologically relevant metabolites in multiple layers-biosynthetic pathways, host immunomodulatory functions and microbiome-level landscapes in the host.
Ferroptosis induced by phenolic compound-iron complex
Authors: Sui Xinyue , Wang Jichao , Zhao Zhiqiang , Liu Bin , Liu Miaomiao , Liu Min , Shi Cong , Feng Xinjun , Fu Yingxin , Shi Dayong , Li Shengying , Qi Qingsheng , Xian Mo , Zhao Guang
Published: May 2023

Phenolic compounds are the most ubiquitously distributed pollutants, and are highly toxic to living organisms, however the detailed mechanism how phenols exert toxic effects remains elusive. Here,Escherichia coliand phloroglucinol are adapted as proxy to elucidate the molecular mechanism of phenols’ toxicity. We demonstrated that phloroglucinol complexed with iron and promoted the generation of hydroxyl radicals in Fenton reaction, leading to reducing power depletion and lipid peroxidation, and further leading to ferroptosis-like cell death ofE. coli. This ferroptotic death can be triggered by various phenols in diverse organisms, from bacteria to mammalian cells. Furthermore, we demonstrated that phloroglucinol-induced ferroptosis suppressed tumor growth in mice effectively, indicating phloroglucinol as promising drug for therapy-resistant cancers. It’s also discovered that repression of this ferroptosis-like cell death benefited microbial degradation or production of desired phenolic compounds, showing great application potential in biotechnology field.
Cardiomyocyte-restricted expression of IL11 causes cardiac fibrosis, inflammation, and dysfunction
Authors: Sweeney Mark , O’Fee Katie , Villanueva-Hayes Chelsie , Rahman Ekhlas , Lee Michael , Vanezis Konstantinos , Andrew Ivan , Lim Wei-Wen , Widjaja Anissa , Barton Paul JR , Cook Stuart A
Published: May 2023

Abstract

Background: Cardiac fibrosis is a common pathological process in heart disease and represents a therapeutic target. TGFβ is the canonical driver of cardiac fibrosis and was recently shown to be dependent on IL11 for its profibrotic effects in fibroblasts. In the opposite direction, recombinant human IL11 has been reported as anti-fibrotic and also anti- inflammatory in the mouse heart. Objectives: In this study, we determined the effects of IL11 expression in cardiomyocytes on cardiac pathobiology and function. Methods: We used the Cre-loxP system to generate a tamoxifen-inducible mouse with cardiomyocyte-restricted murineIl11expression. Using protein assays, bulk RNA-sequencing, andin vivoimaging we analysed the effects of IL11 on myocardial fibrosis, inflammation and cardiac function and challenge previous reports suggesting cardioprotective potential of IL11. Results: TGFβ stimulation of cardiomyocytes causedIl11upregulation. As compared to wild-type controls,Il11expressing hearts demonstrated severe cardiac fibrosis and inflammation that was associated with the upregulation of cytokines, chemokines, complement factors and increased inflammatory cells. IL11 expression also activated a programme of endothelial-to- mesenchymal transition and resulted in left ventricular dysfunction. Conclusion: Our data define species matched IL11 as strongly profibrotic and proinflammatory when secreted from cardiomyocytes and further establish IL11 as a disease factor.
Exploring the Chain Release Mechanism from an Atypical Apicomplexan Polyketide Synthase
Authors: Keeler Aaron M. , Petruzziello Porter E. , Boger Elizabeth G. , D’Ambrosio Hannah K. , Derbyshire Emily R.
Published: May 2023

Polyketide synthases (PKSs) are megaenzymes that form chemically diverse polyketides and are found within the genomes of nearly all classes of life. We recently discovered the type I PKS from the apicomplexan parasiteToxoplasma gondii, TgPKS2, which contains a unique putative chain release mechanism that includes ketosynthase (KS) and thioester reductase (TR) domains. Our bioinformatic analysis of the thioester reductase ofTgPKS2,TgTR, suggests differences in putative apicomplexan reductase domains compared to other systems and hints at a possibly conserved release mechanism within the apicomplexan subclass Coccidia. To evaluate this release module, we first isolatedTgTR and observed that it is capable of 4 electron (4e-) reduction of octanoyl-CoA to the primary alcohol, octanol, utilizing NADH as a cofactor.TgTR was also capable of generating octanol in the presence of octanal and NADH, but no reactions were observed when NADPH was supplied as a cofactor. To biochemically characterize the protein, we measured the catalytic efficiency ofTgTR using a fluorescence assay and determined theTgTR binding affinity for cofactor and substrates using isothermal titration calorimetry (ITC). We additionally show thatTgTR is capable of reducing an acyl carrier protein (ACP)-tethered substrate by liquid chromatography mass spectrometry and determine thatTgTR binds to holo-TgACP4, its predicted cognate ACP, with aKDof 5.75 ± 0.77 µM. Finally, our transcriptional analysis shows thatTgPKS2 is upregulated ∼4-fold in the parasite’s cyst-forming bradyzoite stage compared to tachyzoites. Our study identifies features that distinguishTgPKS2 from well-characterized systems in bacteria and fungi, and suggests it aids theT. gondiicyst stage. Together, this work increases our knowledge of PKS thioester reductase domains and advances our understanding of unconventional polyketide chain termination mechanisms.
Mapping Niche-specific Two-Component System Requirements in UropathogenicEscherichia coli
Authors: Brannon John R. , Reasoner Seth A. , Bermudez Tomas A. , Dunigan Taryn L. , Wiebe Michelle A. , Beebout Connor J. , Ross Tamia , Bamidele Adebisi , Hadjifrangiskou Maria
Published: May 2023

Sensory systems allow pathogens to differentiate between different niches and respond to stimuli within them. A major mechanism through which bacteria sense and respond to stimuli in their surroundings is two-component systems (TCSs). TCSs allow for the detection of multiple stimuli to lead to a highly controlled and rapid change in gene expression. Here, we provide a comprehensive list of TCSs important for the pathogenesis of uropathogenicEscherichia coli(UPEC). UPEC accounts for >75% of urinary tract infections (UTIs) worldwide. UTIs are most prevalent among people assigned female at birth, with the vagina becoming colonized by UPEC in addition to the gut and the bladder. In the bladder, adherence to the urothelium triggersE. coliinvasion of bladder cells and an intracellular pathogenic cascade. IntracellularE. coliare safely hidden from host neutrophils, competition from the microbiota, and antibiotics that kill extracellularE. coli.To survive in these intimately connected, yet physiologically diverse nichesE. colimust rapidly coordinate metabolic and virulence systems in response to the distinct stimuli encountered in each environment. We hypothesized that specific TCSs allow UPEC to sense these diverse environments encountered during infection with built-in redundant safeguards. Here, we created a library of isogenic TCS deletion mutants that we leveraged to map distinct TCS contributions to infection. We identify – for the first time – a comprehensive panel of UPEC TCSs that are critical for infection of the genitourinary tract and report that the TCSs mediating colonization of the bladder, kidneys, or vagina are distinct.

IMPORTANCE

While two-component system (TCS) signaling has been investigated at depth in model strains ofE. coli, there have been no studies to elucidate – at a systems level – which TCSs are important during infection by pathogenicEscherichia coli. Here, we report the generation of a markerless TCS deletion library in a uropathogenicE. coli(UPEC) isolate that can be leveraged for dissecting the role of TCS signaling in different aspects of pathogenesis. We use this library to demonstrate, for the first time in UPEC, that niche-specific colonization is guided by distinct TCS groups.
Long-range repression by ecdysone receptor on complex enhancers of the insulin receptor gene
Authors: Thompson Katie , Suber Will , Nicholas Rachel , Arnosti David N.
Published: May 2023

The insulin signaling pathway is evolutionarily conserved throughout metazoans, playing key roles in development, growth, and metabolism. Misregulation of this pathway is associated with a multitude of disease states including diabetes, cancer, and neurodegeneration. Genome-wide association studies indicate that natural variants in putative intronic regulatory elements of the human insulin receptor gene (INSR)are associated with metabolic conditions, however, this gene’s transcriptional regulation remains incompletely studied.INSRis widely expressed throughout development and was previously described as a ‘housekeeping’ gene. Yet, there is abundant evidence that this gene is expressed in a cell-type specific manner, with dynamic regulation in response to environmental signals. The Drosophila insulin-like receptor gene (InR) is homologous to the humanINSRgene and was previously shown to be regulated by multiple transcriptional elements located primarily within the introns of the gene. These elements were roughly defined in ∼1.5 kbp segments, but we lack an understanding of the potential detailed mechanisms of their regulation, as well as the integrative output of the battery of enhancers in the entire locus. Using luciferase assays, we characterized the substructure of these cis-regulatory elements in Drosophila S2 cells, focusing on regulation through the ecdysone receptor (EcR) and the dFOXO transcription factor. The direct action of EcR on Enhancer 2 reveals a bimodal form of regulation, with active repression in the absence of the ligand, and positive activation in the presence of 20E. By identifying the location of activators of this enhancer, we characterized a long-range of repression acting over at least 475 bp, similar to the action of long-range repressors found in the embryo. dFOXO and 20E have contrasting effects on some of the individual regulatory elements, and for the adjacent enhancers 2 and 3, their influence was/was not found to be additive, indicating that enhancer action on this locus can/cannot be characterized in part by additive models. Other characterized enhancers from within this locus exhibited “distributed” or “localized” modes of action, suggesting that predicting the joint functional output of multiple regulatory regions will require a deeper experimental characterization. The noncoding intronic regions ofInRhave demonstrated dynamic regulation of expression and cell type specificity. This complex transcriptional circuitry goes beyond the simple conception of a ‘housekeeping’ gene. Further studies are aimed at identifying how these elements work together in vivo to generate finely tuned expression in tissue- and temporal-specific manners, to provide a guide to understanding the impact of natural variation in this gene’s regulation, applicable to human genetic studies.
S1basic leucine zipper transcription factors shape plant architecture by controlling C/N partitioning to apical and lateral organs
Authors: Kreisz Philipp , Hellens Alicia M. , Fröschel Christian , Krischke Markus , Maag Daniel , Feil Regina , Wildenhain Theresa , Draken Jan , Braune Gabriel , Erdelitsch Leon , Cecchino Laura , Wagner Tobias C. , Mueller Martin J. , Becker Dirk , Lunn John E. , Hanson Johannes , Beveridge Christine A. , Fichtner Franziska , Barbier Francois F. , Weiste Christoph
Published: May 2023

Plants exhibit an immense plasticity in their architecture. While the impact of hormonal regulation is well-characterised, the importance of sugar-signalling has just recently emerged. Here, we addressed which sugar-signalling components mediate the trade-off between growth of apical versus lateral meristems and how they control organ sink-strength. Thereby, we unravelled a novel developmental function of the sugar-controlled S1basic-leucine-zipper (S1-bZIP) transcription factors in establishing global source-sink interactions. Applying comprehensive molecular, analytical, and genetic approaches, we demonstrate that S1-bZIPs operate in a redundant manner to control tissue-specific expression of definedSWEETsugar-transporters and theGAT1_2.1glutaminase. By these means, S1-bZIPs control carbohydrate (C)-channelling from source leaves to apical shoot and root organs and tune systemic organic nitrogen (N)-supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.
Genomic potential and evolution of Dissimilatory Nitrate Reduction to Ammonium in Cyanobacteria
Authors: Ray Manisha , Manu Shivakumara , Rastogi Gurdeep , Umapathy Govindhaswamy
Published: May 2023

Cyanobacteria play an important role in primary production and nitrogen fixation. Although Cyanobacteria are well-known diazotrophic organisms, their role in other steps Nitrogen Cycle is obscure. Screening of Cyanobacterial genomes from cultured and unculturable species can help identify potentially novel functions. In this study, we assembled Cyanobacterial genomes from metagenomic data generated from environmental DNA isolated from a brackish water lagoon (Chilika, India). We annotated these Cyanobacterial metagenome-assembled genomes (MAG) for all the encoded functions using KEGG Orthology. We found two high-quality Cyanobacterial MAGs containing thenirBDgene andnifHandnifDgenes involved in the nitrogen cycle.nirBDencodes for the Dissimilatory Nitrate Reduction to Ammonium (DNRA) activity, a function previously not ascribed to Cyanobacteria. We validated the presence of NirBD in publicly available isolate genomes of Cyanobacteria and examined its evolution in the phylum by phylogenetic reconciliation of species and gene trees. Our analysis revealed that both horizontal gene transfers and speciation events contributed to the dispersal of thenirBDgene in Cyanobacteria. We observed that mostly filamentous Cyanobacteria served as ancestral donors in horizontal gene transfer events. Further, we found that thenirBDgene is under a purifying selection pressure in Cyanobacteria. This study demonstrates the genomic potential and evolution of DNRA activity in Cyanobacteria for the utilisation of nitrate in the ecosystem which can help these organisms to cope with extreme environmental conditions. It expands our overall comprehension of the contribution of Cyanobacteria in the biogeochemical cycling in aquatic ecosystems.
Organismal landscape of clock cells and circadian gene expression inDrosophila
Authors: Patop Ines L. , Anduaga Ane Martin , Bussi Ivana L. , Ceriani M. Fernanda , Kadener Sebastian
Published: May 2023

Background

Circadian rhythms time physiological and behavioral processes to 24-hour cycles. It is generally assumed that most cells contain self-sustained circadian clocks that drive circadian rhythms in gene expression that ultimately generating circadian rhythms in physiology. While those clocks supposedly act cell autonomously, current work suggests that inDrosophilasome of them can be adjusted by the brain circadian pacemaker through neuropeptides, like the Pigment Dispersing Factor (PDF). Despite these findings and the ample knowledge of the molecular clockwork, it is still unknown how circadian gene expression inDrosophilais achieved across the body.

Results

Here, we used single-cell and bulk RNAseq data to identify cells within the fly that express core-clock components. Surprisingly, we found that less than a third of the cell types in the fly express core-clock genes. Moreover, we identified Lamina wild field (Lawf) and Ponx-neuro positive (Poxn) neurons as putative new circadian neurons. In addition, we found several cell types that do not express core clock components but are highly enriched for cyclically expressed mRNAs. Strikingly, these cell types express the PDF receptor (Pdfr), suggesting that PDF drives rhythmic gene expression in many cell types in flies. Other cell types express both core circadian clock components andPdfr, suggesting that in these cells, PDF regulates the phase of rhythmic gene expression.

Conclusions

Together, our data suggest three different mechanisms generate cyclic daily gene expression in cells and tissues: canonical endogenous canonical molecular clock, PDF signaling-driven expression, or a combination of both.
Bias in the arrival of variation can dominate over natural selection in Richard Dawkins’ biomorphs
Authors: Martin Nora S. , Camargo Chico Q. , Louis Ard A.
Published: May 2023

Biomorphs, Richard Dawkins’ iconic model of morphological evolution, are traditionally used to demonstrate the power of natural selection to generate biological order from random mutations. Here we show that biomorphs can also be used to illustrate how developmental bias shapes adaptive evolutionary outcomes. In particular, we find that biomorphs exhibit phenotype bias, a type of developmental bias where certain phenotypes can be many orders of magnitude more likely than others to appear through random mutations. Moreover, this bias exhibits a strong Occam’s-razor-like preference for simpler phenotypes with low descriptional complexity. Such bias towards simplicity is formalised by an information-theoretic principle that can be intuitively understood from a picture of evolution randomly searching in the space of algorithms. By using population genetics simulations, we demonstrate how moderately adaptive phenotypic variation that appears more frequently upon random mutations will fix at the expense of more highly adaptive biomorph phenotypes that are less frequent. This result, as well as many other patterns found in the structure of variation for the biomorphs, such as high mutational robustness and a positive correlation between phenotype evolvability and robustness, closely resemble findings in molecular genotype-phenotype maps. Many of these patterns can be explained with an analytic model based on constrained and unconstrained sections of the genome. We postulate that the phenotype bias towards simplicity and other patterns biomorphs share with molecular genotype-phenotype maps may hold more widely for developmental systems, which would have implications for longstanding debates about internal versus external causes in evolution.
Gene Expression Profiling and Physiological Adaptations of Pearl Spot (Etroplus suratensis) under Varying Salinity Conditions
Authors: Marbade Pranali Prabhakar , Shanmugam S. A. , Suresh E. , Rathipriya A. , Agarwal Deepak
Published: May 2023

Eutroplus suratensis(Pearl spot) is naturally found in estuarine environments and has been noted to have a high salinity tolerance, with the ability to thrive in freshwater as well as seawater. By examining the impact of various salinity levels on the growth and survival of Pearl spot, the present study aims to enhance aquaculture profitability by assessing their adaptability and physiological adjustments to changes in salinity, as well as determining their potential to acclimate to a broad range of salinity regimes. Pearl spot fingerlings were placed in tanks with varying salinities (15, 25, 35, 45, 60, and 75ppt) and monitored for mortality at 24-hour intervals up to 120 hours. Results revealed no mortality in the control group (0ppt), as well as in the 15, 25, and 35ppt treatment groups. However, the remaining groups (45, 60, and 75ppt) showed differing levels of mortality, with 44% mortality observed in the 45ppt group and 100% mortality in both the 60 and 75ppt groups. The impact of different salinity levels on the expression of pearl spot genes such as IGF-1, SOD, CAT, NaKATPase, OSTF-1, and HSP70 was investigated, along with a histological examination of the gills. The results showed significant physiological and cellular damage caused by the salinity levels. The expression analysis showed that liver IGF-1 mRNA expression increased by 2.6-fold at 15ppt, and HSP70 mRNA expression in the liver also showed a significant increase with rising salinity levels. In addition, OSTF1 expression exhibited an increase at 15ppt, whereas SOD and CAT expression reached their highest levels at 25ppt. At 15ppt, the expression of NKA mRNA increased significantly by 2.8-fold. The study’s overall findings suggested that the fish demonstrated strong molecular-level performance between 15 to 25ppt salinity levels, with the best results observed at 15ppt. These findings suggest that utilizing a salinity level of 15ppt for Pearl spot production could be viable for profitable aquaculture.
Structural principles of peptide-centric Chimeric Antigen Receptor recognition guide therapeutic expansion
Authors: Sun Yi , Florio Tyler J. , Gupta Sagar , Young Michael C. , Marshall Quinlen F. , Garfinkle Samuel E. , Papadaki Georgia F. , Truong Hau V. , Mycek Emily , Li Peiyao , Farrel Alvin , Church Nicole L. , Jabar Shereen , Beasley Matthew D. , Kiefel Ben R. , Yarmarkovich Mark , Mallik Leena , Maris John M. , Sgourakis Nikolaos G.
Published: May 2023

Peptide-Centric Chimeric Antigen Receptors (PC-CARs), which recognize oncoprotein epitopes displayed by human leukocyte antigens (HLAs) on the cell surface, offer a promising strategy for targeted cancer therapy1. We have previously developed a PC-CAR targeting a neuroblastoma- associated PHOX2B peptide, leading to robust tumor cell lysis restricted by two common HLA allotypes2. Here, we determine the 2.1 Å structure of the PC-CAR:PHOX2B/HLA-A*24:02/β2m complex, which reveals the basis for antigen-specific recognition through interactions with CAR complementarity-determining regions (CDRs). The PC-CAR adopts a diagonal docking mode, where interactions with both conserved and polymorphic HLA framework residues permit recognition of multiple HLA allotypes from the A9 serological cross-reactivity group, covering a combined American population frequency of up to 25.2%. Comprehensive characterization using biochemical binding assays, molecular dynamics simulations, and structural and functional analyses demonstrate that high-affinity PC-CAR recognition of cross-reactive pHLAs necessitates the presentation of a specific peptide backbone, where subtle structural adaptations of the peptide are critical for high-affinity complex formation and CAR-T cell killing. Our results provide a molecular blueprint for engineering CARs with optimal recognition of tumor-associated antigens in the context of different HLAs, while minimizing cross-reactivity with self-epitopes.
The genome ofSalmacisia buchloëana, the parasitic puppetmaster pulling strings of sexual phenotypic monstrosities in buffalograss
Authors: Benson Christopher W. , Sheltra Matthew R. , Huff David R.
Published: May 2023

To complete its parasitic lifecycle,Salmacisia buchloëana, a biotrophic fungus, manipulates reproductive organ development, meristem determinacy, and resource allocation in its dioecious plant host, buffalograss (Bouteloua dactyloides;Poaceae). To gain insight intoS. buchloëana’sability to manipulate its host, we sequenced and assembled the 20.1 Mb genome ofS. buchloëanainto 22 chromosome-level pseudomolecules. Phylogenetic analysis suggests thatS. buchloëanais nested within the genusTilletiaand diverged fromT. cariesandT. walkeri ∼40 million years ago. We find thatS. buchloëanahas a novel chromosome arm with no syntenic relationship to other publicly availableTilletiagenomes and that genes on the novel arm are upregulated upon infection, suggesting that this unique chromosomal segment may have played a critical role inS. buchloëana’sevolution and host specificity.Salmacisia buchloëanahas one of the largest fractions of serine peptidases (1.53% of the proteome) and one of the highest GC contents (62.3%) in all classified fungi. Analysis of codon base composition indicated that GC content is controlled more by selective constraints than directional mutation and thatS. buchloëanahas a unique bias for the serine codon UCG. Finally, we identify three inteins within theS. buchloëanagenome, two of which are located in a gene often used in fungal taxonomy. The genomic and transcriptomic resources generated here will aid plant pathologists and breeders by providing insight into the extracellular components contributing to sex determination in dioecious grasses.
Wage dispersion and sports performance: does gender matter?
Authors: Arutiunova Margarita , Gasparetto Thadeu
Published: May 2023

Purpose

Previous studies focused predominantly on wage dispersion within men’ sports teams. This study aims to reveal how the relationship between wage dispersion and team performance applies for women’s sport.

Design/methodology/approach

The sample comprises 168 observations of four consecutive National Basketball Association (NBA) and Women’s National Basketball Association (WNBA) regular seasons (2018–2021). Eight econometric models are performed for comparing the leagues.

Findings

The findings indicate that the wage dispersion within the squads affects the women’s and men’s basketball teams differently. Cohesiveness theory is applicable for WNBA teams, while NBA teams follow the tournament theory.

Originality/value

To the best of the authors’ knowledge, this is the first paper which inspects the relationship between wage dispersion and team performance using data from women’s sports. Further research may examine whether the differences found in sports also apply in different labor markets.