bluuebunny/crossref_metadata_2025 huggingface dataset:
The InternationalOryzaMap Alignment Project (IOMAP): the Americas—past achievements and future directions
Authors: Alsantely Aseel , Gutaker Rafal , Navarrete Rodríguez María E , Arrieta-Espinoza Griselda , Fuchs Eric J , Costa de Oliveira Antonio , Tohme Joe , Zuccolo Andrea , Wing Rod A , Fornasiero Alice
Published: December 2022

The wild relatives of rice hold unexplored genetic diversity that can be employed to feed an estimated population of 10 billion by 2050. The Oryza Map Alignment Project (OMAP) initiated in 2003 has provided comprehensive genomic resources for comparative, evolutionary, and functional characterization of the wild relatives of rice, facilitating the cloning of >600 rice genes, including those for grain width (GW5) and submergence tolerance (SUB1A). Following in the footsteps of the original project, the goal of ‘IOMAP: the Americas’ is to investigate the present and historic genetic diversity of wild Oryza species endemic to the Americas through the sequencing of herbaria and in situ specimens. The generation of a large diversity panel describing past and current genetic status and potential erosion of genetic variation in the populations will provide useful knowledge for the conservation of the biodiversity in these species. The wild relatives of rice in the Americas present a wide range of resistance traits useful for crop improvement and neodomestication approaches. In the race against time for a sustainable food future, the neodomestication of the first cereal species recently accomplished in O. alta opens the door to the potential neodomestication of the other wild Oryza species in Americas.
Central concentration of asymmetric features in post-starburst galaxies at z ∼ 0.8
Authors: Himoto Kazuharu G , Kajisawa Masaru
Published: December 2022

We present morphological analyses of post-starburst galaxies (PSBs) at 0.7 < z < 0.9 in the COSMOS field. We fitted ultraviolet to mid-infrared multiband photometry of objects with i < 24 from COSMOS2020 catalogue with population synthesis models assuming non-parametric, piece-wise constant function of star formation history, and selected 94 of those galaxies that have high specific star formation rates (SSFRs) of more than 10−9.5 yr−1 in 321–1000 Myr before observation and an order-of-magnitude lower SSFRs within recent 321 Myr. We devised a new non-parametric morphological index which quantifies concentration of asymmetric features, CA, and measured it as well as concentration C and asymmetry A on the Hubble Space Telescope/Advanced Camera for Surveys IF814W-band images. While relatively high C and low A values of PSBs are similar to those of quiescent galaxies rather than star-forming galaxies, we found that PSBs show systematically higher values of CA than both quiescent and star-forming galaxies; 36 per cent of PSBs have log CA > 0.8, while only 16 per cent (2 per cent) of quiescent (star-forming) galaxies show such high CA values. Those PSBs with high CA have relatively low overall asymmetry of A ∼ 0.1, but show remarkable asymmetric features near the centre. The fraction of those PSBs with high CA increases with increasing SSFR in 321–1000 Myr before observation rather than residual ongoing star formation. These results and their high surface stellar mass densities suggest that those galaxies experienced a nuclear starburst in the recent past, and processes that cause such starbursts could lead to the quenching of star formation through rapid gas consumption, supernova/active galactic nucleus feedback, and so on.
A Small Change With a Twist Ending: A Single Residue in EGF-CFC Drives Bilaterian Asymmetry
Authors: Truchado-García Marta , Perry Kimberly J , Cavodeassi Florencia , Kenny Nathan J , Henry Jonathan Q , Grande Cristina
Published: December 2022

Asymmetries are essential for proper organization and function of organ systems. Genetic studies in bilaterians have shown signaling through the Nodal/Smad2 pathway plays a key, conserved role in the establishment of body asymmetries. Although the main molecular players in the network for the establishment of left-right asymmetry (LRA) have been deeply described in deuterostomes, little is known about the regulation of Nodal signaling in spiralians. Here, we identified orthologs of the egf-cfc gene, a master regulator of the Nodal pathway in vertebrates, in several invertebrate species, which includes the first evidence of its presence in non-deuterostomes. Our functional experiments indicate that despite being present, egf-cfc does not play a role in the establishment of LRA in gastropods. However, experiments in zebrafish suggest that a single amino acid mutation in the egf-cfc gene in at least the common ancestor of chordates was the necessary step to induce a gain of function in LRA regulation. This study shows that the egf-cfc gene likely appeared in the ancestors of deuterostomes and “protostomes”, before being adopted as a mechanism to regulate the Nodal pathway and the establishment of LRA in some lineages of deuterostomes.
Mutations in CmVPS41 controlling resistance to cucumber mosaic virus display specific subcellular localization
Authors: Real Núria , Villar Irene , Serrano Irene , Guiu-Aragonés Cèlia , Martín-Hernández Ana Montserrat
Published: December 2022

Resistance to cucumber mosaic virus (CMV) in melon (Cucumis melo L.) has been described in several exotic accessions and is controlled by a recessive resistance gene, cmv1, that encodes a vacuolar protein sorting 41 (CmVPS41). cmv1 prevents systemic infection by restricting the virus to the bundle sheath cells, preventing viral phloem entry. CmVPS41 from different resistant accessions carries two causal mutations, either a G85E change, found in Pat-81 and Freeman’s cucumber, or L348R, found in PI161375, cultivar Songwhan Charmi (SC). Here, we analyzed the subcellular localization of CmVPS41 in Nicotiana benthamiana and found differential structures in resistant and susceptible accessions. Susceptible accessions showed nuclear and membrane spots and many transvacuolar strands, whereas the resistant accessions showed many intravacuolar invaginations. These specific structures colocalized with late endosomes. Artificial CmVPS41 carrying individual mutations causing resistance in the genetic background of CmVPS41 from the susceptible variety Piel de Sapo (PS) revealed that the structure most correlated with resistance was the absence of transvacuolar strands. Coexpression of CmVPS41 with viral movement proteins, the determinant of virulence, did not change these localizations; however, infiltration of CmVPS41 from either SC or PS accessions in CMV-infected N. benthamiana leaves showed a localization pattern closer to each other, with up to 30% cells showing some membrane spots in the CmVPS41SC and fewer transvacuolar strands (reduced from a mean of 4 to 1–2) with CmVPS41PS. Our results suggest that the distribution of CmVPS41PS in late endosomes includes transvacuolar strands that facilitate CMV infection and that CmVPS41 re-localizes during viral infection.
Determinants of health-related quality of life across the spectrum of connective tissue diseases using latent profile analysis: results from the LEAP cohort
Authors: Dyball Sarah , Reynolds John A , Herrick Ariane L , Haque Sahena , Chinoy Hector , Bruce Ellen , Naz Sophia , Parker Ben , Bruce Ian N
Published: December 2022

Objectives

Poor health-related quality of life (HRQoL) is well recognized in patients with CTD. We hypothesized that subgroups of patients across the spectrum of CTD experience different HRQoL patterns and aimed to determine patient-level characteristics associated with these different subgroups.

Methods

Using the eight continuous domains of the Medical Outcomes Study 36-item Short Form (SF-36) questionnaire we performed data-driven clustering to derive latent profiles (LPs) of patients with distinct HRQoL patterns. Multivariable ordinal logistic regression was used to determine patient-level characteristics associated with each HRQoL subgroup identified.

Results

A total of 309 CTD patients completed the SF-36 questionnaire. The most impaired SF-36 domains in each disease group were vitality, general health and bodily pain. The physical component of the SF-36 was consistently more impaired compared with the mental component, with similar scores across disease groups. Three LPs were identified with poor [n = 89 (29%)], average [n = 190 (61.4%)] and excellent [n = 30 (9.7%)] HRQoL. LPs were not associated with diagnostic grouping or autoantibody profiles. Black background [odds ratio (OR) 0.22 (95% CI 0.08, 0.63)], Indo-Asian background [OR 0.39 (95% CI 0.19, 0.78)], concomitant fibromyalgia [OR 0.40 (95% CI 0.20, 0.78)], sicca symptoms [OR 0.56 (95% CI 0.32, 0.98)] and multimorbidity [Charlson Comorbidity Index; OR 0.81 (95% CI 0.67, 0.97)] were associated with the ‘poor’ HRQoL LP.

Conclusion

Distinct HRQoL subgroups exist that are not primarily driven by a specific diagnosis or autoantibody profiles. We identified a number of key demographic and clinical factors associated with poor HRQoL. These factors need to be addressed across the whole CTD spectrum as part of a holistic management approach aimed at improving overall patient outcomes.
Endoscopic Ultrasound-guided Transluminal Gallbladder Drainage in Patients With Acute Cholecystitis
Authors: Irani Shayan S. , Sharma Neil R. , Storm Andrew C. , Shah Raj J. , Chahal Prabhleen , Willingham Field F. , Swanstrom Lee , Baron Todd H. , Shlomovitz Eran , Kozarek Richard A. , Peetermans Joyce A. , McMullen Edmund , Ho Evelyne , van der Merwe Schalk W.
Published: December 2022

Objective:

To evaluate the safety and efficacy of endoscopic ultrasound-guided gallbladder drainage (EUS-GBD) using a lumen-apposing metal stent (LAMS).

Background:

For patients with acute cholecystitis who are poor surgical candidates, EUS-GBD using a LAMS is an important treatment alternative to percutaneous gallbladder drainage.

Methods:

We conducted a regulatory-compliant, prospective multicenter trial at 7 tertiary referral centers in the United States of America and Belgium. Thirty consecutive patients with mild or moderate acute cholecystitis who were not candidates for cholecystectomy were enrolled between September 2019 and August 2021. Eligible patients had a LAMS placed transmurally with 30 to 60-day indwell if removal was clinically indicated, and 30-day follow-up post-LAMS removal. Endpoints included days until acute cholecystitis resolution, reintervention rate, acute cholecystitis recurrence rate, and procedure-related adverse events (AEs).

Results:

Technical success was 93.3% (28/30) for LAMS placement and 100% for LAMS removal in 19 patients for whom removal was attempted. Five (16.7%) patients required reintervention. Mean time to acute cholecystitis resolution was 1.6±1.5 days. Acute cholecystitis symptoms recurred in 10.0% (3/30) after LAMS removal. Five (16.7%) patients died from unrelated causes. Procedure-related AEs were reported to the FDA in 30.0% (9/30) of patients, including one fatal event 21 days after LAMS removal; however, no AEs were causally related to the LAMS.

Conclusions:

For selected patients with acute cholecystitis who are at elevated surgical risk, EUS-GBD with LAMS is an alternative to percutaneous gallbladder drainage. It has high technical and clinical success, with low recurrence and an acceptable AE rate. Clinicaltrials.gov, Number: NCT03767881.
PD-L1 regulates inflammatory macrophage development from human pluripotent stem cells by maintaining interferon-gamma signal
Authors: Cao Handi , Xiang Yang , Zhang Shihui , Chao Yiming , Guo Jilong , Ho Joshua W. K. , Huang Yuanhua , Liu Pentao , Sugimura Ryohichi
Published: December 2022

PD-L1 (programmed death-ligand 1) serves as a pivotal immune checkpoint in both the innate and adaptive immune systems. PD-L1 is expressed in macrophages in response to interferon-gamma (IFNγ). We examined whether PD-L1 might regulate macrophage development. We establishedPD-L1-/-human pluripotent stem cells, differentiated them into macrophages, and observed a 60% reduction of CD11B+CD45+macrophages inPD-L1-/-, orthogonally verified with PD-L1 inhibitor BMS-1166 reduced macrophages to the same fold. Single-cell RNA sequencing further confirmed the 60% reduction of macrophages as well as the down-regulation of macrophage-defining transcription factorsSPI1, KLF6, andMAFB. Further,PD-L1-/-macrophages reduced the level of inflammatory signals such as NFκB, TNF, and chemokines CXCL and CCL families. Whilst anti-inflammatory TGF-β was upregulated. Finally, we identified thatPD-L1-/-macrophages significantly down-regulated interferon-stimulated genes (ISGs) despite IFNγ in differentiation media. Mechanistically,PD-L1-/-macrophages reducedIFNGR1expression explaining that cells could not respond to IFNγ. These data suggest that PD-L1 regulates inflammatory macrophage development by maintaining the IFNγ signal.
The impact of study design choices on significance and generalizability of canonical correlation analysis in neuroimaging studies
Authors: Pigeau Grace , Costantino Manuela , Devenyi Gabriel A. , Bussy Aurelie , Parent Olivier , Chakravarty M. Mallar
Published: December 2022

This technical note describes the effects of different data reduction methods and sample sizes for neuroimaging studies in the context of canonical correlation analysis (CCA). CCA is a multivariate statistical technique which has gained increasing popularity in neuroimaging research in recent years. Here, we investigate the parcellation methods’ impact on elucidating neuroanatomical relationships (based on cortical thickness) with known risk factors related to Alzheimer’s disease risk using data from the UK Biobank. The cortical thickness values were parcellated using four common methods in neuroimaging (atlas-based parcellation, spectral clustering, principal component analysis, and independent component analysis) and results from CCA were compared. The results show that the choice of parcellation technique impacts the strength and significance of the correlation between the brain and behaviours. Principal component analysis and independent component analysis result in the strongest correlations.

Additionally, we show that regardless of parcellation technique, smaller sample sizes of participants result in inflated correlation strength and significance.
Towards a General Approach for Bat Echolocation Detection and Classification
Authors: Aodha Oisin Mac , Martínez Balvanera Santiago , Damstra Elise , Cooke Martyn , Eichinski Philip , Browning Ella , Barataud Michel , Boughey Katherine , Coles Roger , Giacomini Giada , Swiney G. M. Cristina Mac , Obrist Martin K. , Parsons Stuart , Sattler Thomas , Jones Kate E.
Published: December 2022

Acoustic monitoring is an effective and scalable way to assess the health of important bioindicators like bats in the wild. However, the large amounts of resulting noisy data requires accurate tools for automatically determining the presence of different species of interest. Machine learning-based solutions offer the potential to reliably perform this task, but can require expertise in order to train and deploy.

We propose BatDetect2, a novel deep learning-based pipeline for jointly detecting and classifying bat species from acoustic data. Distinct from existing deep learning-based acoustic methods, BatDetect2’s outputs are interpretable as they directly indicate at what time and frequency a predicted echolocation call occurs. BatDetect2 also makes use of surrounding temporal information in order to improve its predictions, while still remaining computationally efficient at deployment time.

We present experiments on five challenging datasets, from four distinct geographical regions (UK, Mexico, Australia, and Brazil). BatDetect2 results in a mean average precision of 0.88 for a dataset containing 17 bat species from the UK. This is significantly better than the 0.71 obtained by a traditional call parameter extraction baseline method.

We show that the same pipeline, without any modifications, can be applied to acoustic data from different regions with different species compositions. The data annotation, model training, and evaluation tools proposed will enable practitioners to easily develop and deploy their own models. BatDetect2 lowers the barrier to entry preventing researchers from availing of effective deep learning bat acoustic classifiers. Open source software is provided at:

https://github.com/macaodha/batdetect2
Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants
Authors: Fu Yunfan , Bedő Justin , Papenfuss Anthony T. , Rubin Alan F.
Published: December 2022

Evaluating the impact of amino acid variants has been a critical challenge for studying protein function and interpreting genomic data. High-throughput experimental methods like deep mutational scanning (DMS) can measure the effect of large numbers of variants in a target protein, but because DMS studies have not been performed on all proteins, researchers also model DMS data computationally to estimate variant impacts by predictors. In this study, we extended a linear regression-based predictor to explore whether incorporating data from alanine scanning (AS), a widely-used low-throughput mutagenesis method, would improve prediction results. To evaluate our model, we collected 146 AS datasets, mapping to 54 DMS datasets across 22 distinct proteins. We show that improved model performance depends on the compatibility of the DMS and AS assays, and the scale of improvement is closely related to the correlation between DMS and AS results.
Histology-associated transcriptomic heterogeneity in ovarian folliculogenesis revealed by quantitative single-cell RNA-sequencing for tissue sections with DRaqL
Authors: Ikeda Hiroki , Miyao Shintaro , Nagaoka So , Yamamoto Takuya , Kurimoto Kazuki
Published: December 2022

High-quality single-cell RNA-sequencing (RNA-seq) with spatial resolution remains challenging. Laser capture microdissection (LCM) is a widely used, potent approach to isolate arbitrarily targeted cells from tissue sections for comprehensive transcriptomics. Here, we developed DRaqL (direct RNA recovery and quenching for LCM), an experimental approach for efficient lysis of single cells isolated by LCM from alcohol- and formalin-fixed sections without RNA purification. Single-cell RNA-seq combined with DRaqL allowed transcriptomic profiling from alcohol-fixed sections with efficiency comparable to that of profiling from freshly dissociated cells, together with effective exon– exon junction profiling. Furthermore, the combination of DRaqL and protease treatment enabled robust and efficient single-cell transcriptome analysis from tissue sections strongly fixed with formalin. Applying this method to mouse ovarian sections, we revealed a transcriptomic continuum of growing oocytes quantitatively associated with oocyte size, and detected oocyte-specific splice isoforms. In addition, our statistical model revealed heterogeneity of the relationship between the transcriptome of oocytes and their size, resulting in identification of a size–transcriptome relationship anomaly in a subset of oocytes. Finally, we identified genes that were differentially expressed in granulosa cells in association with the histological affiliations of granulosa cells to the oocytes, suggesting distinct epigenetic regulations and cell-cycle activities governing the germ–soma relationship. Thus, we developed a versatile, efficient approach for robust single-cell cDNA amplification from tissue sections and provided an experimental platform conducive to high-quality transcriptomics, thereby revealing histology-associated transcriptomic heterogeneity in folliculogenesis in ovarian tissues.
Flattening the Curve is Imperative: When China Relaxes the Dynamic Zero COVID-19 Policy
Authors: Zhao Shilei , Sha Tong , Xue Yongbiao , Chen Hua
Published: December 2022

Since December 7, 2022, China relaxed the strict dynamic zero COVID-19 policy. Here we quantitatively analyze its potential impacts on COVID-19 trend with the epidemiological model SUVQC using the population and parameter settings of Beijing as a case. Our results indicate that if non-pharmacological interventions are completely ceased, the ICU bed demand number will peak in 26 days at ∼23.88 thousand, which is 18 times the total number of ICU beds in Beijing. COVID-19 Omicron will cause 31,817 deaths in Beijing in the first year. We urge that the flattening curve strategy is necessary to slow down the infection and avoid overwhelming the healthcare system.
Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliles/OTX regulate early head development in embryos
Authors: Fenelon Kelli D. , Gao Fan , Borad Priyanshi , Abbasi Shiva , Pachter Lior , Koromila Theodora
Published: December 2022

During development, embryonic patterning systems direct a set of initially uncommitted pluripotent cells to differentiate into a variety of cell types and tissues. A core network of transcription factors, such as Zelda/POU5F1, Odd-paired (Opa)/ZIC and Ocelliless (Oc)/OTX, are conserved across animals. While Opa is essential for a second wave of zygotic activation after Zelda, it is unclear whether Opa drives head cell specification past gastrulation onset, in theDrosophilaembryo. Our hypothesis is that Opa and Oc are interacting with distinct cis-regulatory regions for shaping cell fates in the embryonic head. Using super-resolution microscopy and epigenomic meta-analysis of single cell RNAseq datasets we find thatopa’s andoc’s overlapping expression domains are dynamic in the head region, with both factors being simultaneously transcribed at the blastula stage. However, analysis of single-embryo RNAseq data reveals a subgroup of Opa-bound genes to be Opa-independent in the cellularized embryo. Interrogation of these genes against Oc ChIPseq combined with in situ data, suggests that Opa is competing with Oc for the regulation of a subgroup of genes later in gastrulation. Specifically, we find that Oc binds to late, head-specific enhancers independently and activates them in a head-specific wave of zygotic transcription, suggesting distinct roles for Oc in the blastula and gastrula stages.
Replitrons: a new group of eukaryotic transposons encoding HUH endonuclease
Authors: Craig Rory J.
Published: December 2022

HUH endonucleases of the Rep (replication protein) class mediate the replication of highly diverse plasmids and viral genomes across all domains of life. Reps also function as transposases, and three evolutionarily independent groups of transposable elements (TEs) mobilised by Reps have been described: the prokaryotic insertion sequences IS200/IS605and IS91/ISCR, and the eukaryotic Helitrons. Here I present Replitrons, a new group of eukaryotic transposons encoding Rep HUH endonuclease. Replitron transposases feature Rep with one catalytic Tyr (Y1) as their only recognised domain, contrasting with Helitron transposases that feature Rep with two Tyr (Y2) and a fused helicase domain (i.e. RepHel). Protein clustering found no link between Replitron transposases and described Rep transposases, and instead recovered a weak association with Reps of circular Rep-encoding single stranded (CRESS) DNA viruses and their related plasmids (pCRESS). The predicted tertiary structure of the transposase ofReplitron-1, the founding member of the group that is active in the green algaChlamydomonas reinhardtii, closely resembles that of CRESS-DNA viruses and other HUH endonucleases. Replitrons are present in at least three eukaryotic supergroups and reach high copy numbers in non-seed plant genomes. Replitron DNA sequences generally feature short direct repeats at, or potentially near, their termini. Finally, I characterisecopy-and-paste de novoinsertions ofReplitron-1using long-read sequencing ofC. reinhardtiiexperimental lines. Overall, these results support an ancient and evolutionarily independent origin of Replitrons, in line with other major groups of eukaryotic TEs. This work substantially expands the known diversity of both transposons and HUH endonucleases in eukaryotes.
Japanese Encephalitis Virus NS1’ Protein regulates the expression and distribution of TIM-1 to promote viral infection
Authors: Liang Zhenjie , Xie Shengda , Pan Junhui , Yang Xingmiao , Jiao Wenlong , Cao Ruibing
Published: December 2022

Japanese encephalitis virus (JEV) is a mosquito-borneFlavivirus, which may cause severe encephalitis in humans, horses, and other animals. TIM-1 has been identified to be a receptor that promotes various viruses to enter into target cells in recent years. In the present study, we found that TIM-1 protein was significantly increased in A549 cells at the late stage of JEV infection, while the transcription levels of TIM-1 remained unaltered. Interestingly, we found that NS1’ protein plays a key role in increasing the expression of TIM-1 in cells infected with JEV. Further, we found that the NS1’ protein also efficiently regulates TIM-1 protein to distribute in the cytoplasm in JEV-infected cells, and the amount of TIM-1 protein located on the cell membrane was reduced instead. As a consequence, NS1’ protein antagonize TIM-1 mediated viral restriction for further viral infection and propagation in the late stage of infection. In molecular mechanism, the molecular weight of TIM-1 increased a bit in the present of NS1’. Expression of NEU1 down-regulated TIM-1 expression and oseltamivir treatment increased the expression of TIM-1. Therefore, our data indicated that JEV NS1’ protein facilitated the sialylation modification of TIM-1 to up-regulate the level of TIM-1 expression and regulate its distribution. Collectively, our study revealed that JEV NS1’ protein regulates the expression and distribution of TIM-1 by facilitating its sialylation to antagonize TIM-1-mediated JEV restriction for further infection. Understanding the functional interplays between TIM-1 and NS1’ proteins will offer new insights into virushost interaction.

IMPORTANCE

T-cell immunoglobulin and mucin domain protein 1 (TIM-1) is known to promote cellular entry of various enveloped viruses. We discovered a novel phenomenon of dynamic expression and functional regulation of TIM-1 during JEV infection. Firstly, TIM-1 protein increased in the cytoplasm at the late stage of JEV infection. Furthermore, JEV NS1’ protein up-regulated the intracellular expression of TIM-1 and antagonize TIM-1-mediated viral restriction for further viral infection. In molecular mechanism, JEV NS1’ protein facilitated the sialylation of TIM-1 to increase the level of TIM-1 expression and cytoplasm distribution. Taken together, at the late stage of infection, JEV employs a strategy in which NS1’ promotes JEV release by promoting the sialylation of TIM-1, causing it to be primarily localized in the cytoplasm. Therefore, we discovered new functions of TIM-1 and JEV NS1’ during the process of JEV infection, and provide a new insight into the interactions between JEV and cell hosts.
Diversity and ecological function of urease-producing bacteria in the cultivation environment ofGracilariopsis lemaneiformis
Authors: Pei Pengbing , Du Hong , Aslam Muhammad , Wang Hui , Ye Peilin , Li Tangcheng , Liang Honghao , Zhang Zezhi , Ke Xiao , Lin Qi , Chen Weizhou
Published: December 2022

Urease-producing bacteria (UPB) provide inorganic nitrogen for primary producers by hydrolysis of urea. They play an important role in marine nitrogen cycle. However, there is still incomplete understanding of UPB and their ecological functions in the cultivation environment of red macroalageGracilariopsis lemaneiformis. This study comprehensively analyzed the diversity of culturable UPB and explored their effects on urea uptake byG. lemaneiformis. Total 34 isolates belonging to four main bacterial phyla i.e. Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were identified through 16S rRNA sequencing and were screened for UPB by urea agar chromogenic medium assay andureCgene cloning. Our data revealed that only 8 strains were found containing urease. These all UPB exhibited different urease activities by Berthelot reaction colorimetry assay. Furthermore, UPB with highest urease activity was selected to use as co-culture withG. lemaneiformisto explore its role in terms of promotion or inhibition of nitrogen uptake byG. lemaneiformis. The results showed that the urea consumption in culture media and the total cellular nitrogen inG. lemaneiformisfound increased significantly in the UPB-co culture group than control i.e. in the sterile group (p< 0.05). Similarity, isotopic assay revealed that δ15N contents ofG. lemaneiformiswas significant higher in the UPB-co culture than in the control where δ15N-urea was the only nitrogen source in the culture media, indicating the UPB helpedG. lemaneiformisto absorb more nitrogen from urea. Moreover, the highest content of δ15N was found inG. lemaneiformiswith epiphytic bacteria, as compared to sterilized (control) showing that epiphytic bacteria along with UPB have compound effects in helpingG. lemaneiformisabsorb more nitrogen in urea. Taken together, these results provide unique insight into the ecological role of UPB and suggest that urease from macroalgae environment-associated bacteria might be important player in the marine nitrogen cycling.

Importance

To the best of our knowledge, this is the first study ever conducted to isolate the culturable UPB from the cultivation environment ofG. lemaneiformisby urea agar chromogenic medium assay, and also evaluate the effects of UPB on urea utilization inG. lemaneiformisby stable isotopic tracer technique. This study provides a new insight into the mechanism of organic nitrogen uptake and utilization inG. lemaneiformis, and is of great significance for a better understanding of the ecological role of functional bacteria (e.g. urease-producing bacteria) in the marine nitrogen cycling.
Multilevel selection in the evolution of sexual dimorphism in phenotypic plasticity
Authors: Zadorin Anton S. , Rivoire Olivier
Published: December 2022

Phenotypes are partly shaped by the environment, which can impact both short-term adaptation and long-term evolution. In dioecious species, the two sexes may exhibit different degrees of phenotypic plasticity and theoretical models indicate that such differences may confer an adaptive advantage when the population is subject to directional selection, either because of a systematically varying environment or of a load of deleterious mutations. The effect stems from the fundamental asymmetry between the two sexes: female fertility is more limited than male fertility. Whether this asymmetry is sufficient for sexual dimorphism in phenotypic plasticity to evolve is, however, not obvious. Here, we show that even in conditions where it provides an adaptive advantage, dimorphic phenotypic plasticity may be evolutionarily unstable due to sexual selection. This is the case, in particular, for panmictic populations where mating partners are formed at random. However, we show that the effects of sexual selection can be counteracted when mating occurs within groups of related individuals. Under this condition, sexual dimorphism in phenotypic plasticity can not only evolve but offset the twofold cost of males. We demonstrate these points with a simple mathematical model through a combination of analytical and numerical results.
Motility mediates satellite formation in confined biofilms
Authors: Cordero Mireia , Mitarai Namiko , Jauffred Liselotte
Published: December 2022

Bacteria have spectacular survival capabilities and can spread in many, vastly different environments. For instance, when pathogenic bacteria infect a host, the cells expand through proliferation and squeezing through narrow pores and elastic matrices. However, the exact role of surface structures and matrix elasticity in colony expansion and morphogenesis is still largely unknown. Here we show howsatellitecolonies emerge around biofilms embedded in semi-soft agar in controlledin vitroassays. We tested how extra-cellular structures – important for biofilm formation and motility – control this morphology. Moreover, we identify the range of extra-cellular matrix elasticity, where this morphology is possible. When paralleled with mathematical modelling, our results demonstrate that satellite formation allows bacterial communities to spread faster. We anticipate that this strategy is important to speed up expansion in various environments while retaining the close interactions and protection provided by the community.
Divergent associations between auditory activation and inhibition task performance in children and adults
Authors: van Bijnen Sam , Parviainen Tiina
Published: December 2022

Adults and children show remarkable differences in cortical auditory activation which, in children, have shown relevance for cognitive performance, specifically inhibitory control. However, it has not been tested whether these differences translate to functional differences in response inhibition between adults and children. We recorded auditory responses of adults and school-aged children (6-14y) using combined magneto- and electroencephalography (M/EEG) during passive listening conditions and an auditory Go/No-go task. The associations between auditory cortical responses and inhibition performance measures diverge between adults and children; while in children the brain-behavior associations are not significant, or stronger responses are beneficial, adults show negative associations between auditory cortical responses and inhibitory performance. Furthermore, we found qualitative differences in auditory responses between adults and children; the late (∼200 ms post stimulation) adult peak activation shifts from auditory to frontomedial areas. In contrast, children show prolonged obligatory responses in the auditory cortex. Together this likely translates to a functional difference between adults and children in the cortical resources for performance consistency in auditory-based cognitive tasks.
Non-coding autoimmune risk variant accelerates T peripheral helper cell development via ICOS
Authors: Kim Taehyeung , Martínez-Bonet Marta , Wang Qiang , Hackert Nicolaj , Sparks Jeffrey A. , Baglaenko Yuriy , Koh Byung-Hee , Darbousset Roxane , Laza-Briviesca Raquel , Chen Xiaoting , Gutierrez-Arcelus Maria , Westra Harm-Jan , Weirauch Matthew T. , Raychaudhuri Soumya , Rao Deepak A. , Nigrovic Peter A.
Published: December 2022

Fine-mapping and functional studies implicate rs117701653, a common non-coding variant in theCD28/CTLA4/ICOSlocus, as a contributor to risk for rheumatoid arthritis and type 1 diabetes. Using DNA pulldown, mass spectrometry, genome editing and eQTL analysis, we establish that the disease-associated allele reduces affinity for the inhibitory chromosomal regulator SMCHD1 to drive expression of inducible T-cell costimulator (ICOS), enhancing memory CD4+T cell ICOS expression in individuals bearing the risk allele. Higher ICOS expression is paralleled by an increase in circulating T peripheral helper (Tph) cells, and in rheumatoid arthritis patients, of blood and joint fluid Tph cells and circulating plasmablasts, suggesting a causal link. Indeed, ICOS ligation accelerates T cell differentiation into CXCR5-PD-1highTph cells producing IL-21 and CXCL13, as does carriage of the rs117701653 risk allele. Thus, mechanistic dissection of a causal non-coding variant in human autoimmunity discloses a new pathway through which ICOS regulates Tph abundance.
Evaluation of microRNA variant maturation prior to genome edition
Authors: Busseau Isabelle , Mockly Sophie , Houbron Élisabeth , Somaï Hedi , Seitz Hervé
Published: December 2022

* Abstract

Assessment of the functionality of individual microRNA/target sites is a crucial issue. Genome editing techniques should theoretically permit a fine functional exploration of such interactions, allowing the mutation of microRNAs or individual binding sites in a completein vivosetting, therefore abrogating or restoring individual interactions on demand. A major limitation to this experimental strategy is the influence of microRNA sequence on its accumulation level, which introduces a confounding effect when assessing phenotypic rescue by compensatorily mutated microRNA and target site. Here we describe a simple assay to identify microRNA variants most likely to accumulate at wild-type levels even though their sequence has been mutated. In this assay, quantification of a reporter construct in cultured cells predicts the efficiency of an early biogenesis step, the Drosha-dependent cleavage of microRNA precursors, which appears to be a major determinant of microRNA accumulation in our variant collection. This system allowed the generation of a mutantDrosophilastrain expressing abantammicroRNA variant at wild-type levels.
The H163A Mutation Unravels an Oxidized Conformation of the SARS-CoV-2 Main Protease and Opens a New Avenue for Anti-Viral Therapeutic Design
Authors: Tran Norman , Dasari Sathish , Barwell Sarah , McLeod Matthew J. , Kalyaanamoorthy Subha , Holyoak Todd , Ganesan Aravindhan
Published: December 2022

The main protease of SARS-CoV-2 (Mpro) is an important target for developing COVID-19 therapeutics. Recent work has highlighted Mpro’s susceptibility to undergo redox-associated conformational changes in response to cellular and immune-system-induced oxidation. Despite structural evidence indicating large-scale rearrangements upon oxidation, the mechanisms of conformational change and its functional consequences are poorly understood. Here, we present the crystal structure of a new Mpro point mutant (H163A) that shows an oxidized conformation with the catalytic cysteine in a disulfide bond. We hypothesize that Mpro adopts this conformation under oxidative stress to protect against over-oxidation. Our metadynamics simulations illustrated a potential mechanism by which H163 modulates this transition and suggest that this equilibrium exists in the wild-type enzyme. We show that other point mutations can also significantly shift the equilibrium towards this state by altering conformational free energies. New therapeutic strategies against SARS-CoV-2 can be explored by understanding how H163 modulates this equilibrium.
Blockchain innovations and the contribution of the intergovernmental organizations
Authors: Katuu Shadrack
Published: December 2022

Purpose

The United Nations (UN) is globally acknowledged for its unique role as a convening platform to address humanitarian, peace, security and sustainable development challenges. However, it is not often associated with technological innovation. Blockchain technology, an innovation that emerged in the late 2000s, has generated animated discussions that are led, in the most part, by private sector institutions. A dearth of literature highlights the innovative blockchain projects supported by UN entities. The purpose of this study is to provide an overview of blockchain innovations supported by UN entities and explore opportunities for future studies.

Design/methodology/approach

This paper used an exploratory case study approach with the purpose of providing a broad perspective of blockchain innovations undertaken by UN entities in the quest to meet sustainable and equitable development across the world.

Findings

This study found 25 blockchain projects by 13 UN entities in 19 countries. The geographical spread of the case studies revealed that two studies have global jurisdiction, five studies in Africa, three in Europe, four in Latin America and the Caribbean and 11 in Asia, Oceania and the Middle East. Of the 19 countries, three had two projects each. Two countries had three projects and the rest had one project each. Of the 13 UN entities, three dominated with UNICEF (part of six projects), UNDP (part of 10 projects) and WFP (part of four projects). Finally, the 25 projects were divided among three categories of blockchain use cases, as defined by UN guidance documents. Five case studies focused on immutable record keeping, five on transfer of value and 15 on smart contracts.

Originality/value

This study offers a unique overview of blockchain efforts within UN entities. It provides a platform for future studies to reveal implicit assumptions, contrasting explanations and casual connections.
A feminist-affordance lens: examining the power outcomes of the actualization of smartphone affordances
Authors: Salamoun Randa , Karam Charlotte M. , Abdallah Crystel
Published: December 2022

Purpose

The authors explore the entanglement of smartphone technology and power in this paper. This paper explores the following question: In what ways does the actualization of smartphone affordances result in empowering outcomes (i.e. increase or reduce oppression) in the daily lives of refugees? Leveraging both affordance and feminist theories, the authors develop a hybrid lens bringing attention to the contextualized relationship between social process goals and affordances for sociality, upon which the authors introduce the notion of “goal-affordance interrelations”. The authors then trace how the actualization of these interrelations increases or reduces oppression.

Design/methodology/approach

Using an abductive approach, the authors analyze 32 semi-structured interview transcriptions conducted with Syrian refugees in Lebanon.

Findings

The analysis in this study reveals four categories of social process goals (meet financial needs, satisfy security needs, communicate and learn and maintain pre-existing social ties) that are intimate components of contextually meaningful affordances. When actualized, the goal–affordance interrelations fundamentally shape refugee experiences of power outcomes. The findings suggest forms of empowerment where powerlessness, marginalization, violence and exploitation are perceived to be reduced. Actualization outcomes are also found to increase perceived oppression. Additionally, the findings reveal that not all interrelations are actualized, such that the anticipation of an oppressive power outcome may limit the actualization of affordances for sociality.

Originality/value

This research raises considerations concerning technology and oppression, and that efforts to empower refugees through technology should critically question whether the lived experiences of oppression will be reduced. The findings of this study reveal various forms of less empowering (i.e. oppressive) outcomes for the refugees sampled, they also point to the potential politicization of the actualization of goal–affordance interrelations.
Graduate readiness for a professional career in accounting – an investigation of employers’ perspectives in Fiji
Authors: Roy Sandhiya
Published: December 2022

Purpose

The purpose of this paper is to identify and gain recent insights into the extent to which skills expectation gap exists from the perspective of employers in a Pacific Island country, including the competencies perceived essential within the work context of accountants and the support provided by employers to accounting graduates to address the skills expectation gap.

Design/methodology/approach

Using the expectation–performance gap framework developed by Bui and Porter (2010), this study collects and analyses data via semi-structured interviews with employers at chartered accounting firms, large- and medium-sized commercial and industrial firms in Fiji.

Findings

Majority of the employers indicated that graduates from the Fijian universities are adequately prepared and have acquired the necessary attributes to perform at the workplace. However, employers expect universities to do a little more in terms of developing confidence and improving ability to apply theoretical knowledge to practice. The findings also outline that the institutional-, social- and student-related constraints directly affect the quality of graduates, which are not in control of academics.

Research limitations/implications

It is noted that graduate capabilities are developed over two different learning environments. This study focused on how universities prepared graduates to perform at the workplace from the perspective of employers. This serves as a basis for future research to investigate effectiveness of trainings provided by employers to graduates to enable them into becoming successful accounting professionals.

Originality/value

This study adds clarifications to the debate on academic–practice gap by providing recent insights into the extent to which graduates demonstrate capabilities to perform in the accounting profession, the prevailing issues with graduate capabilities and the employers’ contribution towards strengthening graduate capabilities.
Disentangling direct and indirect effects of extreme events on coastal wetland communities
Authors: Davis Courtney L. , Walls Susan C. , Barichivich William J. , Brown Mary E. , Miller David A. W.
Published: December 2022

One of the primary ways in which climate change will impact coastal freshwater wetlands is through changes in the frequency, intensity, timing and distribution of extreme weather events. Disentangling the direct and indirect mechanisms of population‐ and community‐level responses to extreme events is vital to predicting how species composition of coastal wetlands will change under future conditions.

We extended static structural equation modelling approaches to incorporate system dynamics in a multi‐year multispecies occupancy model to quantify the effects of extreme weather events on a coastal freshwater wetland system.

We used data from an 8‐year study (2009–2016) on St. Marks National Wildlife Refuge in Florida, USA, to quantify species‐specific and community‐level changes in amphibian and fish occupancy associated with two flooding events in 2012 and 2013. We examine how physical changes to the landscape, including potential changes in salinity and increased wetland connectivity, may have contributed to or exacerbated the effects of these extreme weather events on the biota of isolated coastal wetlands.

We provide evidence that the primary effects of flooding on the amphibian community were through indirect mechanisms via changes in the composition of the sympatric fish community that may have had lethal (i.e. through direct predation) or non‐lethal (i.e. through direct or indirect competitive interactions) effects. In addition, we have shown that amphibian species differed in their sensitivity to direct flooding effects and indirect changes in the fish community and wetland‐specific conductance, which led to variable responses across the community. These effects led to the overall decline in amphibian species richness from 2009 to 2016, suggesting that wetland‐breeding amphibian communities on St. Marks National Wildlife Refuge may not be resilient to predicted changes in coastal disturbance regimes because of climate change.

Understanding both direct and indirect effects, as well as species interactions, is important for predicting the effects of a changing climate on individual species, communities and ecosystems.