bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harmonizing labeling and analytical strategies to obtain protein turnover rates in intact adult animals
Authors: Hammond Dean E , Simpson Deborah M , Franco Catarina , Muelas Marina Wright , Waters John , Ludwig R W , Prescott Mark C , Hurst Jane L , Beynon Robert J , Lau Edward 
Published: December 2021

AbstractChanges in the abundance of individual proteins in the proteome can be elicited by modulation of protein synthesis (the rate of input of newly synthesized proteins into the protein pool) or degradation (the rate of removal of protein molecules from the pool). A full understanding of proteome changes therefore requires a definition of the roles of these two processes in proteostasis, collectively known as protein turnover. Because protein turnover occurs even in the absence of overt changes in pool abundance, turnover measurements necessitate monitoring the flux of stable isotope labeled precursors through the protein pool such as labeled amino acids or metabolic precursors such as ammonium chloride or heavy water. In cells in culture, the ability to manipulate precursor pools by rapid medium changes is simple, but for more complex systems such as intact animals, the approach becomes more convoluted. Individual methods bring specific complications, and the suitability of different methods has not been comprehensively explored. In this study we compare the turnover rates of proteins across four mouse tissues, obtained from the same inbred mouse strain maintained under identical husbandry conditions, measured using either [13C6]lysine or [2H2]O as the labeling precursor. We show that for long-lived proteins, the two approaches yield essentially identical measures of the first order rate constant for degradation. For short-lived proteins, there is a need to compensate for the slower equilibration of lysine through the precursor pools. We evaluate different approaches to provide that compensation. We conclude that both labels are suitable, but careful determination of precursor enrichment kinetics in amino acid labeling is critical and has a considerable influence on the numerical values of the derived protein turnover rates.
Nucleocapsid 203 mutations enhance SARS-CoV-2 immune evasion
Authors: Lin Xiaoyuan , Xue Weiwei , Zhang Yueping , Fu Beibei , Trimpert Jakob , Xing Na , Kunec Dusan , Tang Wanyan , Xiao Yang , Meng Kaiwen , Shi Shuobo , Wu Haibo , Meng Geng , Zhu Zhenglin 
Published: December 2021

AbstractPrevious work indicated that the nucleocapsid 203 mutation increase the virulence and transmission of the SARS-CoV-2 Alpha variant. However, Delta later outcompeted Alpha and other lineages, promoting a new wave of infections. Delta also possesses a nucleocapsid 203 mutation, R203M. Large-scale epidemiological analyses suggest a synergistic effect of the 203 mutation and the spike L452R mutation, associated with Delta expansion. Viral competition experiments demonstrate the synergistic effect in fitness and infectivity. More importantly, we found that the combination of R203M and L452R brings in a 3.2-fold decrease in neutralizing titers to the neutralizing serum relative to L452R-only virus. R203M/L452R show an increased fitness after the initiation of global vaccination programmes, possibly associated with the enhanced immune evasion. Another rapidly emerging variant Omicron also bears the 203 mutation. Thus, we proposed that nucleocapsid mutations play an essential role for the rise and predominance of variants in concern.
Characterization of antibiotic resistance in clinical isolates of Klebsiella pneumoniae in Denmark
Authors: Fang Xin , Westh Henrik , Kemp Michael , Ellermann-Eriksen Svend , Palsson Bernhard O. , Johansen Helle Krogh , Monk Jonathan M. 
Published: December 2021

ABSTRACTKlebsiella pneumoniae (KP) is a major global health problem as it leads to hospital outbreaks all over the world and is becoming more difficult to treat due to its increasing antimicrobial resistance (AMR). Optimization and development of new treatments of KP requires understanding of its population structure and AMR properties. Therefore, in this study, we collected and sequenced 491 KP strains from four major Danish microbiology departments covering 51% of the Danish population. The isolates were whole genome sequenced (WGS), phenotypically characterized and compared with 2,124 KP strains from 13 different countries (PATRIC strains). We found that while genomic content varies significantly across the Danish strains, they also differ significantly from strains from other countries, due to the lack of certain AMR sequence types (e.g. ST258 and ST307) in Denmark. Genomic and experimental analysis suggest that Danish strains contain fewer virulence mechanisms and are more susceptible to antimicrobials compared to strains from other countries, likely due to the relatively low antibiotic usage in Denmark where 70% of hospital antibiotic usage is penicillins. We also identified potential novel AMR determinants to tigecycline through statistical analysis of genomic and phenotypic data. To conclude, we obtained a more comprehensive understanding of the KP strains in Denmark and provided valuable insights for future experiments and strategies to combat AMR in KP.
Multi-layered networks of SalmoNet2 enable strain comparisons of the Salmonella genus on a molecular level
Authors: Olbei Marton , Bohar Balazs , Fazekas David , Madgwick Matthew , Sudhakar Padhmanand , Hautefort Isabelle , Métris Aline , Baranyi Jozsef , Kingsley Robert A. , Korcsmaros Tamas 
Published: December 2021

AbstractSerovars of the genus Salmonella primarily evolved as gastrointestinal pathogens in a wide range of hosts. Some serotypes later evolved further, adopting a more invasive lifestyle in a narrower host range associated with systemic infections. A system-level knowledge of these pathogens has the potential to identify the complex adaptations associated with the evolution of serovars with distinct pathogenicity, host range and risk to human health. This promises to aid the design of interventions and serve as a knowledge base in the Salmonella research community. Here we present SalmoNet2, a major update to SalmoNet, the first multi-layered interaction resource for Salmonella strains, containing protein-protein, transcriptional regulatory and enzyme enzyme interactions. The new version extends the number of Salmonella genomes from 11 to 20, including strains such as S. Typhimurium D23580, an epidemic multidrug-resistant strain leading to invasive non-typhoidal Salmonella Disease (iNTS), and a strain from Salmonella bongori, another species in the Salmonella genus. The database now uses strain specific metabolic models instead of a generalised model to highlight differences between strains. This has increased the coverage of high-quality protein-protein interactions, and enhances interoperability with other computational resources by adopting standardised formats. The resource website has been updated with tutorials to help researchers analyse their Salmonella data using molecular interaction networks from SalmoNet2. SalmoNet2 is accessible at http://salmonet.org/.ImportanceMulti-layered network databases collate information from multiple sources, and are powerful both as a knowledge base and platform for analysis. Here we present SalmoNet2, an integrated network resource of 20 Salmonella strains, containing protein-protein, transcriptional regulatory, and metabolic interactions. Key improvements to the update include expanding the number of strains, strain-specific metabolic networks, an increase in high quality protein-protein interactions, community standard computational formats to help interoperability, and online tutorials to help users analyse their data using SalmoNet2.
CameraEEG: Synchronized Recording of Video with Electroencephalogram data on an Android Application
Authors: Madhavan Srihari , Hazarika Doli , Gupta Cota Navin 
Published: December 2021

AbstractWe present a novel android application named CameraEEG that enables synchronized acquisition of Electroencephalogram(EEG) and camera data using a smartphone. Audio-visual events of interest experienced by the subject were also recorded using a button press on the CameraEEG app. Unlike lab-restricted experiments, which usually constrain the subject’s mobility, this wearable solution enables monitoring of the human brain during everyday life activities. The app was built using Android SDK version 28 and Smarting mobi SDK from mbraintrain. It works on all android devices having a minimum Android OS - Lollipop.We successfully recorded thirty minutes of synchronized Video and EEG during eyes closed and walking tasks using the app. Event markers enabled by the subject using the app during walking tasks were also recorded. Timing tests showed that temporal synchronization of video and EEG data was good. We analysed the recorded data and were able to identify the task performed by the subject from the event markers. The power spectrum density of the two tasks showed different power spectrums with a peak in the alpha band for eyes closed task. We also provide android studio codes for download and detailed help documentation for the community to test the developed application.
The role of intraspinal sensory neurons in the control of quadrupedal locomotion
Authors: Gerstmann Katrin , Jurčić Nina , Kunz Severine , Wanaverbecq Nicolas , Zampieri Niccolò 
Published: December 2021

SummaryFrom swimming to walking and flying, animals have evolved specific locomotor strategies to thrive in different habitats. All types of locomotion depend on integration of motor commands and sensory information to generate precise movements. Cerebrospinal fluid-contacting neurons (CSF-cN) constitute a vertebrate sensory system that monitors CSF composition and flow. In fish, CSF-cN modulate swimming activity in response to changes in pH and bending of the spinal cord, yet their role in higher vertebrates remains unknown. We used mouse genetics to study their function in quadrupedal locomotion and found that CSF-cN are directly integrated into spinal motor circuits by forming connections with motor neurons and premotor interneurons. Elimination of CSF-cN selectively perturbs the accuracy of foot placement required for skilled movements at the balance beam and horizontal ladder. These results identify an important role for mouse CSF-cN in adaptive motor control and indicate that this sensory system evolved a novel function from lower vertebrates to accommodate the biomechanical requirements of terrestrial locomotion.
Evaluation of Commercially Available Glucagon Receptor Antibodies and Glucagon Receptor Expression
Authors: Bomholt Anna Billeschou , Johansen Christian Dall , Kjeldsen Sasha A. S. , Galsgaard Katrine D. , Christensen Jens Bager , Winther-Sørensen Marie , Serizawa Reza , Hornum Mads , Porrini Esteban , Pedersen Jens , Ørskov Cathrine , Gluud Lise L. , Sørensen Charlotte Mehlin , Holst Jens J. , Albrechtsen Reidar , Albrechtsen Nicolai J. Wewer 
Published: December 2021

AbstractGlucagon is a key regulator of numerous metabolic functions including glucose, protein and lipid metabolism, and glucagon-based therapies are explored for diabetes, fatty liver disease and obesity. Insight into tissue and cell specific expression of the glucagon receptor (GCGR) is important to understand the biology of glucagon as well as to differentiate between direct and indirect actions of glucagon. However, it has been challenging to accurately localize the GCGR in tissue due to low expression levels and lack of specific methodologies. Immunohistochemistry has frequently been used for GCGR localization, but G-protein-coupled receptors (GPCRs) targeting antibodies are notoriously unreliable. In this study, we systematically evaluated all commercially available GCGR antibodies. Initially, twelve GCGR antibodies were evaluated using HEK293 cells transfected with mouse or human GCGR cDNA. Of the twelve antibodies tested, eleven showed positive staining of GCGR protein from both species. Human liver tissue was investigated using the same GCGR antibodies. Five antibodies failed to stain human liver biopsies (despite explicit claims to the contrary from the vendors). Immunohistochemical (IHC) staining demonstrated positive staining of liver tissue from glucagon receptor knockout (Gcgr−/−) mice and their wild-type littermates (Gcgr+/+) with only one out of the twelve available GCGR antibodies. Three antibodies were selected for further evaluation by western blotting and bands corresponding to the predicted size of the GCGR (62 kDa) were identified using two of these. Finally, a single antibody (no. 11) was selected for specific GCGR localization studies in various tissues. In mouse tissue the most intense immunostainings were found in lever, kidney, ileum, heart, and pancreas. Western blotting, performed on liver tissue from Gcgr+/+ and Gcgr−/− mice, confirmed the specificity of antibody no. 11, detecting a band at high intensity in material from Gcgr+/+and no bands in liver tissue from Gcgr−/−mice. Staining of human kidney tissue, with antibody no. 11, showed GCGR localization to the distal tubules. Autoradiography was used as an antibody-independent approach to support the antibody-based findings, revealing specific binding in liver, pancreas, and kidney. As a final approach, RNA-sequencing and single-cell RNA (scRNA)-sequencing were implemented. RNA-sequencing confirmed GCGR presence within liver and kidney tissue. The GCGR was specifically found to be expressed in hepatocytes by scRNA-sequencing and potentially also in collecting and distal tubule cells in the kidney. Our results clearly indicate the liver and the kidneys as the primary targets of glucagon action.
Structural basis for antibody resistance to SARS-CoV-2 omicron variant
Authors: Cerutti Gabriele , Guo Yicheng , Liu Lihong , Zhang Zhening , Liu Liyuan , Luo Yang , Huang Yiming , Wang Harris H. , Ho David D. , Sheng Zizhang , Shapiro Lawrence 
Published: December 2021

SUMMARYThe recently reported B.1.1.529 Omicron variant of SARS-CoV-2 includes 34 mutations in the spike protein relative to the Wuhan strain that initiated the COVID-19 pandemic, including 15 mutations in the receptor binding domain (RBD). Functional studies have shown omicron to substantially escape the activity of many SARS-CoV-2-neutralizing antibodies. Here we report a 3.1 Å resolution cryo-electron microscopy (cryo-EM) structure of the Omicron spike protein ectodomain. The structure depicts a spike that is exclusively in the 1-RBD-up conformation with increased mobility and inter-protomer asymmetry. Many mutations cause steric clashes and/or altered interactions at antibody binding surfaces, whereas others mediate changes of the spike structure in local regions to interfere with antibody recognition. Overall, the structure of the omicron spike reveals how mutations alter its conformation and explains its extraordinary ability to evade neutralizing antibodies.HighlightsSARS-CoV-2 omicron spike exclusively adopts 1-RBD-up conformationOmicron substitutions alter conformation and mobility of RBDA subset of omicron mutations change the local conformation of spikeThe structure reveals the basis of antibody neutralization escape
Expanded FLP toolbox for spatiotemporal protein degradation and transcriptomic profiling in C. elegans
Authors: Fragoso-Luna Adrián , Romero-Bueno Raquel , Eibl Michael , Ayuso Cristina , Muñoz-Jiménez Celia , Benes Vladimir , Cases Ildefonso , Askjaer Peter 
Published: December 2021

AbstractControl of gene expression in specific tissues and/or at certain stages of development allows the study and manipulation of gene function with high precision. Site-specific genome recombination by the Flippase (FLP) and Cre enzymes has proven particularly relevant. Joint efforts of many research groups have led to the creation of efficient FLP and Cre drivers to regulate gene expression in a variety of tissues in Caenorhabditis elegans. Here, we extend this toolkit by the addition of FLP lines that drive recombination specifically in distal tip cells, the somatic gonad, coelomocytes and the epithelial P lineage. In some cases, recombination-mediated gene knockouts do not completely deplete protein levels due to persistence of long-lived proteins. To overcome this, we developed a spatiotemporally regulated degradation system for GFP fusion proteins (GFPdeg) based on FLP-mediated recombination. Using two stable nuclear pore proteins, MEL-28/ELYS and NPP-2/NUP85 as examples, we report the benefit of combining tissue-specific gene knockout and protein degradation to achieve complete protein depletion. We also demonstrate that FLP-mediated recombination can be utilized to identify transcriptomes in a C. elegans tissue of interest. We have adapted RNA polymerase DamID (RAPID) for the FLP toolbox and by focusing on a well-characterized tissue, the hypodermis, we show that the vast majority of genes identified by RAPID are known to be expressed in this tissue. These tools allow combining FLP activity for simultaneous gene inactivation and transcriptomic profiling, thus enabling the inquiry of gene function in various complex biological processes.
Revisiting PFA-mediated tissue fixation chemistry: FixEL enables trapping of small molecules in the brain to visualize their distribution dynamics
Authors: Nonaka Hiroshi , Mino Takeharu , Sakamoto Seiji , Oh Jae Hoon , Watanabe Yu , Ishikawa Mamoru , Tsushima Akihiro , Amaike Kazuma , Kiyonaka Shigeki , Tamura Tomonori , Aricescu A. Radu , Kakegawa Wataru , Miura Eriko , Yuzaki Michisuke , Hamachi Itaru 
Published: December 2021

AbstractVarious small molecules have been used as functional probes for tissue imaging in medical diagnosis and pharmaceutical drugs for disease treatment. The spatial distribution, target selectivity, and diffusion/extrusion kinetics of small molecules in structurally complicated specimens are critical for function. However, robust methods for precisely evaluating these parameters in the brain have been limited. Herein we report a new method termed “Fixation-driven chemical crosslinking of exogenous ligands (FixEL)” which traps and images exogenously administered molecules-of-interest (MOI) in complex tissues. This method relies on proteins-MOI interactions, and chemical crosslinking of amine-tethered MOI with paraformaldehyde used for perfusion fixation. FixEL is used to obtain images of the distribution of the small molecules and their dynamics, which addresses selective/nonselective binding to proteins, time-dependent localization changes, and diffusion/retention kinetics of MOI such as PET tracer derivatives or drug-like small molecules. Clear imaging of a nanobody distributed in the whole brain was also achieved with high spatial resolution using 2D/3D mode.
Application of a simple device for “attracting” and “trapping” glioma cells in situ
Authors: Song Haimin , Yang Runwei , Lai Runbin , Guo Jinglin , Li Kaishu , Ni Bowen , Liu Yawei 
Published: December 2021

AbstractGlioblastoma multiforme (GBM) is the most malignant adult brain tumor. The current adjuvant therapies for GBM are disappointing, which are based on cytotoxicity strategy. Thus, other ways should be explored to improve the curative effect. According to the strong invasive ability of GBM cells, we assume a new treatment strategy for GBM by developing a new cell trap device (CTD) with some kind of “attractive” medium loaded in it to attract and capture the tumor cells. The in vitro experiment showed that Hepatocyte Growth Factor (HGF) presented stronger chemotaxis on C6 and U87 cell line than the Epidermal Growth Factor (EGF) and Fibroblast Growth Factor (FGF). A simple in vitro CTD loaded with HGF was made and in vivo experiments results showed that HGF successfully attracted tumor cells from tumor bed in situ into the CTD. This study proposes the new strategy for GBM treatment of “attract and trap” tumor cells is proved to be feasible.
Depriving mice of sleep also deprives of food
Authors: Đukanović Nina , La Spada Francesco , Emmenegger Yann , Niederhäuser Guy , Preitner Frédéric , Franken Paul 
Published: December 2021

AbstractBoth sleep-wake behavior and circadian rhythms are tightly coupled to energy metabolism and food intake. Altered feeding times in mice are known to entrain clock-gene rhythms in brain and liver and sleep-deprived humans tend to eat more and gain weight. Previous observations in mice showing that sleep deprivation (SD) changes clock-gene expression might thus relate to altered food intake and not to the loss of sleepper se. Whether SD affects food intake in the mouse and how this might affect clock-gene expression is, however, unknown. We therefore quantified i) the cortical expression of the clock genesPer1, Per2, Dbp, andCry1in mice that had access to food or not during a 6h SD, and ii) food intake during baseline, SD, and recovery sleep. We found that food deprivation did not modify the SD-incurred clock-gene changes in the cortex. Moreover, we discovered that although food intake during SD did not differ from baseline, mice lost weight and increased food intake during subsequent recovery. We conclude that SD is associated with food deprivation and that the resulting energy deficit might contribute to the effects of SD that are commonly interpreted as a response to sleep loss.
Intrinsic apoptosis is evolutionarily divergent among metazoans
Authors: Krasovec Gabriel , Quéinnec Éric , Chambon Jean-Philippe 
Published: December 2021

AbstractApoptosis is regulated cell death that depends on caspases. Upstream of each apoptotic signalling pathway is involved a specific initiator caspase. Characterised in nematode, fly and mammals, intrinsic apoptosis is considered to be ancestral and conserved among animals, and depends on shared initiators; caspase-9, Apaf-1 and Bcl-2. However, the biochemical role of mitochondria, the pivotal function of cytochrome c and the modality of caspase activation remain highly heterogeneous and hide profound molecular divergences among apoptotic pathways in animals. Uncovering the phylogenetic history of apoptotic actors, especially caspases, is crucial to shed light on intrinsic apoptosis evolutionary history. Here, we demonstrate by phylogenetic analyses, that caspase-9, the fundamental key of intrinsic apoptosis, is deuterostome-specific, while caspase-2 is ancestral to bilaterians. Our analysis of Bcl-2 and Apaf-1 confirm heterogeneity in functional organisation of apoptotic pathways in animals. Our results support emergence of distinct intrinsic apoptotic pathways during metazoan evolution.
Sex, amitosis, and evolvability in the ciliate Tetrahymena thermophila
Authors: Tarkington Jason , Zhang Hao , Azevedo Ricardo B. R. , Zufall Rebecca A. 
Published: December 2021

AbstractUnderstanding the mechanisms that generate genetic variation, and thus contribute to the process of adaptation, is a major goal of evolutionary biology. Mutation and genetic exchange have been well studied as mechanisms to generate genetic variation. However, there are additional processes that may also generate substantial genetic variation in some populations and the extent to which these variation generating mechanisms are themselves shaped by natural selection is still an open question. Tetrahymena thermophila is a ciliate with an unusual mechanism of nuclear division, called amitosis, which can generate genetic variation among the asexual descendants of a newly produced sexual progeny. We hypothesize that amitosis thus increases the evolvability of newly produced sexual progeny relative to species that undergo mitosis. To test this hypothesis, we used experimental evolution and simulations to compare the rate of adaptation in T. thermophila populations founded by a single sexual progeny to parental populations that had not had sex in many generations. The populations founded by a sexual progeny adapted more quickly than parental populations in both laboratory populations and simulated populations. This suggests that the additional genetic variation generated by amitosis of a heterozygote can increase the rate of adaptation following sex and may help explain the evolutionary success of the unusual genetic architecture of Tetrahymena and ciliates more generally.