bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying the impact of sample, instrument, and data processing on biological signatures detected with Raman spectroscopy
Authors: Wiemann Jasmina , Heck Philipp R.
Published: June 2023

Raman spectroscopy is a popular tool for characterizing complex biological materials and their geological remains1-10. Ordination methods, such as Principal Component Analysis (PCA), rely on spectral variance to create a compositional space1, the ChemoSpace, grouping samples based on spectroscopic manifestations that reflect different biological properties or geological processes1-7. PCA allows to reduce the dimensionality of complex spectroscopic data and facilitates the extraction of relevant informative features into data formats suitable for downstream statistical analyses, thus representing an essential first step in the development of diagnostic biosignatures. However, there is presently no systematic survey of the impact of sample, instrument, and spectral processing on the occupation of the ChemoSpace. Here the influence of sample count, signal-to-noise ratios, spectrometer decalibration, baseline subtraction routines, and spectral normalization on ChemoSpace grouping is investigated using synthetic spectra. Increase in sample size improves the dissociation of sample groups in the ChemoSpace, however, a stable pattern in occupation can be achieved with less than 10 samples per group. Systemic noise of different amplitude and frequency, features that can be introduced by instrument or sample11,12, are eliminated by PCA even when spectra of differing signal-to-noise ratios are compared. Routine offsets (± 1 cm−1) in spectrometer calibration contribute to less than 0.1% of the total spectral variance captured in the ChemoSpace, and do not obscure biological information. Standard adaptive baselining, together with normalization, increase spectral comparability and facilitate the extraction of informative features. The ChemoSpace approach to biosignatures represents a powerful tool for exploring, denoising, and integrating molecular biological information from modern and ancient organismal samples.
The demographic history of the wild crop relativeBrachypodium distachyonis shaped by distinct past and present ecological niches
Authors: Minadakis Nikolaos , Williams Hefin , Horvath Robert , Caković Danka , Stritt Christoph , Thieme Michael , Bourgeois Yann , Roulin Anne C.
Published: June 2023

Abstract

Closely related to economically important crops, the grassBrachypodium distachyonhas been originally established as a pivotal species for grass genomics but more recently flourished as a model for developmental biology. Grasses encompass more than 10,000 species and cover more than 40% of the world land area from tropical to temperate regions. Given that grasses also supply about a fifth of the world’s dietary protein as cereal grains, unlocking the sources of phenotypic variation inB. distachyonis hence of prime interest in fundamental and applied research in agronomy, ecology and evolution. We present here theB. distachyondiversity panel, which encompasses 332 fully sequenced accessions covering the whole species distribution from Spain to Iraq. By combining population genetics, niche modeling and landscape genomics, we suggest thatB. distachyonrecolonized Europe and the Middle East following the last glacial maximum. Consequently, the species faced new environmental conditions which led to clear associations between bioclimatic variables and genetic factors as well as footprints of positive selection in the genome. Altogether, this genomic resource offers a powerful alternative toArabidopsis thalianato investigate the genetic bases of adaptation and phenotypic plasticity in plants and more specifically in monocots.
Single-cell lineage tracing reveals hierarchy and mechanism of adipocyte precursor maturation
Authors: Rivera-Gonzalez Guillermo C. , Butka Emily G. , Gonzalez Carolynn E. , Kong Wenjun , Jindal Kunal , Morris Samantha A.
Published: June 2023

White adipose tissue is crucial in various physiological processes. In response to high caloric intake, adipose tissue may expand by generating new adipocytes. Adipocyte precursor cells (progenitors and preadipocytes) are essential for generating mature adipocytes, and single-cell RNA sequencing provides new means to identify these populations. Here, we characterized adipocyte precursor populations in the skin, an adipose depot with rapid and robust generation of mature adipocytes. We identified a new population of immature preadipocytes, revealed a biased differentiation potential of progenitor cells, and identified Sox9 as a critical factor in driving progenitors toward adipose commitment, the first known mechanism of progenitor differentiation. These findings shed light on the specific dynamics and molecular mechanisms underlying rapid adipogenesis in the skin.
Investigating the impact of paternal aging on murine sperm miRNA profiles and their potential link to autism spectrum disorder
Authors: Miyahara Kazusa , Tatehana Misako , Kikkawa Takako , Osumi Noriko
Published: June 2023

Paternal aging has consistently been linked to an increased risk of neurodevelopmental disorders, including autism spectrum disorder (ASD), in offspring. Recent evidence has highlighted the involvement of epigenetic factors. In this study, we aimed to investigate age-related alterations in microRNA (miRNA) profiles of mouse sperm and analyze target genes regulated by differentially expressed miRNAs (DEmiRNAs). Microarray analyses were conducted on sperm samples from mice at different ages: 3 months (3 M), over 12 M, and beyond 20 M. We identified 26 miRNAs with differential expression between the 3 M and 20 M mice, 34 miRNAs between the 12 M and 20 M mice, and 2 miRNAs between the 3 M and 12 M mice. The target genes regulated by these miRNAs were significantly associated with apoptosis/ferroptosis pathways and the nervous system. We revealed alterations in sperm miRNA profiles due to aging and suggest that the target genes regulated by these DEmiRNAs are associated with apoptosis and the nervous system, implying a potential link between paternal aging and an increased risk of neurodevelopmental disorders such as ASD. The observed age-related changes in sperm miRNA profiles have the potential to impact sperm quality and subsequently affect offspring development.
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

Malaria 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

Human 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

Background

Postpartum 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.

Methods

Single 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.

Results

Unbiased 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.

Conclusion

Our 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

Phospholipase 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

Several 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

The 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

Biological 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.

IMPORTANCE

Azotobacter 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.
Interplay between nutrient transporters ensures fertility in the malaria mosquito Anopheles gambiae
Authors: Stryapunina Iryna , Itoe Maurice , Trinh Queenie , Vidoudez Charles , Du Esrah , Mendoza Lydia , Hulai Oleksandr , Kauffman Jamie , Carew John , Shaw W. Robert , Catteruccia Flaminia
Published: June 2023

Females from many mosquito species feed on blood to acquire nutrients for egg development. The oogenetic cycle has been characterized in the arboviral vector Aedes aegypti, where after a bloodmeal, the lipid transporter lipophorin (Lp) shuttles lipids from the midgut and fat body to the ovaries, and a yolk precursor protein, vitellogenin (Vg), is deposited into the oocyte by receptor-mediated endocytosis. Our understanding of how the roles of these two nutrient transporters are mutually coordinated is however limited in this and other mosquito species. Here, we demonstrate that in the malaria mosquito Anopheles gambiae, Lp and Vg are reciprocally regulated in a timely manner to optimize egg development and ensure fertility. Defective lipid transport via Lp silencing triggers abortive ovarian follicle development, leading to misregulation of Vg and aberrant yolk granules. Conversely, depletion of Vg causes an upregulation of Lp in the fat body in a manner that appears to be at least partially dependent on target of rapamycin (TOR) signaling, resulting in excess lipid accumulation in the developing follicles. Embryos deposited by Vg-depleted mothers are completely infertile, and are arrested early during development, likely due to severely reduced amino acid levels and protein synthesis. Our findings demonstrate that the mutual regulation of these two nutrient transporters is essential to safeguard fertility by ensuring correct nutrient balance in the developing oocyte, and validate Vg and Lp as two potential candidates for mosquito control.
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

The 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.

IMPORTANCE

Influenza 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

Proton-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

Background

HIV 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.

Methods

Using 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.

Results

Our 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.

Conclusions

Non-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 messages

Partial identification bounds are useful for HIV estimation when data are subject to non-response bias

Instrumental variables can narrow the width of the bounds but validity of an instrument variable is an untestable hypothesis

This paper proposes pooling candidate instruments and creating union bounds from the pool

Our 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

Successful 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

Synthetic 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.
Spermidine facilitates the adhesion and subsequent invasion ofSalmonellaTyphimurium into epithelial cells via the regulation of surface adhesive structures and the SPI-1
Authors: Nair Abhilash Vijay , Tatu Utpal Shashikant , Devasurmutt Yashas , Rahman S.A , Chakravortty Dipshikha
Published: June 2023

Polyamines are poly-cationic molecules ubiquitously present in all organisms.Salmonellasynthesizes and also harbors specialized ABC transporters to uptake polyamines. Polyamines assist in pathogenesis and stress resistance inSalmonella; however, the mechanism remains elusive. The virulence trait ofSalmonelladepends on the injection of effector proteins into the host cell and modulation of host machinery and employs an array of arsenals to colonize in the host niche successfully. However, prior to this,Salmonellautilizes multiple surface structures to attach and adhere to the surface of the target cells. Our study solves the enigma of how polyamine spermidine assists in the pathogenesis of Salmonella. We show that spermidine mediates the initial attachment and adhesion ofSalmonellaTyphimurium to Caco-2 cells, facilitating its invasion. In-vivo studies showed that polyamines are required for invasion into the murine Peyer’s patches. Polyamines have previously been shown to regulate the transcription of multiple genes in both eukaryotes and prokaryotes. We show that spermidine controls the RNA expression of the two-component system, BarA/SirA, that further regulates multiple fimbrial and non-fimbrial adhesins inSalmonella. Flagella is also a vital surface structure aiding in motility and attachment to surfaces of host cells and gall stones. Spermidine regulated the expression of flagellin genes by enhancing the translation of s28, which features an unusual start codon and a poor Shine-Dalgarno sequence. Besides regulating the formation of the adhesive structures, spermidine tunes the expression of theSalmonellapathogenicity island-1 encoded genes. Thus, our study unravels a novel mechanism by which spermidine aids in the adhesion and the subsequent invasion ofSalmonellainto host cells.
Manuscript title: Ultra-processed food consumption in UK adolescents: distribution, trends, and sociodemographic correlates using the National Diet and Nutrition Survey 2008/09 to 2018/19
Authors: Chavez-Ugalde Yanaina , De Vocht Frank , Jago Russell , Adams Jean , Ong Ken K. , Forouhi Nita , Colombet Zoé , Ricardo Luiza I.C. , Van Sluijs Esther , Toumpakari Zoi
Published: June 2023

Background

The consumption of ultra-processed foods (UPF) has been proposed as a key driver of the global rise in non-communicable diseases. Evidence from several countries suggests that adolescents are the highest consumers. This study examined UPF consumption in a representative sample of UK adolescents.

Methods

We used data from 4-day food diaries from adolescents (11-18y) in the UK National Diet and Nutrition Survey (2008/09-2018/19) (n=3,270). UPF were identified using the NOVA classification. We estimated the percentage of Total Energy Intake (%TEI) and the absolute weight (grams). Linear regression models quantified differences in UPF consumption across survey years and its association with participant’s individual characteristics.

Results

Mean UPF consumption was 861 (SD 442) g/d and this accounted for 65.9% (SD 13.4%) of TEI. Between 2008 and 2019, mean UPF consumption decreased from 996 to 776 g/d [−211 (95%CI: −302;-120)] and from 67.7% to 62.8% of TEI [−4.8% (95%CI:-8.1;-1.5)]. Higher %TEI was consumed by adolescents with lower socioeconomic status; white ethnicity and living in England North. A higher weight of UPF consumption was associated with being male, white, age 18y, having parents with routine or manual occupation, living in England North, and living with obesity.

Discussion and conclusion

Average energy intake from UPF has decreased over a decade in UK adolescents. We observed a social and regional patterning of UPF consumption, with higher consumption among adolescents from lower socioeconomic backgrounds, from a white ethnicity and living in England North. Our findings suggest a relationship between individual characteristics and UPF consumption by UK adolescents.
Direct phasing algorithm for protein crystals with high solvent content using low-resolution diffraction data
Authors: Jiang Yu-Meng , Miao Han , Pan Xin-Yu , Wang Qi , Dong Zheng , Geng Zhi , Dong Yu-Hui
Published: June 2023

Over the past decade, iterative projection algorithms, an effective approach to recovering phases from a single intensity measurement, have found application in protein crystallography to directly surmount the `phase problem'. However, previous studies have always assumed that some prior knowledge constraints (i.e. a low-resolution envelope about the protein structure in the crystal cell or histogram matching requiring a similar density distribution to the target crystal) must be known for successful phase retrieval, thus hindering its widespread application. In this study, a novel phase-retrieval workflow is proposed that eliminates the need for a reference density distribution by utilizing low-resolution diffraction data in phasing algorithms. The approach involves randomly assigning one out of 12 possible phases at 30° intervals (or two for centric reflections) to produce an initial envelope, which is then refined through density modification after each run of phase retrieval. To evaluate the success of the phase-retrieval procedure, information entropy is introduced as a new metric. This approach was validated using ten protein structures with high solvent content, demonstrating its effectiveness and robustness.
Consumer engagement behavior in the value co-creation process of healthcare services: a scoping review
Authors: Wu Chuanhui , Jiang Shaohai , Zhou Yusheng , Yuan Qinjian
Published: June 2023

Purpose

The purpose of this review is to provide a conceptual framework of consumer engagement behavior in the value co-creation process of healthcare services, and further understand the current knowledge maps and advances.

Design/methodology/approach

Specifically, the scoping review methodology is used to synthesize the extant findings. The authors first develop the inclusion/exclusion criteria to evaluate the source material for the review; then, the authors further conduct the literature refinement to select the final data sample. As such, the authors extract and analyze the information derived from these articles.

Findings

The authors found most related studies focus on exploring patients' engagement behavior in the value co-creation process, especially those with chronic disease; the findings also reveal that consumers are most likely to engage in the value co-creation process of healthcare services by seeking or sharing health information; also, consumers engagement behavior is mainly driven by individual, interactive, and technological factors; moreover, consumer engagement in the value co-creation of healthcare services are more likely to achieve positive health and behavioral outcomes.

Originality/value

The role of consumers has gradually shifted from that of passive recipients to that of active participants in the healthcare value co-creation process. Consumer engagement behavior is the key premise for the realization of healthcare value co-creation, and it has received increasing attention both academically and practically. By unearthing the conceptual framework of consumer engagement behavior in the value co-creation process of healthcare services, this study provides a systematic understanding and serves as a useful resource for future research and practice.
Moral laxity – the cognitive gap between true and pseudo corporate social responsibility
Authors: Hatami Akram , Hermes Jan , Firoozi Naser
Published: June 2023

Purpose

To succeed in today’s dynamic and unpredictable business world, businesses are increasingly required to gain the trust of and inform the society in which they operate about the social and environmental consequences of their actions. Corporations’ claims regarding the responsibility and ethicality of their actions, however, have been shown to be contradictory to some degree. We define corporations’ deceitful implementation of their corporate social responsibility (CSR) policies as pseudo-CSR. We argue that it is the moral characteristics of individuals, i.e. employees, managers and other decision-makers who ignore the CSR policies, which produce pseudo-CSR.

Design/methodology/approach

This is a conceptual paper.

Findings

The authors conceptualize the gap between true CSR and pseudo-CSR on a cognitive individual level as “moral laxity,” resulting from organization-induced lack of effort concerning individual moral development through ethical discourse, ethical sensemaking and subjectification processes. The absence of these processes prohibits individuals in organizations from constructing ethical identities to inhibit pseudo-CSR activities.

Originality/value

This paper contributes to the literature on CSR by augmenting corporate-level responsibility with the hitherto mostly neglected, yet significant, role of the individual in bridging this gap.
Hybridized nanofluidic convection in umbrella-shaped porous thermal systems with identical heating and cooling surfaces
Authors: Biswas Nirmalendu , Mandal Dipak Kumar , Manna Nirmal K. , Gorla Rama S.R. , Chamkha Ali J.
Published: June 2023

Purpose

This study aims to investigate the impact of different heater geometries (flat, rectangular, semi-elliptical and triangular) on hybrid nanofluidic (Cu–Al2O3–H2O) convection in novel umbrella-shaped porous thermal systems. The system is top-cooled, and the identical heater surfaces are provided centrally at the bottom to identify the most enhanced configuration.

Design/methodology/approach

The thermal-fluid flow analysis is performed using a finite volume-based indigenous code, solving the nonlinear coupled transport equations with the Darcy number (10–5≤ Da ≤ 10–1), modified Rayleigh number (10 ≤ Ram≤ 104) and Hartmann number (0 ≤ Ha ≤ 70) as the dimensionless operating parameters. The semi-implicit method for pressure linked equations algorithm is used to solve the discretized transport equations over staggered nonuniform meshes.

Findings

The study demonstrates that altering the heater surface geometry improves heat transfer by up to 224% compared with a flat surface configuration. The triangular-shaped heating surface is the most effective in enhancing both heat transfer and flow strength. In general, flow strength and heat transfer increase with rising Ramand decrease with increasing Da and Ha. The study also proposes a mathematical correlation to predict thermal characteristics by integrating all geometric and flow control variables.

Research limitations/implications

The present concept can be extended to further explore thermal performance with different curvature effects, orientations, boundary conditions, etc., numerically or experimentally.

Practical implications

The present geometry configurations can be applied in various engineering applications such as heat exchangers, crystallization, micro-electronic devices, energy storage systems, mixing processes, food processing and different biomedical systems (blood flow control, cancer treatment, medical equipment, targeted drug delivery, etc.).

Originality/value

This investigation contributes by exploring the effect of various geometric shapes of the heated bottom on the hydromagnetic convection of Cu–Al2O3–H2O hybrid nanofluid flow in a complex umbrella-shaped porous thermal system involving curved surfaces and multiphysical conditions.
Does urbanization cause energy consumption amidst globalization and FDI in South Asia? A pooled mean group estimation
Authors: Islam Md. Saiful
Published: June 2023

Purpose

The purpose of this study is to examine the influence of urbanization on energy consumption, including economic growth, globalization and “foreign direct investment (FDI)” inflow as control variables.

Design/methodology/approach

This study uses yearly panel data from 19071 to 2018 on five selected South Asian economies. It applies the “pooled mean group (PMG)” estimator and the “Dumitrescu-Hurlin (D-H)” panel causality test.

Findings

The PMG estimators reveal that urbanization causes energy consumption negatively in the long run because of an unusual and messy urbanization process. At the same time, it has no impact on the latter in the short run. Per capita income has both long- and short-run positive influences on energy use. Globalization causes energy consumption positively in the long run but does not affect it in the short run. FDI inflow has a strong positive impact on energy use in the long run and adverse effects in the short run. The Dumitrescu–Hurlin causality test reveals feedback relationships between “urbanization and energy consumption,” “globalization and energy consumption” and one-way causation from “per capita income to energy consumption.” It validates the findings of the PMG estimators.

Practical implications

The results of this study indicate that South Asia may focus on enhancing the availability of energy in the region and producing more renewable energy to add to its energy portfolio to meet growing energy demand, particularly among urban dwellers. Moreover, they should raise their real per capita incomes and augment the standard of living of low-income city dwellers to make urbanization more serviceable and comfortable.

Originality/value

This study is original. As far as the author is aware, this is a maiden attempt to investigate urbanization's effects on energy usage in South Asia in the preview of globalization and FDI.
Effects of long‐term fixed fire regimes on African savanna vegetation biomass, vertical structure and tree stem density
Authors: Singh Jenia , Boucher Peter B. , Hockridge Evan G. , Davies Andrew B.
Published: June 2023

Fire plays an integral role in shaping the vegetation structure of savanna ecosystems. However, the effects of fire regime characteristics, such as frequency and season of burn, on savanna vegetation structure, biomass and tree abundance across landscape types are largely unknown.

We used high‐resolution airborne light detection and ranging (LiDAR) to investigate the long‐term effects of fire manipulation on savanna vegetation in Kruger National Park, South Africa. We analysed the effects of fire exclusion and experimental burns every 1, 2, 3, 4 and 6 years and during different seasons on aboveground biomass (AGB), tree stem densities and vegetation vertical height profiles across a rainfall gradient and on contrasting geologies.

Across savanna types, and especially in drier savannas, fire season was more influential for constraining AGB than fire frequency. Plots experiencing fires during the late‐ and mid‐dry season had 44.50% and 43.60%, respectively, lower AGB relative to unburnt plots than wet‐season fires. However, in mesic savannas, fire frequency interacted with fire season to influence AGB: plots subjected to high frequency, dry‐season fires had 55.35% lower AGB than unburnt plots, whereas plots burnt in the wet season at lower frequencies had lower AGB (24.40% lower than unburnt plots) than plots subjected to high frequency, wet‐season fires (13.74% lower AGB than unburnt plots).

Fire regimes had variable effects on tree densities, and effects varied with the savanna type. Woody vertical vegetation profiles showed the largest differences in response to dry‐season fires, with the greatest divergence in vegetation height classes <5 m.

Synthesis and applications. Understanding the influence of fire regimes on vegetation structure has important implications for the management of savanna heterogeneity and for predicting trajectories of change in savanna vegetation as fire regimes vary with climate change. We show that the magnitude of the effect of fire on woody vegetation structure varies with savanna context. Our results suggest that heterogeneous vegetation structure can be achieved by applying fires in the dry season in mesic savannas, whereas in dry savannas, variation in fire regimes is less consequential for constraining biomass accumulation and altering vegetation structure.