bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conserved degronome features governing quality control associated proteolysis
Authors: Mashahreh Bayan , Armony Shir , Johansson Kristoffer Enøe , Chappleboim Alon , Friedman Nir , Gardner Richard G. , Hartmann-Petersen Rasmus , Lindorff-Larsen Kresten , Ravid Tommer 
Published: April 2022

SummaryThe eukaryotic proteome undergoes constant surveillance by quality control systems that either sequester, refold, or eliminate aberrant proteins by ubiquitin-dependent mechanisms. Ubiquitin-conjugation necessitates the recognition of degradation determinants, termed degrons, by their cognate E3 ubiquitin-protein ligases. To learn about the distinctive properties of quality control degrons, we performed an unbiased peptidome stability screen in yeast. The search identified a large cohort of proteome-derived degrons, some of which exhibited broad E3 ligase specificity. Consequent application of a machine-learning algorithm established constraints governing degron potency, including the amino acid composition and secondary structure propensities. According to the set criteria, degrons with transmembrane domain-like characteristics are the most probable sequences to act as degrons. Similar quality control degrons were identified in viral and human proteins, suggesting conserved degradation mechanisms. Altogether, the emerging data indicate that transmembrane domain-like degron features have been preserved in evolution as key quality control determinants of proteins’ half-life.
Identification and calibration of ultrabright localizations to eliminate quantification error in SMLM
Authors: Cao Bo , Ni Jielei , Niu Gang , Chen Danni , Liu Gang , Zhou Lingxiao , Xia Tingying , Feng Fu , Wei Shibiao , Yuan Xiaocong , Ni Yanxiang 
Published: April 2022

AbstractSingle molecule localization microscopy (SMLM) is irreplaceable among super-resolution microscopies in revealing biological ultra-structures, given its unmatched high resolution. However, its sub-optimal quantitative capability, which is critical for characterizing true biomolecular organization of ultra-structures in cells, has hindered its widest application in biomedical research. Here, in SMLM imaging of cellular structures such as lipid rafts and microtubules with saturation labelling, we identified ultra-bright localizations, each of which is contributed by simultaneous emission of multiple molecules within a diffraction-limit region and has been regarded before as a regular localization from single molecule. Consistently, ultra-bright localizations are also observed in simulated SMLM imaging of endoplasmic reticulum or microtubules from public resource. Furthermore, after calibrating each ultrabright localization into multiple single-molecule localizations using the photon-number-based models, the density of total localizations shows linear correlation with the true molecule density, presenting SMLM with new reconstruction method as a quantitative analysis approach. Therefore, identification and dissection of ultra-bright localizations in SMLM enable the close and quantitative estimate of the true biomolecular organization.
Delta-Omicron recombinant escapes therapeutic antibody neutralization
Authors: Duerr Ralf , Zhou Hao , Tada Takuya , Dimartino Dacia , Marier Christian , Zappile Paul , Wang Guiqing , Plitnick Jonathan , Griesemer Sara B. , Girardin Roxanne , Machowski Jessica , Bialosuknia Sean , Lasek-Nesselquist Erica , Hong Samuel L. , Baele Guy , Dittmann Meike , Ortigoza Mila B. , Prasad Prithiv J. , McDonough Kathleen , Landau Nathaniel R. , George Kirsten St. , Heguy Adriana 
Published: April 2022

SummaryBackgroundThe emergence of recombinant viruses is a threat to public health. Recombination of viral variants may combine variant-specific features that together catalyze viral escape from treatment or immunity. The selective advantages of recombinant SARS-CoV-2 isolates over their parental lineages remain unknown.MethodsMulti-method amplicon and metagenomic sequencing of a clinical swab and the in vitro grown virus allowed for high-confidence detection of a novel recombinant variant. Mutational, phylogeographic, and structural analyses determined features of the recombinant genome and spike protein. Neutralization assays using infectious as well as pseudotyped viruses and point mutants thereof defined the recombinant’s sensitivity to a panel of monoclonal antibodies and sera from vaccinated and/or convalescent individuals.ResultsA novel Delta-Omicron SARS-CoV-2 recombinant was identified in an unvaccinated, immunosuppressed kidney transplant recipient treated with monoclonal antibody Sotrovimab. The recombination breakpoint is located in the spike N-terminal domain, adjacent to the Sotrovimab quaternary binding site, and results in a 5’-Delta AY.45 and a 3’-Omicron BA.1 mosaic spike protein. Delta and BA.1 are sensitive to Sotrovimab neutralization, whereas the Delta-Omicron recombinant is highly resistant to Sotrovimab, both with and without the RBD resistance mutation E340D.ConclusionsRecombination between circulating SARS-CoV-2 variants can functionally contribute to immune escape. It is critical to validate phenotypes of mosaic viruses and monitor immunosuppressed COVID-19 patients treated with monoclonal antibodies for the selection of recombinant and immune escape variants. (Funded by NYU, the National Institutes of Health, and others)
Experimental evolution of phosphomannomutase-deficient yeast reveals compensatory mutations in a phosphoglucomutase
Authors: Vignogna Ryan C. , Allocca Mariateresa , Monticelli Maria , Norris Joy W. , Steet Richard , Andreotti Giuseppina , Perlstein Ethan O. , Lang Gregory I. 
Published: April 2022

ABSTRACTThe most common cause of human congenital disorders of glycosylation (CDG) are mutations in the phosphomannomutase gene PMM2, which affect protein N-linked glycosylation. The yeast gene SEC53 encodes a nearly-identical homolog of human PMM2. We evolved 384 populations of yeast harboring one of two human-disease-associated alleles, sec53-V238M and sec53-F126L, or wild-type SEC53. We find that after 1,000 generations, most populations compensate for the slow-growth phenotype associated with the sec53 human-disease-associated alleles. Through whole-genome sequencing we identify compensatory mutations, including known SEC53 genetic interactors. We observe an enrichment of compensatory mutations in other genes whose human homologs are associated with Type 1 CDG, including PGM1, which encodes the minor isoform of phosphoglucomutase in yeast. By genetic reconstruction, we show that evolved pgm1 mutations are dominant and allele-specific genetic interactors that restore both protein glycosylation and growth of yeast harboring the sec53-V238M allele. Finally, we characterize the enzymatic activity of purified Pgm1 mutant proteins. We find that reduction, but not elimination, of Pgm1 activity best compensates for the deleterious phenotypes associated with the sec53-V238M allele. Broadly, our results demonstrate the power of experimental evolution as a tool for identifying genes and pathways that compensate for human-disease associated alleles.
Trim33 conditions the lifespan of primitive macrophages and onset of definitive macrophage production
Authors: Demy Doris Lou , Touret Anne-Lou , Lancino Mylène , Tauzin Muriel , Capuana Lavinia , Pierre Constance , Herbomel Philippe 
Published: April 2022

ABSTRACTTRIM33 (Tif1-γ) is a transcriptional regulator notably involved in several aspects of hematopoiesis. It is essential for the production of erythrocytes in zebrafish, and for the proper functionning and aging of hematopoietic stem and progenitor cells (HSPCs) in mice. Here we have found that in zebrafish development, Trim33 is essential cell-autonomously for the lifespan of the yolk sac derived primitive macrophages, as well as for the initial production of definitive (HSPC-derived) macrophages in the first niche of definitive hematopoiesis, the caudal hematopoietic tissue. Moreover, Trim33 deficiency leads to an excess production of definitive neutrophils and thrombocytes. Our data indicate that Trim33 radically conditions the differentiation ouput of aorta-derived HSPCs in all four erythro-myeloid cell types, in a niche-specific manner.
Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria is Governed by a Global Transcriptional Regulator NagR
Authors: Arzamasov Aleksandr A. , Nakajima Aruto , Sakanaka Mikiyasu , Ojima Miriam N. , Katayama Takane , Rodionov Dmitry A. , Osterman Andrei L. 
Published: April 2022

AbstractBifidobacterium longum subsp. infantis (B. infantis) is a prevalent beneficial bacterium that colonizes the human neonatal gut and is uniquely adapted to efficiently use human milk oligosaccharides (HMOs) as a carbon and energy source. Multiple studies have focused on characterizing the elements of HMO utilization machinery in B. infantis; however, the regulatory mechanisms governing the expression of these catabolic pathways remain poorly understood. A bioinformatic regulon reconstruction approach used in this study implicated NagR, a transcription factor from the ROK family, as a negative global regulator of genomic loci encoding lacto-N-biose/galacto-N-biose (LNB/GNB), lacto-N-tetraose (LNT), and lacto-N-neotetraose (LNnT) utilization pathways in B. infantis. This conjecture was corroborated by transcriptome profiling upon nagR genetic inactivation and experimental assessment of binding of recombinant NagR to predicted DNA operators. The latter approach also implicated N-acetylglucosamine (GlcNAc), a universal intermediate of LNT and LNnT catabolism, and its phosphorylated derivatives as plausible NagR transcriptional effectors. Reconstruction of NagR regulons in various Bifidobacterium lineages revealed multiple regulon expansion events, suggesting evolution from a local regulator of GlcNAc catabolism in ancestral bifidobacteria to a global regulator controlling foraging of mixtures of GlcNAc-containing host-derived glycans in mammalian gut-colonizing B. infantis and Bifidobacterium bifidum.ImportanceThe predominance of bifidobacteria in the gut of breastfed infants is attributed to the ability of these bacteria to utilize human milk oligosaccharides (HMOs). Thus, individual HMOs such as lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT) are considered promising prebiotics that would stimulate the growth of bifidobacteria and confer multiple health benefits to preterm and malnourished children suffering from impaired (stunted) gut microbiota development. However, the rational selection of HMO-based prebiotics is hampered by the incomplete knowledge of regulatory mechanisms governing HMO utilization in target bifidobacteria. This study describes NagR-mediated transcriptional regulation of LNT and LNnT utilization in Bifidobacterium longum subsp. infantis. The elucidated regulatory network appears optimally adapted to simultaneous utilization of multiple HMOs, providing a rationale to add HMO mixtures (rather than individual components) into infant formulas. The study also provides insights into the evolutionary trajectories of complex regulatory networks controlling carbohydrate metabolism in bifidobacteria.
Biochemical characterization of AniA from Neisseria gonorrhoeae
Authors: Barreiro Daniela S. , Oliveira Ricardo N. S. , Pauleta Sofia R. 
Published: April 2022

AbstractAniA, the nitrite reductase from Neisseria gonorrhoeae, has been shown to play a crucial role in the infection mechanism of this microorganism by producing NO and abolishing epithelial exfoliation. This enzyme is a trimer with one type-1 copper center per subunit and one type 2 copper center in the subunits interface, with the latter being the catalytic site. The two centers were characterized by visible, EPR and CD spectroscopy for the first time, indicating that AniA’s type 1 copper center has a high rhombicity, which is attributed to its tetrahedral geometry, and shorter Met-Cu bond, while type 2 copper center has the usual properties, though with a shorter hyperfine coupling constant (A//= 9.1 mT). The thermostability of AniA was analyzed by differential scanning calorimetry showing a single endothermic transition in the thermogram, with a maximum at 95 °C, while the CD spectra in the visible region indicates the presence of copper centers at 85-90 °C. The reoxidation rates of AniA in the presence of nitrite were analyzed by visible spectroscopy showing a pH dependence and being higher at pH 6.0. The high thermostability of this enzyme might be important for maintaining a high activity in the extracellular space and be less prone to denaturation and proteolysis, contributing to the proliferation of N. gonorrhoeae.
Structural and biochemical basis of FANCI-FANCD2 interdependent ubiquitination
Authors: Lemonidis Kimon , Rennie Martin L. , Arkinson Connor , Chaugule Viduth K. , Clarke Mairi , Streetley James , Walden Helen 
Published: April 2022

AbstractThe Fanconi Anaemia pathway operates for the repair of interstrand crosslinks and the maintenance of genomic stability upon replication stalling. Di-monoubiquitination of the FANCI-FANCD2 (ID2) complex is a central and crucial step in this pathway. Evidence suggests that FANCD2 ubiquitination precedes FANCI ubiquitination, and that both the FANCD2-ubiquitinated (ID2Ub) and the di- monoubiquitinated (IUbD2Ub) complex clamp on DNA. However, FANCD2 is deubiquitinated at a faster rate than FANCI, which can result in a FANCI-ubiquitinated ID2 complex (IUbD2). Here, we present a 4.1 Å cryo-EM structure of IUbD2 complex bound to double-stranded DNA. We show that this complex, like ID2Uband IUbD2Ub, is also in the closed ID2 conformation and clamps on DNA. While the target lysine of FANCD2 (K561) is partially buried in the non-ubiquitinated ID2-DNA complex, it becomes fully exposed in the IUbD2-DNA structure, and thus can be ubiquitinated at a faster rate. The IUbD2-DNA complex cannot easily revert to the non-ubiquitinated ID2 state, due to USP1-UAF1-resistance, conferred by the presence of DNA and FANCD2. ID2Ub-DNA, on the other hand, can be efficiently deubiquitinated by USP1-UAF1, unless further ubiquitination on FANCI occurs. FANCI ubiquitination also progresses at a faster rate in ID2Ub-DNA over ID2-DNA complex, and results in partial DNA-dependent protection from FANCD2 deubiquitination. Taken together, our results suggest that, while FANCD2 ubiquitination promotes FANCI ubiquitination, FANCI ubiquitination in turn maintains FANCD2 ubiquitination by two mechanisms: it prevents excessive FANCD2 deubiquitination within an IUbD2Ub-DNA complex, and it enables re-ubiquitination of FANCD2 within a transient, closed-on-DNA, IUbD2 complex.
COP I and II dependent trafficking controls ER-associated degradation in mammalian cells
Authors: Ogen-Shtern Navit , Chang Chieh , Saad Haddas , Mazkereth Niv , Patel Chaitanya , Shenkman Marina , Lederkremer Gerardo Z. 
Published: April 2022

AbstractMisfolded proteins and components of the endoplasmic reticulum (ER) quality control and ER associated degradation (ERAD) machineries concentrate in mammalian cells in the pericentriolar ER-derived quality control compartment (ERQC), suggesting it as a staging ground for ERAD. By tracking the chaperone calreticulin and an established ERAD substrate, asialoglycoprotein receptor H2a, we have now determined that the trafficking to the ERQC is reversible and recycling back to the ER is slower than the movement in the ER periphery. The dynamics suggest vesicular trafficking rather than diffusion. Indeed, using dominant negative mutants of ARF1 and Sar1 or the drugs Brefeldin A and H89, we observed that COPI inhibition causes accumulation in the ERQC and increased retrotranslocation and ERAD, whereas COPII inhibition has the opposite effect. Our results suggest that targeting of misfolded proteins to ERAD involves COPII-dependent transport to the ERQC and that they can be retrieved to the peripheral ER in a COPI-dependent manner.
Primary cilia loss promotes reactivation of morphogenesis and cyst-fission through a deregulated TGFβ-ECM-Integrin axis in polycystic liver disease
Authors: Waddell Scott H , Yao Yuelin , Olaizola Paula , Jarman Edward J , Gournopanos Kostas , Christodoulou Ersi , Gautier Philippe , Drenth Joost PH , Kendall Timothy J , Banales Jesus M , Khamseh Ava , Mill Pleasantine , Boulter Luke 
Published: April 2022

AbstractPathological liver cysts are an important comorbidity in multiple diseases and syndromes(1, 2) driven by dysfunction of the primary cilium (PC), a complex sensory organelle that protrudes from the apical surface of biliary epithelial cells (BECs)(3, 4). The essential nature of PC in liver development(5, 6) makes understanding the molecular role of this organelle in the structural maintenance of the adult bile duct challenging. Here, we show that PC loss deletion of Wdr35 in adult mouse BECs is sufficient to cause bile duct expansion, driving cyst formation through the de novo production of a fibronectin-rich pro-cystic microenvironment. This newly formed niche promotes both cell-autonomous changes in cell shape and duct-level mechanical rearrangements that converge to drive cyst-fission, a novel process whereby single, large cysts undergo morphological splitting. This process gives rise to many, smaller polycystic progeny and can be halted by pharmacological inhibition of a specific pro-cystic integrin receptor.
A CAE-oriented mesh hole-filling algorithm focusing on geometry and quality
Authors: Hai Yongqing , Guo Yufei , Dong Mo 
Published: April 2022

PurposeIntegrality of surface mesh is requisite for computational engineering. Nonwatertight meshes with holes can bring inconvenience to applications. Unlike simple modeling or visualization, the downstream industrial application scenarios put forward higher requirements for hole-filling, although many related algorithms have been developed. This study aims at the hole-filling issue in industrial application scenarios.Design/methodology/approachThis algorithm overcomes some inherent weakness of general methods and generates a high-level resulting mesh. Initially, the primitive hole boundary is filled with a more appropriate triangulation which introduces fewer geometric errors. And in order for better performances on shape approximation of the background mesh, the algorithm also refines the initial triangulation with topology optimization. When obtaining the background mesh defining the geometry and size field, spheres on it are packed to determine the vertex configuration and then the resulting high-level mesh is generated.FindingsThrough emphasizing geometry recovery and mesh quality, the proposed algorithm works well in hole-filling in industrial application scenarios. Many experimental results demonstrate the reliability and the performance of the algorithm. And the processed meshes are capable of being used for industrial simulation computations directly.Originality/valueThis paper makes input meshes more adaptable for solving programs through local modifications on meshes and perfects the preprocessing technology of finite element analysis (FEA).
Hate speech in social media: personal experiences and perceptions of university students in Bangladesh
Authors: Atikuzzaman Md. , Akter Shohana 
Published: April 2022

Purpose
Social media (SM) is a new communication tool that substantially contribute to facilitating online hate speech (OHS). In emphasis of the question “what role can SM play in an individual’s life?”, this study aims to understand Bangladeshi university students’ personal experiences and opinions of OHSs related to SM.

Design/methodology/approach
The authors used an online survey method to collect data and retrieved responses from 410 students. Mann–Whitney U test, Kruskal–Wallis test and Spearman’s rank correlation analysis were used to test the hypotheses.

Findings
This study found that hate speech is a familiar term among students. Students’ political views or opinions, religion and gender have become the most targeted instruments for OHSs. Comparing students’ use of SM, the authors found that Facebook was the most used SM site to spread hate speech in Bangladesh. In terms of personal experiences, the findings indicated that 45.6% of students became victims of OHSs at least once or more times, and the majority of students tended to simply avoid OHSs. Another significant finding was that OHS has real-life effects on the students, resulting in various personal and psychological distress.

Originality/value
Although some research has been conducted on hate speech at the local level, to the best of the authors’ knowledge, no study has focused on the student community. To the best of the authors’ knowledge, this study is the first attempt in Bangladesh to focus on OHSs from a student’s personal viewpoint.
An appraisal of the early impact of COVID-19 on affordable housing finance in Saudi Arabia's Vision 2030
Authors: Alharbi Raed 
Published: April 2022

PurposeAffordable housing provision is one of the visions of the Kingdom of Saudi Arabia (KSA), as highlighted in Vision 2030. For about 21 months now, the coronavirus disease 2019 (COVID-19) pandemic has ravaged the world and has increased the level of economic crisis and financial uncertainty to achieve planned projects. Studies investigating the reality of how the COVID-19 pandemic may streamline the chances of achieving affordable housing for all in 2030 are scarce. Thus, this study examined the relevance of affordable housing, the perceived impact of COVID-19 on affordable housing and proffered measures to promote affordable housing finance in Vision 2030.Design/methodology/approachMedina, Riyadh and Al Qassim were the participants' cities engaged via panel interviews and supported by existing relevant Vision 2030 documents. The Delphi method was adopted to explore the government officials, financial operators (bankers), academicians and employees' opinions, and the analysed data presented in themes.FindingsFindings show that SA Vision 2030 blueprint expresses an exemplary country in all ramifications, including affordable housing finance for the citizens. Findings reveal that the COVID-19 pandemic threatens SA affordable housing finance Vision 2030. The increased housing shortage, high construction housing cost, increased foreclosures, increased eviction, possible homelessness, financial instability and vulnerability emerged as the perceived impact of COVID-19 on affordable housing finance in Vision 2030. Refinancing housing loans to boost Vision 2030, forbearance to promote Vision 2030, improve payment relief, among others, emerged as measures to promote affordable housing in the post-COVID-19 era.Research limitations/implicationsThe research only identified the possible negative impacts of the COVID-19 pandemic on affordable housing finance in Vision 2030 and proffered policy solutions from the engaged participants' perspective. Also, the study covered three cities (Medina, Riyadh and Al Qassim). The suggestions that will emerge from this research may be adopted to address other sectors captured in Vision 2030 that are critical and hit by the ravaging pandemic.Practical implicationsMeasures such as refinancing mortgages and strengthening government housing agencies will promote affordable housing for Vision 2030 if the relevant policymakers and mortgage institutions are well implemented.Originality/valueThis research identified the perceived early threats from the COVID-19 pandemic that could affect affordable housing transformation in Vision 2030 from the participants' perspective. Studies regarding COVID-19 and affordable housing in Vision 2030 are very few.