bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hippocampal-prefrontal theta coupling develops as mice become proficient in associative odorant discrimination learning
Authors: Ramirez-Gordillo Daniel , Parra Andrew A. , Bayer K. Ulrich , Restrepo Diego 
Published: September 2021

AbstractLearning and memory requires coordinated activity between different regions of the brain. Here we studied the interaction between infralimbic medial prefrontal cortex (mPFC) and hippocampal dorsal CA1 during associative odorant discrimination learning in the male mouse. We found that as the animal learns to discriminate odorants in a go- no go task the coupling of high frequency neural oscillations to the phase of theta oscillations (theta-referenced phase-amplitude coupling or tPAC) changes in a manner that results in divergence between rewarded and unrewarded odorant-elicited changes in the theta-phase referenced power (tPRP) for beta and gamma oscillations. In addition, in the proficient animal there was a decrease in the coordinated oscillatory activity between CA1 and mPFC in the presence of the unrewarded odorant. Furthermore, the changes in tPAC resulted in a marked increase in the accuracy for decoding contextual odorant identity from tPRP when the animal became proficient. Finally, we studied the role of Ca2+/calmodulin-dependent protein kinase II α (CaMKIIα), a protein involved in learning and memory, in oscillatory neural processing in this task. We find that the accuracy for decoding the contextual odorant identity from tPRP decreases in CaMKIIα knockout mice and that this accuracy correlates with behavioral performance. These results implicate a role for tPAC and CaMKIIα genotype in olfactory go-no go associative learning in the hippocampal-prefrontal circuit.Significance statementCoupling of neural oscillations between hippocampal CA1 and medial prefrontal cortex (mPFC) is involved in spatial learning and memory, but the role of oscillation coupling for other learning tasks is not well understood. Here we performed local field potential recording in CA1 and mPFC in mice learning to differentiate rewarded from unrewarded odorants in an associative learning task. We find that odorant-elicited changes in the power of bursts of gamma oscillations at distinct phases of theta oscillations become divergent as the animal becomes proficient allowing decoding of contextual odorant identity. Finally, we find that the accuracy to decode contextual odorant identity decreases in mice deficient for the expression of Ca2+/calmodulin-dependent protein kinase II α, a protein involved in synaptic plasticity.
Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing analysis
Authors: Hong Uyen Vu Thuy , Tamiru-Oli Muluneh , Hurgobin Bhavna , Okey Christopher R. , Abreu Artur R. , Lewsey Mathew G. 
Published: September 2021

AbstractOpium poppy (Papaver somniferum) is one of the world’s oldest medicinal plants and a versatile model system to study secondary metabolism. However, our knowledge of its genetic diversity is limited, restricting utilization of the available germplasm for research and crop improvement. We used genotyping-by-sequencing to investigate the extent of genetic diversity and population structure in a collection of poppy germplasm consisting of 91 accessions originating in 30 countries of Europe, North Africa, America, and Asia. We identified five genetically distinct subpopulations using discriminate analysis of principal components and STRUCTURE analysis. Most accessions obtained from the same country were grouped together within subpopulations, likely a consequence of the restriction on movement of poppy germplasm. Alkaloid profiles of accessions were highly diverse, with morphine being dominant. Phylogenetic analysis identified genetic groups that were largely consistent with the subpopulations detected and that could be differentiated broadly based on traits such as number of branches and seed weight. These accessions and the associated genotypic data are valuable resources for further genetic diversity analysis, which could include definition of poppy core sets to facilitate genebank management and use of the diversity for genetic improvement of this valuable crop.
Synthesis of 4-methylvaleric acid, a precursor of pogostone, involves a 2-isobutylmalate synthase related to 2-isopropylmalate synthase of leucine biosynthesis
Authors: Wang Chu , Wang Ying , Chen Jing , Liu Lang , Li Zhengguo , Pichersky Eran , Xu Haiyang 
Published: September 2021

SUMMARYWe show here that the side chain of pogostone, one of the major components of patchouli oil obtained fromPogostemon cablinand possessing a variety of pharmacological activities, is derived from 4-methylvaleric acid.We also show that 4-methylvaleric acid is produced through the one-carbon α- ketoacid elongation pathway with the involvement of the key enzyme 2- isobutylmalate synthase (IBMS), a newly identified enzyme related to isopropylmalate synthase (IPMS) of Leu biosynthesis.Site-directed mutagenesis identified Met132in the N-terminal catalytic region as affecting the substrate specificity of PcIBMS1. And even though PcIBMS1 possesses the C-terminal domain that in IPMS serves to mediate Leu inhibition, it is insensitive to Leu.The observation of the evolution of IBMS from IPMS, as well as previously reported examples of IPMS-related genes involved in making glucosinolates in Brassicaceae, acylsugars in Solanaceae, and flavor compounds in apple, indicate that IPMS genes represent an important pool for the independent evolution of genes for specialized metabolism.One Sentence SummaryWe describe a novel enzyme, 2-isobutylmalate synthase, that is related to 2-isopropylmalate synthase and is able to efficiently convert 4-methyl-2- oxovalerate to 2-isobutylmalate, a key intermediate in the synthesis of the pogostone precursor 4-methylvaleric acid.
Improving older adults’ vaccination uptake: are existing measures of vaccine hesitancy valid and reliable for older people?
Authors: Cogan Nicola , Gallant Allyson J. , Nicholls Louise A. Brown , Rasmussen Susan , Young David , Williams Lynn 
Published: September 2021

ABSTRACTOlder adults are particularly vulnerable to vaccine-preventable diseases (VDU), due to decreased immunity and increased comorbidity. Vaccination can support healthy ageing and help reduce morbidity, mortality, and loss of quality of life associated with VPDs. Despite the availability of effective vaccines, many countries, including the UK, fail to reach recommended coverage levels. Psychosocial factors are recognised as providing important insights into the determinants of vaccination uptake. Little research has sought to establish psychometrically sound scales of vaccine attitudes with older adults. In the present study, a total of 372 UK-based participants (65-92 years, M = 70.5 yrs, SD = 4.6) completed a cross-sectional, online survey measuring health and socio-demographic characteristics in relation to vaccination uptake for influenza, pneumococcal and shingles. Two recently developed vaccination attitude scales, the 5C scale and the Vaccination Attitudes Examination (VAX) scale, were also administered to test their reliability and validity for use with an older adult population. Additional scales used to examine convergent and discriminant validity, the Beliefs about Medicines Questionnaire, the Perceived Sensitivity to Medicines Scale, the Medical Mistrust Index, the Perceived Stress Scale, and the Interpersonal Support Evaluation List, were included. The factor structure of the 5C and VAX scales was confirmed. Both scales showed good internal reliability, convergent, discriminant and concurrent validity, supporting their use with older adult populations. The 5C and VAX scales were found to be reliable and valid psychosocial measures of vaccine hesitancy and acceptance within a UK-based, older adult population. Future research could use these scales to evaluate the impact of psychological antecedents of vaccine uptake, and how concerns about vaccination may be understood and addressed among older adults.Ethics approval & informed consentEthical approval (34/26/11/2019/Staff Williams) was granted by the School of Psychological Sciences and Health Ethics Committee, University of Strathclyde. (SEC19/20: Williams, Nicholls, Rasmussen, Young & Gallant). Approved on 8th January 2020.
Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study
Authors: Popp Bernt , Ekici Arif B. , Knaup Karl X. , Schneider Karen , Uebe Steffen , Park Jonghun , Bafna Vineet , Meiselbach Heike , Eckardt Kai-Uwe , Schiffer Mario , Reis André , Kraus Cornelia , Wiesener Michael 
Published: September 2021

ABSTRACTExome sequencing (ES) studies in chronic kidney disease (CKD) cohorts could identify pathogenic variants in ∼10% of patients. This implies underdiagnosis of hereditary CKD. Tubulointerstitial kidney diseases, showing no typical clinical/histologic finding but tubulointerstitial fibrosis, are particularly difficult to diagnose.We used a custom designed targeted panel (29 genes) and MUC1-SNaPshot to sequence 271 DNA samples, selected by clinical criteria from 5,217 individuals in the German Chronic Kidney Disease (GCKD) cohort.We identified 33 pathogenic small variants. Of these 27 (81.8%) were in COL4-genes, the largest group being 15 COL4A5-variants with nine unrelated individuals carrying c.1871G>A, p.(Gly624Asp). We found three cysteine variants in UMOD, a novel missense, and a novel splice variant in HNF1B and the homoplastic MTTF variant m.616T>C. Copy-number analysis identified a heterozygous COL4A5-deletion, and a HNF1B-duplication/-deletion, respectively. Overall, pathogenic variants were present in 12.5% (34/271) and variants of unknown significance in 9.6% (26/271) of selected individuals. Bioinformatic predictions paired with gold standard diagnostics for MUC1 (SNaPshot) could not identify the typical cytosine duplication (“c.428dupC”) in any individual, implying that ADTKD-MUC1 is rare.Our study shows that >10% of individuals with certain clinical features carry disease variants in genes associated with tubulointerstitial kidney diseases. COL4-genes constitute the largest fraction, implying they are overlooked using clinical Alport-syndrome criteria. We also identified variants easily missed by some ES pipelines. Finally, our results indicate that the filtering criteria applied enrich for an underlying genetic disorder.SIGNIFICANCE STATEMENTCKD affects >10% of the global population and recent studies imply that a considerable portion can be attributed to monogenic diseases, which are likely underappreciated in the clinical routine. Tubulointerstitial kidney diseases are a particularly difficult group of hereditary kidney diseases to diagnose both clinically and genetically. To investigate the prevalence of these disorders in a large CKD cohort we established a set of clinical criteria and designed a custom panel sequencing pipeline. Based on the diagnostic yield of 12.5%, we recommend an algorithm to clinically select and genetically evaluate patients with increased risk for a hereditary tubulointerstitial kidney disease.
Flagellum and toxin phase variation impacts intestinal colonization and disease development in a mouse model of Clostridioides difficile infection
Authors: Trzilova Dominika , Warren Mercedes A. H. , Gadda Nicole C. , Williams Caitlin L. , Tamayo Rita 
Published: September 2021

AbstractClostridioides difficile is a major nosocomial pathogen that can cause severe, toxin-mediated diarrhea and pseudomembranous colitis. Recent work has shown that C. difficile exhibits heterogeneity in swimming motility and toxin production in vitro through phase variation by site-specific DNA recombination. The recombinase RecV reversibly inverts the flagellar switch sequence upstream of the flgB operon, leading to the ON/OFF expression of flagellum and toxin genes. How this phenomenon impacts C. difficile virulence in vivo remains unknown. We identified mutations in the right inverted repeat that reduced or prevented flagellar switch inversion by RecV. We introduced these mutations into C. difficile R20291 to create strains with the flagellar switch “locked” in either the ON or OFF orientation. These mutants exhibited a loss of flagellum and toxin phase variation during growth in vitro, yielding precisely modified mutants suitable for assessing virulence in vivo. In a hamster model of acute C. difficile infection, the phase-locked ON mutant caused greater toxin accumulation than the phase locked OFF mutant but did not differ significantly in the ability to cause acute disease symptoms. In contrast, in a mouse model, preventing flagellum and toxin phase variation affected the ability of C. difficile to colonize the intestinal tract and to elicit weight loss, which is attributable to differences in toxin production during infection. These results show that the ability of C. difficile to phase vary flagella and toxins influences colonization and disease development and suggest that the phenotypic variants generated by flagellar switch inversion have distinct capacities for causing disease.
Two helices control the dynamic crosstalk between the catalytic domains of LRRK2
Authors: Weng Jui-Hung , Aoto Phillip C. , Lorenz Robin , Wu Jian , Schmidt Sven H. , Manschwetus Jascha T. , Kaila-Sharma Pallavi , Mathea Sebastian , Knapp Stefan , Herberg Friedrich W. , Taylor Susan S. 
Published: September 2021

AbstractThe two major molecular switches in biology, kinases and GTPases, are both contained in the Parkinson’s Disease-related Leucine-rich repeat kinase 2 (LRRK2). Using hydrogen-deuterium exchange mass spectrometry (HDX-MS) and Molecular Dynamics (MD) simulations, we generated a comprehensive dynamic allosteric portrait of the C-terminal domains of LRRK2 (LRRK2RCKW). We identified two helices that shield the kinase domain and regulate LRRK2 conformation and function. One docking helix in COR-B (Dk-Helix) tethers the COR-B domain to the αC helix of the kinase domain and faces its Activation Loop, while the C-terminal helix (Ct-Helix) extends from the WD40 domain and interacts with both kinase lobes. The Ct-Helix and the N-terminus of the Dk-Helix create a “cap” that regulates the N-Lobe of the kinase domain. Our analyses reveal allosteric sites for pharmacological intervention and confirm the kinase domain as the central hub for conformational control.
An international report on bacterial communities in esophageal squamous cell carcinoma
Authors: Nomburg Jason , Bullman Susan , Nasrollahzadeh Dariush , Collisson Eric A. , Abedi-Ardekani Behnoush , Akoko Larry O. , Atkins Joshua R. , Buckle Geoffrey C. , Gopal Satish , Hu Nan , Kaimila Bongani , Khoshnia Masoud , Malekzadeh Reza , Menya Diana , Mmbaga Blandina T. , Moody Sarah , Mulima Gift , Mushi Beatrice P. , Mwaiselage Julius , Mwanga Ally , Newton Yulia , Ng Dianna L. , Radenbaugh Amie , Rwakatema Deogratias S. , Selekwa Msiba , Schüz Joachim , Taylor Philip R. , Vaske Charles , Goldstein Alisa , Stratton Michael R. , McCormack Valerie , Brennan Paul , DeCaprio James A. , Meyerson Matthew , Mmbaga Elia J. , Van Loon Katherine 
Published: September 2021

ABSTRACTThe incidence of esophageal squamous cell carcinoma (ESCC) is disproportionately high in the eastern corridor of Africa and parts of Asia. Emerging research has identified a potential association between poor oral health and ESCC. One proposed biological pathway linking poor oral health and ESCC involves the alteration of the microbiome. Thus, we performed an integrated analysis of four independent sequencing efforts of ESCC tumors from patients from high- and low-incidence regions of the world. Using whole genome sequencing (WGS) and RNA sequencing (RNAseq) of ESCC tumors and WGS of synchronous collections of saliva specimens from 61 patients in Tanzania, we identified a community of bacteria, including members of the generaFusobacterium, Selenomonas, Prevotella, Streptococcus, Porphyromonas, Veillonella, andCampylobacter, present at high abundance in ESCC tumors. We then characterized the microbiome of 238 ESCC tumor specimens collected in two additional independent sequencing efforts consisting of patients from other high-ESCC incidence regions (Tanzania, Malawi, Kenya, Iran, China). This analysis revealed a similar tumor enrichment of the ESCC-associated bacterial community in these cancers. Because these genera are traditionally considered members of the oral microbiota, we explored if there is a relationship between the synchronous saliva and tumor microbiomes of ESCC patients in Tanzania. Comparative analyses revealed that paired saliva and tumor microbiomes are significantly similar with a specific enrichment ofFusobacteriumandPrevotellain the tumor microbiome. Together, these data indicate that cancer-associated oral bacteria are associated with ESCC tumors at the time of diagnosis and support a model in which oral bacteria are present in high abundance in both saliva and tumors of ESCC patients. Longitudinal studies of the pre-diagnostic oral microbiome are needed to investigate whether these cross-sectional similarities reflect temporal associations.
Transcriptional interference in toehold switch-based RNA circuits
Authors: Falgenhauer Elisabeth , Mückl Andrea , Schwarz-Schilling Matthaeus , Simmel Friedrich C. 
Published: September 2021

ABSTRACTGene regulation based on regulatory RNA is an important mechanism in cells and is increasingly used for regulatory circuits in synthetic biology. Toehold switches are rationally designed post-transcriptional riboregulators placed in the 5’ untranslated region of mRNA molecules. In the inactive state of a toehold switch, the ribosome-binding site is inaccessible for the ribosome. In the presence of a trigger RNA molecule protein production is turned on. Using antisense RNA against trigger molecules (anti-trigger RNA), gene expression can also be switched off again. We here study the utility and regulatory effect of antisense transcription in this context, which enables a particularly compact circuit design. Our circuits utilize two inducible promoters that separately regulate trigger and anti-trigger transcription, whereas their cognate toehold switch, regulating expression of a reporter protein, is transcribed from a constitutive promoter. We explore various design options for the arrangement of the promoters and demonstrate that the resulting dynamic behavior is strongly influenced by transcriptional interference (TI) effects, leading to more than four-fold differences in expression levels. Our experimental results are consistent with previous findings that enhanced local RNA polymerase concentrations due to active promoters in close proximity lead to an increase in transcriptional activity of the strongest promoter in the circuits. Based on this insight, we selected optimum promoter designs and arrangements for the realization of a genetic circuit comprised of two toehold switches, two triggers and two anti-triggers that function as a post-transcriptional RNA regulatory exclusive OR (XOR) gate.
Monoclonal antibodies targeting surface exposed epitopes of Candida albicans cell wall proteins confer in vivo protection in an infection model
Authors: Palliyil Soumya , Mawer Mark , Alawfi Sami A , Fogg Lily , Tan Tyng H , De Cesare Giuseppe Buda , Walker Louise A , MacCallum Donna M , Porter Andrew J , Munro Carol A 
Published: September 2021

AbstractMAb based immunotherapies targeting systemic and deep-seated fungal infections are still in their early stages of development with currently no licensed antifungal mAbs available for patients at risk. The cell wall glycoproteins of Candida albicans are of particular interest as potential targets for therapeutic antibody generation due to their extracellular location and key involvement in fungal pathogenesis. Here we describe the generation of recombinant human antibodies specifically targeting two key cell wall proteins (CWPs) in C. albicans - Utr2 and Pga31. These antibodies were isolated from a phage display antibody library using peptide antigens representing the surface exposed regions of CWPs expressed at elevated levels during in vivo infection. Reformatted human-mouse chimeric mAbs preferentially recognised C. albicans hyphal forms compared to yeast cells and an increased binding was observed when the cells were grown in the presence of the antifungal agent caspofungin. In J774.1 macrophage interaction assays, mAb pre-treatment resulted in a faster engulfment of C. albicans cells suggesting a role of the CWP antibodies as opsonising agents during phagocyte recruitment. Finally, in a series of clinically predictive, mouse models of systemic candidiasis, our lead mAb achieved an improved survival (83%) and several log reduction of fungal burden in the kidneys, similar to levels achieved for the fungicidal drug caspofungin, and superior to any anti-Candida mAb therapeutic efficacy reported to date.
Versatile and Robust method for Antibody Conjugation to Nanoparticles with High Targeting Efficiency
Authors: Van Zundert Indra , Bravo Maria , Deschaume Olivier , Cybulski Pierre , Bartic Carmen , Hofkens Johan , Uji-i Hiroshi , Fortuni Beatrice , Rocha Susana 
Published: September 2021

AbstractThe application of antibodies in nanomedicine is now standard practice in research since it represents an innovative approach to deliver chemotherapy agents selectively to tumours. The variety of targets or markers that are overexpressed in different types of cancers results in a high demand for antibody conjugated nanoparticles which are versatile and easily customizable. Considering upscaling, the synthesis of antibody conjugated nanoparticles should be simple and highly reproducible. Here, we developed a facile coating strategy to produce antibody conjugated nanoparticles using ‘click chemistry’ and further evaluated their selectivity towards cancer cells expressing different markers. Our approach was consistently repeated for the conjugation of antibodies against CD44 and EGFR, which are prominent cancer cell markers. The functionalized particles presented excellent cell specificity towards CD44 and EGFR overexpressing cells, respectively. Our results indicated that the developed coating method is reproducible, versatile, non-toxic, and can be used for particle functionalization with different antibodies. This grafting strategy can be applied to a wide range of nanoparticles and will contribute to the development of future targeted drug delivery systems.
Iron Status Influences Mitochondrial Disease Progression in Complex I-Deficient Mice
Authors: Grillo Anthony S. , Kelly CJ , Ha Vivian T. , Bodart Camille M. , Huff Sydney , Couch Reid K. , Herrel Nicole T. , Kim Hyunsung D. , Zimmermann Azaad O. , Shattuck Jessica , Pan Yu-Chen , Kaeberlein Matt 
Published: September 2021

AbstractMitochondrial dysfunction caused by aberrant Complex I assembly and reduced activity of the electron transport chain is pathogenic in many genetic and age-related diseases. Mice missing the Complex I subunit NADH dehydrogenase [ubiquinone] iron-sulfur protein 4 (NDUFS4) are a leading mammalian model of severe mitochondrial disease that exhibit many characteristic symptoms of Leigh Syndrome including oxidative stress, neuroinflammation, brain lesions, and premature death. NDUFS4 knockout mice have decreased expression of nearly every Complex I subunit. As Complex I normally contains at least 8 iron-sulfur clusters and more than 25 iron atoms, we asked whether a deficiency of Complex I may lead to intracellular iron perturbations thereby accelerating disease progression. Consistent with this, iron supplementation accelerates symptoms of brain degeneration in these mice while iron restriction delays the onset of these symptoms and increases survival. NDUFS4 knockout mice display signs of iron overload in the liver including increased expression of hepcidin, and show changes in iron responsive element-regulated proteins consistent with increased intracellular iron that were prevented by iron restriction. These results suggest that perturbed iron homeostasis may contribute to pathology in Leigh Syndrome and possibly other mitochondrial disorders.