bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bi-allelic loss-of-function variants in PPFIBP1 cause a neurodevelopmental disorder with microcephaly, epilepsy and periventricular calcifications
Authors: Rosenhahn Erik , O’Brien Thomas J. , Zaki Maha S. , Sorge Ina , Wieczorek Dagmar , Rostasy Kevin , Vitobello Antonio , Nambot Sophie , Alkuraya Fowzan S. , Hashem Mais O. , Alhashem Amal , Tabarki Brahim , Alamri Abdullah S. , Al Safar Ayat H. , Bubshait Dalal K. , Alahmady Nada F. , Gleeson Joseph G. , Abdel-Hamid Mohamed S. , Lesko Nicole , Ygberg Sofia , Correia Sandrina P. , Wredenberg Anna , Alavi Shahryar , Seyedhassani Seyed M. , Nasab Mahya Ebrahimi , Hussien Haytham , Omar Tarek , Harzallah Ines , Touraine Renaud , Tajsharghi Homa , Morsy Heba , Houlden Henry , Shahrooei Mohammad , Ghavideldarestani Maryam , Lemke Johannes R. , Sticht Heinrich , Jamra Rami Abou , Brown Andre E. X. , Maroofian Reza , Platzer Konrad 
Published: April 2022

AbstractPPFIBP1 encodes for the liprin-β1 protein which has been shown to play a role in neuronal outgrowth and synapse formation in Drosophila melanogaster. By exome sequencing, we detected nine ultra-rare homozygous loss-of-function variants in 14 individuals from 10 unrelated families. The individuals presented with moderate to profound developmental delay, often refractory early-onset epilepsy and progressive microcephaly. Further common clinical findings included muscular hypertonia, spasticity, failure to thrive and short stature, feeding difficulties, impaired hearing and vision, and congenital heart defects. Neuroimaging revealed abnormalities of brain morphology with leukoencephalopathy, cortical abnormalities, and intracranial periventricular calcifications as major features. In a fetus with intracranial calcifications, we identified a rare homozygous missense variant that by structural analysis was predicted to disturb the topology of the SAM-domain region that is essential for protein-protein interaction. For further insight in the effects of PPFIBP1 loss-of-function, we performed automated behavioural phenotyping of a Caenorhabditis elegans PPFIBP1/hlb-1 knockout model which revealed defects in spontaneous and light-induced behaviour and confirmed resistance to the acetylcholinesterase inhibitor aldicarb suggesting a defect in the neuronal presynaptic zone. In conclusion, we present bi-allelic loss-of-function variants in PPFIBP1 as a novel cause of an autosomal recessive neurodevelopmental disorder.
Monitoring of SARS-CoV-2 variant dynamics in wastewater by digital RT-PCR : from Alpha to Omicron BA.2 VOC
Authors: Wurtzer Sebastien , Levert Morgane , Dhenain Eloïse , Accrombessi Heberte , Manco Sandra , Fagour Nathalie , Goulet Marion , Boudaud Nicolas , Gaillard Lucie , Bertrand Isabelle , Challant Julie , Masnada Sophie , Azimi Sam , Guillon-Ritz Miguel , Robin Alban , Mouchel Jean-Marie ,   OBEPINE SIG, Moulin Laurent 
Published: April 2022

AbstractThroughout the COVID-19 pandemic, new variants have continuously emerged and spread in populations. Among these, variants of concern (VOC) have been the main culprits of successive epidemic waves, due to their transmissibility, pathogenicity or ability to escape the immune response. Quantification of the SARS-CoV-2 genomes in raw wastewater is a reliable approach well-described and widely deployed worldwide to monitor the spread of SARS-CoV-2 in human populations connected to sewage systems. Discrimination of VOCs in wastewater is also a major issue and can be achieved by genome sequencing or by detection of specific mutations suggesting the presence of VOCs. This study aimed to date the emergence of these VOCs (from Alpha to Omicron BA.2) by monitoring wastewater from the greater Paris area, France, but also to model the propagation dynamics of these VOCs and to characterize the replacement kinetics of the majority populations. These dynamics were compared to various individual-centered public health data, such as regional incidence and proportions of VOCs identified by sequencing of isolated patient strains. The viral dynamics in wastewater highlighted the impact of the vaccination strategy on the viral circulation in human populations but also suggested its potential effect on the selection of variants most likely to be propagated in immunized populations. Normalization of concentrations to capture population movements appeared statistically more reliable using variations in local drinking water consumption rather than using PMMoV concentrations because PMMoV fecal shedding was subject to variability and was not sufficiently relevant in this study. The dynamics of viral spread was observed earlier (about 13 days on the wave related to Omicron VOC) in raw wastewater than the regional incidence alerting to a possible risk of decorrelation between incidence and actual virus circulation probably resulting from a lower severity of infection in vaccinated populations.
Interleukin-6 as a predictor of early weaning from invasive mechanical ventilation in patients with acute respiratory distress syndrome
Authors: Sakai Kazuya , Nishii Mototsugu , Saji Ryo , Matsumura Reo , Ogawa Fumihiro , Takeuchi Ichiro 
Published: April 2022

AbstractBackgroundTherapeutic effects of steroids on acute respiratory distress syndrome (ARDS) requiring mechanical ventilation (MV) have been reported. However, predictive indicators of early weaning from MV post-treatment have not yet been defined, making treating established ARDS challenging. Interleukin (IL)-6 has been associated with the pathogenesis of ARDS.ObjectiveOur aim was to clarify clinical utility of IL-6 level in ventilated patients with established ARDS.MethodsClinical, treatment, and outcome data were evaluated in 119 invasively ventilated patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-mediated ARDS. Plasma levels of IL-6 and C-reactive protein (CRP) were measured on days 1, 4, and 7 after intubation.ResultsFifty-two patients were treated with dexamethasone (steroid group), while the remaining 67 patients were not (non-steroid group). Duration of MV use was significantly shorter in the steroid group compared to non-steroid group (11.5±0.6 vs. 16.1±1.0 days, P = 0.0005, respectively) along with significantly decreased levels of IL-6 and CRP. Even when restricted to the steroid group, among variables post-MV, IL-6 level on day 7 was most closely correlated with duration of MV use (Spearman’s rank correlation coefficient [ρ] = 0.73, P < 0.0001), followed by CRP level on day 7 and the percentage change in IL-6 or CRP levels between day 1 and day 7. Moreover, among these variables, IL-6 levels on day 7 showed the highest accuracy for withdrawal from MV within 11 days (AUC: 0.88), with optimal cutoff value of 20.6 pg/mL. Consistently, the rate of MV weaning increased significantly earlier in patients with low IL-6 (≤ 20.6 pg/mL) than in those with high IL-6 (> 20.6 pg/mL) (log-rank test P < 0.0001).ConclusionsIn invasively ventilated patients with established ARDS due to SARS-CoV-2, plasma IL-6 levels served as a predictor of early withdrawal from MV after dexamethasone administration.
Overlapping and distinct cis-acting requirements for oskar mRNA localization pathways
Authors: Eichler Catherine E. , Grunberg Michelle E. , Gavis Elizabeth R. 
Published: April 2022

ABSTRACTLocalization of oskar mRNA to the posterior of the Drosophila oocyte is essential for abdominal patterning and germline development. oskar localization is a multi-step process involving temporally and mechanistically distinct transport modes. Numerous cis-acting elements and trans-acting factors have been identified that mediate earlier motor-dependent transport steps leading to accumulation of oskar at the posterior. Little is known, however, about what features of oskar are required for the later localization phase, that occurs by diffusion with local entrapment and results in the accumulation of large oskar ribonucleoprotein granules by the end of oogenesis. Here we test whether cis- and trans-acting requirements for kinesin-dependent oskar transport, the structured oskar spliced localization element (SOLE) and the exon junction complex (EJC), are also required for late-phase localization. In contrast to kinesin-dependent motility, late-phase localization is independent of the EJC and depends not only on the structure but also the sequence of the SOLE. Late-phase localization also requires the oskar 3’ UTR and we show that the 3’ UTR is sufficient for ribonucleoprotein granule selectivity.
Prepandemic prevalence estimates of fatty liver disease and fibrosis defined by liver elastography in the United States
Authors: Unalp-Arida Aynur , Ruhl Constance E. 
Published: April 2022

ABSTRACTBackground & AimsFatty liver disease is a growing public health burden with serious consequences. We estimated prepandemic prevalence of fatty liver disease determined by transient elastography assessed hepatic steatosis and fibrosis, and examined associations with lifestyle and other factors in a United States population sample.MethodsLiver stiffness and controlled attenuation parameter (CAP) were assessed on 7,923 non-Hispanic white, non-Hispanic black, non-Hispanic Asian, and Hispanic men and women aged 20 years and over in the National Health and Nutrition Examination Survey (NHANES) 2017-March 2020 prepandemic data.ResultsThe prevalence of fatty liver disease estimated by CAP >300 dB/m was 28.8% and of fibrosis (liver stiffness >8 kPa) was 10.4%. Only 7.2% of participants with fatty liver disease and 10.9% with fibrosis reported being told by a health care provider that they had liver disease. In addition to known risk factors such as metabolic factors and ALT, persons with fatty liver disease were less likely to meet physical activity guidelines, more likely to be sedentary for 12 or more hours a day, and reported a less healthy diet. Persons with fibrosis were less likely to have a college degree and reported a less healthy diet.ConclusionIn the U.S. population, most persons with fatty liver disease are unaware of their condition. Although physical activity and dietary modifications might reduce the fatty liver disease burden, the COVID pandemic has been less favorable for lifestyle changes. There is an urgent need for fatty liver disease management in high-risk individuals using transient elastography or other noninvasive methods to intervene in disease progression.
Immunogenicity of BNT162b2 COVID-19 vaccine in New Zealand adults
Authors: Priddy Frances H. , Williams Michael , Carson Simon , Lavender Brittany , Mathieson Julia , Frampton Chris , Moreland Nicole J. , McGregor Reuben , Williams Georgia , Brewerton Maia , Gell Katie , Ussher James , Gros Graham Le 
Published: April 2022

AbstractBackgroundThere is very little known about SARS-CoV-2 vaccine immune responses in New Zealand populations at greatest risk for serious COVID-19 disease.MethodsThis prospective cohort study assessed immunogenicity in BNT162b2 mRNA vaccine recipients in New Zealand without previous COVID-19, with enrichment for Māori, Pacific peoples, older adults ≥ 65 years of age, and those with co-morbidities. Serum samples were analysed at baseline and 28 days after second dose for presence of quantitative anti-S IgG by chemiluminescent microparticle immunoassay and for neutralizing capacity against Wuhan, Beta, Delta, and Omicron BA.1 strains using a surrogate viral neutralisation assay.Results285 adults with median age of 52 years were included. 55% were female, 30% were Māori, 28% were Pacific peoples, and 26% were ≥65 years of age. Obesity, cardiac and pulmonary disease and diabetes were more common than in the general population. All participants received 2 doses of BNT162b2 vaccine. At 28 days after second vaccination, 99.6% seroconverted to the vaccine, and anti-S IgG and neutralising antibody levels were high across gender and ethnic groups. IgG and neutralising responses declined with age. Lower responses were associated with age ≥75 and diabetes, but not BMI. The ability to neutralise the Omicron BA.1 variant in vitro was severely diminished but maintained against other variants of concern.ConclusionsVaccine antibody responses to BNT162b2 were generally robust and consistent with international data in this COVID-19 naïve cohort with representation of key populations at risk for COVID-19 morbidity. Subsequent data on response to boosters, durability of responses and cellular immune responses should be assessed with attention to elderly adults and diabetics.
PEP7 is a ligand for receptor kinase SIRK1 to regulate aquaporins and root growth
Authors: Wang Jiahui , Xi Lin , Wu Xu Na , König Stefanie , Rohr Leander , Neumann Theresia , Harter Klaus , Schulze Waltraud X. 
Published: April 2022

AbstractPlant receptor kinases constitute a large protein family that regulate various aspects of development and responses to external biotic and abiotic cues. Functional characterization of this protein family and particularly the identification of their ligands remains a major challenge in plant biology. Previously, we identified plasma membrane-intrinsic SUCROSE INDUCED RECEPTOR KINASE 1 (SIRK1) and QIAN SHOU KINASE 1 (QSK1) as a receptor / co-receptor pair involved in regulation of aquaporins in response to osmotic conditions induced by sucrose. Here, we identified a member of the Elicitor Peptide (PEP) family, namely PEP7, as the specific ligand of receptor kinase SIRK1. PEP7 binds to the extracellular domain of SIRK1 with a binding constant of 1.44±0.79 µM and is secreted to the apoplasm specifically in response to sucrose treatment. Stabilization of a signaling complex involving SIRK1, QSK1 and aquaporins as substrates is mediated by alterations in the external sucrose concentration or by PEP7 application. Moreover, the presence of PEP7 induces the phosphorylation of aquaporins in vivo and enhance water influx into protoplasts. The loss-of-function mutant of SIRK1 is not responsive to external PEP7 treatment regarding kinase activity, aquaporin phosphorylation and water influx activity. Our data indicate that the PEP7/SIRK1/QSK1 complex represents a crucial perception and response module mediating sucrose-controlled water flux in plants.
Screening of the optimal CpG-oligodeoxynucleotide for anti-inflammatory responses in avian macrophage cell line HD11
Authors: Ichikawa Kennosuke , Matsuzaki Mei , Ezaki Ryo , Horiuchi Hiroyuki , Yamamoto Yoshinari 
Published: April 2022

ABSTRACTCpG-oligodeoxynucleotides (CpG-ODN) has been shown to possess immunostimulatory features in both mammals and birds. However, compared to its pro-inflammatory effects, little is known about the anti-inflammatory responses triggered by CpG-ODN in avian cells. Hence, in this study, we aimed to characterize the anti-inflammatory response in the chick macrophage cell line HD11 under the stimulation of five kinds of CpG-ODN: CpG-A1585, CpG-AD35, CpG-B1555, CpG-BK3, and CpG-C2395. Single-stimulus CpG-B1555, CpG-BK3, and CpG-C2395 induced the interleukin (IL)-10 expression without causing cellular injury. The effects of pretreatment with each CpG-ODN before subsequent lipopolysaccharide stimulation were also evaluated. Interestingly, only CpG-C2395 maintained a high expression level in this situation. Finally, expression analysis of inflammation-related genes, such as the tumor necrosis factor-α, IL-1β, IL-6, and Toll-like receptor 4, was conducted, and pretreatment with CpG-C2395 significantly reduced their expression. Overall, our results shed light on the anti-inflammatory responses triggered by CpG-C2395 stimulation using a comparative analysis of three major classes of CpG-ODN in chick macrophages.
Cryo-EM reveals an entangled kinetic trap in the folding pathway of a catalytic RNA
Authors: Bonilla Steve L. , Vicens Quentin , Kieft Jeffrey S. 
Published: April 2022

ABSTRACTFunctional RNAs fold through complex pathways that can contain misfolded “kinetic traps.” A complete model of RNA folding requires understanding the formation of such misfolded states, but they are difficult to characterize due to their transient and potentially conformationally dynamic nature. We used cryo-electron microscopy (cryo-EM) to visualize a long-lived misfolded state in the folding pathway of the Tetrahymena thermophila group I intron, a paradigmatic RNA structure-function model system. The structure revealed how this state forms native-like secondary structure and tertiary contacts but contains two incorrectly crossed strands, consistent with a previous model. This incorrect topology mispositions a critical catalytic domain and cannot be resolved locally, as extensive refolding is required. This work provides a structural framework for interpreting decades of biochemical and functional studies and demonstrates the power of cryo-EM for the exploration of RNA folding pathways.
Unaltered T cell responses to common antigens in individuals with Parkinson’s disease
Authors: Williams Gregory P. , Muskat Kaylin , Frazier April , Xu Yaqian , Mateus José , Grifoni Alba , da Silva Antunes Ricardo , Weiskopf Daniela , Amara Amy W. , Standaert David G. , Goldman Jennifer G. , Litvan Irene , Alcalay Roy N. , Sulzer David , Lindestam Arlehamn Cecilia S. , Sette Alessandro 
Published: April 2022

AbstractBackground and ObjectivesParkinson’s disease (PD) is associated with a heightened inflammatory state, including activated T cells. However, it is unclear whether these PD T cell responses are antigen specific or more indicative of generalized hyperresponsiveness. Our objective was to measure and compare antigen-specific T cell responses directed towards antigens derived from commonly encountered human pathogens/vaccines in patients with PD and age-matched healthy controls (HC).MethodsPeripheral blood mononuclear cells (PBMCs) from 20 PD patients and 19 age-matched HCs were screened. Antigen specific T cell responses were measured by flow cytometry using a combination of the activation induced marker (AIM) assay and intracellular cytokine staining.ResultsHere we show that both PD patients and HCs show similar T cell activation levels to several antigens derived from commonly encountered human pathogens/vaccines in the general population. Similarly, we also observed no difference between HC and PD in the levels of CD4 and CD8 T cell derived cytokines produced in response to any of the common antigens tested. These antigens encompassed both viral (coronavirus, rhinovirus, respiratory syncytial virus, influenza, cytomegalovirus) and bacterial (pertussis, tetanus) targets.ConclusionsThese results suggest the T cell dysfunction observed in PD may not extend itself to abnormal responses to commonly encountered or vaccine-target antigens. Our study supports the notion that the targets of inflammatory T cell responses in PD may be more directed towards autoantigens like α-synuclein (α-syn) rather than common foreign antigens.
β-cell responses to high fat feeding: A role and mechanism for redox sensing by SENP1
Authors: Lin Haopeng , Suzuki Kunimasa , Smith Nancy , Li Xi , Nalbach Lisa , Fuentes Sonia , Spigelman Aliya F , Dai Xiaoqing , Bautista Austin , Ferdaoussi Mourad , Aggarwal Saloni , Pepper Andrew R , Roma Leticia P , Ampofo Emmanuel , Li Wen-hong , MacDonald Patrick E 
Published: April 2022

AbstractPancreatic β-cells respond to metabolic stress by upregulating insulin secretion, however the underlying mechanisms remain unclear. In β-cells from overweight humans without diabetes, and mice fed a high-fat diet for 2 days, insulin exocytosis and secretion are enhanced without increased Ca2+influx. β-cell RNA-seq suggests altered metabolic pathways early following HFD, where we find increased basal oxygen consumption, proton leak, but a more reduced cytosolic redox state. Increased β-cell exocytosis after 2-day HFD is dependent on this reduced intracellular redox and requires thesentrin-specific SUMO-protease-1(SENP1). Mice with either pancreas- or β-cell-specific SENP1 deletion fail to up-regulate exocytosis and become rapidly glucose intolerant after 2-day HFD. Mechanistically, redox-sensing by SENP1 requires a thiol group at C535 which together with Zn+-binding suppresses basal protease activity and unrestrained β-cell exocytosis and increases SENP1 sensitivity to regulation by redox signals.
Oncogenic mutations ofPIK3CAlead to increased membrane recruitment driven by reorientation of the ABD, p85 and C-terminus
Authors: Jenkins Meredith L , Ranga-Prasad Harish , Parson Matthew AH , Harris Noah J , Rathinaswamy Manoj K , Burke John E 
Published: April 2022

AbstractPIK3CAencoding the phosphoinositide 3-kinase (PI3K) p110α catalytic subunit is frequently mutated in cancer, with mutations occurring widely throughout the primary sequence. The full set of mechanisms underlying how PI3Ks are activated by all oncogenic mutations on membranes are unclear. Using a synergy of biochemical assays and hydrogen deuterium exchange mass spectrometry (HDX-MS), we reveal unique regulatory mechanisms underlying PI3K activation. Engagement of p110α on membranes leads to disengagement of the ABD of p110α from the catalytic core, and the C2 domain from the iSH2 domain of the p85 regulatory subunit. PI3K activation also requires reorientation of the p110α C-terminus, with mutations that alter the inhibited conformation of the C-terminus increasing membrane binding. Mutations at the C-terminus (M1043I/L, H1047R, G1049R, and N1068KLKR) activate p110α through distinct mechanisms, with this having important implications for mutant selective inhibitor development. This work reveals unique mechanisms underlying how PI3K is activated by oncogenic mutations, and explains how double mutants can synergistically increase PI3K activity.
Organizing laboratory information to analyze the reproducibility of experimental workflows
Authors: Peccoud Jean , Johnson Derek , Peccoud Samuel , Setchell Julia , Zhou Wen 
Published: April 2022

AbstractReproducibility is the cornerstone of scientific experiments. Assessing the reproducibility of an experiment requires analyzing the contribution of different factors to the variation of the observed data. Suitable data structures need to be defined prior to the data collection effort so that data associated with these factors can be recorded and associated with observations of the variable of interest. The resulting datasets can be analyzed statistically to estimate the effect of experimental factors on the observed data using ANOVA models. Custom data structures to document the execution of experimental workflows are defined in a research data management system. The data produced by multiple repetitions of a plasmid purification process and a cell culture process are analyzed using the Kruskal–Wallis H-test to identify factors contributing to their variation. Repetitions of the plasmid purification process do not lead to significant differences in extraction yields. Statistically significant differences in plasmid solution purity are identified but the differences are small enough that are not biologically relevant. The maintenance of two cell lines over many generations leads to similar datasets. However, different media preparations appear to influence the variation of cell viability and harvested cell counts in unexpected ways that may be the indirect expression of hidden effects not captured in the data structure.
Enhancing Prime Editing Efficiency and Flexibility with Tethered and Split pegRNAs
Authors: Feng Ying , Liu Siyuan , Mo Qiqin , Xiao Xiao , Liu Pengpeng , Ma Hanhui 
Published: April 2022

AbstractPrime editing (PE) has advantages for small insertion, deletion or point mutations without double-stranded DNA breaks. The 3’-extension of pegRNAs could negatively affect its stability or folding and comprise the PE activity. Here we generated stem-loop PEs (sPEs) by adding stem-loop aptamers at the 3’-terminal of pegRNA, which can be tethered to Cas9 nickase resulting in tethered PEs (tPEs). sPEs and tPEs increased the small insertion, deletion or point mutations efficiency by 2-4-fold on average in HEK293, U2OS and HeLa cells. We split the modified pegRNAs into sgRNA and prime RNA. The resulting split pegRNA prime editors (SnPEs) maintain the PE activity and increase flexibility.