bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-to-cell variations in subcellular localisation of V2R are independent of its expression level
Authors: Koers Eline J. , Morgan Bradley A. , Heydenreich Franziska M. , Plouffe Bianca , Styles Iain B. , Veprintsev Dmitry B. 
Published: August 2021

AbstractG protein coupled receptors (GPCRs) translate the actions of hormones into intracellular signalling events. Mutations in GPCRs can prevent their correct expression and trafficking to the cell surface and cause disease. We use single cell measurements in HEK293 cells to show that the balance between endoplasmic reticulum (ER) and cell surface localisation of the Vasopressin 2 receptor (V2R) varies significantly from cell to cell. We find that mutations in the V2R affect the proportion of cells able to send this GPCR to the cell surface but do not prevent all cells in the population from correctly trafficking the mutant receptors. These findings reveal that the ability of cells to correctly traffic V2R to the cell surface depends not only on the expressed V2R mutant but also on the individual cell environment.Significance statementMissense mutations in the Vasopressin 2 Receptor (V2R) cause Nephrogenic Diabetes Insipidus. Some of these mutations prevent correct expression and trafficking of V2R to the cell surface resulting in a loss-of-function. We show -using single cell measurements-that the balance between endoplasmic reticulum and cell surface localisation of the V2R varies significantly from cell to cell, independent from its expression level. Mutations affect the proportion of cells able to send V2R to the cell surface but do not prevent all cells in the population from correctly trafficking the mutant receptors. Hence, the ability of cells to correctly traffic V2R to the cell surface depends not only on expressed V2R mutant but also on the cell environment.
Ability of nucleoside-modified mRNA to encode HIV-1 envelope trimer nanoparticles
Authors: Mu Zekun , Wiehe Kevin , Saunders Kevin O. , Henderson Rory , Cain Derek W. , Parks Robert , Martik Diana , Mansouri Katayoun , Edwards Robert J. , Newman Amanda , Lu Xiaozhi , Xia Shi-Mao , Bonsignori Mattia , Montefiori David , Han Qifeng , Venkatayogi Sravani , Evangelous Tyler , Wang Yunfei , Rountree Wes , Tam Ying , Barbosa Christopher , Munir Alam S. , Williams Wilton B. , Pardi Norbert , Weissman Drew , Haynes Barton F. 
Published: August 2021

SUMMARYThe success of nucleoside-modified mRNAs in lipid nanoparticles (mRNA-LNP) as COVID-19 vaccines heralded a new era of vaccine development. For HIV-1, multivalent envelope (Env) trimer protein nanoparticles are superior immunogens compared to trimers alone for priming of broadly neutralizing antibody (bnAb) B cell lineages. The successful expression of complex multivalent nanoparticle immunogens with mRNAs has not been demonstrated. Here we show that mRNAs can encode antigenic Env trimers on ferritin nanoparticles that initiate bnAb precursor B cell expansion and induce serum autologous tier 2 neutralizing activity in bnAb precursor VH + VL knock-in mice. Next generation sequencing demonstrated acquisition of critical mutations, and monoclonal antibodies that neutralized heterologous HIV-1 isolates were isolated. Thus, mRNA- LNP can encode complex immunogens and are of use in design of germline-targeting and sequential boosting immunogens for HIV-1 vaccine development.
Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies)
Authors: Wu Xudong , Rapoport Tom A. 
Published: August 2021

AbstractWe describe a general method that allows structure determination of small proteins by single-particle cryo-electron microscopy (cryo-EM). The method is based on the availability of a target-binding nanobody, which is then rigidly attached to two scaffolds: (1) a Fab-fragment of an antibody directed against the nanobody, and (2) a nanobody-binding protein A fragment fused to maltose binding protein and Fab-binding domains. The overall ensemble of ∼120 kDa, called Legobody, does not perturb the nanobody-target interaction and facilitates particle alignment in cryo-EM image processing. The utility of the method is demonstrated for the KDEL receptor, a 23 kDa membrane protein, resulting in a map at 3.2Å overall resolution with density sufficient forde novomodel building, and for the 22 kDa RBD of SARS-CoV2 spike protein, resulting in a map at 3.6 Å resolution that allows analysis of the binding interface to the nanobody. The Legobody approach thus overcomes the current size limitations of cryo-EM analysis.
Deterministic shifts in molecular evolution correlate with convergence to annualism in killifishes
Authors: Thompson Andrew W. , Black Amanda C. , Huang Yu , Shi Qiong , Furness Andrew I. , Braasch Ingo , Hoffmann Federico G. , Ortí Guillermo 
Published: August 2021

AbstractThe repeated evolution of novel life histories correlating with ecological variables offer opportunities to test scenarios of convergence and determinism in genetic, developmental, and metabolic features. Here we leverage the diversity of aplocheiloid killifishes, a clade of teleost fishes that contains over 750 species on three continents. Nearly half of these are “annual” or seasonal species that inhabit bodies of water that desiccate and are unfeasible for growth, reproduction, or survival for weeks to months at a time. We present a large-scale phylogenomic reconstruction of aplocheiloid killifish evolution using newly sequenced transcriptomes from all major clades. We show that developmental dormancy (diapause) and annualism have up to seven independent origins in Africa and America. We then measure evolutionary rates of orthologous genes and show that annual life history is correlated with higher dN/dSratios. Many of these fast-evolving genes in annual species constitute key developmental genes and nuclear-encoded metabolic genes that control oxidative phosphorylation. Lastly, we compare these fast-evolving genes to genes associated with developmental dormancy and metabolic shifts in killifishes and other vertebrates and thereby identify molecular evolutionary signatures of repeated evolutionary transitions to extreme environments.
Complex feline disease mapping using a dense genotyping array
Authors: Hernandez Isabel , Hayward Jessica J. , Brockman Jeff A. , White Michelle E. , Mouttham Lara , Wilcox Elizabeth A. , Garrison Susan , Castelhano Marta G. , Loftus John P. , Gomes Filipe Espinheira , Balkman Cheryl , Brooks Marjory B. , Fiani Nadine , Forman Marnin , Kern Tom , Kornreich Bruce , Ledbetter Eric , Peralta Santiago , Struble Angela M. , Caligiuri Lisa , Corey Elizabeth , Lin Lin , Jordan Julie , Sack Danny , Boyko Adam R. , Lyons Leslie A. , Todhunter Rory J. 
Published: August 2021

AbstractThe current feline genotyping array of 63k single nucleotide polymorphisms has proven its utility within breeds, and its use has led to the identification of variants associated with Mendelian traits in purebred cats. However, compared to single gene disorders, association studies of complex diseases, especially with the inclusion of random bred cats with relatively low linkage disequilibrium, require a denser genotyping array and an increased sample size to provide statistically significant associations. Here, we undertook a multi-breed study of 1,122 cats, most of which were admitted and phenotyped for nine common complex feline diseases at the Cornell University Hospital for Animals. Using a proprietary 340k single nucleotide polymorphism mapping array, we identified significant genome-wide associations with hyperthyroidism, diabetes mellitus, and eosinophilic keratoconjunctivitis. These results provide genomic locations for variant discovery and candidate gene screening for these important complex feline diseases, which are relevant not only to feline health, but also to the development of disease models for comparative studies.
Karyotype asymmetry in Cuscuta L. subgenus Pachystigma reflects its repeat DNA composition
Authors: Ibiapino Amalia , Báez Mariana , García Miguel A. , Costea Mihai , Stefanović Saša , Pedrosa-Harand Andrea 
Published: August 2021

AbstractCuscuta is a cytogenetically diverse genus, with karyotypes varying 18-fold in chromosome number and 89-fold in genome size. Each of its four subgenera also presents particular chromosomal features, such as bimodal karyotypes in Pachystigma. We used low coverage sequencing of the Cuscuta nitida genome (subgenus Pachystigma), as well as chromosome banding and molecular cytogenetics of three subgenus representatives, to understand the origin of bimodal karyotypes. All three species, C. nitida, C. africana (2n = 28) and C. angulata (2n = 30), showed heterochromatic bands mainly in the largest chromosome pairs. Eighteen satellite DNAs were identified in C. nitida genome, two showing similarity to mobile elements. The most abundant were present at the largest pairs, as well as the highly abundant ribosomal DNAs. The most abundant Ty1/Copia and Ty3/Gypsy elements were also highly enriched in the largest pairs, except for the Ty3/Gypsy CRM, which also labelled the pericentromeric regions of the smallest chromosomes. This accumulation of repetitive DNA in the larger pairs indicates that these sequences are largely responsible for the formation of bimodal karyotypes in the subgenus Pachystigma. The repetitive DNA fraction is directly linked to karyotype evolution in Cuscuta.HighlightsCuscuta subgenus Pachystigma contains species with strikingly bimodal karyotypes. The emergence of these karyotypes is linked to the enrichment of varied repetitive sequences in the largest chromosomal pairs.
The Epithelial and Stromal Immune Microenvironment in Gastric Cancer: A Comprehensive Analysis Reveals Prognostic Factors with Digital Cytometry
Authors: Shen Wenjun , Wang Guoyun , Cooper Georgia R. , Jiang Yuming , Zhou Xin 
Published: August 2021

AbstractBackgroundGastric cancer (GC) is the third leading cause of cancer-related deaths worldwide. Tumor heterogeneity continues to confound researchers’ understanding of tumor growth and the development of an effective therapy. Digital cytometry allows interpretation of heterogeneous bulk tissue transcriptomes at the cellular level.MethodsWe built a novel signature matrix to dissect epithelium and stroma signals using a scRNA-seq data set for GC. We applied cell mixture deconvolution to estimate diverse epithelial, stromal, and immune cell proportions from bulk transcriptome data in four independent GC cohorts. Robust computational methods were applied to identify strong prognostic factors for GC.ResultsWe identified an EMEC population whose proportions were significantly higher in patients with stage I cancer than other stages, and it was predominantly present in tumor samples but not typically found in normal samples. We found that the ratio of EMECs to stromal cells and the ratio of adaptive T cells to monocytes were the most significant prognostic factors within the non-immune and immune factors, respectively. The STEM score, which unifies these two prognostic factors was an independent prognostic factor of overall survival (HR=0.92, 95% CI=0.89-0.94,p= 2.05 × 10−9). The entire GC cohort was stratified into three risk groups (high-, moderate-, and low-risk) which yielded incremental survival times (p< 0.0001). For stage III disease, patients in the moderate- and low-risk groups experienced better survival benefits from radiation therapy ((HR=0.16, 95% CI=0.06-0.4,p< 0.0001), whereas those in the high-risk group did not (HR=0.49, 95% CI=0.14-1.72,p= 0.25).ConclusionsWe conclude that the STEM score is a promising prognostic factor for gastric cancer.
Immuno-proteomic profiling reveals abundant airway CD8 T cells and ongoing epithelial injury in prolonged post-COVID19 respiratory disease
Authors: Vijayakumar Bavithra , Boustani Karim , Ogger Patricia P. , Papadaki Artermis , Tonkin James , Orton Christopher M. , Ghai Poonam , Suveizdyte Kornelija , Hewitt Richard J. , Snelgrove Robert J. , Molyneaux Philip L. , Garner Justin L. , Peters James E. , Shah Pallav L. , Lloyd Clare M. , Harker James A. 
Published: August 2021

SummarySome patients hospitalized with acute COVID19 suffer respiratory symptoms that persist for many months. To characterize the local and systemic immune responses associated with this form of ‘Long COVID’, we delineated the immune and proteomic landscape in the airway and peripheral blood of normal volunteers and patients from 3 to 6 months after hospital discharge. The bronchoalveolar lavage (but not peripheral blood) proteome was abnormal in patients with post-COVID19 lung disease with significantly elevated concentration of proteins associated with apoptosis, tissue repair and epithelial injury. This correlated with an increase in cytotoxic lymphocytes (especially tissue resident CD8+T cells), lactate dehydrogenase and albumin (biomarkers of cell death and barrier integrity). Follow-up of a subset of these patients greater than 1-year post-COVID19 indicated these abnormalities resolved over time. Collectively, these data indicate that COVID-19 results in a prolonged change to the airway immune landscape in those with persistent lung disease, with evidence of cell death and tissue repair linked to ongoing activation of cytotoxic T cells.HighlightsThe post-COVID19 airway is characterized by increased cytotoxic lymphocytes.Distinct airway proteomes are associated with the airway immune cell landscape.The peripheral blood does not predict immune-proteome alterations in the airway post-COVID19.Persistent abnormalities in the airway immune-proteome post-COVID19 airways correlate with ongoing epithelial damage.
Spectral inference reveals principal cone-integration rules of the zebrafish inner retina
Authors: Bartel Philipp , Yoshimatsu Takeshi , Janiak Filip K , Baden Tom 
Published: August 2021

ABSTRACTIn the vertebrate retina, bipolar cells integrate the signals from different cone types at two main sites: directly, via dendritic inputs in the outer retina, and indirectly, via axonal inputs in the inner retina. Of these, the functional wiring of the indirect route, involving diverse amacrine cell circuits, remains largely uncharted. However, because cone-photoreceptor types differ in their spectral sensitivities, insights into the total functional cone-integration logic of bipolar cell might be gained by linking spectral responses across these two populations of neurons. To explore the feasibility of such a “spectral-circuit-mapping” approach, we here recordedin vivoresponses of bipolar cell presynaptic terminals in larval zebrafish to widefield but spectrally resolved flashes of light. We then mapped the results onto the previously established spectral sensitivity functions of the four cones.We find that this approach could explain ∼95% of the spectral and temporal variance of bipolar cell responses by way of a simple linear model that combined weighted inputs from the cones with four stereotyped temporal components. This in turn revealed several notable integration rules of the inner retina. Overall, bipolar cells were dominated by red-cone inputs, often alongside equal sign inputs from blue- and green-cones. In contrast, UV-cone inputs were uncorrelated with those of the remaining cones. This led to a new axis of spectral opponency which was mainly set-up by red-/green-/blue-cone “Off” circuits connecting to “natively-On” UV-cone circuits in the outermost fraction of the inner plexiform layer – much as how key colour opponent circuits are established in mammals. Beyond this, and despite substantial temporal diversity that was not present in the cones, bipolar cell spectral tunings were surprisingly simple. They either approximately resembled both opponent and non-opponent spectral motifs already present in the cones or exhibited a stereotyped non-opponent broadband response. In this way, bipolar cells not only preserved the efficient spectral representations in the cones, but also diversified them to set up a total of six dominant spectral motifs which included three axes of spectral opponency. More generally, our results contribute to an emerging understanding of how retinal circuits for colour vision in ancestral cone-tetrachromats such as zebrafish may be linked to those found in mammals.
ACE2 Pathway Regulates Thermogenesis and Energy Metabolism
Authors: Cao Xi , Shi Tingting , Zhang Chuanhai , Jin Wanzhu , Song Lini , Zhang Yichen , Liu Jingyi , Yang Fangyuan , Rotimi Charles N , Xu Amin , Yang Jinkui 
Published: August 2021

AbstractIdentification of key regulators of energy homeostasis holds important therapeutic promise for metabolic disorders, such as obesity and diabetes. ACE2 cleaves angiotensin II (Ang II) to generate Ang-(1-7) which acts mainly through the Mas receptor. Here, we identify ACE2 pathway as a critical regulator in the maintenance of thermogenesis and energy expenditure. We found that ACE2 is highly expressed in brown adipose tissue (BAT) and that cold stimulation increases ACE2 and Ang-(1-7) levels in BAT and serum. ACE2 knockout mice (ACE2-/y), Mas knockout mice (Mas-/-), and the mice transplanted with brown adipose tissue from Mas-/- mice displayed impaired thermogenesis. In contrast, impaired thermogenesis of db/db obese diabetic mice and high-fat diet-induced obese mice were ameliorated by overexpression of ACE2 or continuous infusion of Ang-(1-7). Activation of ACE2 pathway was associated with improvement of metabolic parameters, including blood glucose, lipids and energy expenditure in multiple animal models. Consistently, ACE2 pathway remarkably enhanced the browning of white adipose tissue. Mechanistically, we showed that ACE2 pathway activated Akt/FoxO1 and PKA pathway, leading to induction of UCP1 and activation of mitochondrial function. Our data propose that adaptive thermogenesis requires regulation of ACE2 pathway and highlight novel therapeutic targets for the treatment of metabolic disorders.
Do high-resolution satellite indices at field level reduce basis risk of satellite-based weather index insurance?
Authors: Kölle Wienand , Buchholz Matthias , Musshoff Oliver 
Published: August 2021

PurposeSatellite-based weather index insurance has recently been considered in order to reduce the high basis risk of station-based weather index insurance. However, the use of satellite data with a relatively low spatial resolution has not yet made it possible to determine the satellite indices free of disturbing landscape elements such as mountains, forests and lakes.Design/methodology/approachIn this context, the Normalized Difference Vegetation Index (NDVI) was used based on both Moderate Resolution Imaging Spectroradiometer (MODIS) (250 × 250 m) and high-resolution Landsat 5/8 (30 × 30 m) images to investigate the effect of a higher spatial resolution of satellite-based weather index contracts for hedging winter wheat yields. For three farms in north-east Germany, insurance contracts both at field and farm level were designed.FindingsThe results indicate that with an increasing spatial resolution of satellite data, the basis risk of satellite-based weather index insurance contracts can be reduced. However, the results also show that the design of NDVI-based insurance contracts at farm level also reduces the basis risk compared to field level. The study shows that higher-resolution satellite data are advantageous, whereas satellite indices at field level do not reduce the basis risk.Originality/valueTo the best of the author’s knowledge, the effect of increasing spatial resolution of satellite images for satellite-based weather index insurance is investigated for the first time at the field level compared to the farm level.
Partnership with stakeholders as innovative model of work-integrated learning for unemployed youths
Authors: Mayombe Celestin 
Published: August 2021

PurposeThe unemployment rate among disadvantaged youths (aged 15–34 years) in large parts of Africa, Asia and Latin America has become a global concern. The concern in this article is that most WIL programmes could not facilitate a smooth WIL-to-work transition. The purpose of the article is to examine the roles of partner stakeholders in the features of an innovative WIL model influencing the labour market entry of the disadvantaged youths.Design/methodology/approachA qualitative approach was suitable for examining the features of an innovative WIL model. Semi-structured interviews were used to collect data from seven managers of different firms and institutions, and ten trainees to examine the roles of partner stakeholders in the features of an innovative WIL model influencing the labour market entry of disadvantaged youths.FindingsThe main findings reveal that local businesses and enterprises played important roles in participating in the design of the WIL curriculum, providing adequate mentorship for work experience and micro-placement to the trainees. Based on the findings, the author concludes that the partnership with stakeholders as an innovative WIL model contributed to the employability of disadvantaged youths through the acquisition of work experience and work-readiness.Practical implicationsThe implication of the findings is that the commitment of partner stakeholders ensures that WIL graduates continue to be employed. The commitment of partner stakeholders evident in this study is likely to continue creating better employment prospects for WIL graduates.Originality/valueThough stakeholder partnerships are common in WIL programmes and TVET, the innovativeness of this model lies in the features of WIL programmes, the roles and commitment of stakeholders including the outcomes of the partnerships.
Revisiting customer loyalty toward mobile e-commerce in the hospitality industry: does brand viscosity matter?
Authors: Wu Jialin Snow , Ye Shun , Zheng Chen Jerry , Law Rob 
Published: August 2021

Purpose
To better understand how to retain hospitality customers in the fierce competition among mobile applications, this study aims to propose and empirically validates an integrative framework, which elaborates how conscious and subconscious factors, together with affective factors, may induce app loyalty and how brand viscosity moderates such effects.

Design/methodology/approach
The authors conducted an online survey to collect data and received a total of 268 valid responses. This study splits the data into two groups (brand viscosity vs non-viscosity). Then, the authors performed a multi-group structural equation modeling with Chi-square difference tests to compare the model between the two groups.

Findings
The findings support the integrative model and reveal that the influence of app satisfaction on loyalty is stronger for app users who do not stick to one brand across the website and mobile app channels. Moreover, for those with brand viscosity, habit and switching cost are two significant determinants that exert positive effects in inducing app loyalty.

Research limitations/implications
Brand viscosity across different channels matters for the effects of habit and switching costs in shaping app loyalty. E-commerce managers should elaborate on brand management among various booking channels and establish effective digital marketing strategies to facilitate the formation of usage habits and switching costs and to enhance brand viscosity across channels.

Originality/value
This research advances the knowledge of app loyalty in hospitality by providing a comprehensive explanatory framework from affective, conscious and subconscious lenses. This research is among the first to unveil the impact of brand viscosity on the links between loyalty and its determinants.