bluuebunny/crossref_metadata_2025 huggingface dataset:
Astrocyte growth during morphogenesis is driven by the Tre1/S1pr1 phospholipid-binding G protein-coupled receptor
Authors: Chen Jiakun , Stork Tobias , Kang Yunsik , Sheehan Amy , Paton Cameron , Monk Kelly R. , Freeman Marc R.
Published: September 2022

Astrocytes play crucial roles in regulating neural circuit function by forming a dense network of synapse-associated membrane specializations, but signaling pathways regulating astrocyte morphogenesis remain poorly defined. Here we show theDrosophilalipid-binding G protein-coupled receptor (GPCR) Tre1, likely acting through Rac1, is required for astrocytes to elaborate their complex morphologyin vivo. The lipid phosphate phosphatases Wunen/Wunen2, which process phospholipid ligands, also regulate astrocyte morphology, and, via Tre1, mediate astrocyte-astrocyte competition for growth promoting lipids. Loss ofs1pr1, the functional analog ofTre1in zebrafish disrupts astrocyte process elaboration. Live-imaging and pharmacology demonstrate that S1pr1 balances proper astrocyte process extension/retraction dynamics during morphogenesis, and that S1pr1 signaling is required throughout astrocyte development. Tre1 and S1pr1 are thus potent evolutionarily conserved regulators of astrocyte growth and elaboration of morphological complexity.

The GPCR Tre1 and LPPs Wun/Wun2 promote astrocyte process outgrowth inDrosophila

Astrocytes compete for a growth­promoting phospholipid in the CNS

Wun/Wun2 act locally to regulate process outgrowth through Tre1

Vertebrate S1pr1 regulates astrocyte growth early, through modulation of process dynamics
Extensive collagen deposition by mesenchymal stem cells cultured in 3D self-assembled peptide scaffolds as revealed by nanoplasmonic colorimetric histology
Authors: Chong Christopher J.H. , Lim Vernise J.T. , Charnley Mirren , Ratcliffe Julian , Field Emily H. , Caballero-Aguilar Lilith M. , Johnson Chad , Orian Jacqueline M. , Caracciolo Kristian , Balaur Eugeniu , Abbey Brian , Moulton Simon E. , Binger Katrina J. , Reynolds Nicholas P.
Published: September 2022

Self-assembling peptides are promising candidates as scaffolds for 3D cell cultures. These hydrogels offer favourable biocompatibility, nanofibrillar structures that mimic native tissues, and the convenient integration of bioactive peptide sequences, such as arginine-glycine-aspartic acid (RGD), which can enable the development of therapeutically valuable cell types.

In the treatment of osteoarthritis (OA) attempts have been made to combine hydrogel scaffolds with mesenchymal stem cells (MSCs) to harness their regenerative potential. This involves the deposition of extracellular matrix (ECM) components like collagen and proteoglycans. Here, we employ the hydrogel-forming peptide Fmoc-diphenylalanine (Fmoc-FF) and incorporate stoichiometric amounts of Fmoc-RGD. We investigate the impact of RGD on nanofibrillar morphologies, hydrogel stability, MSC viability, and the deposition of collagen, proteoglycans, and glycosaminoglycans.

Elevating RGD content enhances cell viability and collagen deposition. However, at higher RGD concentrations, the stability of the hydrogels is compromised. To characterise collagen deposition, we introduce a non-destructive and label-free method using a plasmon-enhanced colorimetric histology technique. This innovation provides a practical means to image collagen without resorting to intricate and destructive sample processing and complex immunohistological staining procedures. This simple approach holds broad potential for routine and label-free quantification of collagen-rich biomaterials, promising widespread applications across various research and clinical settings.
Evaluation of different strategies for efficient sporulation and germination of the MICP bacterium Lysinibacillus sphaericus strain MB284 (ATCC 13805)
Authors: Rahmaninezhad Seyed Ali , Farnam Yaghoob A. , Schauer Caroline L. , Najafi Ahmad Raeisi , Sales Christopher M.
Published: September 2022

Environmental harsh conditions are one of the main challenges to the survivability of bacteria during microbially induced calcium carbonate precipitation (MICP) process. Due to the high resistivity of endospores against inhospitable conditions in comparison with vegetative cells, different sporulation methods were applied to Lysinibacillus sphaericus strain MB284 by changing the environmental conditions to investigate the growth of germinated cells. It was found that the sporulation yield was more when both carbon source starvation and the thermal shock process were applied to this bacterium. In addition, extending the sporulation time of cells into the minimal medium at 2 °C for a couple of weeks had a great impact on improving the sporulation yield. Comparing the growth rate of germinated endospores in natural conditions (pH 7 and 25 °C) and harsh conditions (pH 12, temperature of -10 to 60 °C, salinity up to 100 g/l) showed that endospores generated by thermal shock are able to germinate in almost every inhospitable condition except at low pH (∼3). Finally, exposing generated endospores before germination to harsh conditions (carbon source starving, high and low pH and temperature, and desiccation) for a nearly long period (to 100 days) showed that only low pH(∼3) had a negative effect on the germination process and bacterial growth curve that indicated endospore of strain MB284 can be an appropriate solution for the problem of the survivability of bioagents in MICP. These results will provide helpful information about preparing and applying endospores of L. sphaericus for crack healing in concrete.

Importance

In the bio-self-healing process, bacterial cells are responsible for the production of calcium carbonate to fill cracks in the concrete. Since cracks can happen at any time, cells must survive under harsh conditions in concrete for a long period. This study for the first time investigates different endosporulation methods to find the best well-formed endospores for microbial-inducing calcium carbonate precipitation (MICP). This study shows that the endospores of strain MB284 formed by the thermal shock can survive under inhospitable conditions including different ranges of temperatures (−4 to 60 °C), pH (3 to 14), salinity (up to 100 g/l), and starvation for about 100 days. Furthermore, the bacterial growth rate and the kinetics of calcium carbonate production by germinated endospores and vegetative cells were similar to each other that indicate endospores of strain MB284 formed by the thermal shock method developed in this study are good candidates for the MICP process.

Abstract Figure
Conventional and Bayesian workflows for clinical prediction modelling of severe Covid-19 outcomes based on clinical biomarker test results: LabMarCS: Laboratory Markers of COVID-19 Severity - Bristol Cohort
Authors: Sullivan Brian , Barker Edward , Williams Philip , MacGregor Louis , Bhamber Ranjeet , Thomas Matt , Gurney Stefan , Hyams Catherine , Whiteway Alastair , Cooper Jennifer A , McWilliams Chris , Turner Katy , Dowsey Andrew W. , Albur Mahableshwar
Published: September 2022

We describe several regression models to predict severe outcomes in COVID-19 and challenges present in complex observational medical data. We demonstrate best practices for data curation, cross-validated statistical modelling, and variable selection emphasizing recent Bayesian methods. The study follows a retrospective observational cohort design using multicentre records across National Health Service (NHS) trusts in southwest England, UK. Participants included hospitalised adult patients positive for SARS-CoV 2 during March to October 2020, totalling 843 patients (mean age 71, 45% female, 32% died or needed ICU stay), split into training (n=590) and validation groups (n=253). Models were fit to predict severe outcomes (ICU admission or death within 28-days of admission to hospital for COVID-19, or a positive PCR result if already admitted) using demographic data and initial results from 30 biomarker tests collected within 3 days of admission or testing positive if already admitted. Cross-validation results showed standard logistic regression had an internal validation median AUC of 0.74 (95% Interval [0.62,0.83]), and external validation AUC of 0.68 [0.61, 0.71]; a Bayesian logistic regression (with horseshoe prior) internal AUC of 0.79 [0.71, 0.87], and external AUC of 0.70 [0.68, 0.71]. Variable selection performed using Bayesian predictive projection determined a four variable model using Age, Urea, Prothrombin time and Neutrophil-Lymphocyte ratio, with a median internal AUC of 0.79 [0.78, 0.80], and external AUC of 0.67 [0.65, 0.69]. We illustrate best-practices protocol for conventional and Bayesian prediction modelling on complex clinical data and reiterate the predictive value of previously identified biomarkers for COVID-19 severity assessment.
The Association Between Thyroid Dysfunction, Autoimmune Thyroid Disease, and Rheumatoid Arthritis Disease Severity
Authors: Yazdanifar Mohammad Amin , Bagherzadeh-Fard Mahsa , Vahedian Mostafa , Habibi Mohammad Amin , Bagherzadeh Mohammad , Masoumi Maryam
Published: September 2022

Introduction

Rheumatoid Arthritis (RA) and autoimmune thyroid disease (AITD) are the two most prevalent autoimmune diseases that can coexist due to their similar pathogenesis. Considering the potential effect of AITD on the severity of RA disease, this study aimed to determine the association between thyroid dysfunction, anti-thyroid peroxidase (anti-TPO) positivity, AITD, and RA disease severity in the Iranian population.

Materials and methods

Three hundred and fifty RA patients who presented to Shahid Beheshti tertiary care center, Qom, Iran, were included in this cross-sectional study. The data were collected through the patients’ medical records, interviews, physical examinations, and laboratory investigations. The disease activity score in 28 joints for RA with ESR (DAS-28-ESR) was used to divide patients into three groups, remission (DAS-28-ESR ⍰2.6), mild-to-moderate (2.6 < DAS-28-ESR ⍰5.1), and severe disease activity (DAS-28-ESR > 5.1).

Results

Using the method explained beforehand, 111, 96, 138 patients were sorted into remission, mild-to-moderate, and severe disease activity groups, respectively. Anti-TPO antibody positivity was 2.93 times more prevalent among patients with higher severity of disease than in remission (OR: 2.93; P-value < 0.001). Patients suffering from a more severe form of the disease were almost 2.7 times more probable to have AITD (OR = 2.71; P-value < 0.001) and 82% more likely to have thyroid dysfunction than the patients in remission (OR = 1.82; P-value = 0.006).

Conclusions

It was demonstrated that thyroid dysfunction, anti-TPO antibody positivity, and AITD were significantly more common among RA patients with higher disease activity.
Interference of urinary albumin-to-creatinine ratio measurement by glycosuria: clinical implications when using SGLT-2 inhibitors
Authors: Chapman D , Judge PK , Sardell RJ , Staplin N , Arnold T , Zhu D , Ng S , Moffat S , Landray MJ , Baigent C , Hill M , Haynes R , Clark S , Herrington WG
Published: September 2022

Albuminuria is used for chronic kidney disease (CKD) screening, diagnosis, staging, and monitoring. A change in albuminuria has been proposed as a surrogate outcome for CKD progression. High glucose concentration interferes with Jaffe serum creatinine assays but the extent to which glycosuria biases measurement of urinary albumin-to-creatinine ratio (uACR) is uncertain. Any interference would have implications as the use of sodium-glucose co-transporter-2 (SGLT-2) inhibitors increases. We performed laboratory-based interference studies on urine samples from 333 adults with CKD stages 3-4. Samples were separated into four aliquots: a reference aliquot and three aliquots spiked with increasing concentrations of glucose solution representing the range expected in patients taking SGLT-2 inhibitors (28, 111 and 333 mmol/L). uACR was assayed using Jaffe and enzymatic methods. Median (Q1-Q3) uACR in reference samples was 63 (17-150) mg/mmol. Glucose spiking did not interfere with uACR estimation using enzymatic creatinine assays. For the Jaffe assay, the presence of 28 mmol/L of glucose resulted in a -1.5% mean bias in uACR (95% confidence interval -1.9 to -1.1%) which increased to a -2.5% bias (−3.2 to -1.9%) at a concentration of 333 mmol/L. Overestimation of urinary creatinine concentration increased substantially with decreasing creatinine concentration (i.e. dilute urine). In this cohort, interference of the Jaffe assay by glucose spiking resulted in 2-5% of uACR samples having a ≥10% spurious reduction in uACR (on its original scale). Given the increasing use of SGLT-2 inhibitors, we suggest uACR measured using Jaffe creatinine assays should be avoided.
Prevalence of Shigellosis in Pediatric Diarrheal Patients in Chattogram, Bangladesh: A Molecular Based Approach
Authors: Hossain A K M Zakir , Hasan Md. Zahid , Mina Sohana Akter , Sultana Nahid , Chowdhury A M Masudul Azad
Published: September 2022

Shigella a gram negative, non-motile bacillus, is the primary causative agent of the infectious disease shigellosis, which kills 1.1 million people worldwide every year. The children under the age of five are primarily the victims of this disease. This study has been conducted to assess the prevalence of shigellosis through selective plating, biochemical test and conventional PCR assays, where the samples were collected from suspected diarrheoal patients. Invasive plasmid antigen H (ipaH) and O-antigenic rfc gene were used to identify Shigella spp. and S. flexneri respectively. For validation of these identification, PCR product of ipaH gene of a sample (Shigella flexneri MZS 191) has been sequenced and submitted to NCBI database (GenBank accession no-MW774908.1). Further this strain has been used as positive control. Out of 204, around 14.2% (n=29) pediatric diarrheoal cases were screened as shigellosis. Another interesting finding was that most of shigellosis affected children were 7 months to 1 year. The significance of this study lies in the analyses of the prevalence and the molecular identification of Shigella spp. and S. flexneri that can be utilized in improving the accurate identification and the treatment of the most severe and alarming shigellosis.
The spatio-temporal distribution of musculoskeletal disorders: results of the Global Burden of Disease in 204 countries and 21 subregions between 1990 and 2019
Authors: Bouziri Hanifa , Roquelaur Yves , Descatha Alexis , Dab William , Jean Kévin
Published: September 2022

Objectives

This study aimed to globally assess the prevalence and distribution of primary-origin musculoskeletal disorders (MSDs) from 1990 to 2019 to better understand their temporal trends.

Methods

Using data from the 2019 Global Burden of Diseases, prevalence rates of 6 primary-origin MSDs were analysed across sub-regions, age groups, and genders. Raw and age-standardized data were mapped for over 204 countries. Cochran-Armitage trend tests evaluated temporal prevalence trends. The correlation between MSDs prevalence, national income levels, and medical density was explored.

Results

In 2019, global MSDs prevalence varied significantly among countries. Hip osteoarthritis had a prevalence of 0.56% [95% CI: 0.43-0.70], while low back pain was 8.62% [95% CI: 7.62-9.74]. Most MSDs exhibited an increasing prevalence with age, except for neck pain, which stabilized or decreased after age 45-50. Women generally had higher prevalence rates across all age groups. High-income countries consistently showed higher prevalence rates compared to middle and low-income countries. Over time, most sub-regions experienced a significant increase in MSD prevalence. However, after adjusting for age, the temporal trends for back and neck pain became non-significant, except for hip osteoarthritis, where half of the sub-regions remained significant. Multivariate linear regressions revealed positive associations between MSD prevalence and both national income level and medical density.

Conclusion

The global burden of MSDs is increasing due to population ageing, but other factors should be considered. Longitudinal studies with a wider range of MSDs and additional risk factors are needed for improved prevention strategies.
Low Dimensional Chaotic Attractors in SARS-CoV-2’s Regional Epidemiological Data
Authors: Gonçalves Carlos Pedro
Published: September 2022

Background

Recent studies applying chaos theory methods have found the existence of chaotic markers in SARS-CoV-2’s epidemiological data, evidence that has implications on the prediction, modeling and epidemiological analysis of the SARS-CoV-2/COVID-19 pandemic with implications for healthcare management.

Aim and Methods

We study the aggregate data for the new cases per million and the new deaths per million from COVID-19 in Africa, Asia, Europe, North and South America and Oceania, applying chaos theory’s empirical methods including embedding dimension estimation, Lyapunov spectra estimation, spectral analysis and state-of-the-art topological data analysis methods combining persistent homology, recurrence analysis and machine learning with the aim of characterizing the nature of the dynamics and its predictability.

Results

The results show that for all regions except Oceania there is evidence of low dimensional noisy chaotic attractors that are near the onset of chaos, with a recurrence structure that can be used by adaptive artificial intelligence solutions equipped with nearest neighbors’ machine learning modules to predict with a very high performance the future values of the two target series for each region. The persistent homology analysis uncovers a division into two groups, the first group comprised of Africa and Asia and the second of Europe, North and South America. For Oceania, we found evidence of the occurrence of a bifurcation which we characterize in detail applying a combination of machine learning and topological analysis methods, we find that the bifurcation in the region is related to the emergence of new variants.
Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222
Authors: Chaudhari Aditya S. , Chatterjee Aditi , Domingos Catarina A.O. , Andrikopoulos Prokopis C. , Liu Yingliang , Andersson Inger , Schneider Bohdan , Lórenz-Fonfría Víctor A. , Fuertes Gustavo
Published: September 2022

Photoreceptors containing the light-oxygen-voltage (LOV) domain elicit biological responses upon excitation of their flavin mononucleotide (FMN) chromophore by blue light. The mechanism and kinetics of dark-state recovery are not well understood. Here we incorporated the non-canonical amino acid p-cyanophenylalanine (CNF) by genetic code expansion technology at forty-five positions of the bacterial transcription factor EL222. Screening of light-induced changes in infrared (IR) absorption frequency, electric field and hydration of the nitrile groups identified residues CNF31 and CNF35 as reporters of monomer/oligomer and caged/decaged equilibria, respectively. Time-resolved multi-probe UV/Visible and IR spectroscopy experiments of the lit-to-dark transition revealed four dynamical events. Predominantly, rearrangements around the A’α helix interface (CNF31 and CNF35) precede FMN-cysteinyl adduct scission, folding of α-helices (amide bands), and relaxation of residue CNF151. This study illustrates the importance of characterizing all parts of a protein and suggests a key role for the N-terminal A’α extension of the LOV domain in controlling EL222 photocycle length.

Significance

The kinetics of fold switching between non-illuminated and blue-light-irradiated states in the transcription factor EL222 is important for understanding the signal transduction mechanism of LOV photoreceptors. Here we combine two native probes, the FMN chromophore (absorption bands in the UV/Visible region) and the protein backbone (amide bands in the infrared region), with genetically encoded cyano (C≡N)-containing phenylalanine residues as infrared reporters of protein microenvironments. EL222 structural dynamics is more complex than expected if using a single type of probe. Local changes around residues 31 and 35 precede FMN-protein adduct rupture, which in turn precedes the global protein conformational relaxation. Our findings point the way forward to obtaining comprehensive descriptions of kinetic transitions in LOV and other photosensors.
A new species ofNanhsiungchelys(Testudines: Cryptodira: Nanhsiungchelyidae) from the Upper Cretaceous of Nanxiong Basin, China, and the role of anterolateral processes on the carapace in drag reduction
Authors: Ke Yuzheng , Rahman Imran A. , Song Hanchen , Hu Jinfeng , Niu Kecheng , Han Fenglu
Published: September 2022

Nanhsiungchelyidae are a group of large turtles that lived in Asia and North America during the Cretaceous. Here we report a new species of nanhsiungchelyid,Nanhsiungchelys yangisp. nov., from the Upper Cretaceous of Nanxiong Basin, China. This is the second valid species ofNanhsiungchelys, and the holotype consists of a well-preserved skull and lower jaw, as well as the anterior parts of the carapace and plastron. The diagnostic features ofNanhsiungchelysinclude a huge estimated body size (~55.5 cm), a special network of sculptures on the surface of the skull and shell, weak cheek emargination and temporal emargination, deep nuchal emargination, and a pair of anterolateral processes on the carapace. However,Nanhsiungchelys yangidiffers from the other species ofNanhsiungchelysin having a triangular-shaped snout and wide anterolateral processes. A phylogenetic analysis of nanhsiungchelyids placesNanhsiungchelys yangiandNanhsiungchelys wuchingensisas sister taxa. Some nanhsiungchelyids bear special anterolateral processes on the carapace, which are unknown in extant turtles. Here we test the function of these processes inNanhsiungchelys yangiusing computational fluid dynamics, and the results suggest these processes could enhance locomotory performance by remarkably reducing drag force when the animal was swimming through water.
Mitochondrial sodium/calcium exchanger NCLX regulates glycolysis in astrocytes, impacting on cognitive performance
Authors: Cabral-Costa João Victor , Vicente-Gutiérrez Carlos , Agulla Jesús , Lapresa Rebeca , Elrod John W. , Almeida Ángeles , Bolaños Juan P. , Kowaltowski Alicia J.
Published: September 2022

Intracellular Ca2+ concentrations are strictly controlled by plasma membrane transporters, the endoplasmic reticulum, and mitochondria, in which Ca2+ uptake is mediated by the mitochondrial calcium uniporter complex (MCUc), while efflux occurs mainly through the mitochondrial Na+/Ca2+ exchanger (NCLX). RNAseq database repository searches led us to identify the Nclx transcript as highly enriched in astrocytes when compared to neurons. To assess the role of NCLX in mouse primary culture astrocytes, we inhibited its function both pharmacologically or genetically. This resulted in re-shaping of cytosolic Ca2+ signaling and a metabolic shift that increased glycolytic flux and lactate secretion in a Ca2+-dependent manner. Interestingly, in vivo genetic deletion of NCLX in hippocampal astrocytes improved cognitive performance in behavioral tasks, whereas hippocampal neuron-specific deletion of NCLX impaired cognitive performance. These results unveil a role for NCLX as a novel modulator of astrocytic glucose metabolism, impacting on cognition.
Transcriptome-wide analysis of pseudouridylation inDrosophila melanogaster
Authors: Song Wan , Podicheti Ram , Rusch Douglas B. , Tracey W. Daniel
Published: September 2022

Pseudouridine (Psi) is one of the most frequent post-transcriptional modification of RNA. Enzymatic Psi modification occurs on rRNA, snRNA, snoRNA, tRNA, non-coding RNA and has recently been discovered on mRNA. Transcriptomewide detection of Psi (Psi-seq) has yet to be performed for the widely studied model organismDrosophila melanogaster. Here, we optimized Psi-seq analysis for this species and have identified thousands of Psi modifications throughout the female fly head transcriptome. We find that Psi is widespread on both cellular and mitochondrial rRNAs. In addition, more than a thousand Psi sites were found on mRNAs. When pseudouridylated, mRNAs frequently had many Psi sites. Many mRNA Psi sites are present in genes encoding for ribosomal proteins, and many are found in mitochondrial encoded RNAs, further implicating the importance of pseudouridylation for ribosome and mitochondrial function. The 7SLRNA of the signal recognition particle is the non-coding RNA most enriched for Psi. The three mRNAs most enriched for Psi encode highly-expressed yolk proteins (Yp1, Yp2, Yp3). By comparing the pseudouridine profiles in theRluA-2mutant and thew1118control genotype, we identified Psi sites that were missing in the mutant RNA as potential RluA-2 targets. Finally, differential gene expression analysis of the mutant transcriptome indicates a major impact of loss of RluA-2 on the ribosome and translational machinery.
Transcriptional units form the elementary constraining building blocks of the bacterial chromosome
Authors: Bignaud Amaury , Cockram Charlotte , Allemand Eric , Mozziconnacci Julien , Espeli Olivier , Koszul Romain
Published: September 2022

Transcription generates local topological and mechanical constraints along the DNA fiber, driving for instance the generation of supercoiled chromosomal domains in bacteria. However, the global impact of transcription-based regulation of chromosome organization remains elusive. Notably, the scale of genes and operons in bacteria remains well below the resolution of chromosomal contact maps generated using Hi-C (~ 5 – 10 kb), preventing to resolve the impact of transcription on genomic organization at the fine-scale. Here, we combined sub-kb Hi-C contact maps and chromosome engineering to visualize individual transcriptional units (TUs) while turning off transcription across the rest of the genome. We show that each TU forms a discrete, transcription-induced 3D domain (TIDs). These local structures impose mechanical and topological constraints on their neighboring sequences at larger scales, bringing them closer together and restricting their dynamics. These results show that the primary building blocks of bacteria chromosome folding consists of transcriptional domains that together shape the global genome structure.
Brassinosteroid gene regulatory networks at cellular resolution
Authors: Nolan Trevor M , Vukašinović Nemanja , Hsu Che-Wei , Zhang Jingyuan , Vanhoutte Isabelle , Shahan Rachel , Taylor Isaiah W , Greenstreet Laura , Heitz Matthieu , Afanassiev Anton , Wang Ping , Szekely Pablo , Brosnan Aiden , Yin Yanhai , Schiebinger Geoffrey , Ohler Uwe , Russinova Eugenia , Benfey Philip N
Published: September 2022

Brassinosteroids (BRs) are plant steroid hormones that regulate diverse processes such as cell division and cell elongation. BRs control thousands of genes through gene regulatory networks that vary in space and time. By using time-series single-cell RNA-sequencing to identify BR-responsive gene expression specific to different cell types and developmental stages of the Arabidopsis root, we uncovered the elongating cortex as a site where BRs trigger a shift from proliferation to elongation associated with increased expression of cell wall-related genes. Our analysis revealed HAT7 and GTL1 as BR-responsive transcription factors that regulate cortex cell elongation. These results establish the cortex as an important site for BR-mediated growth and unveil a BR signaling network regulating the transition from proliferation to elongation, illuminating new aspects of spatiotemporal hormone response.
In vitro evaluation of immune responses to bacterial hydrogels for the development of living therapeutic materials
Authors: Yanamandra Archana , Bhusari Shardul , del Campo Aránzazu , Sankaran Shrikrishnan , Qu Bin
Published: September 2022

In living therapeutic materials, organisms genetically programmed to produce and deliver drugs are encapsulated in porous matrices or hydrogels acting as physical barriers between the therapeutic organisms and the host cells. The therapeutic potential of such constructs has been highlighted in in vitro studies, but the translation to in vivo scenarios requires evaluation of the immune response to the presence of the encapsulated, living organisms. In this study, we investigate the responses of human peripheral blood mononuclear cells (PBMCs) exposed to a living therapeutic material consisting of engineered E. coli encapsulated in Pluronic F127-based hydrogels. The release of inflammation-related cytokines (IL-2, IL-4, IL-6, IL-10, IL-17A, TNFα and IFNγ) and cytotoxic proteins (granzyme A, granzyme B, perforin, granulysin, sFas, and sFasL) in response to the bacterial hydrogels, as well as the subsets of natural killer cells and T cells after exposure to the bacterial hydrogel for up to three days were examined. In direct contact with PBMCs, both E. coli and its endotoxin-free variant, ClearColi, induce apoptosis of the immune cells and trigger IL-6 release from the surviving cells. However, we found that encapsulation of the bacteria in Pluronic F127 diacrylate hydrogels considerably lowers their immunogenicity and practically abolishes apoptosis triggered by ClearColi. In comparison with E. coli, free and hydrogel-encapsulated ClearColi induced significantly lower levels of NK cell differentiation into the more cytolytic CD16dim subset. Our results demonstrate that ClearColi-encapsulated hydrogels generate low immunogenic response and are suitable candidates for the development of living therapeutic materials for in vivo testing to assess a potential clinical use. Nevertheless, we also observed a stronger immune response in pro-inflammatory PBMCs, possibly from donors with underlying infections. This suggests that including anti-inflammatory measures in living therapeutic material designs could be beneficial for such recipients.
Molecular Acclimation of Halobacterium salinarum to Halite Brine Inclusions
Authors: Favreau C. , Tribondeau A. , Marugan M. , Guyot F. , Alpha-Bazin B. , Marie A. , Puppo R. , Dufour T. , Huguet A. , Zirah S. , Kish A.
Published: September 2022

1

Halophilic microorganisms have long been known to survive within the brine inclusions of salt crystals, as evidenced by the change in color for salt crystals containing pigmented halophiles. However, the molecular mechanisms allowing this survival has remained an open question for decades. While protocols for the surface sterilization of halite (NaCl) have enabled isolation of cells and DNA from within halite brine inclusions, “-omics” based approaches have faced two main technical challenges: (1) removal of all contaminating organic biomolecules (including proteins) from halite surfaces, and (2) performing selective biomolecule extractions directly from cells contained within halite brine inclusions with sufficient speed to avoid modifications in gene expression during extraction. In this study, we present methods to resolve these two technical challenges. In addition, we apply these methods to perform the first examination of the early acclimation of a model haloarchaeon (Halobacterium salinarum NRC-1) to halite brine inclusions. Examinations of the proteome of Halobacterium cells two months post-evaporation revealed a high degree of similarity with stationary phase liquid cultures, but with a sharp down-regulation of ribosomal proteins. Low quantities of RNA from halite brine inclusions corroborate the hypothesis of low transcriptional and translational activities. While proteins for central metabolism were part of the shared proteome between liquid cultures and halite brine inclusions, proteins involved in cell mobility (archaellum, gas vesicles) were either absent or less abundant in halite samples. Proteins unique to cells within brine inclusions included transporters, suggesting modified interactions between cells and the surrounding brine inclusion microenvironment. The methods and hypotheses presented here enable future studies of the survival of halophiles in both culture model and natural halite systems.
Cycle length flexibility: is the duration of sexual receptivity associated with changes in the social environment?
Authors: Fragkiskos Darmis , Élise Huchard , Guy Cowlishaw , Alecia Carter J.
Published: September 2022

Research in social mammals has revealed the complexity of strategies females use in response to female-female reproductive competition and sexual conflict. One point at which competition and conflict manifests acutely is during sexual receptivity, indicated by swellings in some primates. Whether females can adjust their sexual receptivity from cycle to cycle to decrease reproductive competition and sexual conflict in response to changes in the social environment has not been tested. As a first step, this study explores whether sexual receptivity duration is predicted by the social environment in wild female chacma baboons (Papio ursinus). Given that female baboons face intense reproductive competition and sexual coercion, we predicted that: females could shorten the duration of their sexual receptive period to reduce female-female aggression and male coercion or increase it to access multiple or their preferred male(s). We quantified 157 ovulatory cycles from 46 wild females living in central Namibia recorded over 15 years. We found no support for our hypothesis; however, we found a negative correlation between maximal-swelling duration and group size, a proxy of within-group competition. This study provides further evidence that swelling is costly for females as well as a testable framework for future investigations of ‘cycle length manipulation’.
Detection of neuronal OFF periods as low amplitude neural activity segments
Authors: Harding Christian D. , Guillaumin Mathilde C.C. , Krone Lukas B. , Kahn Martin C. , Blanco-Duque Cristina , Mikutta Christian , Vyazovskiy Vladyslav V.
Published: September 2022

During non-rapid eye movement sleep (NREM), synchronised neuronal activity is reflected in a specific neural oscillation observed in neocortical electrophysiological signals: a low frequency component characterised by depth-positive/surface-negative potentials known as slow waves, corresponding to alternating periods of high (ON period) and low (OFF period) spiking activity. Often overlooked in favour of slow waves, there is an interest in understanding how neuronal silencing during OFF periods leads to the generation of slow waves and whether this relationship changes between cortical layers. The foremost issue in detecting population OFF periods is the absence of a formal, widely adopted definition. Here, we grouped segments of high frequency neural activity containing spikes, recorded from the neocortex, on the basis of amplitude and asked whether the population of low amplitude (LA) segments displayed the expected characteristics of OFF periods. We corroborate previous studies showing that LA segments in neural activity signals are a uniquely identifiable structure with distinct characteristics from the surrounding signal that identify them as OFF periods including NREM sleep predominance and association with a local field potential (LFP) slow wave. In addition, we attribute new characteristics to these segments not previously associated with OFF periods: vigilance-state-dependent duration and duration-dependent homeostatic response. This could suggest that ON/OFF periods are currently underdefined, and their appearance is less binary than previously considered, instead representing a continuum.
Enrichment and application of bacterial sialic acids containing polymers from the extracellular polymeric substances of “Candidatus Accumulibacter”
Authors: Tomás-Martínez Sergio , Chen Le Min , Pabst Martin , Weissbrodt David G. , van Loosdrecht Mark C.M. , Lin Yuemei
Published: September 2022

Pseudaminic and legionaminic acids are a subgroup of nonulosonic acids (NulOs) unique to bacterial species. There is a lack of advances in the study of these NulOs due to their complex synthesis and production. Recently, it was seen that “Candidatus Accumulibacter” can produce Pse or Leg analogues as part of its extracellular polymeric substances (EPS). In order to employ a “Ca. Accumulibacter” enrichment as production platform for bacterial sialic acids, it is necessary to determine which fractions of the EPS of “Ca. Accumulibacter” contain NulOs and how to enrich and/or isolate them. We extracted the EPS from granules enriched with “Ca. Accumulibcater” and used size-exclusion chromatography to separate them into different molecular weight fractions. This separation resulted in two high molecular weight (> 5,500 kDa) fractions dominated by polysaccharides, with a NulO content up to 4 times higher than the extracted EPS. This suggests that NulOs in “Ca. Accumulibacter” are likely located in high molecular weight polysaccharides. Additionally, it was seen that the extracted EPS and the NulO-rich fractions can bind and neutralize histones. This suggest that they can serve as source for sepsis treatment drugs, although further purification needs to be evaluated.

Graphical abstract

Highlights

NulOs in “Ca. Accumulibacter” are likely located in high molecular weight polysaccharides.

Size exclusion chromatography allows to obtain high molecular weight polysaccharide-rich fractions enriched with NulOs.

EPS and the NulOs-rich fractions can serve as source for sepsis treatment drugs.
Notch directs telencephalic development and controls neocortical neuron fate determination by regulating microRNA levels
Authors: Han Jisoo S. , Fishman-Williams Elizabeth , Decker Steven C. , Hino Keiko , Reyes Raenier V. , Brown Nadean L. , Simó Sergi , Torre Anna La
Published: September 2022

The central nervous system (CNS) contains myriads of different types of cells produced from multipotent neural progenitors. Neural progenitors acquire distinct cell identities depending on their spatial position, but they are also influenced by temporal cues to give rise to different cell populations over time. For instance, the progenitors of the cerebral neocortex generate different populations of excitatory projection neurons following a well-known sequence. The Notch signaling pathway plays crucial roles this process but the molecular mechanisms by which Notch impacts progenitor fate decisions have not been fully resolved. Here, we show that Notch signaling is essential for neocortical and hippocampal morphogenesis, and for the development of the corpus callosum and choroid plexus. Our data also indicate that, in the neocortex, Notch controls projection neuron fate determination through the regulation of two microRNA (miRNA) clusters that include let-7, miR-99a/100, and miR-125b. Our findings collectively suggest that balanced Notch signaling is crucial for telencephalic development and that the interplay between Notch and miRNAs is critical to control neocortical progenitor behaviors and neuron cell fate decisions.
GPCR signaling promotes severe stress-induced organismic death inC. elegans
Authors: Wang Changnan , Long Yong , Wang Bingying , Zhang Chao , Ma Dengke K.
Published: September 2022

How an organism dies is a fundamental yet poorly understood question in biology. An organism can die of many causes, including stress-induced phenoptosis, also defined as organismic death that is regulated by its genome-encoded programs. The mechanism of stress-induced phenoptosis is still largely unknown. Here we show that transient but severe freezing-thaw stress (FTS) inC. elegansinduces rapid and robust phenoptosis that is regulated by G-protein coupled receptor (GPCR) signaling. RNAi screens identify the GPCR-encodingfshr-1in mediating transcriptional responses to FTS. FSHR-1 increases ligand interaction upon FTS and activates a cyclic AMP-PKA cascade leading to a genetic program to promote organismic death under severe stress. FSHR-1/GPCR signaling up-regulates the bZIP-type transcription factor ZIP-10, linking FTS to expression of genes involved in lipid remodeling, proteostasis and aging. A mathematical model suggests that genes may promote organismic death under severe stress conditions, potentially benefiting growth of the clonal population with individuals less stressed and more reproductively privileged. Our studies reveal roles of FSHR-1/GPCR-mediated signaling in stress-induced gene expression and phenoptosis inC. elegans, providing empirical new insights into mechanisms of stress-induced phenoptosis with evolutionary implications.
Day-to-day spontaneous social behaviours is quantitatively and qualitatively affected in a 16p11.2 deletion mouse model
Authors: Rusu Anna , Chevalier Claire , de Chaumont Fabrice , Nalesso Valérie , Brault Véronique , Hérault Yann , Ey Elodie
Published: September 2022

Background

Autism spectrum disorders affect more than one percent of the population, impairing social communication and increasing stereotyped behaviours. A micro-deletion of the 16p11.2 BP4-BP5 chromosomic region has been identified in one percent of patients also displaying intellectual disabilities. In mouse models generated to understand the mechanisms of this deletion, learning and memory deficits were pervasive in most genetic backgrounds, while social communication deficits were only detected in some models.

Methods

Based on previous study (Arbogast et al. 2016 PLoS genetics), we itemized the social deficits in the mouse model of 16p11.2 deletion on a hybrid C57BL/6NxC3H.Pde6b+genetic background. We examined whether behavioural deficits were visible over long-term observation periods, to parallel everyday-life assessment of patients. We recorded the individual and social behaviours of 16p11.2 Del/+ mice and their wild-type littermates from both sexes in long-term (over two and three consecutive nights) social interactions of familiar mixed-genotype quartets of males and of females, and of same-genotype unfamiliar female pairs.

Results

We observed that Del/+ mice of both sexes increased significantly their locomotor activity compared to wild-type littermates over long-term monitoring. In the social domain, Del/+ mice of both sexes displayed widespread deficits over long-term monitoring, even more so in males than in females in quartets of familiar individuals. In pairs, significant perturbations of the organisation of the social communication and behaviours appeared in Del/+ females.

Discussion

Altogether, this suggests that, over long recording periods, the phenotype of the 16p11.2 Del/+ mice was differently affected in the locomotor activity and the social domains and between the two sexes. These findings confirm the importance of testing models in long-term conditions to provide a comprehensive view of their phenotype that will refine the study of cellular and molecular mechanisms and complement pre-clinical targeted therapeutic trials.
Characterizing the Resolution and Throughput of the Apollo Direct Electron Detector
Authors: Peng Ruizhi , Fu Xiaofeng , Mendez Joshua H. , Randolph Peter S. , Bammes Benjamin E. , Stagg Scott M.
Published: September 2022

Advances in electron detection have been essential to the success of high-resolution cryo-EM structure determination. A new generation of direct electron detector called the Apollo, has been developed by Direct Electron. The Apollo uses a novel event-based MAPS detector custom designed for ultra-fast electron counting. We have evaluated this new camera, finding that it delivers high detective quantum efficiency (DQE) and low coincidence loss, enabling high-quality electron counting data acquisition at up to nearly 80 input electrons per pixel per second. We further characterized the performance of Apollo for single particle cryo-EM on real biological samples. Using mouse apoferritin, Apollo yielded better than 1.9 Å resolution reconstructions at all three tested dose rates from a half-day data collection session each. With longer collection time and improved specimen preparation, mouse apoferritin was reconstructed to 1.66 Å resolution. Applied to a more challenging small protein aldolase, we obtained a 2.24 Å resolution reconstruction. The high quality of the map indicates that the Apollo has sufficiently high DQE to reconstruct smaller proteins and complexes with high-fidelity. Our results demonstrate that the Apollo camera performs well across a broad range of dose rates and is capable of capturing high quality data that produce high-resolution reconstructions for large and small single particle samples.
Morphological and temporal variation in early embryogenesis contributes to species divergence in Malawi cichlid fishes
Authors: Marconi Aleksandra , Yang Cassandra , McKay Samuel , Santos M. Emília
Published: September 2022

The cichlid fishes comprise the largest extant vertebrate family and are the quintessential example of rapid “explosive” adaptive radiations and phenotypic diversification. Despite low genetic divergence, East African cichlids harbour a spectacular intra- and interspecific morphological diversity, including the hyper-variable, neural crest (NC)-derived traits such as colouration and craniofacial skeleton. Although the genetic and developmental basis of these phenotypes has been investigated, understanding of when, and specifically how early, in ontogeny species-specific differences emerge, remains limited. Since adult traits often originate during embryonic development, the processes of embryogenesis could serve as a potential source of species-specific variation. Consequently, we compared the features of embryogenesis between three Malawi cichlid species – Astatotilapia calliptera, Tropheops sp. ‘mauve’ and Rhamphochromis sp. ‘chilingali’ – representing a wide spectrum of variation in pigmentation and craniofacial morphologies. Our results showed fundamental differences in multiple aspects of embryogenesis that could underlie interspecific divergence in adult adaptive traits. Firstly, we identified variation in the somite number and signatures of temporal variation, or heterochrony, in the rates of somite formation. The heterochrony was also evident within and between species throughout ontogeny, up to the juvenile stages. Finally, the identified interspecific differences in the development of pigmentation and craniofacial cartilages, present at the earliest stages of their overt formation, provide compelling evidence that the species-specific trajectories begin divergence during early embryogenesis, potentially during somitogenesis and NC development. Altogether, our results expand our understanding of fundamental cichlid biology and provide new insights into the developmental origins of vertebrate morphological diversity.

Research highlights

This work details the early development of three divergent Lake Malawi cichlids. A comparative analysis reveals anatomical and timing differences during embryogenesis and indicates divergence of species’ morphologies prior to their overt formation.