bluuebunny/crossref_metadata_2025_split huggingface dataset:
scRNA-Seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with uncomplicated malaria
Authors: Morang’a Collins M. , Drake Riley S. , Miao Vincent N. , Nyakoe Nancy K. , Amuzu Dominic S.Y. , Appiah Vincent , Aniweh Yaw , Bediako Yaw , Bah Saikou Y. , Shalek Alex K. , Awandare Gordon A. , Otto Thomas D. , Amenga–Etego Lucas 
Published: June 2023

AbstractMalaria causes significant morbidity and mortality worldwide, disproportionately impacting sub-Saharan Africa. Disease phenotypes associated with malarial infection can vary widely, from asymptomatic to life-threatening. To date, prevention efforts, particularly those related to vaccine development, have been hindered by an incomplete understanding of which factors impact host immune responses resulting in these divergent outcomes. Here, we conducted a field study in 224 malaria positive individuals (rapid diagnostic test - RDT) from a high transmission area in Ghana, to determine immunological factors associated with uncomplicated malaria “patients” compared to healthy individuals in the community “controls”. Generally, the patients had higher parasite density levels although it had a negative correlation with age, suggesting that, is a key indicator of disease pathogenesis. We applied single-cell RNA-sequencing to compare the immunological phenotypes of 18,176 peripheral blood mononuclear cells (PBMCs) isolated from a subset of the patients and controls (n=11/224), matched on location, age, sex, and parasite density. On average, patients were characterized by a higher fractional abundance of monocytes and an upregulation of innate immune responses, including those to type I and type II interferons and tumor necrosis factor-alpha (TNF-α) signaling via NFκB. Further, in the patients, we identified more putative interactions between antigen-presenting cells and proliferating CD4 T cells and naïve CD8 T cells driven by MHC-I and MHC-II signaling pathways, respectively. Together, these findings highlight transcriptional differences between immune cell subsets associated with malaria that may help guide the development of improved vaccines and new therapeutic interventions for individuals residing in endemic areas.
Fetally-encoded GDF15 and maternal GDF15 sensitivity are major determinants of nausea and vomiting in human pregnancy
Authors: Fejzo M , Rocha N , Cimino I , Lockhart SM , Petry C , Kay RG , Burling K , Barker P , George AL , Yasara N , Premawardhena A , Gong S , Cook E , Rainbow K , Withers DJ , Cortessis V , Mullin PM , MacGibbon KW , Jin E , Kam A , Campbell A , Polasek O , Tzoneva G , Gribble FM , Yeo GSH , Lam BYH , Saudek V , Hughes IA , Ong KK , Perry JRB , Sutton Cole A , Baumgarten M , Welsh P , Sattar N , Smith GCS , Charnock Jones DS , Coll AP , Meek CL , Mettananda S , Hayward C , Mancuso N , O’Rahilly S 
Published: June 2023

AbstractHuman pregnancy is frequently accompanied by nausea and vomiting that may become severe and life-threatening, as in hyperemesis gravidarum (HG), the cause of which is unknown. Growth Differentiation Factor-15 (GDF15), a hormone known to act on the hindbrain to cause emesis, is highly expressed in the placenta and its levels in maternal blood rise rapidly in pregnancy. Variants in the maternalGDF15gene are associated with HG. Here we report that fetal production of GDF15, and maternal sensitivity to it, both contribute substantially to the risk of HG. We found that the great majority of GDF15 in maternal circulation is derived from the feto-placental unit and that higher GDF15 levels in maternal blood are associated with vomiting and are further elevated in patients with HG. Conversely, we found that lower levels of GDF15 in the non-pregnant state predispose women to HG. A rare C211G variant inGDF15which strongly predisposes mothers to HG, particularly when the fetus is wild-type, was found to markedly impair cellular secretion of GDF15 and associate with low circulating levels of GDF15 in the non-pregnant state. Consistent with this, two commonGDF15haplotypes which predispose to HG were associated with lower circulating levels outside pregnancy. The administration of a long-acting form of GDF15 to wild-type mice markedly reduced subsequent responses to an acute dose, establishing that desensitisation is a feature of this system. GDF15 levels are known to be highly and chronically elevated in patients with beta thalassemia. In women with this disorder, reports of symptoms of nausea or vomiting in pregnancy were strikingly diminished. Our findings support a causal role for fetal derived GDF15 in the nausea and vomiting of human pregnancy, with maternal sensitivity, at least partly determined by pre-pregnancy exposure to GDF15, being a major influence on its severity. They also suggest mechanism-based approaches to the treatment and prevention of HG.
Sex-specific Proximal Tubular Cell differentiation pathways identified by single-nucleus RNA sequencing
Authors: Lu Yueh-An , Smith Tanya , Deshpande Sumukh , Liao Chia-Te , Talabani Bnar , Grigorieva Irina , Mason Anna , Andrews Robert , Bowen Timothy , Taylor Philip R. , Fraser Donald 
Published: June 2023

BackgroundPostpartum kidney growth is substantial but proliferation and differentiation pathways underpinning nephron elongation are not well defined. Here we performed sequential characterization of mouse kidney transcriptomics at the single cell level to address this.MethodsSingle nuclear RNA sequencing (snRNA-seq) was performed on kidney tissue from male and female mice at 1, 2, 4 and 12 weeks of age using the 10x Chromium platform.ResultsUnbiased clustering was performed on 68,775 nuclei from 16 animals. 31 discrete cellular clusters were seen, which were identified through comparison of their gene expression profiles to canonical markers of kidney cell populations. High levels of proliferation were evident at early time points in some cell types, especially tubular cells, but not in other cell types, for example podocytes. Proliferation was especially evident in Proximal Tubular Cells (PTCs) which are the most abundant cell type in the adult kidney. Uniquely when compared to other kidney cell types, PTCs demonstrated sex-specific expression profiles at late, but not early, time points. Mapping of PTC differentiation pathways using techniques including trajectory and RNA Velocity analyses delineated increasing PTC specialization and sex-specific phenotype specification.ConclusionOur single-cell transcriptomics data characterise cellular states observed during kidney growth. We have identified PTC differentiation pathways that lead to sex-specific tubular cell phenotypes.
Ectopic Expression of DistinctPLCGenes Identifies ‘Compactness’ as Novel Architectural Shoot Strategy to Cope with Drought Stress
Authors: Hooren van Max , van Wijk Ringo , Vaseva Irina I. , Van Der Straeten Dominique , Haring Michel , Munnik Teun 
Published: June 2023

AbstractPhospholipase C (PLC) has been implicated in several stress responses, including drought. Overexpression (OE) ofPLChas been shown to improve drought tolerance in various plant species.Arabidopsiscontains ninePLCgenes, subdivided into four clades. Earlier, OE ofPLC3, -5or-7were found to increase Arabidopsis’ drought tolerance. Here, we confirm this for three other PLCs:PLC2,the only constitutively expressedAtPLC;PLC4,reported to have reduced salt tolerance; andPLC9,of which the encoded enzyme was presumed to be catalytically inactive. To compare eachPLCand to discover any other potential phenotype, two independent OE lines of six AtPLC genes, representing all four clades, were simultaneously monitored with the GROWSCREEN FLUORO phenotyping platform, under both control- and mild drought conditions. To investigate which tissues were most relevant to achieve drought survival, we additionally expressed AtPLC5using 13 different cell- or tissue-specific promoters. While no significant differences in plant size, biomass or photosynthesis were found betweenPLClines and wild-type (WT) plants, allPLC-OElines, as well as those tissue-specific lines that promoted drought survival, exhibited a stronger decrease in convex hull perimeter (= increase in compactness) under water deprivation compared to WT. Increased compactness has not been associated with drought or decreased water loss before, though a hyponastic decrease in compactness in response to increased temperatures has been associated with water loss. We pose that increased compactness leads to decreased water loss and potentially provides a new breeding trait to select for drought tolerance.
Stress- and phospholipid signalling responses in Arabidopsis PLC4-KO and -overexpression lines under salt- and osmotic stress
Authors: Hooren Max van , Darwish Essam , Munnik Teun 
Published: June 2023

ABSTRACTSeveral drought- and salt tolerant phenotypes have been reported when overexpressing (OE) phospholipase C(PLC) genes across plant species. In contrast, a negative role for ArabidopsisPLC4in salinity stress was recently proposed by Xia et al., (2017) since they reported roots ofPLC4-OEseedlings to be were more sensitive to NaCl whileplc4-KO mutants were more tolerant. To investigate this apparent contradiction, and to analyse the phospholipid signalling responses associated with salt stress, we performed root growth- and phospholipid analyses onplc4-KO andPLC4-OEseedlings subjected to salinity (NaCl) or osmotic (sorbitol) stress, and compared these to wild type (WT) plants. Only very minor differences between PLC4 mutants and WT were observed, which even disappeared after normalization of the data, while in soil, PLC4-OE plants were clearly more drought tolerant than WT plants, as was found earlier when overexpressing ArabidopisisPLC2, -3, -5, -7or -9. We conclude that PLC4 plays no opposite role in salt-or osmotic stress and rather behaves like the other Arabidopsis PLCs.GRAPHICAL ABSTRACT
Mechanism of substrate binding and transport in BASS transporters
Authors: Becker Patrick , Naughton Fiona B. , Brotherton Deborah H. , Pacheco-Gomez Raul , Beckstein Oliver , Cameron Alexander D. 
Published: June 2023

AbstractThe Bile Acid Sodium Symporter (BASS) family transports a wide array of molecules across membranes, including bile acids in humans, and small metabolites in plants. These transporters, many of which are sodium-coupled, have been shown to use an elevator mechanism of transport, but exactly how substrate binding is coupled to sodium ion binding and transport is not clear. Here we solve the crystal structure at 2.3 Å of a transporter fromNeisseria Meningitidis(ASBTNM) in complex with pantoate, a potential substrate of ASBTNM. The BASS family is characterised by two helices that cross-over in the centre of the protein in an arrangement that is intricately held together by two sodium ions. We observe that the pantoate binds, specifically, between the N-termini of two of the opposing helices in this cross-over region. During molecular dynamics simulations the pantoate remains in this position when sodium ions are present but is more mobile in their absence. Comparison of structures in the presence and absence of pantoate demonstrates that pantoate elicits a conformational change in one of the cross-over helices. This modifies the interface between the two domains that move relative to one another to elicit the elevator mechanism. These results have implications, not only for ASBTNMbut for the BASS family as a whole and indeed other transporters that work through the elevator mechanism.
A hybrid nitrogenase with regulatory elasticity inAzotobacter vinelandii
Authors: Rivier Alex J. , Myers Kevin S. , Garcia Amanda K. , Sobol Morgan S. , Kaçar Betül 
Published: June 2023

ABSTRACTBiological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, engineering of nitrogen fixation requires an integrated understanding of how the gene regulatory dynamics of host diazotrophs restrict the available sequence-function space of its central catalytic metalloenzyme, nitrogenase. Here, we interrogate this relationship by analyzing the transcriptome ofAzotobacter vinelandiiengineered with a phylogenetically inferred, ancestral nitrogenase protein variant. The engineered strain exhibits reduced cellular nitrogenase activity but recovers wild-type growth rates following an extended lag period. We find that expression of genes within the immediate nitrogen fixation network is resilient to nitrogenase sequence-level perturbations. Rather, physiological compatibility with the ancestral nitrogenase variant is restored by reducing trace metal and electron resource allocation to nitrogenase. Our results spotlight cellular processes adjacent to nitrogen fixation as productive engineering targets to improve compatibility between remodeled nitrogenase proteins and engineered host diazotrophs.IMPORTANCEAzotobacter vinelandiiis a key model bacterium for the study of biological nitrogen fixation, an important metabolic process catalyzed by nitrogenase enzymes. Here, we demonstrate that compatibilities between engineeredA. vinelandiistrains and remodeled nitrogenase variants can be modulated at the regulatory level. Engineered cells respond by adjusting expression of proteins involved in cellular processes adjacent to nitrogen fixation, rather than that of nitrogenase proteins themselves. These insights can inform future strategies to transfer nitrogenase variants to non-native hosts.
Targeting host sialic acids in the upper respiratory tract with a broadly-acting neuraminidase to inhibit influenza virus transmission
Authors: Ortigoza Mila B. , Mobini Catherina L. , Rocha Hedy L. , Bartlett Stacey , Loomis Cynthia A. , Weiser Jeffrey N. 
Published: June 2023

ABSTRACTThe ongoing transmission of influenza A viruses (IAV) for the past century continues to be a burden to humans. IAV binds terminal sialic acids (SA) of sugar molecules present within the upper respiratory tract (URT) in order to successfully infect hosts. The two most common SA structures that are important for IAV infection are those with α2,3- and α2,6-linkages. While mice were once considered to be an unsuitable system for studying IAV transmission due to their lack of α2,6-SA in the trachea, we have successfully demonstrated that IAV transmission in infant mice is remarkably efficient. This finding led us to reevaluate the SA composition of the URT of mice usingin situimmunofluorescence and examine itsin vivocontribution to transmission for the first time. We demonstrate that mice express both α2,3- and α2,6-SA in the URT and that the difference in expression between infants and adults contribute to the variable transmission efficiencies observed. Furthermore, selectively blocking α2,3-SA or α2,6-SA within the URT of infant mice using lectins was necessary but insufficient at inhibiting transmission, and simultaneous blockade of both receptors was crucial in achieving the desired inhibitory effect. By employing a broadly-acting neuraminidase (ba-NA) to indiscriminately remove both SA moietiesin vivo, we effectively suppressed viral shedding and halted the transmission of different strains of influenza viruses. These results emphasize the utility of the infant mouse model for studying IAV transmission, and strongly indicate that broadly targeting host SA is an effective approach that inhibits IAV contagion.IMPORTANCEInfluenza virus transmission studies have historically focused on viral mutations that alter hemagglutinin binding to sialic acid (SA) receptorsin vitro. However, SA binding preference doesn’t fully account for the complexities of IAV transmission in humans. Our previous findings reveal that viruses that are known to bind α2,6-SAin vitrohave different transmission kineticsin vivo, suggesting that diverse SA interactions may occur during their life-cycle. In this study, we examine the role of host SA on viral replication, shedding, and transmissionin vivo. We highlight the critical role of SA presence during virus shedding, such that attachment to SA during virion egress is equally important as detachment from SA during virion release. These insights support the potential of broadly-acting neuraminidases as therapeutic agents capable of restraining viral transmissionin vivo. Our study unveils intricate virus-host interactions during shedding, highlighting the necessity to develop innovative strategies to effectively target transmission.
Depression events associated with proton-pump inhibitors in postmarketing drug surveillance data
Authors: Makunts Tigran , Joulfayan Haroutyun , Ta Kenneth , Abagyan Ruben 
Published: June 2023

AbstractProton-pump inhibitors, PPIs, are widely prescribed and are available over the counter for prolonged reduction of stomach acid production and related disorders. PPIs irreversibly inhibit the hydrogen/potassium ATPase in gastric parietal cells. Recent retrospective studies have described an association between PPI use and depression. However, there is conflicting evidence that PPI therapy improves depressive symptoms. Considering the widespread use and over the counter availability of these drugs, further investigation into depression adverse event was warranted with a larger scale postmarketing set of reports. Here we analyzed over 68,178 reports from the FDA Adverse Event Reporting System consisting of PPI and histamine-2 receptor antagonist monotherapy records and found a statistically significant association between use of PPIs and depression. Additionally, we analyzed each of the six currently marketed PPIs individually and observed the association with the depression adverse reaction for all of them.
HIV ESTIMATION USING POPULATION-BASED SURVEYS WITH NON-RESPONSE: A PARTIAL IDENTIFICATION APPROACH*
Authors: Adegboye Oyelola A. , Fujii Tomoki , Leung Denis Heng-Yan , Siyu Li 
Published: June 2023

AbstractBackgroundHIV estimation using data from the Demographic and Health Surveys (DHS) is limited by the presence of non-response and test refusals. Conventional adjustments such as imputation require the data to be missing at random. Methods that use instrumental variables allow the possibility that prevalence is different between the respondents and non-respondents, but their performance depends critically on the validity of the instrument.MethodsUsing Manski’s partial identification approach, we form instrumental variable bounds for HIV prevalence from a pool of candidate instruments. Our method does not require all candidate instruments to be valid. We use a simulation study to evaluate our method and compare it against its competitors. We illustrate the proposed method using DHS data from Zambia.ResultsOur simulations show that imputation leads to seriously biased results even under mild violations of non-random missingness. Using worst case identification bounds that do not make assumptions about the non-response mechanism is robust but not informative. By taking the union of instrumental variable bounds balances informativeness of the bounds and robustness to inclusion of some invalid instruments.ConclusionsNon-response and refusals are ubiquitous in population based HIV data such as those collected under the DHS. Partial identification bounds provide a robust solution to HIV prevalence estimation without strong assumptions. Union bounds are significantly more informative than the worst case bounds, without sacrificing credibility.Key messagesPartial identification bounds are useful for HIV estimation when data are subject to non-response biasInstrumental variables can narrow the width of the bounds but validity of an instrument variable is an untestable hypothesisThis paper proposes pooling candidate instruments and creating union bounds from the poolOur approach significantly reduces the width of the worst case bounds without sacrificing robustness
A high throughput assay provides novel insight into type VII secretion inStaphylococcus aureus
Authors: Yang Yaping , Scott Aaron A. , Kneuper Holger , Alcock Felicity , Palmer Tracy 
Published: June 2023

AbstractSuccessful colonisation by the opportunistic pathogenStaphylococcus aureusdepends on its ability to interact with other microorganisms.S. aureusstrains harbour a T7b-subtype type VII secretion system (T7SSb), a protein secretion system found in a wide variety of Bacillota which functions in bacterial antagonism and virulence. Assessment of T7SSb activity inS. aureushas been hampered by low secretion activity under laboratory conditions, and the lack of a sensitive assay to measure secretion. Here we have utilised NanoLuc Binary Technology to develop a simple assay to monitor protein secretion via detection of bioluminescence. Fusion of the 11 amino acid NanoLuc fragment to the conserved substrate EsxA permits its extracellular detection upon supplementation with the large NanoLuc fragment and luciferase substrate. Following miniaturisation of the assay to 384 well format, we use high-throughput analysis to demonstrate that T7SSb-dependent protein secretion differs across strains and growth temperature. We further show that the same assay can be used to monitor secretion of the surface-associated toxin substrate TspA. Using this approach we identify three conserved accessory proteins required to mediate TspA secretion. Co-purification experiments confirm that all three proteins form a complex with TspA.
Autotrophic growth of E. coli is achieved by a small number of genetic changes
Authors: Ben-Nissan Roee , Milshtein Eliya , Pahl Vanessa , de Pins Benoit , Jona Ghil , Levi Dikla , Yung Hadas , Nir Noga , Ezra Dolev , Gleizer Shmuel , Link Hannes , Noor Elad , Milo Ron 
Published: June 2023

AbstractSynthetic autotrophy is a promising avenue to sustainable bioproduction from CO2. Here, we use iterative laboratory evolution to generate several distinct autotrophic strains. Utilising this genetic diversity, we identify that just three mutations are sufficient forE. colito grow autotrophically, when introduced alongside non-native energy (formate dehydrogenase) and carbon-fixing (RuBisCO, phosphoribulokinase, carbonic anhydrase) modules. The mutated genes are involved in glycolysis (pgi), central-carbon regulation (crp), and RNA transcription (rpoB). Thepgimutation reduces the enzyme’s activity, thereby stabilising the carbon-fixing cycle by capping a major branching flux. For the other two mutations, we observe down-regulation of several metabolic pathways and increased expression of native genes associated with the carbon-fixing module (rpiB) and the energy module (fdoGH), as well as an increased ratio of NADH/NAD+ - the cycle’s electron-donor. This study demonstrates the malleability of metabolism and its capacity to switch trophic modes using only a small number of genetic changes and could facilitate transforming other heterotrophic organisms into autotrophs.