bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA Binding of Syntaxin 5 Synergises Membrane Fusion to Accelerate miRNA Export, Activate Macrophage and Clear Pathogens
Authors: Hom Choudhury Sourav , Bhattacharjee Shreya , Mukherjee Kamalika , Bhattacharyya Suvendra N.
Published: September 2023

Intercellular miRNA exchange acts as a key mechanism to control gene expression post-transcriptionally in mammalian cells. Regulated export of repressive miRNAs allows the expression of inflammatory cytokines in activated macrophages. Intracellular trafficking of miRNAs from endoplasmic reticulum to endosomes is a rate determining step in miRNA export process and plays an important role in controlling cellular miRNA level and inflammatory processes in macrophages. We have identified the SNARE protein Syntaxin5 to show a synchronized expression pattern with miRNA activity loss in activated mammalian macrophage cells. Syntaxin 5 is both necessary and sufficient for macrophage activation and clearance of the intracellular pathogenLeishmania donovanifrom infected macrophages. Exploring the mechanism of how Syntaxin5 acts as an immunostimulant, we have identified thede novoRNA binding property of this SNARE protein that binds specific miRNAs and facilitates their accumulation in endosomes in a cooperative manner with human ELAV protein HuR to ensure export of miRNAs and allows the expression of miRNA-repressed cytokines. Conversely, in its dual role in miRNA export, this SNARE protein prevents lysosomal targeting of endosomes by enhancing the fusion of miRNA-loaded endosomes with plasma membrane to ensure accelerated release of extracellular vesicles and associated miRNAs.

Graphical Abstract

HuR transfers miRNAs to STX5 for export

STX5 utilizes its N-terminal disordered domain to bind and target miRNAs to endosomes.

In its dual role, STX5 uses the SNARE domain to export miRNA by promoting EV biogenesis and release.

STX5-mediated miRNA export activates macrophage to clear internalized parasites.
Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis
Authors: Vignale Federico A. , Hernandez Garcia Andrea , Modenutti Carlos P. , Sosa Ezequiel J. , Defelipe Lucas A. , Oliveira Renato R.M. , Nunes Gisele L. , Acevedo Raúl M. , Burguener German F. , Rossi Maximiliano , Zapata Pedro D. , Marti Dardo A. , Sansberro Pedro A. , Oliveira Guilherme , Smith Madeline N. , Dubs Nicole M. , Nair Satish , Barkman Todd J. , Turjanski Adrian G.
Published: September 2023

Yerba mate (Ilex paraguariensis) is an economically important crop marketed for the elaboration of mate, the third-most widely consumed caffeine-containing infusion worldwide. Here we report the first genome assembly of this species, which has a total length of 1.06 Gb and contains 53,390 protein-coding genes. Comparative analyses revealed that the large yerba mate genome size is partly due to a whole-genome duplication (Ip-α) during the early evolutionary history ofIlex, in addition to the hexaploidization event (γ) shared by core eudicots. Characterization of the genome allowed us to clone the genes encoding methyltransferase enzymes that catalyse multiple reactions required for caffeine production. To our surprise, this species has converged upon a different biochemical pathway compared to that of its relatives, coffee and tea. In order to gain insight into the structural basis for the convergent enzyme activities, we obtained a crystal structure for the terminal enzyme in the pathway that forms caffeine. The structure reveals that convergent solutions have evolved for substrate positioning because different amino acid residues facilitate a different substrate orientation such that efficient methylation occurs in the independently evolved enzymes in yerba mate and coffee. While our results show phylogenomic constraint limits the genes coopted for convergence of caffeine biosynthesis, the x-ray diffraction data suggests structural constraints are minimal for the convergent evolution of individual reactions.
A General Method to Accurately Count Molecular Complexes and Determine the Degree of Labelling in Cells Using Protein Tags
Authors: Tashev Stanimir Asenov , Euchner Jonas , Yserentant Klaus , Hänselmann Siegfried , Hild Felix , Chmielewicz Wioleta , Hummert Johan , Schwörer Florian , Tsopoulidis Nikolaos , Germer Stefan , Saßmannshausen Zoe , Fackler Oliver T. , Klingmüller Ursula , Herten Dirk-Peter
Published: September 2023

Determining the label to target ratio, also known as degree of labelling (DOL), is crucial for quantitative fluorescence microscopy and a high DOL with minimal unspecific labelling is beneficial for fluorescence microscopy in general. Yet, robust, versatile, and easy-to-use tools for measuring cell-specific labelling efficiencies are not available. This study presents a novel DOL determination technique named Protein-tag DOL (ProDOL), which enables fast DOL measurements and optimisation of protein-tag labelling. With ProDOL various factors affecting labelling efficiency, including substrate type, incubation time, and concentration, as well as sample fixation and cell type can be easily assessed. We applied ProDOL to investigate how HIV-1 pathogenesis factor Nef modulates CD4 T cell activation measuring total and activated copy numbers of the adaptor protein SLP-76 in signalling microclusters. ProDOL proved to be a versatile and robust tool for labelling calibration, enabling determination of labelling efficiencies, optimisation of strategies, and quantification of protein stoichiometry.
Tradeoffs of increasing temperatures for the spread of antimicrobial resistance in river biofilms
Authors: Bagra Kenyum , Kneis David , Padfield Daniel , Szekeres Edina , Teban-Man Adela , Coman Cristian , Singh Gargi , Berendonk Thomas U. , Klümper Uli
Published: September 2023

River microbial communities regularly act as the first defense barrier against the spread of antimicrobial resistance genes (ARG) that enter environmental microbiomes through wastewaters. However, how the invasion dynamics of wastewater-born ARGs into river biofilm communities will shift due to increasing average and peak temperatures worldwide through climate change remains unknown. Here we aimed at elucidating the effects of increasing temperatures on both, the natural river biofilm resistome, as well as the river biofilms invadability by foreign, wastewater-born ARGs. To achieve this, natural biofilms were grown in a pristine German river and transferred to artificial laboratory recirculation flume systems at three different temperatures (20°C, 25°C, 30°C). Already after one week of acclimatization to the temperatures, significant increases in the abundance of most naturally occurring ARGs were detected in the biofilms exposed to the highest temperature. Thereafter, biofilms were exposed to a single pulse of wastewater and the invasion dynamics of wastewater-born ARGs were analyzed over a period of two weeks. While initially after one day ARGs were able to invade all biofilms successfully and in equal proportions, the foreign invading ARGs were lost at a far increased rate at 30°C over time. ARG levels dropped to the initial natural levels at 30°C after 14 days. Contrary at the lower temperatures ARGs remained far elevated and certain ARGs were able to establish themselves in the biofilms. Overall, we here demonstrate tradeoffs of increasing temperature between increases in naturally occurring and faster loss dynamics of invading ARGs.
Comparative transcriptomics reveal a novel tardigrade specific DNA binding protein induced in response to ionizing radiation
Authors: Anoud M. , Delagoutte E. , Helleu Q. , Brion A. , Duvernois-Berthet E. , As M. , Marques X. , Lamribet K. , Senamaud C. , Jourdren L. , Adrait A. , Heinrich S. , Toutirais G. , Hamlaoui S. , Gropplero G. , Giovannini I. , Ponger L. , Gèze M. , Blugeon C. , Coute Y. , Guidetti R. , Rebecchi L , Giovannangeli C. , De Cian A. , Concordet J-P.
Published: September 2023

Tardigrades, microscopic animals found in virtually all ecosystems, are renowned for their remarkable ability to withstand extreme conditions. Recent studies have identified novel tardigrade specific protein families that aid in resistance to desiccation and ionizing radiation (IR). Notably, a tardigrade specific DNA binding protein called Dsup (for DNA damage suppressor) has been found to protect from X-ray damage in human cells and from hydroxyl radicalsin vitro. However, Dsup has only been found in two species within the Hypsibioidea superfamily.

To better understand mechanisms underlying radio-resistance in the Tardigrada phylum, we first characterized DNA damage and repair in response to IR in the model speciesHypsibius exemplaris. By analysis of phosphorylated H2AX, we demonstrated the induction and repair of DNA double-strand breaks after IR exposure. Importantly, the rate of single-strand breaks induced was roughly equivalent to that in human cells, suggesting that DNA repair plays a predominant role in the remarkable radio-resistance of tardigrades. In order to identify novel tardigrade specific genes involved, we next conducted a comparative transcriptomics across three species,H. exemplaris,Acutuncus antarcticusandParamacrobiotus fairbanksi, the latter belonging to the Macrobiotoidea superfamily known to lack Dsup homologs. In all three species, many genes of DNA repair were among the most strongly overexpressed genes alongside a novel tardigrade specific gene, namedTardigradeDNA damageResponse protein1(TDR1). We found that TDR1 protein interacts with DNA and forms aggregates at high concentration suggesting it may condensate DNA and act by preserving chromosome organization until DNA repair is accomplished. Remarkably, when expressed in human cells, TDR1 improved resistance to Bleomycin, a radiomimetic drug. Based on these findings, we propose that TDR1 is a novel tardigrade specific gene responsible for conferring resistance to IR. Our study sheds light on mechanisms of DNA repair helping to cope with high levels of DNA damage. Furthermore, it suggests that at least two tardigrade specific genes, respectively for Dsup and TDR1, have independently evolved DNA-binding functions that contribute to radio-resistance in the Tardigrada phylum.
Development of evolutionarily conserved viral integration sites as safe harbors for human gene therapy
Authors: Quezada-Ramírez Marco A. , Loncar Shannon , Campbell Matthew A. , Parsi Krishna M. , Gifford Robert J. , Kotin Robert M.
Published: September 2023

Gene transfer into CD34+hematopoietic stem and progenitor cells (HSPCs) involving integrating viral vectors has unpredictable outcomes including potential adverse events like leukemogenesis, resulting from insertional mutagenesis. Therefore, identifying and characterizing genome safe harbor (GSH) sites where exogenous gene material can be safely integrated into adult progenitor and stem cells is critically important for therapeutic gene addition. Here, we present a novel approach to identify new GSH sites based on a proven system of stable transgene insertion: the evolutionarily conserved integration of parvovirus DNA into the germlines of host species. From a dataset of 199 unique endogenous parvovirus (EPV) integration events identified in host species genomes, 102 loci were mapped to the human genome with 17 being experimentally evaluated as GSHs in primary human CD34+HSPCs. Nine promising GSHs resulted in cells edited using nucleofection alone or in combination with rAAV transduction. Of the nine GSH sites, six edited loci displayed sustained transgene expression in both erythroid and immune phenotypes while three clearly exhibited immune branch specific-regulation. Following this approach, additional GSH sites are likely to emerge from the remaining mapped loci for gene addition in hematopoietic stem and progenitor cells. Since it is unlikely that the GSH-lineage-restricted transgene expression is exclusive to hematopoietic stem cells, this approach extends the options for gene knock-ins while reducing the risks of insertional mutagenesis, unpredictable expression profiles, effects on differentiation, and increasing therapeutic effects.
Top-down biological motion perception does not differ between adults scoring high versus low on autism traits
Authors: Oomen Danna , Wiersema Jan R. , Orgs Guido , Cracco Emiel
Published: September 2023

The perception of biological motion is an important social cognitive ability. Models of biological motion perception recognize two processes that contribute to the perception of biological motion: a bottom-up process that binds optic-flow patterns into a coherent percept of biological motion and a top-down process that binds sequences of body-posture ‘snapshots’ over time into a fluent percept of biological motion. The vast majority of studies on autism and biological motion perception have used point-light figure stimuli, which elicit biological motion perception predominantly via bottom-up processes. Here, we investigated whether autism is associated with deviances in the top-down processing of biological motion. For this, we tested a sample of adults scoring lowvshigh on autism traits on a recently validated EEG paradigm in which apparent biological motion is combined with frequency tagging (Cracco et al., 2022) to dissociate between two percepts: 1) the representation of individual body postures, and 2) their temporal integration into movements. In contrast to our hypothesis, we found no evidence for a diminished temporal body posture integration in the high-scoring group. We did, however, find a group difference that suggests that adults scoring high on autism traits have a visual processing style that focuses more on a single percept (i.e. either body postures or movements, contingent on saliency) compared to adults scoring low on autism traits who instead seemed to represent the two percepts included in the paradigm in a more balanced manner. Although unexpected, this finding aligns well with the autism literature on perceptual stability(/rigidity).
Mechanosensitive recruitment of Vinculin maintains junction integrity and barrier function at epithelial tricellular junctions
Authors: van den Goor Lotte , Iseler Jolene , Koning Katherine , Miller Ann L.
Published: September 2023

Apical cell-cell junctions, including adherens junctions (AJs) and tight junctions (TJs), adhere epithelial cells to one another and regulate selective permeability at both bicellular junctions (BCJs) and tricellular junctions (TCJs). Although several specialized proteins are known to localize at TCJs, it remains unclear how actomyosin-mediated tension transmission at TCJs contributes to the maintenance of junction integrity and barrier function at these sites. Here, utilizing gastrula-stageXenopus laevisembryos as a model system, we describe a mechanism by which Vinculin, a mechanosensitive protein, anchors the actomyosin network at TCJs, thus maintaining TJ stability and barrier function. Using an optogenetic approach, we found that acutely increasing junctional tension results in robust recruitment of Vinculin to apical junctions immediately surrounding TCJs. In Vinculin knockdown (KD) embryos, junctional actomyosin intensity is decreased and becomes disorganized at TCJs. Using fluorescence recovery after photobleaching (FRAP), we show that loss of Vinculin results in reduced Actin stability at TCJs. Vinculin knockdown also destabilizes Angulin-1, a key protein involved in regulating barrier function at TCJs. When Vinculin KD embryos are subjected to increased tension, TCJs cannot maintain their proper morphology. Finally, using a live imaging barrier assay, we detect increased barrier leaks at TCJs in Vinculin KD embryos. Together, our findings show that Vinculin-mediated actomyosin organization is required to maintain junction integrity and barrier function at TCJs and reveal new information about the interplay between adhesion and barrier function at TCJs.

Highlights

Vinculin is mechanosensitively recruited to tricellular junctions

Vinculin’s actin-binding function is needed for tricellular actomyosin organization

Tricellular tight junctions are unstable when Vinculin is knocked down

Vinculin is required to maintain barrier function at tricellular junctions
Inhibition of human immunodeficiency virus (HIV-1) infectivity by expression of poorly or broadly neutralizing antibodies against Env in virus-producing cells
Authors: Wang Qian , Zhang Shijian , Nguyen Hanh T. , Sodroski Joseph
Published: September 2023

The human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) precursor (gp160) trimerizes, is modified by high-mannose glycans in the endoplasmic reticulum, and is transported via Golgi and non-Golgi secretory pathways to the infected cell surface. In the Golgi, gp160 is partially modified by complex carbohydrates and proteolytically cleaved to produce the mature functional Env trimer, which is preferentially incorporated into virions. Broadly neutralizing antibodies (bNAbs) generally recognize the cleaved Env trimer, whereas poorly neutralizing antibodies (pNAbs) bind the conformationally flexible gp160. We found that expression of bNAbs, pNAbs or soluble/membrane forms of the receptor, CD4, in cells producing HIV-1 all decreased viral infectivity. Four patterns of co-expressed ligand:Env were observed: 1) Ligands (CD4, soluble CD4-Ig and some pNAbs) that specifically recognize the CD4-bound Env conformation resulted in uncleaved Envs lacking complex glycans that were not incorporated into virions; 2) Other pNAbs produced Envs with some complex carbohydrates and severe defects in cleavage, which were relieved by brefeldin A treatment; 3) bNAbs that recognize gp160 as well as mature Envs resulted in Envs with some complex carbohydrates and moderate decreases in virion Env cleavage; and 4) bNAbs that preferentially recognize mature Envs produced cleaved Envs with complex glycans in cells and on virions. The low infectivity observed upon co-expression of pNAbs or CD4 could be explained by disruption of Env trafficking, reducing the level of Env and/or increasing the fraction of uncleaved Env on virions. In addition to bNAb effects on virion Env cleavage, the secreted bNAbs neutralized the co-expressed viruses.

IMPORTANCE

The envelope glycoprotein (Env) trimers on the human immunodeficiency virus (HIV-1) mediate virus entry into host cells. Env is synthesized in infected cells, modified by complex sugars and cleaved to form a mature, functional Env, which is incorporated into virus particles. Env elicits antibodies in infected individuals, some of which can neutralize the virus. We found that antibodies co-expressed in the virus-producing cell can disrupt Env transit to the proper compartment for cleavage and sugar modification and, in some cases, block incorporation into viruses. These studies provide insights into the processes by which Env becomes functional in the virus-producing cell and may assist attempts to interfere with these events to inhibit HIV-1 infection.
Service evaluation of “GP at Door” of Accident and Emergency Services in Eastern England
Authors: Brainard Julii , Rice Aiden , Hughes Gareth , Everden Paul
Published: September 2023

Aims

To describe activity and outcomes after streaming low urgency attenders to general practice services at door of Accident and Emergency departments (GDAE), including possible benefits to co-located emergency departments.

Methods

As a service evaluation, we describe GDAE users, their reasons for presentation, wait times, outcomes and co-located emergency department performance metrics at two hospitals in eastern England.

Findings

Each GDAE saw about 928 patients per month. Wait times for usual A&E care relatively shortened at only one site. Reattendances were common (about 10% of attenders), 75% of GDAE attenders were seen within 1 hour of arrival, 7% of patients initially allocated to GDAE were referred back to A&E for further investigations, 59% of GDAE patients were treated and discharged with no further treatment or referral required. Pain, injury, infection or feeling generally unwell each comprised > 10% of primary reasons for attendance. Referrals to specialist health services were outcome for 4% and 16% at respective sites.

Conclusions

About 26,000 A&E attendances appear to have been prevented. Patients were seen quickly at both GDAE sites, while there were more specialist referrals or shorter wait times for usual A&E services at only one site. Process evaluation could illuminate reasons for these differences.
Proposal of a vaccination needs index to prioritize municipal interventions in Brazil
Authors: Diaz-Quijano Fredi Alexander , Schrarstzhaupt Isaac Negretto , Fantinato Francieli Fontana Sutile Tardetti , Guzmán-Barrera Lely Stella , Croda Julio
Published: September 2023

Introduction

To address the health needs of a population, it is essential to integrate several indicators that are expressed on non-comparable scales. Vaccination is a crucial aspect of public health, and prioritizing vaccination needs through immunization registries can help allocate resources and funding to integral approaches.

Objective

To propose and implement an index of vaccination needs (VNI) based on national administrative data on tracer vaccines for children, born between 2019 and 2022, to help prioritize Brazilian municipalities.

Methodology

We analyzed data from 5,570 municipalities in Brazil. The VNI integrated indicators of vaccination coverage and the number of susceptible children regarding tracer vaccines for children including DTP – Diphtheria-Tetanus-Pertussis (third dose), polio (third dose), and MMR – Measles-Mumps and Rubella (second dose). We assessed how the VNI could identify a group of municipalities in challenging situations to improve vaccination.

Results

Compared with criteria based only on the absolute number of unvaccinated children (susceptible children) or the vaccination coverage, the group prioritized for having high VNI exhibited more similar proportions of large, medium, and small municipalities. Additionally, this group included more municipalities located in the Legal Amazon region and Special Sanitary Indigenous Districts than groups prioritized with the other criteria. The VNI also outperformed the other criteria to prioritize municipalities that differed from the rest regarding the Gini coefficient.

Conclusion

The proposed VNI can facilitate the identification of populations that need differentiated interventions to prevent the resurgence of eliminated or controlled vaccine-preventable diseases.
Structure of γ-secretase (PSEN1/APH-1B) in complex with Aβ46 provides insights into amyloid-β processing and modulation by the APH-1B isoform
Authors: Odorcic Ivica , Hamed Soliman Mohamed Belal , Lismont Sam , Chávez-Gutiérrez Lucía , Efremov Rouslan G.
Published: September 2023

Deposition of amyloid-β (Aβ) peptides in the brain is a hallmark of Alzheimer’s disease. Aβs are generated through sequential proteolysis of the amyloid precursor protein by the γ-secretase complexes (GSECs). Aβ peptide length, which is modulated by the Presenilin (PSEN) and APH-1 subunits of GSEC, is critical for Alzheimer’s pathogenesis. Despite high relevance, mechanistic understanding of the proteolysis of Aβ, and its modulation by APH-1, remain incomplete. Here, we report cryo-EM structures of human GSEC (PSEN1/APH-1B) reconstituted into lipid nanodiscs in apo form and in complex with the intermediate Aβ46 substrate. We found a divergent APH-1 loop to be involved with PSEN1 in substrate-binding-induced concerted rearrangements. Upstream the catalytic site, Aβ46 structure is similar to the endopeptidase substrates and is stabilised by polar interactions including a previously unseen interaction with PSEN1 loop1. The hybrid β-sheet was not observed downstream the catalytic site.
DelSIEVE: cell phylogeny model of single nucleotide variants and deletions from single-cell DNA sequencing data
Authors: Kang Senbai , Borgsmüller Nico , Valecha Monica , Markowska Magda , Kuipers Jack , Beerenwinkel Niko , Posada David , Szczurek Ewa
Published: September 2023

With rapid advancements in single-cell DNA sequencing (scDNA-seq), various computational methods have been developed to study evolution and call variants on single-cell level. However, modeling deletions remains challenging because they affect total coverage in ways that are difficult to distinguish from technical artifacts. We present DelSIEVE, a statistical method that infers cell phylogeny and single-nucleotide variants, accounting for deletions, from scDNA-seq data. DelSIEVE distinguishes deletions from mutations and artifacts, detecting more evolutionary events than previous methods. Simulations show high performance, and application to cancer samples reveals varying amounts of deletions and double mutants in different tumors.
Evolutionarily Conserved CKI1-Mediated Two-Component Signaling is Required for Female Germline Specification inMarchantia polymorpha
Authors: Bao Haonan , Sun Rui , Iwano Megumi , Yoshitake Yoshihiro , Aki Shiori S , Umeda Masaaki , Nishihama Ryuichi , Yamaoka Shohei , Kohchi Takayuki
Published: September 2023

In land plants, gametes derive from a small number of dedicated haploid cells.1In angiosperms, one central cell and one egg cell are differentiated in the embryo sac as female gametes for double fertilization, while in non-flowering plants, only one egg cell is generated in the female sexual organ, called the archegonium.2,3The central cell specification ofArabidopsis thalianais controlled by the histidine kinase CYTOKININ-INDEPENDENT 1 (CKI1), which is a two-component signaling (TCS) activator sharing downstream regulatory components with the cytokinin signaling pathway.4–7Our phylogenetic analysis suggested that CKI1 orthologs broadly exist in land plants. However, the role of CKI1 in the archegonium-bearing non-flowering plants remains unclear. Here we found that the sole CKI1 ortholog in the liverwortMarchantia polymorpha, MpCKI1, which functions through conserved downstream TCS components, regulates the female germline specification for egg cell development in the archegonium. InM. polymorpha, the archegonium develops three-dimensionally from a single cell, accumulating MpBONOBO (MpBNB), a master regulator for germline initiation and differentiation.8We visualized female germline specification by capturing the distribution pattern of MpBNB in the discrete stages of early archegonium development, and found that the MpBNB accumulation is restricted to female germline cells. MpCKI1 is required for the proper MpBNB accumulation in the female germline, and is critical for the asymmetric cell divisions that specify the female germline cells. These results suggest that CKI1-mediated TCS originated during early land plant evolution and participates in female germ cell specification in deeply-diverged plant lineages.
Decision bias and sampling asymmetry in reward-guided learning
Authors: Cao Yinan , Tsetsos Konstantinos
Published: September 2023

Human economic decisions are highly sensitive to contexts. Deciding between two competing alternatives can be notoriously biased by their overall value (‘magnitude effect’) or by a third decoy option (‘distractor effect’). Some prominent explanations appeal to diminishing value sensitivity and divisive normalization in value representations, i.e., representational bias, that feed into the choice stage. However, these explanations have recently come under scrutiny due to empirical inconsistencies and mounting alternative theories. Here, we posit that context-sensitive choices may not stem from representational biases but rather emerge as by-products of asymmetric sampling during value learning. In a reward-guided choice task, participants aimed to maximize cumulative rewards through trial and error. The task introduced alternating blocks with either a colored distractor or a neutral ‘notional’ distractor. We observed decreased choice accuracy when higher-value distractors were present, a pattern that persisted even in the notional distractor blocks. Using computational modeling, we show that this phenomenon falls out naturally from a simple learning rule without relying on any additional mechanism such as divisive normalization or nonlinear utility. Furthermore, we found that, contrary to divisive normalization, choice accuracy was not influenced by distractor value but strongly depended on the magnitude of the targets’ values per se. This ‘magnitude sensitivity’ was also found in the ‘notional distractor’ conditions and could lawfully be reproduced by the learning model. Importantly, when counterfactual feedback eliminated sampling asymmetry, the observed decision bias vanished. Our results suggest that the genesis of context-sensitive choices may lie in the learning dynamics themselves, specifically sampling asymmetry, rather than in pre-decisional representational biases. This finding reframes the discourse on irrational decision-making, attributing it to acquired biases during the learning process, not necessarily computational intricacies at the choice stage.
Interplay of Race and Neighborhood Deprivation on Ambulatory Blood Pressure in Young Adults
Authors: Jeong Soolim , Linder Braxton A. , Barnett Alex M. , Tharpe McKenna A. , Hutchison Zach J. , Culver Meral N. , Sanchez Sofia O. , Nichols Olivia I. , Grosicki Gregory J. , Bunsawat Kanokwan , Nasci Victoria L. , Gohar Eman Y. , Fuller-Rowell Thomas E. , Robinson Austin T.
Published: September 2023

Background

Ambulatory blood pressure (BP) monitoring measures nighttime BP and BP dipping, which are superior to in-clinic BP for predicting cardiovascular disease (CVD), the leading cause of death in America. Compared with other racial/ethnic groups, Black Americans exhibit elevated nighttime BP and attenuated BP dipping, including in young adulthood. Social determinants of health contribute to disparities in CVD risk, but the contribution of neighborhood deprivation on nighttime BP is unclear. Therefore, we examined associations between neighborhood deprivation with nighttime BP and BP dipping in young Black and White adults.

Methods

We recruited 21 Black and 26 White participants (20 M/27 F, mean age: 21 years, body mass index: 25±4 kg/m2) for 24-hour ambulatory BP monitoring. We assessed nighttime BP and BP dipping (nighttime:daytime BP ratio). The area deprivation index (ADI) was used to measure neighborhood deprivation. Associations between ADI and ambulatory BP were examined.

Results

Black participants exhibited higher nighttime diastolic BP compared with White participants (63±8 mmHg vs 58±7 mmHg,p=0.003), and attenuated BP dipping ratios for both systolic (0.92±0.06 vs 0.86±0.05,p=0.001) and diastolic BP (0.86±0.09 vs 0.78±0.08,p=0.007). Black participants experienced greater neighborhood deprivation compared with White participants (ADI scores: 110±8 vs 97±21,p<0.001), and ADI was associated with attenuated systolic BP dipping (ρ=0.342,p=0.019).

Conclusions

Our findings suggest neighborhood deprivation may contribute to higher nighttime BP and attenuated BP dipping, which are prognostic of CVD, and more prevalent in Black adults. Targeted interventions to mitigate the effects of neighborhood deprivation may help to improve nighttime BP.

Clinical Trial Registry

URL:https://www.clinicaltrials.gov; Unique identifier:NCT04576338

Clinical Perspective

We demonstrate young Black adults exhibit higher nighttime blood pressure and attenuated nighttime blood pressure dipping compared with young White adults.

Black adults were exposed to greater neighborhood deprivation, which was associated with attenuated blood pressure dipping, irrespective of race.

Our findings add to a growing body of literature indicating neighborhood deprivation may contribute to increased cardiovascular disease risk.
Rab35 is required for embryonic development and kidney and ureter homeostasis through regulation of epithelial cell junctions
Authors: Clearman Kelsey R. , Timpratoom Napassawon , Patel Dharti , Rains Addison B. , Haycraft Courtney J. , Croyle Mandy J. , Reiter Jeremy F. , Yoder Bradley K.
Published: September 2023

Structured Abstract

Background

Rab35 is a member of a GTPase family of endocytic trafficking proteins. Studies in cell lines have indicated that Rab35 participates in cell adhesion, polarity, cytokinesis, and primary cilia length and composition. Additionally, sea urchin Rab35 regulates actin organization and is required for gastrulation. In mice, loss of Rab35 in the CNS disrupts hippocampal development and neuronal organization. Outside of the CNS, the functions of mammalian Rab35in vivoare unknown.

Methods

We generated and analyzed the consequences of both congenital and conditional nullRab35mutations in mice. Using a LacZ reporter allele, we assessedRab35expression during development and postnatally. We assessed Rab35 loss in the kidney and ureter using histology, immunofluorescence microscopy, and western blotting.

Results

CongenitalRab35loss of function caused embryonic lethality: homozygous mutants arrested at E7.5 with cardiac edema. Conditional loss of Rab35, either during gestation or postnatally, caused hydronephrosis. The kidney and ureter phenotype were associated with disrupted actin cytoskeletal architecture, altered Arf6 epithelial polarity, reduced adherens junctions, loss of tight junction formation, defects in EGFR expression and localization, disrupted cell differentiation, and shortened primary cilia.

Conclusion

Rab35 is essential for mammalian development and the maintenance of kidney and ureter architecture. Loss of Rab35 leads to non-obstructive hydronephrosis, making theRab35mutant mouse a novel mammalian model to study mechanisms underlying this disease.

Significance Statement

Hydronephrosis, distention of the renal calyces and pelvis, affects 1 in 100 infants. Most cases of hydronephrosis are associated with obstruction. Non-obstructive hydronephrosis is typically associated with impaired ureter development, and requires surgical intervention. Here, we describe a mouse model of non-obstructive hydronephrosis caused by mutations inRab35.Hydronephrosis inRab35mutants is associated with the inability to maintain epithelial cell junctions, defects in EGFR expression, and altered urothelium and smooth muscle integrity of the ureter. TheRab35mutant mouse is a novel model to study mechanisms and treatment strategies for non-obstructive hydronephrosis.
A novel workflow for unbiased quantification of autophagosomes in 3D inArabidopsis thalianaroots
Authors: Daněk Michal , Kocourková Daniela , Podmanická Tereza , Eliášová Kateřina , Nesvadbová Kristýna , Krupař Pavel , Martinec Jan
Published: September 2023

Macroautophagy is frequently quantified by live imaging of autophagosomes decorated with a marker of fluorescently tagged ATG8 protein (FT-ATG8) inArabidopsis thaliana. This requires generation of suitable plant material by time-consuming crossing or transformation with FT-ATG8 marker. Autophagosome quantification by image analysis often relies on their counting in individual focal planes. This approach is prone to deliver biased results due to inappropriate sampling of the regions of interest in the Z-direction, as the actual 3D distribution of autophagosomes is usually not taken into account. To overcome such drawbacks, we have developed and tested a workflow consisting of immunofluorescence microscopy of autophagosomes labelled with anti-ATG8 antibody followed by stereological image analysis employing the optical disector and the Cavalieri principle. Our immunolabelling protocol specifically recognized autophagosomes in epidermal cells ofA. thalianaroot. Higher numbers of immunolabelled autophagosomes were observed when compared with those recognized with FT-AtATG8e marker, suggesting that singleAtATG8 isoform markers cannot detect all autophagosomes in a cell. Therefore, immunolabelling provides more precise information as the anti-ATG8 antibody recognizes virtually allAtATG8 isoforms. The number of autophagosomes per tissue volume determined by stereological methods correlated with the intensity of autophagy induction treatment. Compared to autophagosome quantifications in maximum intensity projections, stereological methods detected autophagosomes present in a given volume with higher accuracy. Our novel application of immunolabelling combined with stereological methods constitutes a powerful toolbox for unbiased and reproducible quantification of autophagosomes and offers a convenient alternative to the standard of live imaging using FP-ATG8 marker.
GC content across insect genomes: phylogenetic patterns, causes and consequences
Authors: Kyriacou Riccardo G. , Mulhair Peter O. , Holland Peter W. H.
Published: September 2023

The proportions of A:T and G:C nucleotide pairs are often unequal and can vary greatly between animal species and along chromosomes. The causes and consequences of this variation are incompletely understood. The recent release of high-quality genome sequences from the Darwin Tree of Life and other large-scale genome projects provides an opportunity for GC heterogeneity to be compared across a large number of insect species. Here we analyse GC content along chromosomes, and within protein-coding genes and codons, of 150 insect species from four holometabolous orders: Coleoptera, Diptera, Hymenoptera, and Lepidoptera. We find that protein-coding sequences have higher GC content than the genome average, and that Lepidoptera generally have higher GC content than the other three insect orders examined. GC content is higher in small chromosomes in most Lepidoptera species, but this pattern is less consistent in other orders. GC content also increases towards subtelomeric regions within protein-coding genes in Hymenoptera, Coleoptera and, most strikingly, Lepidoptera. Two species of Diptera,Bombylius majorandB. discolor, have very atypical genomes with ubiquitous increase in AT content, especially at third codon positions. Despite dramatic AT-biased codon usage, we find no evidence that this has driven divergent protein evolution. We argue that the GC landscape of Lepidoptera, Hymenoptera and Coleoptera genomes is influenced by GC-biased gene conversion, strongest in Lepidoptera, with some outlier taxa affected drastically by counteracting processes.
Clustering of cortical dynein regulates the mechanics of spindle orientation in human mitotic cells
Authors: Anjur-Dietrich Maya I. , Hererra Vicente Gomez , Farhadifar Reza , Wu Haiyin , Merta Holly , Bahmanyar Shirin , Shelley Michael J. , Needleman Daniel J.
Published: September 2023

The forces which orient the spindle in human cells remain poorly understood due to a lack of direct mechanical measurements in mammalian systems. We use magnetic tweezers to measure the force on human mitotic spindles. Combining the spindle’s measured resistance to rotation, the speed it rotates after laser ablating astral microtubules, and estimates of the number of ablated microtubules reveals that each microtubule contacting the cell cortex is subject to ∼1 pN of pulling force, suggesting that each is pulled on by an individual dynein motor. We find that the concentration of dynein at the cell cortex and extent of dynein clustering are key determinants of the spindle’s resistance to rotation, with little contribution from cytoplasmic viscosity, which we explain using a biophysically based mathematical model. This work reveals how pulling forces on astral microtubules determine the mechanics of spindle orientation and demonstrates the central role of cortical dynein clustering.

Highlights

Cytoplasmic viscosity does not determine the spindle’s resistance to rotation

Each astral microtubule that contacts the cell cortex is pulled on by a single dynein motor

Pulling forces on astral microtubules determine the mechanics of spindle orientation

The mechanics of spindle orientation is regulated by clustering of dynein motors at the cell cortex

Graphical Abstract
Instinct to insight: Neural correlates of ethological strategy learning
Authors: Lu Kai , Wong Kelvin T. , Zhou Lin N. , Shi Yike T. , Yang Chengcheng J. , Liu Robert C.
Published: September 2023

In ethological behaviors like parenting, animals innately follow stereotyped patterns of choices to decide between uncertain outcomes but can learn to modify their strategies to incorporate new information. For example, female mice in a T-maze instinctively use spatial-memory to search for pups where they last found them but can learn more efficient strategies employing pup-associated acoustic cues. We uncovered neural correlates for transitioning between these innate and learned strategies. Auditory cortex (ACx) was required during learning. ACx firing at the nest increased with learning and correlated with subsequent search speed but not outcome. Surprisingly, ACxsuppressionrather than facilitation during search was more prognostic of correct sound-cued outcomes – even before adopting a sound-cued strategy. Meanwhile medial prefrontal cortex encoded the last pup location, but this decayed as the spatial-memory strategy declined. Our results suggest a neural competition between a weakening spatial-memory and strengthening sound-cued neural representation to mediate strategy switches.
Stakeholder management challenges in a health-care medical device project in India – an SME perspective
Authors: Kaur Amrinder
Published: September 2023

Learning outcomes

The learning outcomes are as follows: understanding the impact on company growth through identification and alignment of stakeholder priorities in a project for SME in an emerging market; analyzing the impact of stakeholder alignment and relationship management on the project outcome; and evaluating the importance of Stakeholder Management for effective Project Management.

Case overview/synopsis

The case of ‘Hospedia Medicare,’ a medical device manufacturing company based in India, was started by a family involved in the medical devices business for over two decades. The company began operations in a new avatar and focused on one medical device or product by 2013. The product was designed with quality features to solve customer problems, making the cost relatively high compared to other domestic peers. Creating new product lines or updating the existing product attributes was imperative for the company to attain its growth objectives. The protagonist was dealing with a dilemma involving managing various stakeholders, aligning the project scope to create a growth story for the company in line with its vision and managing the stakeholders by understanding and analyzing their needs, expectations and interest, thus influencing the project outcome. The case can be used by instructors to identify, understand and evaluate the importance of different stakeholders on project outcome or success. Furthermore, it can be used to analyze and critique the impact of stakeholders on project scope, which can affect the long-term sustainability of the company, as different stakeholders have different expectations and needs. The case also details how regular communication, collaboration and awareness became essential for the project's success. Lack of an effective engagement strategy at the project planning stage can have risks concerning cost and achieving the overall vision, which creates a positive outcome for all the stakeholders.

Complexity academic level

The case study can be introduced to graduate and undergraduate students to reflect on and critique the importance of Stakeholder Management in Project Management. It can be used for, entrepreneurship, project management, operations and strategy, particularly emphasizing for small and medium enterprises (SMEs).

Supplementary material

Teaching notes are available for educators only.

Subject code

CSS 9: Operations and Logistics.
Toward a simple and accurate Lagrangian-based error estimator for the BDF algorithms and adaptive time-stepping
Authors: Wang Yazhou , Luo Dehong , Zhang Xuelin , Wang Zhitao , Chen Hui , Zhang Xiaobo , Xie Ningning , Mei Shengwei , Xue Xiaodai , Zhang Tong , Tamma Kumar K.
Published: September 2023

Purpose

The purpose of this paper is to design a simple and accurate a-posteriori Lagrangian-based error estimator is developed for the class of backward differentiation formula (BDF) algorithms with variable time step size, and the adaptive time-stepping in BDF algorithms is demonstrated for efficient time-dependent simulations in fluid flow and heat transfer.

Design/methodology/approach

The Lagrange interpolation polynomial is used to predict the time derivative, and then the accurate primary result is obtained by the Gauss integral, which is applied to evaluate the local error. Not only the generalized formula of the proposed error estimator is presented but also the specific expression for the widely applied BDF1/2/3 is illustrated. Two essential executable MATLAB functions to implement the proposed error estimator are appended for practical applications. Then, the adaptive time-stepping is demonstrated based on the newly proposed error estimator for BDF algorithms.

Findings

The validation tests show that the newly proposed error estimator is accurate such that the effectivity index is always close to unity for both linear and nonlinear problems, and it avoids under/overestimation of the exact local error. The applications for fluid dynamics and coupled fluid flow and heat transfer problems depict the advantage of adaptive time-stepping based on the proposed error estimator for time-dependent simulations.

Originality/value

In contrast to existing error estimators for BDF algorithms, the present work is more accurate for the local error estimation, and it can be readily extended to practical applications in engineering with a few changes to existing codes, contributing to efficient time-dependent simulations in fluid flow and heat transfer.
Co-production in clinical practice: a case-study of engagement with patients with dementia and Huntington's disease to develop meaningful cognitive activities
Authors: Girardi Alessandra , Webb Elanor , Stewart Inga , Stokes Simon , Breen Kieran
Published: September 2023

Purpose

The development and clinical application of digital devices to support individuals with dementia can be challenging due to difficulties meeting the needs of a patient population with largely heterogeneous and progressive symptoms. Memjo Ltd has developed a digital interactive prototype tablet to promote cognitive stimulation and reminiscence. This proof-of-concept case-study aims to understand whether the engagement of individuals with dementia and Huntington's disease (HD) at an early stage is a useful approach to inform the initial development of meaningful digital activities and ultimately its potential introduction into clinical practice.

Design/methodology/approach

Five patients with dementia and HD at different stages of progression were recruited from an inpatient secure psychiatric hospital. Engagement, usability and preliminary benefits were assessed using a mixed-methods approach through observations, open-ended questions and subjective ratings.

Findings

The content of the tool triggered reminiscence, discussion and positive behavioural and emotional responses. The participants were confident using the tablet but needed support interacting with the touchscreen and, at times, to encourage communication. “Music” and “Videos”, were particularly successful in engaging most participants despite their cognitive and physical difficulties.

Originality/value

This case-study shows that co-production in clinical practice can be successfully implemented to develop activities that meet the interests and needs of patients with dementia and Huntington's disease. The varied and flexible assessment provided rich feedback that will be used to improve the device. This highlights avenues of focus for the development of future pools of activities.