bluuebunny/crossref_metadata_2025 huggingface dataset:
Sex-stratified genomic structural equation models of posttraumatic stress inform PTSD etiology
Authors: Moo-Choy Ashley , Stein Murray , Gelernter Joel , Wendt Frank R
Published: September 2023

Posttraumatic stress disorder (PTSD) affects 3.9%-5.6% of the worldwide population, with well-documented sex-related differences. While psychosocial and hormonal factors affecting sex differences in PTSD and posttraumatic stress (PTS) symptom etiology have been explored, there has been limited focus on genetic bases of these differences. Many symptom combinations may confer a PTSD diagnosis. We hypothesized that these symptom combinations have sex-specific patterns, the examination of which could inform etiological differences in PTSD genetics between males and females. To investigate this, we performed a sex-stratified multivariate genome-wide association study (GWAS) in unrelated UK Biobank (UKB) individuals of European ancestry. Using GWAS summary association data, genomic structural equation modeling was performed to generate sex-specific factor models using six indicator variables: trouble concentrating, feeling distant from others, irritability, disturbing thoughts, upset feelings, and avoidance of places/activities which remind the individual of a traumatic event. Models of male and female PTSD symptoms differed substantially (local standardized root mean square difference=3.12) and significantly (χ2(5)=28.03, p=3.6x10-5). Independent two-factor models best fit the data in both males and females; these factors were subjected to GWAS in each sex, revealing three genome-wide significant loci in females, mapping to SCAND3, WDPCP, and FAM120A. No genome-wide significant loci were identified in males. All four PTS factors (2 in males and 2 in females) were heritable (p<0.05): male PTS-f1h2-SNP=1.85%, male PTS-f2h2-SNP=1.47%, female PTS-f1h2-SNP=3.87%, female PTS-f2h2-SNP=3.53%. Male PTS-f1was enriched for medication-related putative causal relationships (3.73-fold, p=0.032) while male PTS-f2was enriched for body structure (2.84-fold, p=5.512x10-7) and cognitive (3.22-fold, p=0.009) putative causal relationships. In females, PTS-f1was enriched for metabolic putative causal relationships (28.08-fold, p=0.035). By assessing the relationship between sex and PTSD symptoms, this study informs correlative and putatively causal etiological differences between males and females which support further investigation of sex differences in PTSD genetics.
Maternal obesity shapes the B lymphocyte and antibody repertoires of human colostrum
Authors: Sánchez-Salguero Erick , Bonilla-Ruelas Diana , Alcorta-García Mario René , Lara-Diaz Víctor Javier , López-Villaseñor Claudia Nohemí , Brunck Marion E G
Published: September 2023

The prevalence of obesity is rapidly increasing worldwide and its impact on future generations must be assessed. We recently showed that colostrum from mothers with obesity contained a significantly reduced B lymphocytes (CD19+) fraction. Here, in a subsequent transversal cohort study of 48 mothers, we exhaustively characterize the B lymphocytes subsets present in peripheral blood and colostrum from obese mothers and describe a pervasive alteration of the B lymphocytes compartment of human colostrum accompanied by a dysregulated antibody composition. We describe significant decreases in regulatory B cells and soluble IgA concentrations, combined with increases in soluble IgG and double negative 2 (CD19+, CD27-, IgD-, CD38-, CD24-, CD21-, CD11c+) B lymphocytes. These alterations correlated with maternal BMI and corporal fat %. We provide evidence for possibly autoimmune IgG present in obese colostrum, and for the proinflammatory consequences of obese colostrumin vitro. Beyond the impact of obesity, we evidence the selective presence of B lymphocyte subtypes in colostrum andin situproduction of IgG antibodies, which expands our current understanding of the origin of colostrum IgG. As maternal milk antibodies play a crucial role in regulating neonatal gut immune development, this work uncovers maternal obesity as a potential risk factor for compromised breastmilk immune components, calling for more research on the long-term health of lactating infants.
Development and validation of nomograms for predicting the prognosis of early and late recurrence of advanced gastric cancer after radical surgery
Authors: Liu Chenming , Lu Jialiang , An Liang
Published: September 2023

Objective

In this study, we aimed to explore the risk factors influencing post recurrence survival (PRS) of early recurrence (ER) and late recurrence (LR) in stage advanced gastric cancer (AGC) patients after radical surgery, respectively, and to develop predictive models in turn.

Methods

Medical records of 192 AGC patients who recurred after radical gastrectomy were retrospectively reviewed. They were randomly divided into the training and validation set at a ratio of 2:1. Nomograms were built based on risk factors influencing PRS of ER and LR explored by Cox regression analyses, respectively. Concordance index (C-index) values and calibration curves were used to evaluate predictive power of nomograms.

Results

Body mass index < 18.5 kg/m2, prealbumin level < 70.1 mg/l, positive lymph nodes ratio ≥ 0.486 and palliative treatment after recurrence were independent risk factors for the prognosis of ER. In contrast, prealbumin level < 170.1 mg/l, CEA ≥ 18.32 μg/l, tumor diameter ≥ 5.5 cm and palliative treatment after recurrence were independent risk factors for the prognosis of LR. The C-index value was 0.801 and 0.772 for ER and LR in the training set, respectively. The calibration curves of validation set showed a C-index value of 0.744 and 0.676 for ER and LR, respectively.

Conclusions

Nomograms which were constructed to predict the prognosis of ER and LR of AGC after surgery showed great predictive power and could provide reference for clinicians’ treatment strategies to some extent.
Effect of post-activation potentiation on the sports performance of athletes: a systematic review
Authors: Li Jiazhe , Soh Kim Goek , Loh Su Peng , Luo Shengyao , Bashir Marrium , Yu Xiao
Published: September 2023

Background

This study aimed to investigate the effects of post-activation potentiation (PAP) on sport performance.

Methods

The data used in this study were reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2020 guidelines. Researchers extracted relevant randomized controlled trials from the available literature using prominent scientific indexing databases such as EBSCOhost, PubMed, Scopus, Web of Science, as well as Google Scholar. Ten of the 125 studies that met the inclusion criteria were included. The overall quality of each study was determined using the PEDro scale. Ten studies had scores ranging from 3 to 5.

Results

In PAP interventions, power (n = 4) was the primary aspect of sports performance, followed by endurance (n = 1), speed (n = 2), and jumping ability (n = 2). Meanwhile, PAP significantly affects the power, endurance, speed, and jumping abilities of athletes in basketball, volleyball, track and field, and soccer.

Conclusion

Compared with conventional training, PAP is a relatively novel dynamic warm-up routine that can greatly enhance the sports performance of athletes in terms of endurance, power, speed, and jumping ability. As a phenomenon of rapid increase in muscle strength and power caused by high-intensity warm-up activities, PAP can help athletes quickly adjust the physical condition to the best state in the pre-match warm- up. However, since some study findings did not reflect the effect of PAP on the sports performance of athletes, more high-quality randomized controlled trials are required to further prove the effect of PAP. Additionally, the existing evidence does not consider the effect of PAP on agility and flexibility performance. In formulating the PAP induction program, it is also necessary to consider the impact of the gender and age of the inducer, exercise level, pre-stimulation load, and interval time on PAP.

Systematic Review Registration:[https://inplasy.com/], identifier: [INPLASY202330120].
The Impact of Social Determinants of Health and Lifestyle on the Association of Lipoprotein(a) with Myocardial Infarction and Stroke
Authors: Brandt Eric J. , Kirch Matthias , Patel Nimai , Chennareddy Chaitanya , Murthy Venkatesh L. , Goonewardena Sascha N.
Published: September 2023

Background

In European cohorts, a higher Mediterranean diet or Life’s Simple 7 (LS7) score abolished or attenuated the risk associated with increasing Lipoprotein(a) [Lp(a)] on cardiovascular outcomes. This is unstudied in US cohorts. The impact of social determinants of health (SDOH) on the association of Lp(a) with cardiovascular outcomes remains unstudied. We sought to test if a SDOH score and LS7 score impacts the association of Lp(a) with myocardial infarction (MI) or stroke.

Methods

Observational Cohort of US Adults from the Atherosclerosis Risk in Communities (ARIC) and Multi-Ethnic Study of Atherosclerosis (MESA) cohorts. We performed sequential multivariable Cox proportional hazard analysis, first adjusting for age, gender, non-HDL-C, race and ethnicity, then added SDOH and LS7 scores sequentially. The primary outcomes were time until first fatal or nonfatal MI or stroke.

Results

ARIC (n=15,072; median Lp(a)=17.3 mg/dL) had 16.2 years average follow up. MESA (n=6,822; median Lp(a)=18.3 mg/dL had 12.3 years average follow-up. In multivariable analyses adjusted for age, gender, race and ethnicity, and non-HDL-C, Lp(a) was associated (HR, p-value) with MI in ARIC (1.10, <0.001) and MESA (1.09, <0.001), and stroke in ARIC (1.08, <0.001) but not MESA (0.97, 0.50). With SDOH and LS7 added to the model associations remained similar (association of Lp(a) with MI in ARIC 1.09, <0.001 and in MESA 1.10, 0.001, with stroke in ARIC 1.06, <0.003 and in MESA 0.96, 0.39). In models with all covariates, each additional SDOH correlated positively with MI (ARIC 1.13, <0.001; MESA 1.11, <0.001) and stroke (ARIC 1.17, <0.001; HR 1.07, p=0.11) and each additional LS7 score point correlated negatively with MI (ARIC 0.81, <0.001; MESA 0.84, <0.001) and stroke (ARIC 0.82, <0.001; MESA 0.84, <0.001).

Conclusions and Relevance

SDOH and lifestyle factors were predictors for MI and stroke that did not impact the association between Lp(a) and cardiovascular events. Our findings support that Lp(a) is an independent risk factor for MI and possibly stroke.
Respective contribution of Appl to mushroom body axon growth and long-term memory inDrosophila
Authors: Marquilly Claire , Boulanger Ana , Busto Germain U. , Pasquer Laure , Zinzen Robert P , Hassan Bassem A , Fradkin Lee G , Preat Thomas , Dura Jean-Maurice
Published: September 2023

The Amyloid Precursor Protein (APP) is linked to Alzheimer’s disease.Applis the singleDrosophilaAPP ortholog and is expressed in all neurons throughout development. Appl was previously shown to modulate, cell-autonomously, axon outgrowth in the mushroom bodies (MBs), the fly olfactory memory center. Furthermore,Applknockdown in the MBs results in loss of memory following the association of odorants with electric shocks. Nevertheless, the memory defects of flies devoid of Appl remains unknown becauseAppldflies, carrying the only known null allele, show an abnormal response to electric shock. We found thatAppldaffects the normal function ofvnd, the gene just proximal toAppl. We report here thatvndis required for MB β-branch axon outgrowth. Moreover,vndis expressed in neurons close to, but not within, the MB during development and is required non-cell-autonomously for MB axon outgrowth. To decipher developmental and memory defects specifically due to a loss of onlyApplfunction, we generated a preciseApplnull allele (ApplC2.1) by CRISPR/Cas9 genomic engineering. WithApplC2.1, we confirmed the partial requirement forApplin MB axon outgrowth but found no defects of electric shock avoidance, allowing us to test for potential memory defects.ApplC2.1flies showed a complete loss of long-term memory which was fully rescued by MB-restricted expression ofAppl+only during the adult stage. Therefore, we demonstrate that the complete lack of Appl affects memory independently from structural developmental defects.
In vivo perturb-seq of cancer and microenvironment cells dissects oncologic drivers and radiotherapy responses in glioblastoma
Authors: Liu S. John , Pak Joanna , Zou Christopher , Casey-Clyde Timothy , Borah Ashir A. , Wu David , Seo Kyounghee , O’Loughlin Thomas , Lim Daniel A. , Ozawa Tomoko , Berger Mitchel S. , Weiss William A. , Raleigh David R. , Gilbert Luke A.
Published: September 2023

Genetic perturbation screens with single cell readouts have enabled rich phenotyping of gene function and regulatory networks. These approaches have been challengingin vivo,especially in adult disease models such as cancer, which include mixtures of malignant and microenvironment cells. Glioblastoma (GBM) is a fatal cancer, and methods of systematically interrogating gene function and therapeutic targetsin vivo, especially in combination with standard of care treatment such as radiotherapy, are lacking. Here, we iteratively develop a multiplexin vivoperturb-seq CRISPRi platform for single cell genetic screens in cancer and tumor microenvironment cells that leverages intracranial convection enhanced delivery (CED) of sgRNA libraries into models of GBM. Our platform enables potent silencing of drivers ofin vivogrowth and tumor maintenance, as well as genes that sensitize GBM to radiotherapy. We find radiotherapy rewires transcriptional responses to genetic perturbations in anin vivodependent manner, revealing heterogenous patterns of treatment sensitization or resistance in GBM. Furthermore, we demonstrate targeting of genes that function in the tumor microenvironment, enabling alterations of ligand-receptor interactions between immune/stromal cells followingin vivoCRISPRi perturbations. In sum, we demonstrate the utility of multiplexed perturb-seq forin vivosingle cell dissection of adult cancer and normal tissue biology across multiple cell types in the context of therapeutic intervention, a platform with potential for broad application.
Tropomyosin 1 deficiency facilitates cell state transitions to enhance hemogenic endothelial cell specification during hematopoiesis
Authors: Wilken Madison B , Fonar Gennadiy , Nations Catriana , Pavani Giulia , Tsao Victor , Garifallou James , Tober Joanna , Bennett Laura , Maguire Jean Ann , Gagne Alyssa , Okoli Nkemdilim , Gadue Paul , Chou Stella T , Speck Nancy A , French Deborah L , Thom Christopher S
Published: September 2023

Tropomyosins coat actin filaments and impact actin-related signaling and cell morphogenesis. Genome-wide association studies have linkedTropomyosin 1(TPM1) with human blood trait variation. Prior work suggested thatTPM1regulated blood cell formation in vitro, but it was unclear how or whenTPM1affected hematopoiesis. Using gene-edited induced pluripotent stem cell (iPSC) model systems,TPM1knockout was found to augment developmental cell state transitions, as well as TNFα and GTPase signaling pathways, to promote hemogenic endothelial (HE) cell specification and hematopoietic progenitor cell (HPC) production. Single-cell analyses showed decreasedTPM1expression during human HE specification, suggesting thatTPM1regulated in vivo hematopoiesis via similar mechanisms. Indeed, analyses of aTPM1gene trap mouse model showed thatTPM1deficiency enhanced the formation of HE during embryogenesis. These findings illuminate novel effects ofTPM1on developmental hematopoiesis.
Mechanisms used for cDNA synthesis and site-specific integration of RNA into DNA genomes by a reverse transcriptase-Cas1 fusion protein
Authors: Mohr Georg , Yao Jun , Park Seung Kuk , Markham Laura M. , Lambowitz Alan M.
Published: September 2023

Reverse transcriptase-Cas1 (RT-Cas1) fusion proteins found in some CRISPR systems enable spacer acquisition from both RNA and DNA, but the mechanism of RNA spacer acquisition has remained unclear. Here, we foundMarinomonas mediterraneaRT-Cas1/Cas2 adds short 3’-DNA (dN) tails to RNA protospacers enabling their direct integration into CRISPR arrays as 3’-dN-RNA/cDNA duplexes or 3’-dN-RNAs at rates comparable to similarly configured DNAs. Reverse transcription of RNA protospacers occurs by multiple mechanisms, including recently describedde novoinitiation, protein priming with any dNTP, and use of short exogenous or synthesized DNA oligomer primers, enabling synthesis of cDNAs from diverse RNAs without fixed sequence requirements. The integration of 3’-dN-RNAs or single-stranded (ss) DNAs is favored over duplexes at higher protospacer concentrations, potentially relevant to spacer acquisition from abundant pathogen RNAs or ssDNA fragments generated by phage-defense nucleases. Our findings reveal novel mechanisms for site-specifically integrating RNA into DNA genomes with potential biotechnological applications.
Transgenic expression ofcifgenes fromWolbachiastrainwAlbB recapitulates cytoplasmic incompatibility inAedes aegypti
Authors: McNamara Cameron J , Ant Thomas H , Harvey-Samuel Tim , White-Cooper Helen , Martinez Julien , Alphey Luke , Sinkins Steven P
Published: September 2023

The endosymbiotic bacteriaWolbachiacan invade insect populations by modifying host reproduction through cytoplasmic incompatibility (CI), an effect that results in embryonic lethality whenWolbachia-carrying males mate withWolbachia-free females. Here we describe a transgenic system for recreating CI in the major arbovirus vectorAedes aegyptiusing CI factor (cif) genes fromwAlbB, aWolbachiastrain currently being deployed to reduce dengue transmission. CI-like sterility was induced whencifAandcifBwere co-expressed in testes; this sterility could be rescued by maternalcifAexpression, thereby reproducing the pattern ofWolbachia-induced CI. Expression ofcifBalone was associated with extensive DNA damage and disrupted spermatogenesis. The strength of rescue by maternalcifAexpression was dependent on the comparative levels ofcifA/cifBexpression in males. These findings are consistent with CifB acting as a toxin and CifA as an antitoxin, with CifA attenuating CifB toxicity in both the male germline and in developing embryos.
Dual α-globin and truncated EPO receptor knockin restores hemoglobin production in α-thalassemia-derived red blood cells
Authors: Chu Simon N. , Soupene Eric , Wienert Beeke , Yin Han , Sharma Devesh , McCreary Travis , Jia Kun , Homma Shota , Hampton Jessica P. , Gardner James M. , Conklin Bruce R. , MacKenzie Tippi C. , Porteus Matthew H. , Cromer M. Kyle
Published: September 2023

Alpha-thalassemia is an autosomal recessive disease with increasing worldwide prevalence. The molecular basis is due to mutation or deletion of one or more duplicated α-globin genes, and disease severity is directly related to the number of allelic copies compromised. The most severe form, α-thalassemia major (αTM), results from loss of all four copies of α-globin and has historically resulted in fatalityin utero. However,in uterotransfusions now enable survival to birth. Postnatally, patients face challenges similar to β-thalassemia, including severe anemia and erythrotoxicity due to imbalance of β-globin and α-globin chains. While curative, hematopoietic stem cell transplantation (HSCT) is limited by donor availability and potential transplant-related complications. Despite progress in genome editing treatments for β-thalassemia, there is no analogous curative option for patients suffering from α-thalassemia. To address this, we designed a novel Cas9/AAV6-mediated genome editing strategy that integrates a functional α-globin gene into the β-globin locus in αTM patient-derived hematopoietic stem and progenitor cells (HSPCs). Incorporation of a truncated erythropoietin receptor transgene into the α-globin integration cassette dramatically increased erythropoietic output from edited HSPCs and led to the most robust production of α-globin, and consequently normal hemoglobin. By directing edited HSPCs toward increased production of clinically relevant RBCs instead of other divergent cell types, this approach has the potential to mitigate the limitations of traditional HSCT for the hemoglobinopathies, including low genome editing and low engraftment rates. These findings support development of a definitiveex vivoautologous genome editing strategy that may be curative for α-thalassemia.

Graphical abstract
Finding Expression of MUC1 and MUC4 in the Respiratory System of the Iraqi Common Quail (Coturnix coturnix)
Authors: Murad AL-Mamoori Nabeel Abd , Almhanna Hazem , Kadhim Abdulrazzaq B , Kilroy David , Kumar Arun HS
Published: September 2023

Background

This study focused on the major components of mucus, known as mucins, within the mucosal epithelium of the respiratory system in Iraqi Common Quail. Six quail were utilized in accordance with animal ethics guidelines from the College of Veterinary Medicine at the University of Al-Qadisiyah. Histological analysis, utilizing H&E staining, aimed to identify key respiratory system structures. PAS plus Alcian blue stains were employed to identify specific carbohydrates in the trachea, bronchi, and lungs. RT-qPCR was used to assess the gene expression levels of MUC1 and MUC4.

Results

The trachea and bronchi encompassed four distinct layers: tunica mucosa, tunica submucosa, hyaline cartilage, and tunica adventitia. The mucosa consisted of pseudostratified epithelium that transitioned into simple columnar cells toward the primary and secondary bronchioles. This transition further progressed into simple cuboidal and squamous epithelium at smaller tertiary branches of the secondary bronchioles. Notably, the bronchial tunica submucosa was thinner than the trachea. While hyaline cartilage was prominently present in the trachea, it became fragmented in the bronchi and diminished towards the lungs and secondary bronchioles. Lung tissue was characterized by numerous lobules housing alveoli connected to alveolar ducts and sacs, alongside an intricate network of blood vessels. The respiratory tissues, including the trachea, bronchi, and lungs, exhibited a strong affinity for PAS-combined Alcian blue stains. This confirmed the substantial presence of both acidic and neutral mucins within the epithelial cells and glands. The trachea demonstrated significantly elevated levels of acidic mucins and a concentrated amount? of neutral mucins. Transcriptome analysis indicated the expression of both MUC1 and MUC4 genes. Importantly, MUC4 expression surpassed that of MUC1 in the trachea, bronchi, and lungs.

Conclusion

This study highlights the similarity of histological structures in the trachea, bronchi, and lungs of quail to typical avian species. Moreover, it underscored the substantial presence of both acidic and neutral mucins, with MUC4 being the predominant mucin, potentially playing a pivotal role in regulating mucosal barrier functions and interacting with pathogens. Nonetheless, further investigation is warranted to elucidate MUC4’s role in respiratory epithelial cells.
Novel substrate prediction for the TAM family of RTKs using phosphoproteomics and structure-based modeling
Authors: Widstrom Naomi E. , Andrianov Grigorii V. , Heier Jason L. , Heier Celina , Karanicolas John , Parker Laurie L.
Published: September 2023

The TAM family of receptor tyrosine kinases is implicated in multiple distinct oncogenic signaling pathways. However, to date there are no FDA-approved small molecule inhibitors for the TAM kinases. Inhibitor design and screening rely on tools to study kinase activity. Our goal was to address this gap by designing a set of synthetic peptide substrates for each of the TAM family members: Tyro3, Axl and Mer. We used an in vitro phosphoproteomics workflow to determine the substrate profile of each TAM kinase and input the identified substrates into our data processing pipeline, KINATEST-ID, producing a position-specific scoring matrix for each target kinase and generating a list of candidate synthetic peptide substrates. We synthesized and characterized a set of those substrate candidates, systematically measuring their initial phosphorylation rate with each TAM kinase by LC-MS. We also used the multimer modeling function of AlphaFold2 to predict peptide-kinase interactions at the active site for each of the novel candidate peptide sequences against each of the TAM family kinases, and observed that remarkably, every sequence for which it predicted a putatively catalytically competent interaction was also demonstrated biochemically to be a substrate for one or more of the TAM kinases. This work shows that kinase substrate design can be achieved using a combination of preference motifs and structural modeling, and it provides the first demonstration of peptide-protein interaction modeling for predicting likelihood of constructive catalytic interactions.
Lipid levels correlate with neuronal and dopaminergic markers during the differentiation of SH-SY5Y cells
Authors: Marlet Frederik Ravnkilde , Muñoz Sonia Sanz , Sotiraki Nefeli , Eliasen Jannik Nicklas , Woessmann Jakob Paul , Weicher Jan , Dreier Jesper Elmsted , Schoof Erwin , Kohlmeier Kristi A , Maeda Kenji , Galvagnion Céline
Published: September 2023

Parkinson’s Disease (PD) is characterized by the loss of dopaminergic neurons and the deposition in the remaining cells of protein inclusions called Lewy Bodies (LBs). LBs are heterogeneous structures composed of protein and lipid molecules and their main constituent is the presynaptic protein α-synuclein. SH-SY5Y cells are neuroblastoma cells commonly used to model PD because they express dopaminergic markers and α-synuclein and they can be differentiated into neuronal cells using established protocols. Despite increasing evidence pointing towards a role of lipids in the initiation of PD, limited knowledge is available on the lipidome of undifferentiated and differentiated SH-SY5Y cells. In this study, we show that the levels and chemical properties of negatively charged phospholipids, diacyl glycerol and sphingolipids are specifically altered along the differentiation process of SH-SY5Y cells and that the levels of these lipids’ species correlate with those of dopaminergic and neuronal markers. These results are supported by proteomic data showing that the main biological processes affected by the differentiation of SH-SY5Y cells are lipid metabolism and processes associated with neuron maturation. Finally, our results show that electrophysiological activity can be detected in differentiated SH-SY5Y cells at a stage where most of the lipid changes have reached their maximal value. These results provide the first complete and quantitative characterisation of the changes in lipidome associated with the differentiation of SH-SY5Y cells into more neuronal and dopaminergic-like phenotype and serve as a basis for further characterisation of lipid disruptions in association with PD and its risk factors in this dopaminergic-like neuronal cell model.
Characterization of erythroferrone oligomerization and its impact on BMP antagonism
Authors: Mast Jacob F , Leach Edmund A E , Thompson Thomas B
Published: September 2023

Hepcidin, a peptide hormone that negatively regulates iron metabolism, is expressed by bone morphogenetic protein (BMP) signaling. Erythroferrone (ERFE) is an extracellular protein that binds and inhibits BMP ligands, thus positively regulating iron import by indirectly suppressing hepcidin. This allows for rapid erythrocyte regeneration after blood loss. ERFE belongs to the C1Q/TNF related protein (CTRP) family and is suggested to adopt multiple oligomeric forms: a trimer, a hexamer, and a high molecular weight species. The molecular basis for how ERFE binds BMP ligands and how the different oligomeric states impact BMP inhibition are poorly understood. In this study, we demonstrated that ERFE activity is dependent on the presence of stable dimeric or trimeric ERFE, and that larger species are dispensable for BMP inhibition. Additionally, we used anin-silicoapproach to identify a helix, termed the ligand binding domain (LBD), that was predicted to bind BMPs and occlude the type I receptor pocket. We provide evidence that the LBD is crucial for activity through luciferase assays and surface plasmon resonance (SPR) analysis. Our findings provide new insight into how ERFE oligomerization impacts BMP inhibition, while identifying critical molecular features of ERFE essential for binding BMP ligands.
Pseudorabies virus causes splenic injury via inducing the oxidative stress and apoptpsos related factors in mice
Authors: Sun Wei , Liu Shanshan , Yan Yi , Wang Qingyan , Fan Yu , Okyere Samuel Kumi
Published: September 2023

Pseudorabies virus (PRV) is an immunosuppressive disease that causes significant damage to the pig industry. This study aimed to detect the effects of PRV on oxidative stress related factors and cell apoptosis in the spleen, providing a basis for the research on the pathogenesis of PRV in mice model. Pathological observation was performed by hematoxylin and eosin Y staining. Biochemical and Flow cytometry method were performed to determine the reactive oxygen species profile of the spleen post-infection and apoptosis detection. In addition, q-PCR and Western blot were adopted to measure the apoptotic conditions of the spleen infected with PRV. The results indicated that the ROS level in the PRV infection group was remarkedly increased (p<0 01) at a time-dependent pattern. Furthermore, the Malondialdehyde levels in the spleen of mice in the infection group increased significantly (p<0.01) in a time-dependent mode. However, the Catalase, Superoxide dismutase, and Glutathione activity and expression levels in the infection group were significantly decreased with the control group (p<0 01) in a time-dependent manner. Furthermore, the ratio of splenocyte apoptosis in the infection group significantly increased (p<0 05,p<0 01) in a time-dependent manner. In conclusion, PRV infection causes apoptosis of the spleen via oxidative stress in mice.
Comparison of insect and human cytochrome b561 proteins: Insights into candidate ferric reductases in insects
Authors: Holst Jessica D. , Murphy Laura G. , Gorman Maureen J. , Ragan Emily J.
Published: September 2023

Cytochrome b561 (cytb561) proteins comprise a family of transmembrane oxidoreductases that transfer single electrons across a membrane. Most eukaryotic species, including insects, possess multiple cytb561 homologs. To learn more about this protein family in insects, we carried out a bioinformatics-based investigation of cytb561 family members from nine species representing eight insect orders. We performed a phylogenetic analysis to classify insect cytb561 orthologous groups. We then conducted sequence analyses and analyzed protein models to predict structural elements that may impact the biological functions and localization of these proteins, with a focus on possible ferric reductase activity. Our study revealed three orthologous groups, designated CG1275, Nemy, and CG8399, and a fourth group of less-conserved genes. We found that CG1275 and Nemy proteins are similar to a human ferric reductase, duodenal cytochrome b561 (Dcytb), and have many conserved amino acid residues that function in substrate binding in Dcytb. Notably, CG1275 and Nemy proteins contain a conserved histidine and other residues that play a role in ferric ion reduction by Dcytb. Nemy proteins were distinguished by a novel cysteine-rich cytoplasmic loop sequence. CG8399 orthologs are similar to a putative ferric reductase in humans, stromal cell-derived receptor 2. Like other members of the CYBDOM class of cytb561 proteins, these proteins contain reeler, DOMON, and cytb561 domains.Drosophila melanogasterCG8399 is the only insect cytb561 with known ferric reductase activity. Our investigation of the DOMON domain in CG8399 proteins revealed a probable heme-binding site and a possible site for ferric reduction. The fourth clade includes a group of proteins with a conserved “KXXXXKXH” non-cytoplasmic loop motif that may be a substrate binding site and is present in a potential ferric reductase, human tumor suppressor cytochrome b561. This study provides a foundation for future investigations of the biological functions of cytb561 genes in insects.
A rapid and dynamic role for FMRP in the plasticity of adult neurons
Authors: Gundermann Daniel G. , Lymer Seana , Blau Justin
Published: September 2023

Fragile X syndrome (FXS) is a neuro-developmental disorder caused by silencingFmr1, which encodes the RNA-binding protein FMRP. AlthoughFmr1is expressed in adult neurons, it has been challenging to separate acute from chronic effects of loss ofFmr1in models of FXS. We have used the precision ofDrosophilagenetics to test ifFmr1acutely affects adult neuronal plasticityin vivo, focusing on the s-LNv circadian pacemaker neurons that show 24 hour rhythms in structural plasticity. We found that over-expressingFmr1for only 4 hours blocks the activity-dependent expansion of s-LNv projections without altering the circadian clock or activity- regulated gene expression. Conversely, acutely reducingFmr1expression prevented s-LNv projections from retracting. One FMRP target that we identified in s-LNvs issif, which encodes a Rac1 GEF. Our data indicate that FMRP normally reducessifmRNA translation at dusk to reduce Rac1 activity. Overall, our data reveal a previously unappreciated rapid and direct role for FMRP in acutely regulating neuronal plasticity in adult neurons, and underscore the importance of RNA-binding proteins in this process.
Phage libraries screening on P53 : yield improvement by zinc and a new parasites-integrating analysis and rationale
Authors: Ben Abid Sihem , Ketata Emna , Yacoubi-Hadj Amor Ines , Abdelmoula-Souissi Salma , Djemal Lamia , Koubaa Aida , Mokdad-Gargouri Raja , Gargouri Ali
Published: September 2023

P53 is a transcription factor that controls a variety of genes, primarily involved in cell cycle and other processes related to cell survival and death. We have isolated peptides targeting P53 (protein and domains) using the “phage display” technique. Interestingly, adding ZnCl2 at 5-10 mM in panning solutions helped to recover more plaque-forming units at least at round one of the screening. Subtractive docking analyses were designed by using a pool of common redundant peptides known asparasites. This rationale helped us differentiate between possibly specific and non-specific bindings. We found notable differences in docking characteristics between different sets of peptides either related to different targets or related to zinc-conditions. The set of zinc-related peptides shows advantageous docking profiles: sharper binding for some positions and distinct exclusive bound residues, including the relevant R248 and R273. Zinc would have modulating/helping role in the targeting of protein P53 by phage displayed peptides in addition to an enhancement action on bacterial infection.
Disruption of Synaptic Endoplasmic Reticulum Luminal Protein Containment inDrosophila AtlastinMutants
Authors: Quiñones-Frías Mónica C. , Ocken Dina M. , Rodal Avital
Published: September 2023

The endoplasmic reticulum (ER) extends throughout neurons and regulates many neuronal functions, including neurite outgrowth, neurotransmission, and synaptic plasticity. Mutations in proteins that control ER shape are linked to the neurodegenerative disorder Hereditary Spastic Paraplegia (HSP), yet the ultrastructure and dynamics of neuronal ER remain largely unexplored, especially at presynaptic terminals. Using super-resolution and live imaging inD. melanogasterlarval motor neurons, we investigated ER structure at presynaptic terminals of wild-type animals and null mutants of the ER shaping protein and HSP-linked gene, Atlastin. Previous studies using an ER luminal marker reported diffuse localization atAtlastinmutant presynaptic terminals, which was attributed to ER fragmentation. However, using an ER membrane marker, we discovered thatAtlastinmutant ER forms robust networks with only mild defects in structural dynamics, indicating the primary defect is functional rather than architectural. We demonstrate thatAtlastinmutants progressively displace overexpressed luminal ER proteins to the cytosol during larval development, specifically at synapses, while these proteins remain correctly localized in cell bodies, axons, and muscles. This synaptic-specific displacement phenotype, previously unreported in non-neuronal cells, emphasizes the importance of studying neurons to understand HSP pathogenesis.
The role offruitlessin specifying courtship behaviors differs acrossDrosophilaspecies
Authors: Baker Christa A. , Guan Xiao-Juan , Choi Minseung , Murthy Mala
Published: September 2023

Sex-specific behaviors are critical for reproduction and species survival. The sex-specifically spliced transcription factorfruitless(fru) helps establish male courtship behaviors in invertebrates. Forcing male-specificfru(fruM) splicing inDrosophila melanogasterfemales produces male-typical behaviors, while disrupting female-specific behaviors. However, whetherfru’s joint role in specifying male and inhibiting female behaviors is conserved across species is unknown. We used CRISPR/Cas9 to force FruM expression in femaleD. virilis, a species in which males and females produce sex-specific songs. In contrast toD. melanogaster, in which onefruMallele is sufficient to generate male behaviors in females, two alleles are needed inD. virilisfemales.D. virilisfemales expressing FruM maintain the ability to sing female-typical song as well as lay eggs, whereasD. melanogasterFruM females cannot lay eggs. These results reveal important differences infrufunction between divergent species and underscore the importance of studying diverse behaviors and species for understanding the genetic basis of sex differences.
UK healthcare professionals’ attitudes towards the introduction of varicella vaccine into the routine childhood vaccination schedule and their preferences for delivery
Authors: Sherman Susan M. , Allerton-Price Charlotte , Lingley-Heath Nicola , Lai Jasmine , Bedford Helen
Published: September 2023

Background

Varicella (chickenpox) is a highly contagious disease caused by the varicella-zoster virus. Although typically a mild disease, varicella can cause complications leading to severe illness and even death. Safe and effective varicella vaccines are available. The Joint Committee on Vaccination and Immunisation is planning to review the evidence regarding the introduction of varicella vaccine into the UK’s routine childhood immunisation schedule.

Objectives

To explore UK healthcare professionals’ (HCPs) knowledge and attitudes towards varicella vaccination, its introduction to the UK routine childhood immunisation schedule, and their preferences for how it should be delivered.

Design

We conducted an online cross-sectional survey exploring HCPs’ attitudes towards varicella, varicella vaccine, and their preferences for delivery of the vaccine between August and September 2022.

Participants

91 HCPs working in the UK (96.7% female, 3.3% male, mean age 48.7 years).

Results

General vaccine attitudes in this group were very positive. Gaps in knowledge about varicella were revealed: 21.0% of respondents disagreed or were unsure that chickenpox can cause serious complications, while 41.8% were unsure or did not believe chickenpox was serious enough to vaccinate against. After receiving some basic information about chickenpox and the vaccine, almost half of the HCPs (47.3%) in our survey would prefer to administer the varicella vaccine combined with MMR.

Conclusions

Given the positive influence of HCPs on parents’ decisions to vaccinate their children, it is important to understand HCPs’ views regarding the introduction of varicella vaccine into the routine schedule. Our findings highlighted areas for training and HCPs’ preferences which will have implications for policy and practice should the vaccine be introduced.
Delayed localization of A-type lamins to the rupture sites in Hutchinson–Gilford progeria syndrome
Authors: Kono Yohei , Pack Chan-Gi , Ichikawa Takehiko , Komatsubara Arata , Adam Stephen A. , Miyazawa Keisuke , Rolas Loïc , Nourshargh Sussan , Medalia Ohad , Goldman Robert D. , Fukuma Takeshi , Kimura Hiroshi , Shimi Takeshi
Published: September 2023

The nuclear lamina (NL) lines the nuclear envelope (NE) to maintain nuclear structure in metazoan cells. The major NL components, the nuclear lamins contribute to the protection against NE rupture induced by mechanical stress. Lamin A (LA) and a short form of the splicing variant lamin C (LC) are diffused from the nucleoplasm to sites of NE rupture in immortalized mouse embryonic fibroblasts (MEFs). LA localization to the rupture sites is significantly slow and weak compared to LC because of its relatively small pool in the nucleoplasm, but the precise mechanism remains unknown. In this study, we induce NE rupture in wild-type and LA/C-knockout MEFs, and Hutchinson–Gilford Progeria syndrome (HGPS) knock-in MEFs that express progerin, a LA mutant lacking the second proteolytic cleavage site, by laser microirradiation and AFM indentation. The farnesylation at the CaaX motif of unprocessed LA and the inhibition of the second proteolytic cleavage decrease the nucleoplasmic pool and slow the localization to the rupture sites in a long-time window (60-70 min) after the induction of NE rupture. Our data could explain the defective repair of NE rupture in HGPS through the farnesylation at the CaaX motif of unprocessed progerin. In addition, unique segments in LA-specific tail region cooperate with each other to inhibit the rapid accumulation within a short-time window (3 min) that is also observed with LC.

Significance Statement

Nuclear lamins are the major components of the nuclear lamina (NL) that lies the nuclear envelope (NE). Lamin A (LA) is slowly localized to sites of nuclear envelope (NE) rupture compared to lamin C (LC). This study reveals that the farnesylation at the CaaX motif of unprocessed LA and the inhibition of the second proteolytic cleavage decrease the nucleoplasmic pool and slow the localization to the rupture sites within a long-time window (60-70 min) after the induction of NE rupture, which could explain the defective repair of NE rupture in Hutchinson–Gilford Progeria syndrome (HGPS). Additionally, unique segments in LA-specific tail region are critical for inhibiting the rapid accumulation within a short-time window (3 min).
Regulation of an antibiotic resistance efflux pump by quorum sensing and a TetR-family repressor inChromobacterium subtsugae
Authors: Koirala Pratik , Doody Cassie , Blackwell Helen , Chandler Josephine R.
Published: September 2023

The soil bacteriumChromobacterium substugaeuses a single LuxI-R-type quorum-sensing system, CviI-R, to regulate genes in a cell density-dependent manner. CviI synthesizes the signalN-hexanoyl-homoserine lactone (C6-HSL) and CviR is a C6-HSL-responsive cytoplasmic transcription regulator. C6-HSL-bound CviR activates dozens of genes, for example thecdeAB-oprMcluster coding for an efflux pump conferring antibiotic resistance. ThecdeAB-oprMgenes are also regulated by an antibiotic-responsive transcription factor, CdeR, which represses expression of these genes. We are interested in understanding howC. subtsugaeintegrates different environmental cues to regulate antibiotic resistance. In this study, we sought to delineate the mechanism of regulation of thecdeAB-oprMgenes by CviR and CdeR. In recombinantE. coli,thecdeApromoter is activated by CviR and repressed by CdeR. We identify non-overlapping sequence elements in thecdeApromoter that are required for CviR activation and CdeR repression, respectively. We also examined the role of CdeR in modulatingcdeAactivation by C6-HSL inC. subtsugae. We show that CviR and CdeR can independently modulate transcription from thecdeApromoter inC. subtsugae, consistent with the conclusion that CviR and CdeR regulate thecdeAB-oprMgenes by interacting directly with different binding sites in thecdeApromoter. These results contribute to a molecular understanding of how thecdeAB-oprMgenes are regulated and provide new insight into howC. subtsugaeintegrates different environmental cues to regulate antibiotic resistance.

Importance

Many bacteria regulate antibiotic resistance in response to antibiotics and other cues from the environment. In many cases the regulatory mechanisms are best understood in the context of clinical isolates where mutations frequently emerge in resistance regulation pathways. However, an understanding of the role of antibiotic resistance regulators in integrating environmental information is less well understood. In the soil bacteriumChromobacterium subtsugae,an antibiotic-resistance gene cluster is regulated by population density and antibiotics through two different transcription factors; the quorum sensing signal receptor CviR and an antibiotic-responsive transcription factor CdeR. In this study, we show that these factors independently modulate the transcription of the antibiotic resistance genes and coordinate to ensure sensitive responses to changes in cell density. The results give new insight into antibiotic resistance regulation inC. subtsugaeand contribute to a broader understanding of how bacteria optimize the regulation of antibiotic resistance in response to changes in the environment.
Structural insight into translation initiation of theλcl leaderless mRNA
Authors: Acosta-Reyes Francisco J. , Bhattacharjee Sayan , Gottesman Max , Frank Joachim
Published: September 2023

In bacteriophageλlysogens, theλcI repressor is encoded by the leaderless transcript (lmRNA) initiated at theλpRM promoter. Translation is enhanced inrpsBmutants deficient in ribosomal protein uS2. Although translation initiation of lmRNA is conserved in bacteria, archaea, and eukaryotes, structural insight of a lmRNA translation initiation complex is missing. Here, we use cryo-EM to solve the structures of the uS2-deficient 70S ribosome of hostE. colimutantrpsB11and the wild-type 70S complex withλcI lmRNA and fmet-tRNAfMet. Importantly, the uS2-deficient 70S ribosome also lacks protein bS21. The anti-Shine-Dalgarno (aSD) region is structurally supported by bS21, so that the absence of the latter causes the aSD to divert from the normal mRNA exit pathway, easing the exit of lmRNA. A π-stacking interaction between the monitor base A1493 and A(+4) of lmRNA potentially acts as a recognition signal. Coulomb charge flow, along with peristalsis-like dynamics within the mRNA entry channel due to the increased 30S head rotation caused by the absence of uS2, are likely to facilitate the propagation of lmRNA through the ribosome. These findings lay the groundwork for future research on the mechanism of translation and the co-evolution of lmRNA and mRNA that includes the emergence of a defined ribosome-binding site of the transcript.