bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-organizing Single-Rosette Brain Organoids from Human Pluripotent Stem Cells
Authors: Tidball Andrew M. , Niu Wei , Ma Qianyi , Takla Taylor N. , Walker J. Clayton , Margolis Joshua L. , Mojica-Perez Sandra P. , Sudyk Roksolana , Moore Shannon J. , Chopra Ravi , Shakkottai Vikram G. , Murphy Geoffrey G. , Li Jun Z. , Parent Jack M.
Published: March 2022

The field of brain organoid research is complicated by morphological variability with multiple neural rosette structures per organoid. We have developed a new human brain organoid technique that generates self-organizing, single-rosette spheroids (SOSRS) with reproducible size, cortical-like lamination, and cell diversity. Rather than patterning a 3-dimensional embryoid body, we initiate brain organoid formation from a 2-dimensional monolayer of human pluripotent stem cells (hPSCs) that is patterned with small molecules into neuroepithelium and differentiated to cells of the developing dorsal cerebral cortex. This approach recapitulates the 2D to 3D transition from neural plate to neural tube that occurs during neurodevelopment. The vast majority of monolayer fragments form spheres with a single central lumen and consistent growth rates. Over time, the SOSRS develop appropriately ordered lamination consistent with six cortical layers by immunocytochemistry and single cell RNA-sequencing. The reproducibility of this method has allowed us to demonstrate robust structural phenotypes arising from chemical teratogen exposure or when modeling a genetic neurodevelopmental epileptic disorder. This platform should advance studies of human cortical development, brain disorder mechanisms, and precision therapies.

SUMMARY STATEMENT

Simple procedure for generating reproducible single rosette cortical brain organoids used to identify robust structural phenotypes with neuroteratogen exposure and in a genetic neurodevelopmental disease model.
Sex differences in contextual pattern separation, activation of new neurons, and functional connectivity within the limbic system
Authors: Yagi Shunya , Lee Amanda , Truter Nadine , Galea Liisa AM
Published: March 2022

Sex differences in the structure and function of hippocampus exist. Here, we examined sex differences in contextual pattern separation, functional connectivity, and activation of new neurons during fear memory. Two-month-old male and female Sprague-Dawley rats were injected with the DNA synthesis markers, iododeoxyuridine (IdU) and chlorodeoxyuridine (CldU) three weeks and four weeks before perfusion, respectively. One week after CldU injection, the rats underwent a context discrimination task in which rats were placed in context A (shock) and context A’ (no shock) every day for 12 days. On the test day, rats were placed in the shock context (context A) to measure fear memory and expression of zif268, an immediate early gene across 15 different limbic and reward regions. We found that females, but not males, showed contextual discrimination during the last days of training. On the test day, both sexes displayed similar levels of freezing, indicating equivalent fear memory for context A. Despite similar fear memory, males showed more positive correlations of zif268 activation between the limbic regions and the striatum, whereas females showed more negative correlations among these regions. Females showed greater activation of the frontal cortex, dorsal CA1, and 3-week-old adult-born dentate granular cells compared to males. These results highlight the importance of studying sex differences in fear memory and the contribution of adult neurogenesis to the neuronal network and may contribute to differences in susceptibility to fear related disorders such as posttraumatic stress disorder.
A quartz crystal microbalance method to quantify the size of hyaluronan and other glycosaminoglycans on surfaces
Authors: Srimasorn Sumitra , Souter Luke , Green Dixy E. , Djerbal Lynda , Goodenough Ashleigh , Duncan James A. , Roberts Abigail R. E. , Zhang Xiaoli , Débarre Delphine , DeAngelis Paul L. , Kwok Jessica C. F. , Richter Ralf P.
Published: March 2022

Hyaluronan (HA) is a major component of peri- and extra-cellular matrices and plays important roles in many biological processes such as cell adhesion, proliferation and migration. The abundance, size distribution and presentation of HA dictate its biological effects and are also useful indicators of pathologies and disease progression. Methods to assess the molecular mass of free-floating HA and other glycosaminoglycans (GAGs) are well established. In many biological and technological settings, however, GAGs are displayed on surfaces, and methods to obtain the size of surface-attached GAGs are lacking. Here, we present a method to size HA that is end-attached to surfaces. The method is based on the quartz crystal microbalance with dissipation monitoring (QCM-D) and exploits that the softness and thickness of films of grafted HA increase with HA size. These two quantities are sensitively reflected by the ratio of the dissipation shift (ΔD) and the negative frequency shift (-Δf) measured by QCM-D upon the formation of HA films. Using a series of size-defined HA preparations, ranging in size from ∼2 kDa tetrasaccharides to ∼1 MDa polysaccharides, we establish a monotonic yet non-linear standard curve of the ΔD/-Δf ratio as a function of HA size, which reflects the distinct conformations adopted by grafted HA chains depending on their size and surface coverage. We demonstrate that the standard curve can be used to determine the mean size of HA, as well as other GAGs, such as chondroitin sulfate and heparan sulfate, of preparations of previously unknown size in the range from 1 to 500 kDa, with a resolution of better than 10%. For polydisperse samples, our analysis shows that the process of surface-grafting preferentially selects smaller GAG chains, and thus reduces the average size of GAGs that are immobilised on surfaces comparative to the original solution sample. Our results establish a quantitative method to size HA and other GAGs grafted on surfaces, and also highlight the importance of sizing GAGs directly on surfaces. The method should be useful for the development and quality control of GAG-based surface coatings in a wide range of research areas, from molecular interaction analysis to biomaterials coatings.
Hedgehog signaling is non-cell autonomously activated in the cystic kidney of Arl13b mutant mice
Authors: Hsieh Chia-Ling , Jerman Stephanie Justine , Sun Zhaoxia
Published: March 2022

Background

Polycystic kidney disease (PKD) is a ciliopathy characterized by fluid-filled epithelial cysts in the kidney. Although it is well established that the primary cilium is essential for Hedgehog (HH) signalling and HH signalling is abnormally activated in cystic kidneys of multiple PKD models, the mechanism and function of HH activation in PKD pathogenesis remains incompletely understood.

Methods

We used a transgenic HH reporter line to identify the target tissue of HH signalling in Arl13f/f;Ksp-Cre mutant kidney, in which the cilia biogenesis gene Arl13b is specifically deleted in epithelial cells of the distal nephron. In addition, we treated Arl13bf/f;Ksp-Cre mice with the GLI inhibitor GANT61 and analyzed its impact on PKD progression in this model.

Results

In vivo in the mouse kidney, deletion of Arl13b in epithelial cells led to non-cell autonomous activation of the HH pathway in the interstitium. In addition, whole body inhibition of the HH pathway by GANT61 reduced cyst burden, suppressed fibrosis and reduced kidney function decline in Arl13bf/f;Ksp-Cre mice.

Conclusions

Our results reveal non-cell autonomous activation of HH signalling in the interstitium of the cystic kidney of Arl13bf/f;Ksp-Cre mice and suggest that abnormal activation of the HH pathway contributes to PKD progression.
Insights into the role of Nup62 and Nup93 in assembling cytoplasmic ring and central transport channel of the nuclear pore complex
Authors: Madheshiya Pankaj K. , Shukla Ekta , Singh Jyotsna , Bawaria Shrankhla , Ansari Mohammed Yousuf , Chauhan Radha
Published: March 2022

The nuclear pore complex (NPC) is a highly modular assembly of 34 distinct nucleoporins (Nups), to form a versatile transport channel between the nucleus and cytoplasm. Among them, Nup62 is known as an essential component for nuclear transport while, Nup93 for the proper nuclear envelope assembly. These Nups constitute various NPC subcomplexes: such as central transport channel (CTC), cytoplasmic ring (CR) and inner ring (IR). However, how they play their role in the NPC assembly and transport activity is not clear. Here we delineated the interacting regions, conducted biochemical reconstitution and structural characterization of the mammalian CR complex to reveal its intrinsic dynamic behaviour and a distinct ‘4’ shaped architecture resembling the CTC complex. Our data demonstrate that Nup62 coiled-coil domain is critical to form both Nup62•Nup88 and Nup62•Nup88•Nup214 heterotrimers and both can bind to the Nup93. We therefore propose that Nup93 act as a ‘sensor’ to bind to Nup62 shared heterotrimers including Nup62•Nup54 heterotrimer of the CTC, which was not shown previously as an interacting partner. Altogether, our study establishes that the Nup62 via its coiled-coil domain is central to form compositionally distinct yet structurally similar heterotrimers, and the Nup93 anchors these diverse heterotrimers by recognizing them non-selectively.
CircRNA_33702 promotes renal fibrosis by targeting the miR-29b-3p/WISP1 pathway
Authors: Ai Kai , Yi Lei , Wang Yinhuai
Published: March 2022

Growing evidence suggest that circular RNAs (circRNAs) are critical mediators in renal diseases. However, there have been very few reports about the role of circRNAs in renal fibrosis. In this study, circRNA_33702 was found to be upregulated, both in UUO mice and in TGF-β 1-treated BUMPT cells. Whilst knockdown of circRNA_33702 was shown to relieve the TGF-β 1-induced expression of collagen I, collagen III and fibronectin; overexpression of circRNA_33702 was found to exert an inhibitory effect on the expression of the same genes. Mechanistically, circRNA_33702 was demonstrated to bind directly with miR-29b-3p and inhibit its expression. Moreover, WISP1 was identified as a target of miR-29b-3p and the expression of WISP1 was observed to be repressed by miR-29b-3p. Notably, knockdown of circRNA_33702 was found to attenuate the expression of collagen I, collagen III and fibronectin by inhibiting the expression of WISP1, and the observed inhibitory effect can be reversed by miR-29b-3p inhibitor. Finally, inhibition of circRNA_33702 was shown to attenuate interstitial fibrosis in UUO mice via the miR-29b-3p/WISP1 axis. In general, our data show that circRNA_33702 may promote renal fibrosis via the miR-29b-3p/WISP1 axis, which may potentially be developed as a new therapeutic target.
Variability in SARS-Cov-2 IgG Antibody Affinity To Omicron and Delta Variants in Convalescent and Community mRNA Vaccinated Individuals
Authors: Tu Michael K. , Chiang Samantha H. , Wong David T.W. , Strom Charles M
Published: March 2022

The emergence of Omicron and Delta variants of SARS-CoV-2 has begun a number of discussions regarding breakthrough infection, waning immunity, need and timing for vaccine boosters and whether existing mRNA vaccines for the wildtype strain are adequate. Our work leverages a biosensor-based technique to evaluate the binding efficacy of SARS-CoV-2 S1 specific salivary antibodies to the Omicron and Delta variants using a cohort of mRNA vaccinated (n=109) and convalescent (n=19) subjects. We discovered a wide range of binding efficacies to the variant strains, with a mean reduction of 60.5%, 26.7%, and 14.7% in measurable signal to the Omicron strain and 13.4%, 2.4%, and −6.4% percent mean reduction to the Delta Variant for convalescent, Pfizer, and Moderna vaccinated groups respectively. This assay may be an important tool in determining susceptibility to infection or need for booster immunization as the pandemic evolves.

Key Points

AMPERIAL assay developed to quantify salivary SARS-CoV-2 S1 IgG antibodies to Omicron and Delta variants

There was a reduction in affinity to both Delta and Omicron Variants

The reduction in affinity was more pronounced to Omicron than for Delta Variants

There was a significant difference between IgG affinities in Individuals vaccinated with Pfizer versus Moderna Vaccines
Association of the medical therapy with beta-blockers or inhibitors of renin-angiotensin system with clinical outcomes in patients with mildly reduced left ventricular ejection fraction after acute myocardial infarction
Authors: Joo Seung-Jae , Kim Song-Yi , Lee Jae-Geun , Choi Joon-Hyouk , Park Hyeung Keun , Beom Jong Wook , Boo Ki Yung , Yoon Chang-Hwan , Lee Jung-Hee , Hur Seung-Ho , Chae Jei Keon , Jeong Myung Ho
Published: March 2022

In the era of the initial optimal interventional and medical therapy for acute myocardial infarction (AMI), a number of patients with mildly reduced left ventricular ejection fraction (EF) (41 - 49%) have been increasing. This observational study aimed to investigate the association between the medical therapy with oral beta-blockers or inhibitors of renin-angiotensin system (RAS) and 2-year clinical outcomes in patients with mildly reduced EF after AMI. Among patients enrolled in the Korea Acute Myocardial Infarction Registry-National Institute of Health, propensity-score matched patients who survived the initial attack and had mildly reduced EF were selected according to beta-blocker or RAS inhibitor therapy at discharge. Beta-blocker therapy at discharge was associated with lower 2-year major adverse cardiac events which was a composite of cardiac death, myocardial infarction, revascularization and re-hospitalization due to heart failure (8.7 vs. 12.8/100 patient-years; hazard ratio [HR] 0.68; 95% confidence interval [CI] 0.50-0.93; P=0.015), and no significant interaction between EF ≤45% and >45% was observed (Pinteraction=0.354). This association was mainly driven by lower myocardial infarction in patients with beta-blockers (HR 0.50; 95% CI 0.26-0.95; P=0.035). Inhibitors of RAS at discharge were associated with lower re-hospitalization due to heart failure (1.8 vs. 3.5/100 patient-years; HR 0.53; 95% CI 0.33-0.86; P=0.010) without a significant interaction between EF ≤45% and >45% (Pinteraction=0.333). In patients with mildly reduced EF after AMI, the medical therapy with beta-blockers or RAS inhibitors at discharge was associated with better 2-year clinical outcomes.
COVID-19 in Tunisia (North Africa): IgG and IgG subclass antibody responses to SARS-CoV-2 according to disease severity
Authors: Benabdessalem Chaouki , Marzouki Soumaya , Hamouda Wafa Ben , Trabelsi Khaled , Boumaiza Mohamed , Hamouda Sonia Ben , Ouni Rym , Bchiri Soumaya , Chaaban Amani , Gdoura Meriem , Gorgi Yousr , Sfar Imen , Yalaoui Sadok , Khelil Jalila Ben , Hamzaoui Agnes , Abdallah Meya , Cherif Yosra , Petres Stéphane , Pun Mok Chris Ka , Escriou Nicolas , Quesney Sébastien , Dellagi Koussay , Bettaieb Jihene , Rourou Samia , Barbouche Mohamed Ridha , Ahmed Melika Ben
Published: March 2022

Coronavirus disease 2019 (COVID-19) expresses a wide spectrum of disease severity. We investigated the profile of IgG and IgG subclass antibody responses to SARS– CoV-2 in Tunisian patients with COVID-19 according to disease severity (86 patients with severe disease and 63 with mild to moderate disease). Two in house developed ELISA with excellent performance were used to test for antibodies to the nucleocapsid (N) protein and the receptor-binding domain of the spike antigen (S-RBD) of SARS-CoV-2. IgG, IgG1 and IgG3 antibodies were significantly higher in patients with severe disease compared to non-severe disease. Antibodies to S-RBD or the N protein were dominated by IgG1 and IgG3 or IgG1/IgG3 and IgG2 subclasses respectively. In patients with severe disease, IgG antibodies ‘ appearance to S-RBD was delayed compared to the N protein. IgG subclass imbalance may reflect the pathophysiology of COVID-19 and may herald disease aggravation. This study brings information on the immune responses to SARS-CoV-2 in North African patients and completes the picture drawn on COVID-19 in different African populations and worldwide.
First detection of Powassan Virus lineage I in field-collected Dermacentor variabilis from New York, USA
Authors: Hart Charles , Hassett Erin , Vogels Chantal B.F. , Shapley Daniel , Grubaugh Nathan D. , Thangamani Saravanan
Published: March 2022

Powassan virus (POWV) is a tick-borne flavivirus that can cause lethal or debilitating neurological illness. It is canonically transmitted by Ixodes genus ticks but may interact with sympatric Dermacentor species. Here, we report the first detection of POWV lineage I from a pool of field-collected D. variabilis in New York state.
HIF1A modulate glycolysis function to governs mouse ovarian microenvironment metabolic plasticity in aging single cell resolution
Authors: Zhang Xiaoyu , Gunewardena Sumedha , Liu Yan , Wang Ning
Published: March 2022

The molecular machinery of ovarian aging and female age-related pathway remain unclear. Here, we utilized single-cell RNA-seq to profile over 9815 cells from both young and old female mouse and identified age-related alterations in the female somatic microenvironment. Interestingly, by aging-related signature calculation, we examined HIF1A in mouse ovarian cell aging regulated roles which effect pathways included glycolysis, TCA, OXPHOS and fatty acid metabolism. Additionally, inactivated HIF1A, decreased glycolysis was observed. Comparison analysis reveals the aging related regulon; metabolic and nutrient absorption changes provides a comprehensive understanding of the cell-type-specific mechanisms underlying mouse ovarian aging at single-cell resolution. This study, revealing new potential candidate biomarkers for the diagnosis of aging-associated ovary pathology.
PhD and postdoc training outcomes at EMBL: changing career paths for life scientists in Europe
Authors: Lu Junyan , Velten Britta , Klaus Bernd , Ramm Mauricio , Huber Wolfgang , Coulthard-Graf Rachel
Published: March 2022

The life sciences are training growing numbers of PhDs and postdocs, who increasingly engage in collaborative research. The impact of these changes on the careers of researchers is, however, unclear. Here, we report an analysis of the training outcomes for 2284 researchers who completed a PhD or postdoc at the European Molecular Biology Laboratory (EMBL) between 1997 and 2020. This is the first such study published from a European institute and first time-resolved analysis globally. The most common career outcomes were in academic research, service and teaching (1263 alumni, 55%), including 636 principal investigators (PIs). A broad spectrum of other career paths was also represented, including in industry research (332, 15%) and science-related professions (349, 15%). Our analysis indicates that, although there is increased competition for PI roles, life scientists continue to enter and excel in careers that drive research and innovation.
Integrating temporal single-cell gene expression modalities for trajectory inference and disease prediction
Authors: Ranek Jolene S. , Stanley Natalie , Purvis Jeremy E.
Published: March 2022

Current methods for analyzing single-cell datasets have relied primarily on static gene expression measurements to characterize the molecular state of individual cells. However, capturing temporal changes in cell state is crucial for the interpretation of dynamic phenotypes such as the cell cycle, development, or disease progression. RNA velocity infers the direction and speed of transcriptional changes in individual cells, yet it is unclear how these temporal gene expression modalities may be leveraged for predictive modeling of cellular dynamics. Here, we present the first task-oriented benchmarking study that investigates integration of temporal sequencing modalities for dynamic cell state prediction. We benchmark eight integration approaches on eight datasets spanning different biological contexts, sequencing technologies, and species. We find that integrated data more accurately infers biological trajectories and achieves increased performance on classifying cells according to perturbation and disease states. Furthermore, we show that simple concatenation of spliced and unspliced molecules performs consistently well on classification tasks and can be used over more memory intensive and computationally expensive methods. This work provides users with practical recommendations for task-specific integration of single-cell gene expression modalities.
A Morphogenetic Wave that Generates Mesenchymal-to-Epithelial Transition in the Lateral Plate Mesoderm
Authors: Asleh Manar Abboud , Zaher Mira , Jadon Julian , Shaulov Lihi , Yelin Ronit , Schultheiss Thomas M.
Published: March 2022

Most mesodermal cells undergo multiple cycles of transition between an epithelial and mesenchymal state during embryonic development. While many studies have addressed the process of epithelial-to-mesenchymal transition (EMT), comparatively less is known regarding the complementary process, mesenchymal-to-epithelial transition (MET), which is essential for organogenesis and has also been proposed to be important for cancer metastasis. The current study investigated MET using the lateral plate mesoderm (LPM) of the chick embryo as a model system. We find that MET in the LPM proceeds as a wave, which divides the LPM into distinct mesenchymal, transition, and epithelial zones. In the multilayered mesenchymal zone, many apical epithelial markers, including N-Cadherin (N-Cad), Par-3 and Zo-1, but not atypical protein kinase C (aPKC), are detected as dispersed, partially co-localizing aggregates associated with cell-cell contacts. The transition zone is characterized by the appearance of aPKC and the formation of rosette-like structures characterized by wedge-shaped cells that are apical-basal polarized, with strong co-localization of apical polarity markers, but not yet arranged into distinct epithelial sheets. The transition zone is also enriched in mitotic cells. Subsequently, the rosettes resolve into two well-defined epithelial sheets that constitute the coelomic epithelium, the lining of the internal body cavity.

Prior to any overt signs of apical-basal polarity, fibronectin (FN) begins to accumulate at the future basal side of the incipient epithelium. Interference with Extracellular Matrix (ECM)-integrin signaling through disruption of focal adhesion kinase (FAK) or Talin function hindered the normal progression of the epithelialization process. Cells with disrupted FAK or Talin function retained mesenchymal-like characteristics with respect to cellular morphology and apical-basal marker distribution.

We propose a two-stage process for MET in the LPM. Initially, in the polarization phase, ECM-integrin-dependent signaling imparts apical-basal polarity, culminating in the activation of aPKC, to drive cell intercalation and rosette formation. Subsequently in the resolution phase, polarized rosette cells, perhaps facilitated by the weakening of cell-cell interactions that occurs during mitosis, expand their apical surface, and spread out to form new connections laterally to their fully epithelial neighbors. This sequence of events is propagated as a wave through the LPM, thus generating an integrated coelomic epithelium.
Rule-based habitat suitability modelling for the reintroduction of the grey wolf (Canis lupus) in Scotland
Authors: Gwynn Vashti , Symeonakis Elias
Published: March 2022

Though native to Scotland, the grey wolf (Canis lupus) was extirpated c.250 years ago as part of a global eradication drive. The global population has recently expanded, now occupying 67% of its former range. Evidence is growing that apex predators provide a range of ecological benefits, most stemming from the reduction of overgrazing by deer – something from which Scotland suffers. In this study, we build a rule-based habitat suitability model for wolves on the Scottish mainland. From existing literature, we identify the most important variables as land cover, prey density, road density and human density, and establish thresholds of suitability for each. Fuzzy membership functions are used to assign suitability values to each variable, followed by fuzzy overlay to combine all four: a novel approach to habitat suitability modelling for terrestrial mammals. Model sensitivity is tested for land cover and prey density, as these variables constitute a knowledge gap and an incomplete dataset, respectively. The Highlands and Grampian mountains emerge strongly and consistently as the most suitable areas, largely due to high negative covariance between prey density and road/human density. Sensitivity testing reveals the models are fairly robust to changes in prey density, but less robust to changes in the scoring of land cover, with the latter altering the distribution of land mainly through the 70 – 100% suitability range. However, in statistical significance tests, only the least and most generous versions of the model emerge as giving significantly different results. Depending on the version of the model, a contiguous area of between 10,139km2 and 18,857km2 is shown to be 80 to 100% suitable. This could be sufficient to support between 50 and 94 packs of four wolves, if the average pack range size is taken to be 200km2. We conclude that in terms of habitat availability, reintroduction should be feasible.
Individually unique, fixed stripe configurations ofOctopus chierchiaeallow for photoidentification in long-term studies
Authors: Liu Benjamin , Song Leo , Kelkar Saumitra , Ramji Anna , Caldwell Roy
Published: March 2022

The Lesser Pacific Striped Octopus,Octopus chierchiae, is a small iteroparous octopus known to inhabit intertidal regions of the Pacific coast of Central America. Many details about its life history and ecology remain unknown. For apparently rare and delicate animals such asO. chierchiae, non-extractive sampling methods are necessary to study individuals and populations over time. After photographically documenting the physical development of 25 octopuses from hatching, we have concluded thatO. chierchiaehas individually unique stripe configurations that remain constant throughout their post-hatchling lifetimes. Furthermore, using photographs taken of animals in captivity on different dates over many months, we show that untrained volunteers can accurately identify whether or not a pair of images depicts the same individual octopus. These results demonstrate that laboratory-reared individuals could be identified via photographs taken at different points in their lifetimes, which suggests wild individuals can also be recognized and observed for longitudinal field studies. In addition, our results imply potential for photoidentification and community science to be used as non-extractive, non-intrusive sampling methods for future studies of wildO. chierchiae.
Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant
Authors: Calderón-Franco David , Sarelse Roel , Christou Stella , Pronk Mario , van Loosdrecht Mark C.M. , Abeel Thomas , Weissbrodt David G.
Published: March 2022

In the One Health context, wastewater treatment plants (WWTPs) are central to safeguard water resources. Nonetheless, many questions remain about their effectiveness to prevent the dissemination of antimicrobial resistance (AMR). Most surveillance studies monitor the levels and removal of selected antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in intracellular DNA (iDNA) extracted from WWTP influents and effluents. The role of extracellular free DNA (exDNA) in wastewater is mostly overlooked. In this study, we analyzed the transfer of ARGs and MGEs in a full-scale Nereda® reactor removing nutrients with aerobic granular sludge. We tracked the composition and fate of the iDNA and exDNA pools of influent, sludge, and effluent samples. Metagenomics was used to profile the microbiome, resistome, and mobilome signatures of iDNA and exDNA extracts. Selected ARGs and MGEs were analyzed by qPCR. From 2,840 ARGs identified, the genesarr-3(2%), tetC(1.6%), sul1(1.5%), oqxB(1.2%), andaph(3”)-Ib(1.2%) were the most abundant among all sampling points and bioaggregates.Pseudomonas,Acinetobacter,Aeromonas,Acidovorax,Rhodoferax,andStreptomycespopulations were the main hosts of ARGs in the sludge. In the effluent, 478 resistance determinants were detected, of which 89% from exDNA potentially released by cell lysis during aeration in the reactor. MGEs and multiple ARGs were co-localized on the same extracellular genetic contigs. These can pose a risk for AMR dissemination by transformation into microorganisms of receiving water bodies. Total intracellular ARGs decreased 3-42% as a result of wastewater treatment. However, theermBandsul1genes increased by 2 and 1 log gene copies mL-1, respectively, in exDNA from influent to effluent. The exDNA fractions need to be considered in AMR surveillance, risk assessment, and mitigation.

Graphical abstract

Highlights

A DNA database from an AGS reactor was constructed to study the system resistome, mobilome, and microbiome.

The generaPseudomonasandRhodoferaxwere the predominant ARG carriers in the system.

MGEs and ARGs often co-localize on contigs recovered from the exDNA of the effluent.

AGS plants are efficient at reducing ARB.

The exDNA is an underestimated DNA fraction containing ARGs in the effluent.
The periplasmic chaperone Skp prevents misfolding of the secretory lipase A from Pseudomonas aeruginosa
Authors: Papadopoulos Athanasios , Busch Max , Reiners Jens , Hachani Eymen , Bäumers Miriam , Schmitt Lutz , Jaeger Karl-Erich , Kovacic Filip , Smits Sander H.J. , Kedrov Alexej
Published: March 2022

Pseudomonas aeruginosa is a wide-spread opportunistic human pathogen and a high-risk factor for immunodeficient people and patients with cystic fibrosis. The extracellular lipase A belongs to the virulence factors of P. aeruginosa. The lipase undergoes folding and activation in the periplasm prior the secretion. Here, we demonstrate that the ubiquitous periplasmic chaperone Skp of P. aeruginosa, but not SurA, FkpA, PpiD or YfgM, efficiently prevents misfolding of the aggregation-prone lipase A and facilitates its activation by a specific foldase LipH. Small-angle X-ray scattering visualizes the trimeric architecture of P. aeruginosa Skp and identifies two primary conformations of the chaperone, a compact and a widely open. We describe two binding modes of Skp to the lipase, with affinities of 20 nM and 2 μM, which correspond to 1:1 and 1:2 stoichiometry of the lipase:Skp complex. Two Skp trimers are required to stabilize the lipase via the apolar interactions, which are not affected by high salt concentrations typical for the sputum of cystic fibrosis patients. The chaperoning effect of Skp points to its potent role in maturation and secretion of the lipase in Pseudomonas species.
Molecular Basis for Variations in the Sensitivity of Pathogenic Rhodopsin Variants to 9-cis-Retinal
Authors: Roushar Francis J. , McKee Andrew G. , Kuntz Charles P. , Ortega Joseph T. , Penn Wesley D. , Woods Hope , Chamness Laura M. , Most Victoria , Meiler Jens , Jastrzebska Beata , Schlebach Jonathan P.
Published: March 2022

Over 100 mutations in the rhodopsin gene have been linked to a spectrum of retinopathies that include retinitis pigmentosa and congenital stationary night blindness. Though most of these variants exhibit a loss of function, the molecular defects caused by these underlying mutations vary considerably. In this work, we utilize deep mutational scanning to quantitatively compare the plasma membrane expression of 123 known pathogenic rhodopsin variants in the presence and absence of the stabilizing cofactor 9-cis-retinal. We identify 69 retinopathy variants, including 20 previously uncharacterized variants, that exhibit diminished plasma membrane expression in HEK293T cells. 67 of these apparent class II variants exhibit a measurable increase in expression in the presence of 9-cis-retinal. However, the magnitude of the response to this molecule varies considerably across this spectrum of mutations. Evaluation of the observed shifts in relation to thermodynamic estimates for the coupling between binding and folding suggests underlying differences in stability constrains the magnitude of their response to retinal. Nevertheless, estimates from computational modeling suggest many of the least sensitive variants also directly compromise binding. Finally, we evaluate the functional properties of three previous uncharacterized, retinal-sensitive variants (ΔN73, S131P, and R135G) and show that two retain residual function in vitro. Together, our results provide a comprehensive experimental characterization of the proteostatic properties of retinopathy variants and their response to retinal.
ColorBayes: Improved color correction of high-throughput plant phenotyping images to account for local illumination differences
Authors: Lozano-Claros Diego , Custovic Eddie , Deng Guang , Whelan James , Lewsey Mathew G.
Published: March 2022

Background

Color distortion is an inherent problem in image-based phenotyping systems that are illuminated by artificial light. This distortion is problematic when examining plants because it can cause data to be incorrectly interpreted. One of the leading causes of color distortion is the non-uniform spectral and spatial distribution of artificial light. However, color correction algorithms currently used in plant phenotyping assume that a single and uniform illuminant causes color distortion. These algorithms are consequently inadequate to correct the local color distortion caused by multiple illuminants common in plant phenotyping systems, such as fluorescent tubes and LED light arrays. We describe here a color constancy algorithm, ColorBayes, based on Bayesian inference that corrects local color distortions. The algorithm estimates the local illuminants using the Bayes’ rule, the maximum a posteriori, the observed image data, and prior illuminant information. The prior is obtained from light measurements and Macbeth ColorChecker charts located on the scene.

Results

The ColorBayes algorithm improved the accuracy of plant color on images taken by an indoor plant phenotyping system. Compared with existing approaches, it gave the most accurate metric results when correcting images from a dataset of Arabidopsis thaliana images.

The software is available at https://github.com/diloc/Color_correction.git.
Rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought
Authors: Venkataraman Krithika , Shai Nadav , Lakhiani Priyanka , Zylka Sarah , Zhao Jieqing , Herre Margaret , Zeng Joshua , Neal Lauren A. , Molina Henrik , Zhao Li , Vosshall Leslie B.
Published: March 2022

Female Aedes aegypti mosquitoes impose a severe global public health burden as vectors of multiple viral pathogens. Under optimal environmental conditions, Aedes aegypti females have access to human hosts that provide blood proteins for egg development, conspecific males that provide sperm for fertilization, and freshwater that serves as an egg-laying substrate suitable for offspring survival. As global temperatures rise, Aedes aegypti females are faced with climate challenges like intense droughts and intermittent precipitation, which create unpredictable, suboptimal conditions for egg-laying. Here we show that under drought-like conditions simulated in the laboratory, females retain mature eggs in their ovaries for extended periods, while maintaining the viability of these eggs until they can be laid in freshwater. Using transcriptomic and proteomic profiling of Aedes aegypti ovaries, we identify two previously uncharacterized genes named tweedledee and tweedledum, each encoding a small, secreted protein that both show ovary-enriched, temporally-restricted expression during egg retention. These genes are mosquito-specific, linked within a syntenic locus, and rapidly evolving under positive selection, raising the possibility that they serve an adaptive function. CRISPR-Cas9 deletion of both tweedledee and tweedledum demonstrates that they are specifically required for extended retention of viable eggs. These results highlight an elegant example of taxon-restricted genes at the heart of an important adaptation that equips Aedes aegypti females with “insurance” to flexibly extend their reproductive schedule without losing reproductive capacity, thus allowing this species to exploit unpredictable habitats in a changing world.
Uncovering the ligandome of low-density lipoprotein receptor-related protein 1 in cartilage: a top-down approach to identify therapeutic targets
Authors: Yamamoto Kazuhiro , Scavenius Carsten , Meschis Maria M , Mogensen Emilie H , Gremida Abdulrahman M E , Thøgersen Ida B , Bonelli Simone , Scilabra Simone D , Santamaria Salvatore , Ahnström Josefin , Bou-Gharios George , Enghild Jan J , Nagase Hideaki
Published: March 2022

The low-density lipoprotein receptor-related protein 1 (LRP1) is a cell-surface receptor ubiquitously expressed in adult tissues. It plays tissue-specific physiological roles by mediating endocytosis of a diverse range of extracellular molecules. Dysregulation of LRP1 is involved in multiple conditions including Alzheimer’s disease, atherosclerosis and osteoarthritis (OA). However, little information is available about the specific ligand profile (ligandome) for each tissue, which would lead to better understanding of its role in disease states. Here, we investigated adult articular cartilage where impaired LRP1-mediated endocytosis leads to tissue destruction. We used a top-down approach involving analysis of human chondrocyte secretome, direct binding assays and validation in LRP1-deficient fibroblasts, as well as a novel Lrp1 conditional knockout (KO) mouse model. We found that inhibition of LRP1-mediated endocytosis results in cell death, alteration of the entire secretome and transcriptional modulations in human chondrocytes. We have identified more than 50 novel ligand candidates and confirmed direct LRP1 binding of HGFAC, HMGB1, HMGB2, CEMIP, SLIT2, ADAMTS1, IGFBP7, SPARC and LIF. Our in vitro endocytosis assay revealed the correlation of their affinity for LRP1 and the rate of endocytosis. Moreover, a conditional LRP1 KO mouse model demonstrated a critical role of LRP1 in regulating the high-affinity ligands in cartilage in vivo. This systematic approach revealed the extent of the chondrocyte LRP1 ligandome and identified potential novel therapeutic targets for OA.
The effectiveness of Tamarindus Indica extracts as a metal corrosion inhibitor in various circumstances
Authors: Nasser Rabab M. , Masmali Nora M.
Published: March 2022

Purpose

Plant development and use as green corrosion inhibitors are already recognized as one of the most environmentally friendly and effective protocols. In recent years, efforts have been made to find green corrosion inhibitors as an alternative to synthetic inhibitors for metals in acid medium. This paper aims to report the investigation of use of aqueous extracts of Tamarindus Indica as green inhibitors for corrosion of metals within different circumstances.

Design/methodology/approach

The use of Tamarindus Indica extracts (leaves, stem, fruit pulp and fruit husk) as corrosion inhibitors for mild steel and aluminum in different mediums (HCl, H2SO4, formic acid and citric acid) at different temperatures was investigated.

Findings

The inhibitory efficiency of Tamarindus Indica extracts increases with increasing concentration and decreases with increasing temperature. Langmuir is the adsorption isotherm, and the extract (inhibitor) is a mixed-type inhibitor (physisorption and chemisorption).

Practical implications

Tamarindus extracts (leaves, stem, fruit pulp and fruit husk) are effective inhibitors and can be used to protect metals from corrosion at different circumstances.

Originality/value

To the best of the authors’ knowledge, this is the first review that discusses the use of Tamarindus Indica extracts as corrosion inhibitors for metals.
Intellectual capital, sustainable economic and financial performance and value creation in emerging markets: the case of Brazil
Authors: Jordão Ricardo Vinícius Dias , Almeida Vander Ribeiro de , Novas Jorge
Published: March 2022

Purpose

The purpose of this paper is to analyze the influence of intellectual capital (IC) on sustainable economic and financial performance (EFP) and value creation (VC) in Brazilian companies.

Design/methodology/approach

Based on finance and accounting theories, a quantitative and descriptive long-term study was carried out in the companies listed on the Brazil Stock Exchange and Over-the-Counter Market (B3), covering 20 years period.

Findings

The results indicate that IC positively influences profitability, corporate return and organizational value sustainably; the most intangible-intensive Brazilian companies listed on B3 presented more robust results than the least intangible-intensive; and IC contributes to a systematic increase in EFP and VC over time.

Research limitations/implications

Using a well-established metric, the IC-INDEX, the IC and its effects were measured, obtaining theoretical contributions (expanding the understanding of the IC influence in sustainable EFP and VC from a long-term perspective – one subject still unexplored in the literature); and empirical (increasing the understanding of the IC’s role as a driver of competitiveness, performance and organizational value).

Practical implications

This study increases the understanding of the theoretical and practical effects of IC, also providing a competitive benchmarking process to access sustainable EFP and VC of companies and their industries.

Originality/value

The originally applied and validated proposal extends existing theory by offering a set of indicators to scale the contribution of IC to competitiveness from the perspective of long-term (historical) corporate outcomes.
Analysis of contractors' administrative characteristics in bid decision factors
Authors: Olatunji Oluwole Alfred , Ramanayaka Chamil Dilhan Erik , Rotimi Funmilayo Ebun , Rotimi James Olabode Bamidele
Published: March 2022

Purpose

The normative literature suggests that there are more than seventy decision factors that contractors must consider if they intend to success in their bid and projects. In addition, such factors have been grouped in relation to project characteristics, client attributes, contractors' business administration and external factors. The extant literature suggests that the relationships between many of the bid decision factors are orthogonal and may not explain how bid-decisions shape project outcomes.

Design/methodology/approach

This knowledge gap has stagnated research in this area. Building on findings of recent studies, this study unbundles bid decision themes by analysing key factors amongst contractors' administrative characteristics. In addition, the study determines intrinsic predictive correlation between the sub-themes. A total of 17 variables were listed in a structured questionnaire survey and presented to participants recruited through purposive snowballing. In total, 50 responses were received and formed the basis of descriptive and inferential statistical analyses.

Findings

The study found that the 17 factors are significant in bid decisions and consequently in bid successes. However, the explanatory variables attached to the themes are most efficient if categorised into six sub-themes. These are contractor's administration depth, strategic direction, commercial intention and own market advantage, resources, experience as well as openness to technology imposed by new projects. Furthermore, four theoretical positions are significant. Contractors bid for projects strategically; they are less reliant on their resource capabilities in bid decisions; every bid decision aligns with a risk strategy, and financial stability enables them to establish appropriate risk mitigation arrangements that could ensure project success.

Originality/value

These findings provide some support for the conceptual premise that bid decisions need to be rational, considered and strategically contribute to project outcomes.
Ambivalence toward bureaucracy: responses from Korean school principals
Authors: Joo Hyun-Jun , Kim Taeyeon
Published: March 2022

Purpose

Given the context of accountability-driven policy environments, research has shown that school leaders perceive bureaucratic rules and protocols in negative ways, but they also utilize organizational structures and routines to lead changes. To better understand both enabling and hindering mechanisms of bureaucracy in schools, this study explores how Korean school principals understand and perceive bureaucratic structures using a lens of ambivalence. The authors draw on Weber's theory of bureaucracy, with a particular focus on the paradoxical aspect of bureaucracy that might be experienced by individuals within the system.

Design/methodology/approach

This study analyzed qualitative data collected from 26 in-depth interviews with 10 Korean school principals between 2013 and 2015. The authors used the multiple cycles of coding to explore patterns and themes that emerged from the participants' responses.

Findings

The analysis of this study showed that the participants' ambivalent responses toward bureaucracy were particularly salient in three areas where formal organizational structures were changing through policy initiatives: teacher evaluation, electronic approval system and school-based management promoting decentralized decision making. The study participants reflected on how such changes can enable and/or hinder schools to achieve organizational goals and collective values, from the viewpoints of multiple aspects, which led to their ambivalent responses to bureacratic structures in school settings.

Originality/value

This study contributes to the understanding of school organizations by revisiting Weber's theory of bureaucracy in school settings. Using the lens of ambivalence enabled us to reconcile school principals' contradictory perceptions toward bureaucracy, which complicates analyses of tensions and paradoxical responses found in leadership practices within school systems.
A novel utilization-aware and power-delay-aware intelligent DMA controller for video streaming used in AI applications
Authors: Kumar B. Santosh , E. Krishna Kumar
Published: March 2022

Purpose

In real-time entertainment processing applications, processing of the multiple data streams demands high efficient multiple transfers, which leads to the computational overhead for system-on-chip (SoC), which runs the artificial intelligence algorithms. High-performance direct memory access controller (DMAC) is incorporated in SoC to perform the multiple data transfers without the participation of main processors. But achieving the area-efficient and power-aware DMAC suitable for streaming the multiple data remains to be a daunting challenge among the researchers.

Design/methodology/approach

The purpose of this paper to provide the DMA operations without intervention of central processing unit (CPU) for bulk video data transmissions.

Findings

The proposed DMAC has been developed based on the hybrid advanced extensible interface (AXI)-PCI bus subsystem to handle the multiple data streams from the video sources. The proposed model consists of bus selector module, user control signal, status register, DMA-supported address and AXI-PCI subsystems to achieve better performance in analysing the video frames.

Originality/value

The extensive experimentation is carried out with Xilinx Zynq SoC architecture using Very High Speed integrated circuit hardware description language (VHDL) programming, and performance metrics such as utilization area and power are calculated and compared with the other existing DMA controllers such as Scatter-DMA, Gather-DMA and Enhanced DMA. Simulation results demonstrate that the proposed DMAC has outperformed other existing DMAC in terms of less area, less delay and power, which makes the proposed model suitable for streaming multiple video streams.