bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of the early gene expression profile inPopulus ussuriensisunder cold stress using PacBio SMRT sequencing integrated with RNA-seq reads
Authors: Li Wenlong , Fu Yanrui , Lv Wanqiu , Zhao Shicheng , Feng He , Shao Liying , Li Chenghao , Yang Jingli
Published: September 2021

Populus ussuriensis is an important and fast-growing afforestation plant species in north-eastern China. The whole-genome sequencing of P. ussuriensis has not been completed. Also, the transcriptional network of P. ussuriensis response to cold stress remains unknown. To unravel the early response of P. ussuriensis to chilling (3 °C) stress and freezing (−3 °C) stresses at the transcriptional level, we performed single-molecule real-time (SMRT) and Illumina RNA sequencing for P. ussuriensis. The SMRT long-read isoform sequencing led to the identification of 29,243,277 subreads and 575,481 circular consensus sequencing reads. Approximately 50,910 high-quality isoforms were generated, and 2272 simple sequence repeats and 8086 long non-coding RNAs were identified. The Ca2+ content and abscisic acid (ABA) content in P. ussuriensis were significantly increased under cold stresses, while the value in the freezing stress treatment group was significantly higher than the chilling stress treatment group. A total of 49 genes that are involved in the signal transduction pathways related to perception and transmission of cold stress signals, such as the Ca2+ signaling pathway, ABA signaling pathway and MAPK signaling cascade, were found to be differentially expressed. In addition, 158 transcription factors from 21 different families, such as MYB, WRKY and AP2/ERF, were differentially expressed during chilling and freezing treatments. Moreover, the measurement of physiological indicators and bioinformatics observations demonstrated the altered expression pattern of genes involved in reactive oxygen species balance and the sugar metabolism pathway during chilling and freezing stresses. This is the first report of the early responses of P. ussuriensis to cold stress, which lays the foundation for future studies on the regulatory mechanisms in cold-stress response. In addition the full-length reference transcriptome of P. ussuriensis deciphered could be used in future studies on P. ussuriensis.
Predictors of rheumatic fever in sore throat patients: a systematic review and meta-analysis
Authors: Kulik Ellen , Stuart Beth , Willcox Merlin
Published: September 2021

Background

Concerns about rheumatic fever (RF) drive antibiotic prescriptions for sore throat (ST) in endemic areas. Better guidance is needed on which patients are likely to develop RF in order to avoid misuse and overuse of antibiotics. Our aim was to identify predictive factors for RF in ST patients.

Methods

Multiple databases were searched to identify cohort, case–control, cross-sectional or randomised controlled trials that measured RF incidence in ST patients. An inverse variance random effects model was used to pool the data and calculate odds ratios (ORs).

Results

Seven studies with a total of 6890 participants were included: three RCTs and four observational studies. Factors significantly associated with RF development following ST were positive group A streptococcal (GAS) swab (OR 1.74 [95% confidence interval {CI} 1.13 to 2.69]), previous RF history (OR 13.22 [95% CI 4.86 to 35.93]) and a cardiac murmur (OR 3.55 [95% CI 1.81 to 6.94]). Many potential risk factors were not reported in any of the included studies, highlighting important evidence gaps.

Conclusions

ST patients in endemic areas with a positive GAS swab, previous RF history and a cardiac murmur are at increased risk of developing RF. This review identifies vital gaps in our knowledge of factors predicting RF development in ST patients. Further research is needed to develop better clinical prediction tools and rationalise antibiotic use for ST.
Analysis of Differentially Expressed Rice Genes Reveals the ATP-Binding Cassette Transporters as Candidate Genes Against the Sheath Blight Pathogen, Rhizoctonia solani
Authors: Oh Youngjae , Lee Seonghee , Rioux Renee , Singh Pratibha , Jia Melissa H. , Jia Yulin , Mysore Kirankumar S.
Published: September 2021

Sheath blight is a serious rice disease worldwide, and genes involved in resistance remain unclear. In the present study, a virulent field isolate of Rhizoctonia solani was used to inoculate detached leaves of a sheath blight-resistant rice cultivar, Jasmine 85; a suppression subtractive cDNA library was constructed using RNA isolated 16 h postinoculation (hpi); and differentially expressed genes were identified from the cDNA library. A total of 159 uniquely expressed sequence tags were identified, including 105 from rice with enrichment in categories related to cellular response, molecular signaling, and host defense. Coupled with gene expression studies by DNA microarray, 27 highly induced genes involved in signal transduction and defense responses were identified within 16 hpi. Three members of the ATP-binding cassette (ABC) transporter gene family ( OsABC1, OsABC9, and OsABC12) encoding pleiotropic drug resistance-like ABC transporters were mapped to different sheath blight resistance quantitative trait loci (QTLs), and their differential expressions were validated. Three high-resolution melting (HRM) markers were developed from these ABC gene family members to distinguish alleles between sheath blight-susceptible cultivar Lemont and resistant cultivar Jasmine 85. Association of sheath blight resistance to these HRM markers was examined in 77 recombinant inbred lines derived from the cross between Jasmine 85 and Lemont. The OsABC9 gene located in a major sheath blight resistance QTL qShB9-2 showed a major contribution to sheath blight resistance. These results are useful for marker-assisted selection and functional validation of the ABC genes in sheath blight disease resistance.

[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.
The S. Typhi leuO gene contains multiple functional promoters
Authors: Fernández-Mora Marcos , Sánchez-Popoca Diego , Altamirano-Cruz Gloria , López-Méndez Grecia , Téllez-Galicia Andrea Teresa , Guadarrama Carmen , Calva Edmundo
Published: September 2021

The S. Typhi leuO gene, which codes for the LysR-type transcriptional regulator LeuO, contains five forward promoters named P3, P1, P2, P5 and P4, and two reverse promoters, P6 and P7. The activity of the forward promoters was revealed by primer extension using gene reporter fusions in an S. Typhi hns lrp mutant strain. Likewise, the activity of the reverse promoters was revealed in an hns background. Derepression of the transcription of the chromosomal gene was confirmed by RT-PCR in the hns lrp mutant. The leuOP1 transcriptional reporter fusion, which contained only the major P1 promoter, had a lower expression in a relA spoT mutant strain, indicating that the steady-state levels of the (p)ppGpp alarmone positively regulate it. In contrast, the leuOP3, leuOP5P4, leuOP6 and leuOP7 transcriptional fusions were derepressed in the relA spoT background, indicating that the alarmone has a negative effect on their expression. Thus, the search for genetic regulators and environmental cues that would differentially derepress leuO gene expression by antagonizing the action of the H-NS and Lrp nucleoid-associated proteins, or that would fine-tune the expression of the various promoters, will further our understanding of the significance that multiple promoters have in the control of LeuO expression.
Effects of Diet on the Microbiome and Serum Metabolome of South Asian Infants at 1 Year
Authors: Bruce Colin Y. , Shanmuganathan Meera , Azab Sandi M. , Britz-McKibbin Philip , Anand Sonia S. , de Souza Russell J. , Stearns Jennifer C.
Published: September 2021

Diet is known to affect the gut microbiome and metabolome composition in adults, but this has not been fully explored in infants. Dietary patterns from 1 year-old infants (n=182) from the South Asian Birth Cohort (START) study were compared to gut microbiome alpha and beta diversity and to taxa abundance differences. Diet – serum metabolite associations were identified using multivariate analysis (partial least squares-discriminant analysis, PLS-DA) and univariate analysis (T-Test). Dietary biomarkers identified from START were also examined in a separate cohort of white Caucasian infants (CHILD Cohort Study, n=82). Lastly, the association of diet with gut microbiome and serum biomarkers, considering maternal, perinatal and infant characteristics was investigated using multivariate forward stepwise regression. A dietary pattern characterized by breastfeeding, supplemented by formula and dairy was the strongest predictor of the gut microbiome that also differentiated the serum metabolome of infants. The formula and dairy dietary pattern was associated with a panel of circulating metabolites in both cohorts, including: S-methylcysteine, branched-chain/aromatic amino acids, lysine, dimethylglycine, and methionine. Breastfeeding status, the prominent feature of the dietary pattern, was also associated with a sub-set of serum metabolites in both cohorts. In START, this diet pattern was associated with the metabolites tryptophan betaine, 2-hydroxybutyric acid, tyrosine, phenylalanine, and trimethyl-N-oxide. In the CHILD Cohort Study(CHILD), breastfeeding status was associated with the metabolites aminooctanoic acid, 3-hydroxybutyric acid, and methyl-proline. The results of our study suggest that breastfeeding has the largest effect on the composition of the gut microbiome and the serum metabolome at 1 year, even when solid food diet and other covariates are considered.
An Accurate and Explainable Deep Learning System Improves Interobserver Agreement in the Interpretation of Chest Radiograph
Authors: Pham Hieu H. , Nguyen Ha Q. , Lam Khanh , Le Linh T. , Nguyen Dung B. , Nguyen Hieu T. , Le Tung T. , Nguyen Thang V. , Dao Minh , Vu Van
Published: September 2021

Interpretation of chest radiographs (CXR) is a difficult but essential task for detecting thoracic abnormalities. Recent artificial intelligence (AI) algorithms have achieved radiologist-level performance on various medical classification tasks. However, only a few studies addressed the localization of abnormal findings from CXR scans, which is essential in explaining the image-level classification to radiologists. Additionally, the actual impact of AI algorithms on the diagnostic performance of radiologists in clinical practice remains relatively unclear. To bridge these gaps, we developed an explainable deep learning system called VinDr-CXR that can classify a CXR scan into multiple thoracic diseases and, at the same time, localize most types of critical findings on the image. VinDr-CXR was trained on 51,485 CXR scans with radiologist-provided bounding box annotations. It demonstrated a comparable performance to experienced radiologists in classifying 6 common thoracic diseases on a retrospective validation set of 3,000 CXR scans, with a mean area under the receiver operating characteristic curve (AUROC) of 0.967 (95% confidence interval [CI]: 0.958–0.975). The sensitivity, specificity,F1-score, false-positive rate (FPR), and false-negative rate (FNR) of the system at the optimal cutoff value were 0.933 (0.898–0.964), 0.900 (0.887–0.911), 0.631 (0.589–0.672), 0.101 (0.089– 0.114) and 0.067 (0.057–0.102), respectively. For the localization task with 14 types of lesions, our free-response receiver operating characteristic (FROC) analysis showed that the VinDr-CXR achieved a sensitivity of 80.2% at the rate of 1.0 false-positive lesion identified per scan. A prospective study was also conducted to measure the clinical impact of the VinDr-CXR in assisting six experienced radiologists. The results indicated that the proposed system, when used as a diagnosis supporting tool, significantly improved the agreement between radiologists themselves with an increase of 1.5% in mean Fleiss’ Kappa. We also observed that, after the radiologists consulted VinDr-CXR’s suggestions, the agreement between each of them and the system was remarkably increased by 3.3% in mean Co-hen’s Kappa. Altogether, our results highlight the potentials of the proposed deep learning system as an effective assistant to radiologists in clinical practice. Part of the dataset used for developing the VinDr-CXR system has been made publicly available athttps://physionet.org/content/vindr-cxr/1.0.0/.
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

Learning 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 statement

Coupling 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

Opium 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

We 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 Summary

We 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

Older 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 consent

Ethical 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

Exome 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 STATEMENT

CKD 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

Clostridioides 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

The 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

The 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

Gene 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

MAb 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

The 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

Mitochondrial 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.
Dynamics in Fip1 regulate eukaryotic mRNA 3′ end processing
Authors: Kumar Ananthanarayanan , Yu Conny W.H. , Rodríguez-Molina Juan B. , Li Xiao-Han , Freund Stefan M.V. , Passmore Lori A.
Published: September 2021

Cleavage and polyadenylation factor (CPF/CPSF) is a multiprotein complex essential for mRNA 3′ end processing in eukaryotes. It contains an endonuclease that cleaves pre-mRNAs, and a polymerase that adds a poly(A) tail onto the cleaved 3′ end. Several CPF subunits, including Fip1, contain intrinsically disordered regions (IDRs). IDRs within multiprotein complexes can be flexible, or can become ordered upon interaction with binding partners. Here, we show that yeast Fip1 anchors the poly(A) polymerase Pap1 onto CPF via an interaction with zinc finger 4 of another CPF subunit, Yth1. We also reconstitute a fully recombinant 850-kDa CPF. By incorporating selectively labeled Fip1 into recombinant CPF, we could study the dynamics of Fip1 within the megadalton complex using nuclear magnetic resonance (NMR) spectroscopy. This reveals that a Fip1 IDR that connects the Yth1- and Pap1-binding sites remains highly dynamic within CPF. Together, our data suggest that Fip1 dynamics within the 3′ end processing machinery are required to coordinate cleavage and polyadenylation.
Sustainable meat consumption intentions: conceptualisation, scale development and validation
Authors: Zahra Sadaf , McCarthy Breda , Chaiechi Taha
Published: September 2021

Purpose

This study aims to propose and validate a new, comprehensive scale of sustainable meat consumption intentions (SMCI) from the Pakistani consumers' perspective.

Design/methodology/approach

The SMCI scale was developed in four phases, following a mixed-methods approach. Phase 1 generated a pool of items through an extensive literature review and seven focus groups. Phase 2 established the face and content validity of the items. Phase 3 resulted in scale purification in Study 1 (n = 222), followed by Study 2, using exploratory factor analysis (n = 412) to derive an initial factor structure, along with reliability assessment and confirmatory factor analysis (n = 310) to test the theoretical structure. Phase 4 validated the results (n = 355).

Findings

The results from the three studies yielded a ten-item, three-dimensional SMCI scale: “meat detachment”, “meat curtailment” and “organic meat purchase”.

Originality/value

No study at present fully measures the aspects of sustainable meat consumption in Muslim market segments and emerging economies. The formation of the SMCI scale is an important academic contribution that identifies three facets of consumers' SMCI.
Role of collaborative culture and knowledge management process for stimulating radical and incremental innovation: a comparative moderation approach
Authors: Shehzad Muhammad Usman , Zhang Jianhua , Le Phong Ba
Published: September 2021

Purpose

The primary objective of this study is to assess the role of a collaborative culture in the organization’s knowledge management process (KMP) and how it is associated with radical and incremental innovation under the moderating role of ownership formapjm in Pakistani firms.

Design/methodology/approach

This research used the quantitative method and structural equation modeling approach to examine hypotheses with data obtained by the survey from 280 participants in 85 Pakistani firms.

Findings

The findings of this study indicate that the KMP significantly mediates between collaborative culture and two specific types of innovation, namely radical innovation and incremental innovation. In addition, the ownership form can serve as a moderator in the relationship between KMP and innovation capability.

Research limitations/implications

Future research should explore the moderating impact of other strategic or behavioral factors, such as self-efficacy, job experience, education level, optimism and organizational support, to better clarify the association between these latent constructs.

Practical implications

This research provides leaders with a better view of the mechanism of knowledge management and the impact of ownership form and possible influences in their organizations to foster innovation capabilities.

Originality/value

This paper has prompted theoretical and practical attempts on innovation management theory that allow firms to recognize the necessary factors and processes to improve the firm’s innovation capability.
Same scandal, different moral judgments: the effects of consumer-firm affiliation on weighting transgressor-related information and post-scandal patronage intentions
Authors: Lo Carolyn Jia’En , Tsarenko Yelena , Tojib Dewi
Published: September 2021

Purpose

Corporate scandals involving senior executives plague many businesses. Although customers and noncustomers may be exposed to news of the same scandal, they may appraise dimensions of the transgression differently, thereby affecting post-scandal patronage intentions. The purpose of this study is to investigate whether and how consumer-firm affiliation affects future patronage intentions by examining nuances in customers’ vs noncustomers’ reactions toward the transgressor’s professional performance and immoral behavior.

Design/methodology/approach

Four between-subjects experimental studies were used to test whether performance-relevant and/or immorality-relevant pathways drive customers’ vs noncustomers’ post-scandal patronage intentions. The results were analyzed using analysis of variance, parallel mediation and serial mediation.

Findings

The results demonstrate that performance judgment, and not immorality judgment, drive the relationship between consumer-firm affiliation and post-scandal patronage intentions (Study 1a), regardless of the order of information presented (Study 1b). Customers form more positive performance judgments because they give more weight to performance-related information (Study 2), demonstrating a sequential effect of consumer-firm affiliation on post-scandal patronage intentions only through the performance-relevant, and not immorality-relevant, pathway (Study 3).

Research limitations/implications

This research contributes to the literature on social distance and moral judgments. Future research should examine other deleterious outcomes such as brand sabotage and negative word-of-mouth, as well as potential moderators including repeated transgressions and prevalence of the infraction in other firms.

Practical implications

This research offers important nuances for understanding how performance and immorality judgments differentially operate and affect post-scandal patronage intentions. The findings highlight the strategic value of communicating the leader’s performance (e.g. professional contributions) as a buffer against potential declining patronage.

Originality/value

Offering new insights into the extant literature and lay beliefs which contend that harsh moral judgment reduces patronage intentions, this research uncovers why and how exposure to the same scandal can result in varying moral judgments that subsequently influence patronage intentions. Importantly, this research shows that the performance-relevant pathway can explain why customers have higher post-scandal patronage intentions compared to noncustomers.
Building and construction quality: systematic literature review, thematic and gap analysis
Authors: Yarnold Jemima , Banihashemi Saeed , Lemckert Charles , Golizadeh Hamed
Published: September 2021

Purpose

The purpose of this study is to examine, review and analyse the current literature on building and construction quality and determine the related themes and gaps.

Design/methodology/approach

A systematic review approach was adopted on the building quality literature, and keywords such as “construction” or “building”; “defect” and “quality” or “rework” were searched through the Scopus, Web of Science and Google Scholar databases. A number of articles were found and filtered by title, abstract and keyword relevancy. Further articles were cross-referenced from these and again filtered by title, abstract and keyword relevancy. The time period for the search was 2000–2020. A total of 97 articles were found and analysed on the topic.

Findings

A number of recurring themes were found throughout the literature. They are safety, occupier satisfaction, cost, time, licensing, culture, training, software and building quality frameworks, classifications and recommendations. These themes were linked to display relationships between them from the literature. Based on the project lifecycle stages, an amalgamated classification system was developed and is presented here. The gaps in the current literature have been analysed and reported on.

Originality/value

A comprehensive descriptive, thematic and gap analysis was conducted on the available literature of building and construction quality. The emerging themes were discovered, their relationships were demonstrated and the research gaps were identified. A new classification system positioned in the project lifecycle stages is presented.
Gender-based perception of civil engineering and construction students towards infrastructure and community resilience
Authors: Rokooei Saeed , Vahedifard Farshid , Belay Solomon
Published: September 2021

Purpose

The purpose of this study is to investigate the effect of gender differences in the perception of civil engineers and construction (CEC) students toward resilience to natural hazards and extreme events in a changing climate. This study also explores to what extent CEC students perceive the status of the US infrastructure systems similar to an external evaluation model (i.e. American Society of Civil Engineers Infrastructure Report Card).

Design/methodology/approach

An empirical study was conducted to examine the perception of resilience among 103 females and 279 male CEC students from 15 universities across the USA. The obtained data were quantified, and different statistical methods were used to explore the similarities and differences in the gender group responses.

Findings

The results indicated a significant mean difference (disagreement) between male and female groups in the importance of community resilience, management and handling of natural hazards. In addition, while there was no meaningful difference between female and male students in their content knowledge, female students showed a more accurate perception about impacting factors involved.

Originality/value

The findings of this study offer new insight into the impacts of gender differences in the perception of resilience, which can be used to enhance the educational experience of CEC female students in areas related to community and infrastructure resilience.