bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shotgun Immunoproteomics for Identification of Nonhuman Leukocyte Antigens Associated With Cellular Dysfunction in Heart Transplant Rejection
Authors: Gates Katherine V. , Panicker Anjali J. , Biendarra-Tiegs Sherri M. , Vetr Nikolai G. , Lopera Higuita Manuela , Nelson Timothy J. , Pereira Naveen L. , Griffiths Leigh G. 
Published: December 2021

Background.The International Society for Heart and Lung Transplant consensus panel notes that too little data exist regarding the role of non-HLA in allograft rejection. We developed a novel shotgun immunoproteomic approach to determine the identities and potential roles non-HLA play in antibody-mediated rejection (AMR) in heart transplant recipients.Methods.Serum was collected longitudinally from heart transplant recipients experiencing AMR in the absence of donor-specific anti-HLA antibodies (n = 6) and matched no rejection controls (n = 7). Antidonor heart affinity chromatography columns were formed by recipient immunoglobulin G immobilization at transplantation, acute rejection, and chronic postrejection time points. Affinity chromatography columns were used to capture antigens from individual patient’s donor heart biopsies collected at transplantation. Captured proteins were subjected to quantitative proteomic analysis and the longitudinal response was calculated.Results.Overlap in antigen-specific response between AMR and non-AMR patients was only 8.3%. In AMR patients, a total of 155 non-HLAs were identified, with responses toward 43 high prevalence antigens found in ≥50% of patients. Immunofluorescence staining for representative high prevalence antigens demonstrated that their abundance increased at acute rejection, correlating with their respective non-HLA antibody response. Physiological changes in cardiomyocyte and endothelial cell function, following in vitro culture with patient immunoglobulin G, correlated with response toward several high prevalence antigens.Conclusions.This work demonstrates a novel high-throughput strategy to identify clinically relevant non-HLA from donor endomyocardial biopsy. Such a technique has the potential to improve understanding of longitudinal timing of antigen-specific responses and their cause and effect relationship in graft rejection.
Rapid fluoroquinolone resistance detection inPseudomonas aeruginosausing mismatch amplification mutation assay-based real-time PCR
Authors: Madden Danielle E. , McCarthy Kate L. , Bell Scott C. , Olagoke Olusola , Baird Timothy , Neill Jane , Ramsay Kay A. , Kidd Timothy J. , Stewart Adam G. , Subedi Shradha , Choong Keat , Fraser Tamieka A. , Sarovich Derek S. , Price Erin P. 
Published: December 2021

AbstractBackgroundAntimicrobial resistance (AMR) is an ever-increasing global health concern. One crucial facet in tackling the AMR epidemic is earlier and more accurate AMR diagnosis, particularly in the dangerous and highly multi-drug resistant ESKAPE pathogen,Pseudomonas aeruginosa.ObjectivesWe aimed to develop two SYBR Green-based mismatch amplification mutation assays (SYBR-MAMAs) targeting GyrA T83I (gyrA248), and GyrA D87N, D87Y, and D87H (gyrA259). Together, these variants cause the majority of fluoroquinolone (FQ) AMR inP. aeruginosa.MethodsFollowing assay validation, thegyrA248 andgyrA259 SYBR-MAMAs were tested on 84 clinicalP. aeruginosaisolates from Queensland, Australia, 45 of which demonstrated intermediate/full ciprofloxacin resistance according to antimicrobial susceptibility testing.ResultsOur two SYBR-MAMAs correctly predicted an AMR phenotype in the majority (84%) of isolates with intermediate/full FQ resistance. Importantly, all FQ-sensitive strains were predicted to have a sensitive phenotype. Whole-genome sequencing confirmed 100% concordance with SYBR-MAMA genotypes.ConclusionsOur GyrA SYBR-MAMAs provide a rapid and cost-effective method for same-day identification of FQ AMR inP. aeruginosa. An additional SYBR-MAMA targeting the GyrB S466Y/S466F variants would increase FQ AMR prediction to 91%. Clinical implementation of our assays will permit more timely treatment alterations in cases where decreased FQ susceptibility is identified, leading to improved patient outcomes and antimicrobial stewardship.
Data-Driven Real-Time Strategic Placement of Mobile Vaccine Distribution Sites
Authors: Mehrab Zakaria , Wilson Mandy L. , Chang Serina , Harrison Galen , Lewis Bryan , Telionis Alex , Crow Justin , Kim Dennis , Spillmann Scott , Peters Kate , Leskovec Jure , Marathe Madhav V. 
Published: December 2021

AbstractThe deployment of vaccines across the US provides significant defense against serious illness and death from COVID-19. Over 70% of vaccine-eligible Americans are at least partially vaccinated, but there are pockets of the population that are under-vaccinated, such as in rural areas and some demographic groups (e.g. age, race, ethnicity). These unvaccinated pockets are extremely susceptible to the Delta variant, exacerbating the healthcare crisis and increasing the risk of new variants. In this paper, we describe a data-driven model that provides real-time support to Virginia public health officials by recommending mobile vaccination site placement in order to target under-vaccinated populations. Our strategy uses fine-grained mobility data, along with US Census and vaccination uptake data, to identify locations that are most likely to be visited by unvaccinated individuals. We further extend our model to choose locations that maximize vaccine uptake among hesitant groups. We show that the top recommended sites vary substantially across some demographics, demonstrating the value of developing customized recommendation models that integrate fine-grained, heterogeneous data sources. In addition, we used a statistically equivalent Synthetic Population to study the effect of combined demographics (eg, people of a particular race and age), which is not possible using US Census data alone. We validate our recommendations by analyzing the success rates of deployed vaccine sites, and show that sites placed closer to our recommended areas administered higher numbers of doses. Our model is the first of its kind to consider evolving mobility patterns in real-time for suggesting placement strategies customized for different targeted demographic groups. Our results will be presented at IAAI-22, but given the critical nature of the pandemic, we offer this extended version of that paper for more timely consideration of our approach and to cover additional findings.
Whole genome sequencing identifies common and rare structural variants contributing to hematologic traits in the NHLBI TOPMed program
Authors: Wheeler Marsha M. , Stilp Adrienne M. , Rao Shuquan , Halldórsson Bjarni V. , Beyter Doruk , Wen Jia , Mikhaylova Anna V. , McHugh Caitlin P. , Lane John , Jiang Min-Zhi , Raffield Laura M. , Jun Goo , Sedlazeck Fritz J. , Metcalf Ginger , Yao Yao , Bis Joshua B. , Chami Nathalie , de Vries Paul S. , Desai Pinkal , Floyd James S. , Gao Yan , Kammers Kai , Kim Wonji , Moon Jee-Young , Ratan Aakrosh , Yanek Lisa R. , Almasy Laura , Becker Lewis C. , Blangero John , Cho Michael H. , Curran Joanne E. , Fornage Myriam , Kaplan Robert C. , Lewis Joshua P. , Loos Ruth J.F. , Mitchell Braxton D. , Morrison Alanna C. , Preuss Michael , Psaty Bruce M. , Rich Stephen S. , Rotter Jerome I. , Tang Hua , Tracy Russell P. , Boerwinkle Eric , Abecasis Goncalo , Blackwell Thomas W. , Smith Albert V. , Johnson Andrew D. , Mathias Rasika A. , Nickerson Deborah A. , Conomos Matthew P. , Li Yun ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Þorsteinsdóttir Unnur , Magnússon Magnús K. , Stefansson Kari , Pankratz Nathan D. , Bauer Daniel E. , Auer Paul L. , Reiner Alex P. 
Published: December 2021

ABSTRACTGenome-wide association studies (GWAS) have identified thousands of single nucleotide variants and small indels that contribute to the genetic architecture of hematologic traits. While structural variants (SVs) are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of SVs to quantitative blood cell trait variation is unknown. Here we utilized SVs detected from whole genome sequencing (WGS) in ancestrally diverse participants of the NHLBI TOPMed program (N=50,675). Using single variant tests, we assessed the association of common and rare SVs with red cell-, white cell-, and platelet-related quantitative traits. The results show 33 independent SVs (23 common and 10 rare) reaching genome-wide significance. The majority of significant association signals (N=27) replicated in independent datasets from deCODE genetics and the UK BioBank. Moreover, most trait-associated SVs (N=24) are within 1Mb of previously-reported GWAS loci. SV analyses additionally discovered an association between a complex structural variant on 17p11.2 and white blood cell-related phenotypes. Based on functional annotation, the majority of significant SVs are located in non-coding regions (N=26) and predicted to impact regulatory elements and/or local chromatin domain boundaries in blood cells. We predict that several trait-associated SVs represent the causal variant. This is supported by genome-editing experiments which provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression.
Proximal binding pocket Arg717 substitutions in Escherichia coli AcrB cause clinically relevant divergencies in resistance profiles
Authors: Zwama Martijn , Nishino Kunihiko 
Published: December 2021

AbstractMultidrug resistance (MDR) in bacteria can be caused by the over-expression of multidrug efflux pumps belonging to the Resistance-Nodulation-Division (RND) superfamily of proteins. These intrinsic or acquired pumps can export a wide range of antibiotics. Recently, amino acid substitutions within these pumps have been observed in resistant clinical strains. Among others, two of these worrying gain-of-function mutations are R717L and R717Q in the proximal binding pocket of efflux pump AcrB (AcrB-Sa) found in azithromycin-resistant Salmonella enterica spp. We investigated the ramifications of these (and other) mutations in phylogenetically closely related AcrB from Escherichia coli (AcrB-Ec). We found that AcrB-Ec harboring Arg717 substitutions were significantly more effective in exporting all tested macrolides, with an up to 8-fold increase in the minimum inhibitory concentration (MIC) values (from 16 to 128 μg/mL for azithromycin). Interestingly, gain-of-function was also seen for fluoroquinolones (2-fold higher MICs), while there was a consistent loss-of-function for the export of novobiocin and β-lactam cloxacillin (2-fold lower MICs), pointing to a protein adaptation, which simultaneously partly compromised the efflux ability of other compounds with different molecular properties. Disk diffusion susceptibility testing corroborated the findings, as the R717Q and R717L mutant strains had significantly smaller inhibition zones for macrolides and fluoroquinolones and a larger inhibition zone for novobiocin, compared to the wild type. The spread and independent emergences of these potent efflux pump mutations highlight the necessity of control of, and adjustments to, treatments with antibiotics and the need for novel antibiotics and efflux pump inhibitors.ImportanceThe over-expression of multidrug efflux pumps is a major cause of multidrug-resistant bacteria. The emergence of gain-of-function mutations in these pumps is additionally worrying, as these render last-resort antibiotic treatment options ineffective. The Arg717-mutations in related Salmonella Typhi and Paratyphi A AcrB caused azithromycin-resistant strains, with resistance levels past breakpoints. This is worrying, as azithromycin is a last-resort antibiotic after fluoroquinolones to treat typhoid and paratyphoid fever. Our findings that the same substitutions in closely related Escherichia coli AcrB cause an increase in MICs for both fluoroquinolones and macrolides is worrying as it shows the effect of one amino acid substitution on a multitude of treatment options. Additionally, the finding that the substitutions negatively impact the export of other drugs, such as β-lactam cloxacillin, suggests that treatment with multiple antibiotics may mitigate resistance and improve treatment. Our findings also imply the urge to develop novel antibiotics and inhibitors.
Carbon dioxide, COVID-19 and the importance of restaurant ventilation: a case study from Spain approaching Christmas 2021
Authors: Moreno Teresa , Gibbons Wes 
Published: December 2021

AbstractRestaurants present an especial challenge in the prevention of the spread of COVID-19 via exhalatory bioaerosols because customers are unprotected by facemasks while eating, so that ventilation protocols in such establishments become particularly important. However, despite the fact that this pandemic airborne disease has been with us for two full years, many restaurants are still not successfully prioritising air renovation as a key tool for reducing infection risk. We demonstrate this in the run-up to the 2021 Christmas celebrations by reporting on CO2 concentration data obtained from a hotel breakfast room and restaurants during the 5-day Spanish holiday period of 4th-8th December. In the case of the breakfast room, inadequate ventilation resulted in average CO2 levels ranging from 868 to 1237ppm on five consecutive days, with the highest levels coinciding with highest occupancy numbers. Inside the five restaurants, three of these were well ventilated, maintaining stable average CO2 concentrations below 700ppm. In contrast, two restaurants failed to keep average CO2 levels below 1000ppm, despite sporadic, but ineffective, attempts by one of them to ventilate the establishment. More effort needs to be made to foster in both restaurant managers and the general public an improved awareness of the value of CO2 concentrations as an infection risk proxy and the relevance of ventilation issues to the propagation of respiratory diseases.
Seroresponse to Inactivated and Recombinant Influenza Vaccines among Maintenance Hemodialysis Patients
Authors: Manley Harold J. , Lacson Eduardo K. , Aweh Gideon , Weiner Daniel E. , Miskulin Dana C. , Hsu Caroline M. , Kapoian Toros , Hayney Mary S. , Meyer Klemens B. , Johnson Doug S. 
Published: December 2021

AbstractRationale & ObjectivesHigh dose influenza vaccine provides better protection against influenza infection in older adults than standard dose vaccine. We compared vaccine seroresponse among hemodialysis patients over 4 months after high dose inactivated (HD-IIV3), standard dose inactivated (SD-IIV4) or recombinant (RIV4) influenza vaccine.Study DesignProspective observational study.Setting & ParticipantsPatients at four hemodialysis clinics who received influenza vaccination. Hemagglutination inhibition titers were measured at baseline and at 1, 2, 3 and 4 months following vaccination with HD-IIV3, SD-IIV4 or RIV4 influenza vaccine.OutcomeThe primary outcome was seroprotection rates at ≥1:40 and ≥1:160 (which correspond to antibody levels providing protection from infection in about 50% and 95% immunocompetent individuals, respectively) at 1, 3 and 4 months after vaccination.Analytical approachWe determined GMT and seroprotection and seroconversion rates. Chi-square or Fisher exact tests were used for categorical data; continuous values were analyzed using Wilcoxon rank-sum tests. Generalized estimating equation was used to determine association between GMT and age.Results254 HD patients received HD-IIV3 (n=141), SD-IIV4 (n=36) or RIV4 (n=77) vaccine. A robust initial seroresponse to influenza A strains was observed after all 3 vaccines, with no difference in seroprotection rates at either the ≥1:40 or ≥1:160 titer at 1 and 2 months. Seroresponses to RIV4 and SD-IIV4 waned thereafter, such that by month 3 and 4, seroprotection by HD-IIV3 was significantly higher. Seroprotection rates were lower to the B strains across all three vaccines. Results trended similarly across patients aged below 65 years.LimitationsDue to use of observational data, bias by unmeasured confounders may exist. Some of the subgroups by age were low in number.ConclusionsHemodialysis patients achieved high seroprotection rates after all 3 vaccines. The seroresponse waned more slowly with HD-IIV3 as compared to SD-IIV4 or RIV4 vaccine.
Rational Protein Engineering of Bacterial N-demethylases to Create Biocatalysts for the Production of Methylxanthines
Authors: Mills Shelby Brooks , Mock Meredith B. , Summers Ryan M. 
Published: December 2021

AbstractMethylxanthines have a rich history as therapeutics and pharmaceuticals. However, natural dimethyl- and monomethylxanthines are difficult to produce synthetically, which has limited further exploration of these compounds in medicinal applications. A biosynthetic method for production of methylxanthines from whole cell biocatalysts is an attractive alternative. The bacterium Pseudomonas putida CBB5 contains a set of five enzymes, NdmABCDE, which are responsible for methylxanthine metabolism via N-demethylation to xanthine. The recent elucidation of the crystal structures of NdmA and NdmB, which remove the N1- and N3-methyl groups of caffeine, respectively, has opened new avenues to create biocatalysts for methylxanthine production. We have created a set of fifteen N-demethylase mutants and expressed them in E. coli BL21(DE3) as whole cell biocatalysts. The activity of each mutant was characterized for their affinity towards caffeine, theobromine, and theophylline. Two mutant enzymes in particular, labeled NdmA3 and NdmA4, both exhibited selectivity towards the N3-methyl group instead of the N1-methyl group. We also discovered that specific point mutations in NdmD resulted in the ability to tune the rate of the N-demethylase reaction. These new enzymes provide the capability of producing high-value methylxanthines, such as paraxanthine and 1-methylxanthine, through a biocatalytic route.
Ataxin-2, Twenty-four and Dicer-2 are components of a non-canonical cytoplasmic polyadenylation complex
Authors: Nadimpalli Hima Priyanka , Guitart Tanit , Coll Olga , Gebauer Fátima 
Published: December 2021

ABSTRACTCytoplasmic polyadenylation is a mechanism to promote mRNA translation in a wide variety of biological contexts. A canonical complex centered around the conserved RNA-binding protein family CPEB has been shown to be responsible for this process. We have previously reported evidence for an alternative non-canonical, CPEB-independent complex inDrosophila, of which the RNA-interference factor Dicer-2 is a component. Here, we investigate Dicer-2 mRNA targets and protein co-factors in cytoplasmic polyadenylation. Using RIP-Seq analysis we identify hundreds of novel Dicer-2 target transcripts, ∼50% of which were previously found as targets of the cytoplasmic poly(A) polymerase Wispy, suggesting widespread roles of Dicer-2 in cytoplasmic polyadenylation. Large-scale immunoprecipitation revealed Ataxin-2 and Twenty-four among the high-confidence interactors of Dicer-2. Functional analysis indicate that both factors form an RNA-independent complex with Dicer-2, and are required for cytoplasmic polyadenylation of Dicer-2 targets. Our results reveal the composition of a novel cytoplasmic polyadenylation complex that operates duringDrosophilaearly embryogenesis.
Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation
Authors: Kim Tae-Eun , Tsuboyama Kotaro , Houliston Scott , Martell Cydney M. , Phoumyvong Claire M. , Lemak Alexander , Haddox Hugh K. , Arrowsmith Cheryl H. , Rocklin Gabriel J. 
Published: December 2021

AbstractDesigning entirely new protein structures remains challenging because we do not fully understand the biophysical determinants of folding stability. Yet some protein folds are easier to design than others. Previous work identified the 43-residue □ββ□ fold as especially challenging: the best designs had only a 2% success rate, compared to 39-87% success for other simple folds (1). This suggested the □ββ□ fold would be a useful model system for gaining a deeper understanding of folding stability determinants and for testing new protein design methods. Here, we designed over ten thousand new □ββ□ proteins and found over three thousand of them to fold into stable structures using a high-throughput protease-based assay. Nuclear magnetic resonance, hydrogen-deuterium exchange, circular dichroism, deep mutational scanning, and scrambled sequence control experiments indicated that our stable designs fold into their designed □ββ□ structures with exceptional stability for their small size. Our large dataset enabled us to quantify the influence of universal stability determinants including nonpolar burial, helix capping, and buried unsatisfied polar atoms, as well as stability determinants unique to the □ββ□ topology. Our work demonstrates how large-scale design and test cycles can solve challenging design problems while illuminating the biophysical determinants of folding.SignificanceMost computationally designed proteins fail to fold into their designed structures. This low success rate is a major obstacle to expanding the applications of protein design. In previous work, we discovered a small protein fold that was paradoxically challenging to design (only a 2% success rate) even though the fold itself is very simple. Here, we used a recently developed high-throughput approach to comprehensively examine the design rules for this simple fold. By designing over ten thousand proteins and experimentally measuring their folding stability, we discovered the key biophysical properties that determine the stability of these designs. Our results illustrate general lessons for protein design and also demonstrate how high-throughput stability studies can quantify the importance of different biophysical forces.
Physico-chemical principles of HDL-small RNA binding interactions
Authors: Michell Danielle L. , Allen Ryan M. , Cavnar Ashley B. , Contreras Danielle M. , Yu Minzhi , Semler Elizabeth M. , Ramirez Marisol A. , Zhu Wanying , May-Zhang Linda , Raby Chase A. , Castleberry Mark , Ifrim Anca , Carr John Jeffrey , Terry James G. , Schwendeman Anna , Davies Sean S. , Sheng Quanhu , Linton MacRae F. , Vickers Kasey C. 
Published: December 2021

ABSTRACTExtracellular small RNAs (sRNA) are abundant in many biofluids, but little is known about their mechanisms of transport and stability in RNase-rich environments. We previously reported that high-density lipoproteins (HDL) of mice were enriched with multiple classes of sRNA derived from the endogenous transcriptome, but also exogenous organisms. Here, we show that human HDL transports tRNA-derived sRNAs (tDRs) from host and non-host species which were found to be altered in human atherosclerosis. We hypothesized that HDL binds to tDRs through apolipoprotein A-I (apoA-I) and these interactions are conferred by RNA-specific features. We tested this using microscale thermophoresis and electrophoretic mobility shift assays and found that HDL bind tDRs and other single-stranded sRNAs with strong affinity, but not doublestranded RNA or DNA. Natural and synthetic RNA modifications influenced tDR binding to HDL. Reconstituted HDL bound tDRs only in the presence of apoA-I and purified apoA-I alone was sufficient for binding sRNA. Conversely, phosphatidylcholine vesicles did not bind tDRs. In summary, HDL preferentially binds to single-stranded sRNAs likely through non-ionic interactions with apoA-I. These studies highlight binding properties that likely enable extracellular RNA communication and provide a foundation for future studies to manipulate HDL-sRNA for therapeutic approaches to prevent or treat disease.