bluuebunny/crossref_metadata_2025 huggingface dataset:
Apoptosis-resistance of senescent cells is an intrinsic barrier for senolysis induced by cardiac glycosides
Authors: Deryabin Pavel I. , Shatrova Alla N. , Marakhova Irina I. , Nikolsky Nikolay N. , Borodkina Aleksandra V.
Published: December 2020

Targeted elimination of senescent cells – senolysis – is one of the core trends in the anti-aging therapy. Cardiac glycosides were recently proved to be a broad-spectrum senolytics. Here we tested senolytic properties of cardiac glycosides towards human mesenchymal stem cells (hMSCs). Cardiac glycosides had no senolytic ability towards senescent hMSCs of various origins. Using biological and bioinformatic approaches we compared senescence development in ‘cardiac glycosides–sensitive’ A549 and ‘–insensitive’ hMSCs. The absence of senolysis was found to be mediated by the effective potassium import and increased apoptosis-resistance in senescent hMSCs. We revealed that apoptosis-resistance, previously recognized as a common characteristic of senescence, in fact, is not a general feature of senescent cells. Moreover, only apoptosis-prone senescent cells are sensitive to cardiac glycosides-induced senolysis. Thus, we can speculate that the effectiveness of senolysis might depend on whether senescent cells indeed become apoptosis-resistant compared to their proliferating counterparts.
Glycosylation Limits Forward Trafficking of the Tetraspan Membrane Protein PMP22
Authors: Marinko Justin T. , Wright Madison T. , Heintzman Darren R. , Plate Lars , Sanders Charles R.
Published: December 2020

Peripheral myelin protein 22 (PMP22) folds and traffics inefficiently, a phenomenon closely related to the mechanisms by which this tetraspan membrane protein causes Charcot-Marie-Tooth disease (CMTD). We report that elimination of N-glycosylation results in a 3-fold increase in the cell surface trafficking of wild type (WT) PMP22 and a 10-fold increase in trafficking of the unstable L16P disease mutant form. Studies of the interactions of PMP22 with oligosaccharyltransferases A and B as well as quantitative proteomic experiments established that critical endoplasmic reticulum (ER) quality control decisions occur earlier in the biogenesis to cell surface trafficking pathway for the L16P mutant than for WT. CRISPR knock-out cell lines for ER proteins calnexin, RER1, and UGGT1 illuminated the role of each protein in glycosylation dependent and independent surface trafficking of WT PMP22, as well as for a series of disease mutants of varying folding stabilities.

One Sentence Summary

N-linked glycosylation was seen to dramatically limit the cell surface trafficking of PMP22, with some key quality control factors in PMP22 biogenesis being identified.
EloR interacts with the lytic transglycosylase MltG at midcell inStreptococcus pneumoniaeR6
Authors: Winther Anja Ruud , Kjos Morten , Herigstad Marie Leangen , Håvarstein Leiv Sigve , Straume Daniel
Published: December 2020

The ellipsoid shape ofStreptococcus pneumoniaeis determined by the synchronized actions of the elongasome and the divisome, which have the task of creating a protective layer of peptidoglycan (PG) enveloping the cell membrane. The elongasome is necessary for expanding PG in the longitudinal direction whereas the divisome synthesizes the PG that divides one cell into two. Although there is still little knowledge about how these two modes of PG synthesis are coordinated, it was recently discovered that two RNA-binding proteins called EloR and KhpA are part of a novel regulatory pathway controlling elongation inS. pneumoniae. EloR and KhpA form a complex that work closely with the Ser/Thr kinase StkP to regulate cell elongation. Here, we have further explored how this regulation occur. EloR/KhpA is found at midcell, a localization fully dependent on EloR. Using a bacterial two-hybrid assay we probed EloR against several elongasome proteins and found an interaction with the lytic transglycosylase homolog MltG. By using EloR as bait in immunoprecipitation assays, MltG was pulled down confirming that they are part of the same protein complex. Fluorescent microscopy demonstrated that the Jag domain of EloR is essential for EloR’s midcell localization and its interaction with MltG. Since MltG is found at midcell independent of EloR, our results suggest that MltG is responsible for recruitment of the EloR/KhpA complex to the division zone to regulate cell elongation.

Importance

Bacterial cell division has been a successful target for antimicrobial agents for decades. How different pathogens regulate cell division is, however, poorly understood. To fully exploit the potential for future antibiotics targeting cell division, we need to understand the details of how the bacteria regulate and construct cell wall during this process. Here we have revealed that the newly identified EloR/KhpA complex, regulating cell elongation inS. pneumoniae, forms a complex with the essential peptidoglycan transglycosylase MltG at midcell. EloR, KhpA and MltG are conserved among many bacterial species and the EloR/KhpA/MltG regulatory pathway is most likely a common mechanism employed by many Gram-positive bacteria to coordinate cell elongation and septation.
Sex-specific Associations Between Traumatic Experiences and Resting-state Functional Connectivity in the Philadelphia Neurodevelopmental Cohort
Authors: Wang Shiying , Malins Jeffrey G. , Zhang Heping , Gruen Jeffrey R.
Published: December 2020

Background

Traumatic experiences during childhood or adolescence are a significant risk factor for multiple psychiatric disorders and adversely affect cognitive functions. Resting-state functional magnetic resonance imaging has been used to investigate the effects of traumatic experiences on functional connectivity, but the impact of sex differences has not been well documented. This study investigated sex-specific associations between resting-state functional connectivity and traumatic experiences in typically developing youth.

Methods

The sample comprised 1395 participants, ages 8 to 21 years, from the Philadelphia Neurodevelopmental Cohort. Resting-state functional connectivity was characterized by voxel-wise intrinsic connectivity distribution parameter values derived from resting-state functional magnetic resonance imaging. Traumatic experiences were assessed based on a structured psychiatric evaluation. Sex, the number of traumatic events, and their interaction were regressed onto voxel-wise intrinsic connectivity distribution parameter values. Brain regions that passed cluster correction were used as seeds to define resting-state networks.

Results

After quality control, the final sample included 914 participants (mean (SD) age, 14.6 (3.3) years; 529 (57.8%) females; 437 (47.8%) experienced at least one kind of traumatic event). Four discrete anatomical clusters showed decreased functional connectivity as the number of traumatic events increased. The resting-state networks defined by using these four clusters as seeds corresponded with the somatomotor network. Sex-specific associations were identified in another four clusters for which males showed increased connectivity, and females showed decreased connectivity as the number of traumatic events increased. The resting-state networks defined by the four sex-specific clusters corresponded with the default mode network.

Conclusions

Traumatic experiences are associated with an alteration of resting-state functional connectivity in the somatomotor network in youth without psychiatric diagnoses. The associations differ in direction between males and females in the default mode network, suggesting sex-specific responses to early exposure to trauma.
Coupling of Cdc20 inhibition and activation by BubR1
Authors: Hein Jamin , Garvanska Dimitriya H , Nasa Isha , Kettenbach Arminja , Nilsson Jakob
Published: December 2020

Tight regulation of the APC/C-Cdc20 ubiquitin ligase that targets Cyclin B1 for degradation is important for mitotic fidelity. The spindle assembly checkpoint (SAC) inhibits Cdc20 through the mitotic checkpoint complex (MCC). In addition, phosphorylation of Cdc20 by Cyclin B1-Cdk1 independently inhibits APC/C-Cdc20 activation. This creates a conundrum for how Cdc20 gets activated prior to Cyclin B1 degradation. Here we show that the MCC component BubR1 harbours both Cdc20 inhibition and activation activities, allowing for cross-talk between the two Cdc20 inhibition pathways. Specifically BubR1 acts as a substrate specifier for PP2A-B56 to enable efficient Cdc20 dephosphorylation in the MCC. A mutant Cdc20 mimicking the dephosphorylated state escapes a mitotic checkpoint arrest arguing that restricting Cdc20 dephosphorylation to the MCC is important. Collectively our work reveals how Cdc20 can be dephosphorylated in the presence of Cyclin B1-Cdk1 activity without causing premature anaphase onset.
KLF17 promotes human naïve pluripotency but is not required for its establishment
Authors: Lea Rebecca A. , McCarthy Afshan , Boeing Stefan , Niakan Kathy K.
Published: December 2020

Current knowledge of the transcriptional regulation of human pluripotency is incomplete, with lack of inter-species conservation observed. Single-cell transcriptomics of human embryos previously enabled us to identify transcription factors, including the zinc-finger protein KLF17, that are enriched in the human epiblast and naïve hESCs. Here we show that KLF17 is expressed coincident with the known pluripotency factors NANOG and SOX2 across human blastocyst development. We investigate the function of KLF17 in pluripotency using primed and naïve hESCs for gain- and loss-of-function analyses. We find that ectopic expression of KLF17 in primed hESCs is sufficient to induce a naïve-like transcriptome and that KLF17 can drive transgene-mediated resetting to naïve pluripotency. This implies a role for KLF17 in establishing naïve pluripotency. However, CRISPR-Cas9-mediated knockout studies reveal that KLF17 is not required for naïve pluripotency acquisitionin vitro. Transcriptome analysis of naïve hESCs identifies subtle effects on metabolism and signalling following KLF17 loss of function, and possible redundancy with the related factor, KLF5. Overall, we show that KLF17 is sufficient, but not necessary, for naïve pluripotency under the givenin vitroconditions.

Summary statement

Investigating KLF17 in human pluripotency reveals that it is sufficient, but not necessary, to establish naïve hESCs. We posit that KLF17 is a peripheral regulator, like KLF2 in the mouse.
TRPM channels mediate learned pathogen avoidance following intestinal distention
Authors: Filipowicz Adam , Aballay Alejandro
Published: December 2020

Upon exposure to harmful microorganisms, hosts engage in protective molecular and behavioral immune responses, both of which are ultimately regulated by the nervous system. Using the nematode Caenorhabditis elegans, we show that ingestion of E. faecalis leads to a fast pathogen avoidance behavior that results in aversive learning. We have identified multiple sensory mechanisms involved in the regulation of avoidance of E. faecalis, including the GPCR NPR-1-dependent oxygen-sensing pathway, an ASE neuron-dependent pathway, and an AWB and AWC neuron-dependent pathway. Colonization of the anterior part of the intestine by E. faecalis leads to AWB and AWC mediated olfactory aversive learning. Finally, two transient receptor potential melastatin (TRPM) channels, GON-2 and GTL-2, mediate this newly described rapid pathogen avoidance. These results suggest a mechanism by which TRPM channels may sense the intestinal distension caused by bacterial colonization to elicit pathogen avoidance and aversive learning by detecting changes in host physiology.
The Hard Limits of Decoding Mental States: The Decodability of fMRI
Authors: Jabakhanji R. , Vigotsky A.D. , Bielefeld J. , Huang L. , Baliki M.N. , Iannetti G.D. , Apkarian A.V.
Published: December 2020

High-profile studies claim to assess mental states across individuals using multi-voxel decoders of brain activity. The fixed, fine-grained, multi-voxel patterns in these “optimized” decoders are purportedly necessary for discriminating between, and accurately identifying, mental states. Here, we present compelling evidence that the efficacy of these decoders is overstated. Across a variety of tasks, decoder patterns were not necessary. Not only were “optimized decoders” spatially imprecise and 90% redundant, but they also performed similarly to simpler decoders, built from average brain activity. We distinguish decoder performance when used for discriminating between, in contrast to identifying, mental states, and show even when discrimination performance is strong, identification can be poor. Using similarity rules, we derived novel and intuitive discriminability metrics that capture 95% and 68% of discrimination performance within- and across-subjects, respectively. These findings demonstrate that current across-subject decoders remain inadequate for real-life decision making.
Machine Leaning-based Determination of Sampling Depth for Complex Environmental Systems: Case Study with Single-Cell Raman Spectroscopy Data in EBPR Systems
Authors: Li Guangyu , Wu Chieh , Wang Dongqi , Srinivasan Varun , Kaeli David R. , Dy Jennifer G. , Gu April Z.
Published: December 2020

Rapid progress in various advanced analytical methods such as single-cell technologies enable unprecedented and deeper understanding of microbial ecology beyond the resolution of conventional approaches. A major application challenge exists in the determination of sufficient sample size without sufficient prior knowledge of the community complexity and, the need to balance between statistical power and limited time or resources. This hinders the desired standardization and wider application of these technologies. Here, we proposed, tested and validated a computational sampling size assessment protocol taking advantage of a metric, named kernel divergence. This metric has two advantages: First, it directly compares dataset-wise distributional differences with no requirements on human intervention or prior knowledge-based pre-classification. Second, minimal assumptions in distribution and sample space are made in data processing to enhance its application domain. This enables test-verified appropriate handling of datasets with both linear and non-linear relationships. The model was then validated in a case study with eight SCRS phenotyping datasets each sampled from a different enhanced biological phosphorus removal (EBPR) activated sludge community located across North America. The model allows the determination of sufficient sampling size for any targeted or customized information capture capacity or resolution level. For example, an approximated sampling size of 50 or 100 spectra for full-scale EBPR-related ecosystems at 5% or 2% OPU cluster resolution. Promised by its flexibility and minimal restriction of input data types, the proposed method is expected to be a standardized approach for sampling size optimization, enabling more comparable and reproducible experiments and analysis on complex environmental samples. Finally, these advantages exhibit the capability of generalizing to other single-cell technologies or environmental applications, provided that the input datasets contain only continuous features.

TOC
SARS-CoV-2 escapes CD8 T cell surveillance via mutations in MHC-I restricted epitopes
Authors: Agerer Benedikt , Koblischke Maximilian , Gudipati Venugopal , Smyth Mark , Popa Alexandra , Genger Jakob-Wendelin , Endler Lukas , Florian David M. , Mühlgrabner Vanessa , Lercher Alexander , Gattinger Pia , Torralba-Gombau Ricard , Penz Thomas , Fae Ingrid , Wenda Sabine , Traungott Marianna , Walder Gernot , Fischer Gottfried , Hoepler Wolfgang , Pawelka Erich , Zoufaly Alexander , Valenta Rudolf , Bock Christoph , Huppa Johannes B. , Aberle Judith H. , Bergthaler Andreas
Published: December 2020

CD8+ T cell immunity to SARS-CoV-2 has been implicated in COVID-19 severity and virus control, though direct evidence has been lacking so far. Here, we identified non-synonymous mutations in MHC-I restricted CD8+ T cell epitopes after deep sequencing of 747 SARS-CoV- 2 virus isolates. Mutant peptides exhibited diminished or abrogated MHC-I binding, which was associated with a loss of recognition and functional responses by CD8+ T cells isolated from HLA-matched COVID-19 patients. Our findings highlight the capacity of SARS-CoV-2 to subvert CD8+ T cell surveillance through escape mutations in MHCI-restricted viral epitopes. This provides evolutionary evidence for CD8+ T cell immunity controlling SARS-CoV-2 with consequences for COVID-19 vaccine design.
Reliability of neural entrainment in the human auditory system
Authors: Cabral-Calderin Yuranny , Henry Molly J.
Published: December 2020

Auditory stimuli are often rhythmic in nature. Brain activity synchronizes with auditory rhythms via neural entrainment, and entrainment seems to be beneficial for auditory perception. However, it is not clear to what extent neural entrainment in the auditory system is reliable over time – a necessary prerequisite for targeted intervention. The current study aimed to establish the reliability of neural entrainment over time and to predict individual differences in auditory perception from associated neural activity. Across two different sessions, human listeners detected silent gaps presented at different phase locations of a 2-Hz frequency modulated (FM) noise while EEG activity was recorded. As expected, neural activity was entrained by the 2-Hz FM noise. Moreover, gap detection was sinusoidally modulated by the phase of the 2-Hz FM into which the gap fell. Critically, both the strength of neural entrainment as well as the modulation of performance by the stimulus rhythm were highly reliable over sessions. Moreover, gap detection was predictable from pre-gap neural 2-Hz phase and alpha amplitude. Our results demonstrate that neural entrainment in the auditory system and the resulting behavioral modulation are reliable over time, and that both entrained delta and non-entrained alpha oscillatory activity contribute to near-threshold stimulus perception. The latter suggests that improving auditory perception might require simultaneously targeting entrained brain rhythms as well as the alpha rhythm.
Early IFNβ secretion determines variable downstream IL-12p70 responses upon TLR4 activation in health and disease
Authors: Posseme Celine , Llibre Alba , Charbit Bruno , Bondet Vincent , Rouilly Vincent , Saint-André Violaine , Boussier Jeremy , Bergstedt Jacob , Smith Nikaïa , Rotival Maxime , Kobor Michael S , Scriba Tom , Mottez Estelle , Pol Stanislas , Patin Etienne , Albert Matthew L. , Quintana-Murci Lluis , Duffy Darragh ,   Milieu Intérieur Consortium
Published: December 2020

The IL-12 family of cytokines comprises the only heterodimeric cytokines mediating diverse functional effects. We previously observed a bi-modal IL-12p70 response to LPS in healthy donors of theMilieu Interieurcohort. Herein, we demonstrate that IFNβ expression serves as an upstream determinant of variable IL-12p70 production. Integrative modelling of proteomic, genetic, epigenomic and cellular data confirmed IFNβ as key for regulation of LPS inducedIL12Aand IL-12p70 variability. The clinical relevance was supported by reduced and variable IL-12p70 responses in individuals infected with the hepatitis C virus (HCV), and findings that IFN-based therapy for HCV is more likely to fail in those patients with dysregulated pre-treatment IL-12p70 responses. In sum, our systems immunology approach has defined a better understanding of IL-12p70 and IFNβ in healthy and infected persons, providing insights into how common genetic and epigenetic variation may impact immune responses to bacterial infection in health and disease.
LungAI: A Deep Learning Convolutional Neural Network for Automated Detection of COVID-19 from Posteroanterior Chest X-Rays
Authors: Gulati Aryan
Published: December 2020

COVID-19 is an infectious disease caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). As of December 2020, more than 72 million cases have been reported worldwide. The standard method of diagnosis is by Real-Time Reverse Transcription Polymerase Chain Reaction (rRT-PCR) from a Nasopharyngeal Swab. Currently, there is no vaccine or specific antiviral treatment for COVID-19. Due to rate of spreading of the disease manual detection among people is becoming more difficult because of a clear lack of testing capability. Thus there was need of a quick and reliable yet non-labour intensive detection technique. Considering that the virus predominantly appears in the form of a lung based abnormality I made use of Chest X-Rays as our primary mode of detection. For this detection system we made use of Posteroanterior (PA) Chest X-rays of people infected with Bacterial Pneumonia (2780 Images), Viral Pneumonia (1493 Images), Covid-19 (729 Images) as well as those of perfectly Healthy Individuals (1583 Images) procured from various Publicly Available Datasets and Radiological Societies. LungAI is a novel Convolutional Neural Network based on a Hybrid of the DarkNet and AlexNet architecture. The network was trained on 80% of the dataset with 20% kept for validation. The proposed Coronavirus Detection Model performed exceedingly well with an accuracy of 99.16%, along with a Sensitivity value of 99.31% and Specificity value of 99.14%. Thus LungAI has the potential to prove useful in managing the current Pandemic Situation by providing a reliable and fast alternative to Coronavirus Detection given strong results.
From SARS-CoV-2 infection to COVID-19 disease: a proposed mechanism for viral spread to the lower airway based on in silico estimation of virion flow rates
Authors: Basu Saikat , Chakravarty Arijit
Published: December 2020

While the nasopharynx in the upper respiratory airway is the dominant initial infection site for SARS-CoV-2, the physiologic mechanism that launches the infection in the lower airway is still not well-understood. Based on the rapidity with which SARS-CoV-2 infection progresses to the lungs, it has been conjectured that the nasopharynx acts as the seeding zone for subsequent contamination of the lower airway via aspiration of virus-laden boluses of nasopharyngeal fluids. In this study, we examine the plausibility of this proposed mechanism. To this end, we have developed computational fluid mechanics models of the inhalation process in two medical imaging based airway reconstructions and have quantified the nasopharyngeal liquid volume ingested into the lower airspace during each aspiration. The numerical predictions are validated by comparing the number of projected aspirations (approximately 2 – 4) during an eight-hour sleep cycle with prior observational findings of 3 aspirations in human subjects. Extending the numerical trends on aspiration volume to earlier records on aspiration frequency for the entire day indicates a total aspirated nasopharyngeal liquid volume of 0.3 – 0.76 ml per day. We then used sputum assessment data from hospitalized COVID-19 patients to estimate the number of virions that are transmitted daily to the lungs via nasopharyngeal liquid boluses. For mean sputum viral load, our modeling projects that the number of virions penetrating to the lower airway per day will range over 2.1 × 106 – 5.3 × 106; for peak viral load, the corresponding number of penetrating virions hovers between 7.1 × 108 – 17.9 × 108. These findings fill in a key piece of the mechanistic puzzle of the progression from SARS-CoV-2 infection of the nasopharynx to the development of COVID-19 disease within a patient, and point to dysphagia as a potential underlying risk factor for COVID-19. The findings also have significant practical implications in the design of COVID-19 prophylactics and therapeutics that aim to constrain the pathogenic progress of the disease within the limits of the upper airway.
Anti-cancer Potential ofMoringa oleiferaon BRCA1 Gene: Systems Biology
Authors: Balogun Toheeb A. , Buliaminu Kaosarat D. , Chukwudozie Onyeka S. , Tiamiyu Zainab A
Published: December 2020

Breast Cancer has always been a global challenge that is prevalent among women. There is a continuous increase in the high number of women mortality rates as a result of breast cancer and affecting countries at all levels of modernization. Women with high-risk factors including hereditary, obesity, and menopause have the possibility of developing breast cancer. With the advent of radiotherapy, chemotherapy, hormone therapy, and surgery in the treatment of breast cancer, there has an increased number of breast cancer survivors. Also, the design and development of drugs targeting therapeutic enzymes are helping to effectively treat the tumor cells at an early stage. However, long term use of anti-cancer drugs has been linked to severe side effects. This research aims to develop potential drug candidates fromMoringa oleiferawhich could serve as anti-cancer agents.In silicoanalysis using Schrödinger Molecular Drug Discovery Suite and SWISS ADME was employed to determine the therapeutic potential of phytochemicals fromM. oleiferaagainst breast cancer via molecular docking, pharmacokinetic parameters, and drug-like properties. The result shows that Rutin, Vicenin-2, and Quercetin-3-O-glucoside have the highest binding energy of −7.522, −6.808, −6.635kcal/mol respectively in the active site of BRCA1. The essential amino acids involved in the protein-ligand interaction following active site analysis are ASN 1678, ASN 1774, GLY 1656, LEU 1657, GLN 1779, LYS 1702, SER 1655, PHE 1662, ARG 1699, GLU 1698, and VAL 1654. Thus, we propose that bioactive compounds fromM. oleiferamay be potential hit drug candidates against breast cancer.
TWO CLASSES OF MYOSIN INHIBITORS, BLEBBISTATIN AND MAVACAMTEN, STABILIZE β-CARDIAC MYOSIN IN DIFFERENT STRUCTURAL AND FUNCTIONAL STATES
Authors: Gollapudi Sampath K. , Ma Weikang , Chakravarthy Srinivas , Combs Ariana C. , Sa Na , Langer Stephen , Irving Thomas C. , Nag Suman
Published: December 2020

In addition to a conventional relaxed state, a fraction of myosins in the cardiac muscle exists in a newly-discovered low-energy consuming super-relaxed (SRX) state, which is kept as a reserve pool that may be engaged under sustained increased cardiac demand. The conventional and the super-relaxed states are widely assumed to correspond respectively to a structure where myosin heads are in anopenconfiguration, free to interact with actin, and aclosedconfiguration, inhibiting binding to actin. Disruption of the SRX population in different heart diseases, such as hypertrophic cardiomyopathy, results in unwarranted muscle contraction, and stabilizing them using myosin inhibitors is budding as an attractive therapeutic strategy. Here we examine the structure-function relationships of two myosin ATPase inhibitors, mavacamten, and blebbistatin, and found that binding of mavacamten to myosin at a site different than blebbistatin populates myosin into the SRX state. Blebbistatin, and para-nitroblebbistatin, binding to a distal pocket to the myosin lever arm near the nucleotide-binding site, does not affect the usual myosin SRX state but instead appears to render myosin into a new, perhaps non-functional, ‘ultra-relaxed’ state. X-ray scattering-based rigid body modeling shows that both mavacamten and para-nitroblebbistatin induce novel conformations that diverge significantly from the hypotheticalopenandclosedstates and furthermore, mavacamten treatment causes a greater compaction than para-nitroblebbistatin. Taken together, we conclude that mavacamten and blebbistatin stabilize myosin in different structural states, and such states may give rise to different functional energy-sparing SRX states.
Identification of NPC1 as a novel SARS-CoV-2 intracellular target
Authors: Garcia-Dorival Isabel , Ángel Cuesta-Geijo Miguel , Barrado-Gil Lucía , Galindo Inmaculada , Urquiza Jesús , del Puerto Ana , Gil Carmen , Campillo Nuria , Martínez Ana , Alonso Covadonga
Published: December 2020

Niemann-Pick type C1 (NPC1) receptor is an endosomal membrane protein that regulates intracellular cholesterol trafficking, which is crucial in the Ebola virus (EBOV) cycle. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the cell by binding of the viral spike (S) protein to the ACE2 receptor. This requires S-protein processing either by the surface transmembrane serine protease TMPRSS2 for plasma membrane fusion or cathepsin L for endosomal entry. Additional host factors are required for viral fusion at endosomes. Here, we report a novel interaction of the SARS-CoV-2 nucleoprotein (N) with the cholesterol transporter NPC1. Moreover, small molecules interfering with NPC1 that inhibit EBOV entry, also inhibited human coronavirus. Our findings suggest an important role for NPC1 in SARS-CoV-2 infection, a common strategy shared with EBOV, and a potential therapeutic target to fight against COVID-19.
Placing ancient DNA sequences into reference phylogenies
Authors: Martiniano Rui , De Sanctis Bianca , Hallast Pille , Durbin Richard
Published: December 2020

During the last decade, large volumes of ancient DNA (aDNA) data have been generated as part of whole-genome shotgun and target capture sequencing studies. This includes sequences from non-recombining loci such as the mitochondrial or Y chromosomes. However, given the highly degraded nature of aDNA data, post-mortem deamination and often low genomic coverage, combining ancient and modern samples for phylogenetic analyses remains difficult. Without care, these factors can lead to incorrect placement.

For the Y chromosomes, current standard methods focus on curated markers, but these contain only a subset of the total variation. Examining all polymorphic markers is particularly important for low coverage aDNA data because it substantially increases the number of overlapping sites between present-day and ancient individuals which may lead to higher resolution phylogenetic placement. We provide an automated workflow for jointly analysing ancient and present-day sequence data in a phylogenetic context. For each ancient sample, we effectively evaluate the number of ancestral and derived alleles present on each branch and use this information to place ancient lineages to their most likely position in the phylogeny. We provide both a parsimony approach and a highly optimised likelihood-based approach that assigns a posterior probability to each branch.

To illustrate the application of this method, we have compiled and make available the largest public Y-chromosomal dataset to date (2,014 samples) which we used as a reference for phylogenetic placement. We process publicly available African ancient DNA Y-chromosome sequences and examine how patterns of Y-chromosomal diversity change across time and the relationship between ancient and present-day lineages. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree.
Astrocyte-secreted chordin-like 1 regulates spine density after ischemic stroke
Authors: Blanco-Suarez Elena , Allen Nicola J
Published: December 2020

Ischemic stroke occurs when the brain is deprived of blood flow, preventing cells from receiving nutrients necessary to perform basic vital functions. In the peri-infarct area neurons undergo an acute loss of dendritic spines along with morphological alterations, which ultimately modify synaptic plasticity and determine neuronal survival. Astrocytes have been shown to play protective or detrimental roles in neuronal survival post-stroke, depending on the specific stage, yet we lack a clear understanding of the underlying mechanisms triggered at these different time points. Recently chordin-like 1 (Chrdl1) was identified as an astrocyte-secreted protein that promotes synaptic maturation and limits experience-dependent plasticity in the mouse visual cortex, leading us to ask if Chrdl1 regulates spine density and recovery from stroke. Using photothrombosis to model ischemic stroke, we studied Chrdl1 KO mice during the acute and subacute phases post-stroke (1 and 7 days after injury, respectively) to assess the potential of Chrdl1 to regulate spine density, glial reactivity and injury volume, characteristics that are involved in functional recovery after ischemia. We find that the absence of Chrdl1 prevents ischemia-induced spine loss in the peri-infarct area, a feature that indicates an important role of astrocytes in recovery from ischemic stroke.
Myogenetic oligodeoxynucleotide (myoDN) complexed with berberine promotes differentiation of chicken skeletal muscle myoblasts
Authors: Nihashi Yuma , Shinji Sayaka , Umezawa Koji , Shimosato Takeshi , Ono Tamao , Kagami Hiroshi , Takaya Tomohide
Published: December 2020

Skeletal muscle myoblasts are myogenic precursors that develop into myofibers during muscle formation. Improvement of myoblast differentiation is important for advancing meat production by domestic animals. We recently identified novel oligodeoxynucleotides (ODNs) termed myogenetic ODNs (myoDNs) that promote the differentiation of mammalian myoblasts. An isoquinoline alkaloid, berberine, forms a complex with one of the myoDNs, iSN04, and enhances its activities. This study investigated the effects of myoDNs on chicken myoblasts to elucidate their species-specific actions. Seven myoDNs (iSN01-iSN07) were found to facilitate the differentiation of chicken myoblasts into myosin heavy chain (MHC)-positive myocytes. The iSN04-berberine complex exhibited a higher myogenetic activity than iSN04 alone, which was shown to enhance the differentiation of myoblasts into myocytes, myotube formation, and myogenic gene expression (MyoD, myogenin, MHC, and myomaker). These data indicate that myoDNs promoting chicken myoblast differentiation may be used as potential feed additives in broiler diets.
Development and external validation of a logistic regression derived formula based on repeated routine hematological measurements predicting survival of hospitalized Covid-19 patients
Authors: Heber Stefan , Pereyra David , Schrottmaier Waltraud C. , Kammerer Kerstin , Santol Jonas , Pawelka Erich , Hana Markus , Scholz Alexander , Liu Markus , Hell Agnes , Heiplik Klara , Lickefett Benno , Havervall Sebastian , Traugott Marianna T. , Neuböck Matthias , Schörgenhofer Christian , Seitz Tamara , Firbas Christa , Karolyi Mario , Weiss Günter , Jilma Bernd , Thålin Charlotte , Bellmann-Weiler Rosa , Salzer Helmut J.F. , Fischer Michael J.M. , Zoufaly Alexander , Assinger Alice
Published: December 2020

Background

The Covid-19 pandemic has become a global public health crisis and providing optimal patient care while preventing a collapse of the health care system is a principal objective worldwide.

Objective

To develop and validate a prognostic model based on routine hematological parameters to predict uncomplicated disease progression to support the decision for an earlier discharge.

Design

Development and refinement of a multivariable logistic regression model with subsequent external validation. The time course of several hematological variables until four days after admission were used as predictors. Variables were first selected based on subject matter knowledge; their number was further reduced using likelihood ratio-based backward elimination in random bootstrap samples.

Setting

Model development based on three Austrian hospitals, validation cohorts from two Austrian and one Swedish hospital.

Participants

Model development based on 363 survivors and 78 non-survivors of Covid-19 hospitalized in Austria. External validation based on 492 survivors and 61 non-survivors hospitalized in Austria and Sweden.

Outcome

In-hospital death.

Main Results

The final model includes age, fever upon admission, parameters derived from C-reactive protein (CRP) concentration, platelet count and creatinine concentration, approximating their baseline values (CRP, creatinine) and change over time (CRP, platelet count). In Austrian validation cohorts both discrimination and calibration of this model were good, with c indices of 0.93 (95% CI 0.90 - 0.96) in a cohort from Vienna and 0.93 (0.88 - 0.98) in one from Linz. The model performance seems independent of how long symptoms persisted before admission. In a small Swedish validation cohort, the model performance was poorer (p = 0.008) compared with Austrian cohorts with a c index of 0.77 (0.67 - 0.88), potentially due to substantial differences in patient demographics and clinical routine.

Conclusions

Here we describe a formula, requiring only variables routinely acquired in hospitals, which allows to estimate death probabilities of hospitalized patients with Covid-19. The model could be used as a decision support for earlier discharge of low-risk patients to reduce the burden on the health care system. The model could further be used to monitor whether patients should be admitted to hospital in countries with health care systems with emphasis on outpatient care (e.g. Sweden).
In vitro measurements of protein–protein interactions show that antibody affinity governs the inhibition of SARS-CoV-2 spike/ACE2 binding in convalescent serum
Authors: Fiedler Sebastian , Piziorska Monika A. , Denninger Viola , Morgunov Alexey S. , Ilsley Alison , Malik Anisa Y. , Schneider Matthias M. , Devenish Sean R. A. , Meisl Georg , Aguzzi Adriano , Fiegler Heike , Knowles Tuomas P. J.
Published: December 2020

The humoral immune response plays a key role in suppressing the pathogenesis of SARS-CoV-2. The molecular determinants underlying the neutralization of the virus remain, however, incompletely understood. Here, we show that the ability of antibodies to disrupt the binding of the viral spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor on the cell, the key molecular event initiating SARS-CoV-2 entry into host cells, is controlled by the affinity of these antibodies to the viral antigen. By using microfluidic antibody-affinity profiling, we were able to quantify the serum-antibody mediated inhibition of ACE2–spike binding in two SARS-CoV-2 seropositive individuals. Measurements to determine the affinity, concentration, and neutralization potential of antibodies were performed directly in human serum. Using this approach, we demonstrate that the level of inhibition in both samples can be quantitatively described using the binding energies of the binary interactions between the ACE2 receptor and the spike protein, and the spike protein and the neutralizing antibody. These experiments represent a new type of in-solution receptor binding competition assay, which has further potential areas of application ranging from decisions on donor selection for convalescent plasma therapy, to identification of lead candidates in therapeutic antibody development, and vaccine development.
Post-transcriptional gene regulation by the RNA binding protein IGF2BP3 is critical for MLL-AF4 mediated leukemogenesis
Authors: Tran Tiffany M , Philipp Julia , Bassi Jaspal , Nibber Neha , Draper Jolene , Lin Tasha , Palanichamy Jayanth Kumar , Jaiswal Amit Kumar , Silva Oscar , Paing May , King Jennifer , Katzman Sol , Sanford Jeremy R , Rao Dinesh S
Published: December 2020

Despite recent advances in therapeutic approaches, patients with MLL-rearranged leukemia still have poor outcomes and a high risk of relapse. Here, we found that MLL-AF4, the most common MLL fusion protein in patients, transcriptionally induces IGF2BP3 and that IGF2BP3 strongly amplifies MLL-Af4 mediated leukemogenesis. Deletion of Igf2bp3 significantly increases the survival of mice with MLL-Af4 driven leukemia and greatly attenuates disease, with a minimal impact on baseline hematopoiesis. At the cellular level, MLL-Af4 leukemia-initiating cells require Igf2bp3 for their function in leukemogenesis. eCLIP and transcriptome analysis of MLL-Af4 transformed stem and progenitor cells and MLL-Af4 bulk leukemia cells reveals a complex IGF2BP3-regulated post-transcriptional operon governing leukemia cell survival and proliferation. Regulated mRNA targets include important leukemogenic genes such as those in the Hoxa locus and numerous genes within the Ras signaling pathway. Together, our findings show that IGF2BP3 is an essential positive regulator of MLL-AF4 mediated leukemogenesis and represents an attractive therapeutic target in this disease.
Mutation Landscape of SARS COV2 in Africa
Authors: Nassir Angus A. , Musanabaganwa Clarisse , Mwikarago Ivan
Published: December 2020

COVID-19 disease has had a relatively less severe impact in Africa. To understand the role of SARS CoV2 mutations on COVID-19 disease in Africa, we analysed 282 complete nucleotide sequences from African isolates deposited in the NCBI Virus Database. Sequences were aligned against the prototype Wuhan sequence (GenBank accession:NC_045512.2) in BWA v. 0.7.17. SAM and BAM files were created, sorted and indexed in SAMtools v. 1.10 and marked for duplicates using Picard v. 2.23.4. Variants were called with mpileup in BCFtools v. 1.11. Phylograms were created using Mr. Bayes v 3.2.6. A total of 2,349 single nucleotide polymorphism (SNP) profiles across 294 sites were identified. Clades associated with severe disease in the United States, France, Italy, and Brazil had low frequencies in Africa (L84S=2.5%, L3606F=1.4%, L3606F/V378I/=0.35, G251V=2%). Sub Saharan Africa (SSA) accounted for only 3% of P323L and 4% of Q57H mutations in Africa. Comparatively low infections in SSA were attributed to the low frequency of the D614G clade in earlier samples (25% vs 67% global). Higher disease burden occurred in countries with higher D614G frequencies (Egypt=98%, Morocco=90%, Tunisia=52%, South Africa) with D614G as the first confirmed case. V367F, D364Y, V483A and G476S mutations associated with efficient ACE2 receptor binding and severe disease were not observed in Africa. 95% of all RdRp mutations were deaminations leading to CpG depletion and possible attenuation of virulence. More genomic and experimental studies are needed to increase our understanding of the temporal evolution of the virus in Africa, clarify our findings, and reveal hot spots that may undermine successful therapeutic and vaccine interventions.
Patch characteristics and domestic dogs differentially affect carnivore space use in fragmented landscapes in Southern Chile
Authors: Malhotra Rumaan , Jiménez Jaime E. , Harris Nyeema C.
Published: December 2020

In an increasingly anthropogenic world, native species face multiple interacting threats. Habitat fragmentation and domestic dogs are two such perturbations threatening terrestrial mammals globally. Here, we implemented a camera trap survey in the fragmented central valley/Andean foothills transition of the Los Lagos Region in Southern Chile to evaluate space use of native carnivores in a landscape comprised of patches of native forest amidst a matrix of pastureland. Using an occupancy modeling framework to account for imperfect detection, we examined the impacts of dogs and landscape metrics of fragmentation on three mesocarnivores – the foxes culpeo (Lycalopex culpaeus) and chilla (Lycalopex griseus) and the wild cat güiña (Leopardus guigna). Factors driving occupancy differed for each of the native species, while detection rates for both canid species increased with dog occupancy. We found that a small (12%) simulated increase in dog occupancy negatively impacted the spatial use of the culpeo. Habitat loss and fragmentation were positive drivers for the chilla and the dog, and indirectly impacted the culpeo through the domestic dog. The güiña did not respond to fragmentation and other habitat covariates or dog occupancy. Instead, all native carnivore species temporally partitioned diel activity with dogs. We highlight that the effects of dogs or fragmentation are not ubiquitous across the carnivore guild with varied tolerance. However, future conditions of increased fragmentation and habitat loss will likely increase the potential contact between domestic dogs and native carnivores.
Calibrating Hall-Effect valvometers accounting for electromagnetic properties of the sensor and dynamic geometry of the bivalves shell
Authors: Guarini Jean-Marc , Coston-Guarini Jennifer , Comeau Luc A.
Published: December 2020

Hall-Effect valvometry (HES) is being used to describe bivalve valve gape variations and infer environmental perturbations in a variety of aquatic environments. Surprisingly, the published calibrations in ecological literature ignore both the electromagnetic properties of HES and that the valves rotate around their hinge when they move. The high sensitivity of HES suggests these features should be accounted for explicitly to estimate measurement accurately. To address these issues, two calibration functions were developed based on the electromagnetic properties of the HES: one assumes that the HES and magnet are maintained on the same linear axis, and the second model accounts for the geometric properties of the system (i.e. variations of the angle between HES and the magnet during shell rotation). The great scallop (Pecten maximus) was used as biological model because of its large range of valve openings. HES were installed on the flat valve and magnets installed on the opposing rounded valve; 12 individuals of similar size (10 ± 1(SD) cm), were equipped and placed in controlled experimental conditions. A calibration was done for each individual once time series recordings were completed. The variability of parameter estimates was calculated with a bootstrap method. The second model (with rotatation) improves valve gape distance estimates for larger openings despite the decrease of sensor sensitivity. To infer valve gape dynamics, the reciprocal calculation of the calibration function was formalized and applied to the Hall voltage time series. Our analysis suggests that under controlled laboratory conditions, scallops are partially open most of the time (inter-valve distance equalca. 27 mm on average, or 45 % of the average maximum opening distance). Interspersed in this continuous regime, individual scallops performed closing events at a frequency ofca. 2.5 closings per hour. A closing event is a movement that is fast enough relative to the recording frequency (10 Hz) to qualify as discrete. We find that the inversed calibration model without rotation allows negative value estimates, which indicates that this calibration function is incorrect. In contrast, the inversed calibration model with valve rotation around the hinge constrains gape distance values in their domain of definition which automatically excludes sensor readings that produce negative values from estimated gape time series.
Investigation of the underlying hub genes and molecular pathogenesis in gastric cancer by integrated bioinformatic analyses
Authors: Vastrad Basavaraj Mallikarjunayya , Vastrad Chanabasayya Mallikarjunayya
Published: December 2020

The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a protein‑protein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes. The pathways and GO functions of the up and down regulated genes were mainly enriched in pyrimidine deoxyribonucleosides degradation, extracellular structure organization, allopregnanolone biosynthesis and digestion. FN1, PLK1, ANLN, MCM7, MCM2, EEF1A2, PTGER3, CKB, ERBB4 and PRKAA2 were identified as the most important genes of GC, and validated by TCGA database, The Human Protein Atlas database, receiver operating characteristic curve (ROC) analysis and RT-PCR. Bioinformatics analysis might be useful method to explore the molecular pathogensis of GC. In addition, FN1, PLK1, ANLN, MCM7, MCM2, EEF1A2, PTGER3, CKB, ERBB4 and PRKAA2 might be the most important genes of GC.