bluuebunny/crossref_metadata_2025 huggingface dataset:
Basrah experience among 6404 patients with COVID-19
Authors: Hamadi Al-Taher Saad S. , AlKanan Abbas K , Fares Mohammad N. , Mohammed Nihad Q. , Al-Jabery Ali Raheem , Habeeb Awatif A. , Mansour Abbas Ali
Published: October 2020

Abstracts

Background

The first case of COVID-19 report in Basrah was in early March 2020. This study aimed to assess some of the characteristics of patients with COVID-19 in Basrah for the period from March, 4th to September, 8th 2020.

Methods

Retrospective database analysis of the University of Basrah database. All RT-PCR positive patients during the study period were enrolled.

Results

Of 6404 patients included, male constituted 54.8%. Healthcare workers constituted 11.4% of the infected people. Of health care workers 16.1% were physicians. The mean age for the whole cohort was 39±16.7 years; adolescents and children younger than 20 years constituted 12.4%. The peak age was 31-40 years, those aged 61 years or more constituted 9.8% only. The case fatality rate was 3% (males 55.2% and females 44.8%). No death was reported in adolescents or children. The highest death rate was among those age 61 years or more.

Conclusion

The situation of COVID-19 infection in Basrah, Iraq is evolving like other countries. Furthers studies are needed to assess associated comorbidities, treatment lines, outcomes and variables associated with mortality.
The ANTsX ecosystem for quantitative biological and medical imaging
Authors: Tustison Nicholas J. , Cook Philip A. , Holbrook Andrew J. , Johnson Hans J. , Muschelli John , Devenyi Gabriel A. , Duda Jeffrey T. , Das Sandhitsu R. , Cullen Nicholas C. , Gillen Daniel L. , Yassa Michael A. , Stone James R. , Gee James C. , Avants Brian B. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: October 2020

The Advanced Normalizations Tools ecosystem, known as ANTsX, consists of multiple open-source software libraries which house top-performing algorithms used worldwide by scientific and research communities for processing and analyzing biological and medical imaging data. The base software library, ANTs, is built upon, and contributes to, the NIH-sponsored Insight Toolkit. Founded in 2008 with the highly regarded Symmetric Normalization image registration framework, the ANTs library has since grown to include additional functionality. Recent enhancements include statistical, visualization, and deep learning capabilities through interfacing with both the R statistical project (ANTsR) and Python (ANTsPy). Additionally, the corresponding deep learning extensions ANTsRNet and ANTsPyNet (built on the popular TensorFlow/Keras libraries) contain several popular network architectures and trained models for specific applications. One such comprehensive application is a deep learning analog for generating cortical thickness data from structural T1-weighted brain MRI, both cross-sectionally and longitudinally. These pipelines significantly improve computational efficiency and provide comparable-to-superior accuracy over multiple criteria relative to the existing ANTs workflows and simultaneously illustrate the importance of the comprehensive ANTsX approach as a framework for medical image analysis.
Early prognostication of COVID-19 to guide hospitalisation versus outpatient monitoring using a point-of-test risk prediction score
Authors: Chua Felix , Vancheeswaran Rama , Draper Adrian , Vaghela Tejal , Knight Matthew , Mogal Rahul , Singh Jaswinder , Spencer Lisa G , Thwaite Erica , Mitchell Harry , Calmonson Sam , Mahdi Noor , Assadullah Shershah , Leung Matthew , O’Neill Aisling , Popat Chayya , Kumar Radhika , Humphries Thomas J , Talbutt Rebecca , Raghunath Sarika , Molyneaux Philip L , Schechter Miriam , Lowe Jeremy , Barlow Andrew
Published: October 2020

Introduction

Risk factors of adverse outcomes in COVID-19 are defined but stratification of mortality using non-laboratory measured scores, particularly at the time of pre-hospital SARS-CoV-2 testing, is lacking.

Methods

Multivariate regression with bootstrapping was used to identify independent mortality predictors in a derivation cohort of COVID-19 patients. Predictions were externally validated in a large random sample of the ISARIC cohort (N=14,231) and a smaller cohort from Aintree (N=290).

Results

983 patients (median age 70, IQR 53-83; in-hospital mortality 29.9%) were recruited over an 11-week study period. Through sequential modelling, a 5-predictor score termed SOARS (SpO2, Obesity, Age, Respiratory rate, Stroke history) was developed to correlate COVID-19 severity across low, moderate and high strata of mortality risk. The score discriminated well for in-hospital death, with area under the receiver operating characteristic values of 0.82, 0.80 and 0.74 in the derivation, Aintree and ISARIC validation cohorts respectively. Its predictive accuracy (calibration) in both external cohorts was consistently higher in patients with milder disease (SOARS 0-1), the same individuals who could be identified for safe outpatient monitoring. Prediction of a non-fatal outcome in this group was accompanied by high score sensitivity (99.2%) and negative predictive value (95.9%).

Conclusion

The SOARS score uses constitutive and readily assessed individual characteristics to predict the risk of COVID-19 death. Deployment of the score could potentially inform clinical triage in pre-admission settings where expedient and reliable decision-making is key. The resurgence of SARS-CoV-2 transmission provides an opportunity to further validate and update its performance.
Cortical Spikes use Analog Sparse Coding
Authors: Ballard Dana H. , Zhang Ruohan
Published: October 2020

Quantifying the message communicated by neurons in the cortex by averaging action potentials over repeated trials of a given stimulus can reveal neuronal tuning features. For example, simple cells in the visual cortex have been characterized by reverse correlation based on the detailed structure of their oriented receptive fields. This structure, in turn, has been modeled using large libraries of such receptive fields to allow the simultaneous coding of visual stimuli with small numbers of appropriate combinations of cells selected from the library. This strategy, known assparse coding, has been shown to produce excellent approximations for natural visual inputs. In concert with this mathematical development has been the discovery of cells’ use of oscillations in the gamma frequency range for general coding tasks, such as a mechanism for synchronizing distal networks of neurons. More recently, spikes timed with oscillations have been shown to exhibit local phase delays within a single gamma cycle, but such delays have resisted a behavioral functional interpretation. We show here that a specific coordinate system for the gamma cycle allows resultant phase delays to be interpreted quantitatively in classical terms. Specifically, extracted phase delays from mice viewing oriented sinusoidal grating images are shown to have the same distributions as those from a computer sparse coding model using natural images, suggesting for the first time a direct link between experimentally measured phase delays and model receptive fields.

Significance Statement

Networks of pyramidal cells in the cortex exhibit action potentials (spikes) that are characterized by randomness and low firing rates. Spike averaging methods have been ordinarily useful in dealing with these features to reveal behavioral task structure, but the randomness and slowness so far prevented the specification of a satisfactory generative spike model. We show that a spike can be analyzed using the context of a specific phase of the gamma component of its membrane potential. The result is each spike can be can be assigned a scalar, which makes it immediately useful for network models.
A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit
Authors: Schedlbauer Andreas , Iturrioz Idoia , Ochoa-Lizarralde Borja , Diercks Tammo , López-Alonso Jorge Pedro , Lavin José Luis , Kaminishi Tatsuya , Capuni Retina , Dhimole Neha , de Astigarraga Elisa , Gil-Carton David , Fucini Paola , Connell Sean R.
Published: October 2020

While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria employ an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-EM to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30S ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16S rRNA central to decoding site maturation, and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.
Hierarchical Bayesian Models of Reinforcement Learning: Introduction and comparison to alternative methods
Authors: van Geen Camilla , Gerraty Raphael T.
Published: October 2020

Reinforcement learning models have been used extensively to capture learning and decision-making processes in humans and other organisms. One essential goal of these computational models is the generalization to new sets of observations. Extracting parameters that can reliably predict out-of-sample data can be difficult, however. The use of prior distributions to regularize parameter estimates has been shown to help remedy this issue. While previous research has suggested that empirical priors estimated from a separate dataset improve predictive accuracy, this paper outlines an alternate method for the derivation of empirical priors: hierarchical Bayesian modeling. We provide a detailed introduction to this method, and show that using hierarchical models to simultaneously extract and impose empirical priors leads to better out-of-sample prediction while being more data efficient.
Self-Organized Amphiphiles are Poor Hydroxyl Radical Scavengers in Fast Photochemical Oxidation of Proteins Experiments
Authors: Cheng Zhi , Mobley Charles , Misra Sandeep K. , Sharp Joshua S.
Published: October 2020

The analysis of membrane protein topography using fast photochemical oxidation of protein (FPOP) has been reported in recent years, but still underrepresented in literature. Based on the hydroxyl radical reactivity of lipids and other amphiphiles, it is believed that the membrane environment acts as a hydroxyl radical scavenger decreasing effective hydroxyl radical doses and resulting in less observed oxidation of proteins. Here, we investigated the effect of bulk hydroxyl radical scavenging in FPOP using both isolated cellular membranes as well as detergent micelles. We found no significant change in radical scavenging activity upon the addition of disrupted cellular membranes with the membrane concentration in the range of 0-25600 cell/μL using an inline radical dosimeter. We confirmed the non-scavenging nature of the membrane with the FPOP results of a soluble model protein in the presence of cell membranes, which showed no significant difference in oxidation with or without membranes. The use of detergents revealed that, while soluble detergent below the critical micelle concentration acts as a potent hydroxyl radical scavenger as expected, additional detergent has little to no hydroxyl radical scavenging effect once the critical micelle concentration is reached. These results suggest that any scavenging effect of membranes or organized amphiphilic membrane mimetics in FPOP experiments are not due to bulk hydroxyl radical scavenging, but may be due to a localized scavenging phenomenon.
Hypothalamic NMDA receptors stabilize NREM sleep and are essential for REM sleep
Authors: Miracca Giulia , Soto Berta Anuncibay , Tossell Kyoko , Yustos Raquel , Vyssotski Alexei L. , Franks Nicholas P. , Wisden William
Published: October 2020

The preoptic hypothalamus regulates both NREM and REM sleep. We found that calcium levels in mouse lateral preoptic (LPO) neurons were highest during REM. Deleting the core GluN1 subunit of NMDA receptors from LPO neurons abolished calcium signals during all vigilance states, and the excitatory drive onto LPO neurons was reduced. Mice had less NREM sleep and were incapable of generating conventionally classified REM sleep episodes: cortical theta oscillations were greatly reduced but muscle atonia was maintained. Additionally, mice lacking NMDA receptors in LPO neurons had highly fragmented sleep-wake patterns. The fragmentation persisted even under high sleep pressure produced by sleep deprivation. Nevertheless, the sleep homeostasis process remained intact, with an increase in EEG delta power. The sedative dexmedetomidine and sleeping medication zolpidem could transiently restore consolidated sleep. High sleep-wake fragmentation, but not sleep loss, was also produced by selective GluN1 knock-down in GABAergic LPO neurons. We suggest that NMDA glutamate receptor signalling stabilizes the firing of “GABAergic NREM sleep-on” neurons and is also essential for the theta rhythm in REM sleep.
Single-cell analysis of cell fate bifurcation in the chordateCiona
Authors: Winkley Konner M. , Reeves Wendy M. , Veeman Michael T.
Published: October 2020

Inductive signaling interactions between different cell types are a major mechanism for the further diversification of embryonic cell fates. Most blastomeres in the model chordateCiona robustabecome restricted to a single predominant fate between the 64-cell and mid-gastrula stages. We used single-cell RNAseq spanning this period to identify 53 distinct cell states, 25 of which are dependent on a MAPK-mediated signal critical to earlyCionapatterning. Divergent gene expression between newly bifurcated sibling cell types is dominated by upregulation in the induced cell type. These upregulated genes typically include numerous transcription factors and not just one or two key regulators. The Ets family transcription factor Elk1/3/4 is upregulated in almost all the putatively direct inductions, indicating that it may act in an FGF-dependent feedback loop. We examine several bifurcations in detail and find support for a ‘broad-hourglass’ model of cell fate specification in which many genes are induced in parallel to key tissue-specific transcriptional regulators via the same set of transcriptional inputs.
Purification and Characterization of Aspartic Protease Produced fromAspergillus oryzaeDRDFS13 under Solid-State Fermentation
Authors: Mamo Jermen , Orellana Jorge Fernando Suarez , Yelemane Vikas , Kangwa Martin , Fernandez-Lahore Hector Marcelo , Assefa Fassil
Published: October 2020

Aspartic proteases (E.C.3.4.23.) are endopeptidases with molecular masses ranging between 30–45 kDa. They depend on aspartic acid residues for their catalytic activity and show maximal activity at low pH. Thus the main objective of the present study was to purify and characterize aspartic protease from locally identified fungi by solid-state fermentation. The aspartic protease in the current study was obtained fromA. oryzaeDRDFS13 under SSF. The crude enzyme extract was purified by size-exclusion (SEC) and ion-exchange (IEC) chromatography. The protein contents of crude enzyme and IEC fractions were determined by BCA methods while the presence of N-glycosylation was checked using Endo-H. Inhibition studies were conducted using protease inhibitors. The milk-clotting activity (MCA), protease activity (PA); molecular weight and enzyme kinetics were determined using standard methods. Optimum temperature and stability, optimum pH and stability, and the effect of cations on MCA were assessed using standard methods. The maximum MCA (477.11 U/mL) was recorded from IEC fraction A8. The highest specific activity (183.50 U/mg), purification fold (6.20) and yield (9.2%) were also obtained from the same fraction (IEC A8). The molecular weight of 40 kDa was assigned for the purified enzyme (IEC A8). However, its molecular weight was decreased to 30 KDa upon deglycosylation assay which infers that the protein is glycosylated. Incubation of the pure enzyme (IEC A8) with pepstatin A caused a 94 % inhibition on MCA. The dialyzed enzyme showed a Km and Vmax values of 17.50 mM and 1369 U, respectively. The enzyme showed maximum MCA at 60 °C and pH 5.0 with stability at pH 4.5-6.5 and temperature 35-45 °C. Most cat-ions stimulate the activity of the enzyme; moreover, the highest MCA was detected at 50 mM of MnSO4. Furthermore, the results obtained in the present study confirmed that the aspartic protease enzyme produced fromA. oryzaeDRDFS13 and purified in ion-exchange chromatography could be used as a substitute source of rennet enzyme for cheese production.

Importance

The production of pure aspartic protease enzyme from local microbes which is useful to substitute shortage of calf rennet enzyme and valuable to diversify cheese production throughout the world.
Formaldehyde-responsive proteins, TtmR and EfgA, reveal a tradeoff between formaldehyde resistance and efficient transition to methylotrophy inMethylorubrum extorquens
Authors: Bazurto Jannell V. , Bruger Eric L. , Lee Jessica A. , Lambert Leah B. , Marx Christopher J.
Published: October 2020

For bacteria to thrive they must be well-adapted to their environmental niche, which may involve specialized metabolism, timely adaptation to shifting environments, and/or the ability to mitigate numerous stressors. These attributes are highly dependent on cellular machinery that can sense both the external and intracellular environment.Methylorubrum extorquensis an extensively studied facultative methylotroph, an organism that can use single-carbon compounds as their sole source of carbon and energy. In methylotrophic metabolism, carbon flows through formaldehyde as a central metabolite; thus, formaldehyde is both an obligate metabolite and a metabolic stressor. Via the one-carbon dissimilation pathway, free formaldehyde is rapidly incorporated by formaldehyde activating enzyme (Fae), which is constitutively expressed at high levels. In the presence of elevated formaldehyde levels, a recently identified formaldehyde-sensing protein, EfgA, induces growth arrest. Herein, we describe TtmR, a formaldehyde-responsive transcription factor that, like EfgA, modulates formaldehyde resistance. TtmR is a member of the MarR family of transcription factors and impacts the expression of 75 genes distributed throughout the genome, many of which are transcription factors and/or involved in stress response, includingefgA.Notably, whenM. extorquensis adapting its metabolic network during the transition to methylotrophy,efgAandttmRmutants experience an imbalance in formaldehyde production and a notable growth delay. Although methylotrophy necessitates thatM. extorquensmaintain a relatively high level of formaldehyde tolerance, this work reveals a tradeoff between formaldehyde resistance and the efficient transition to methylotrophic growth and suggests that TtmR and EfgA play a pivotal role in maintaining this balance.

Importance

All organisms produce formaldehyde as a byproduct of enzymatic reactions and as a degradation product of metabolites. The ubiquity of formaldehyde in cellular biology suggests all organisms have evolved mechanisms of mitigating formaldehyde toxicity. However, formaldehyde-sensing is poorly described and prevention of formaldehyde-induced damage is primarily understood in the context of detoxification. Here we use an organism that is regularly exposed to elevated intracellular formaldehyde concentrations through high-flux one-carbon utilization pathways to gain insight into the role of formaldehyde-responsive proteins that modulate formaldehyde resistance. Using a combination of genetic and transcriptomic analyses, we identify dozens of genes putatively involved in formaldehyde resistance, determined the relationship between two different formaldehyde response systems and identified an inherent tradeoff between formaldehyde resistance and optimal transition to methylotrophic metabolism.
Comprehensive analysis of HIV elite controllers’ and progressors’ transcriptional profiles from CD8+T lymphocytes demonstrates heterogeneity of pathways and master regulators, which may be essential for disease nonprogression
Authors: Ivanov Sergey , Filimonov Dmitry , Tarasova Olga
Published: October 2020

Cytotoxic and noncytotoxic CD8+T lymphocyte responses are essential for the control of HIV infection. Understanding the mechanisms underlying HIV control in elite controllers (ECs), who do not progress to AIDS for many years without treatment, may facilitate the development of new effective therapeutic strategies.

We performed a comprehensive analysis of the transcriptional profiles of CD8+cells from ECs and treated and untreated progressors using an original pipeline. Cluster analysis enabled the identification of five distinct groups (EC groups 1-5) of ECs based on their transcription profiles. Profiles of EC groups 2-4 were associated with different numbers of differentially expressed genes, but the corresponding genes shared the same cellular processes. These three groups were associated with increased metabolism, survival, proliferation, and the absence of an “exhausted” phenotype of CD8+lymphocytes, compared to untreated progressors. The transcriptional profiles of EC group 1 were opposite to those of EC groups 2-4 and similar to those of the treated progressors. This group may be associated with residual dysfunction of T lymphocytes. The EC group 5 was indistinguishable from normal. EC groups 1 and 5 can have mechanisms of nonprogression unrelated to CD8+cells.

The transcription changes in CD8+lymphocytes from ECs may be attributable to the receptors that modulate the functional states of CD8+cells. We identified 22 receptors, which are potential master regulators and may be responsible for the observed expression changes of CD8+cells in ECs. These receptors can be considered potential targets of therapeutic intervention, which may decelerate disease progression.

IMPORTANCE

A small group of HIV-infected individuals, known as elite controllers (ECs), do not develop AIDS for many years, despite being untreated. Understanding the mechanisms governing HIV control in ECs may help develop new effective therapeutic strategies. Since CD8+T lymphocytes seem to play a significant role in HIV control, we analyzed the large number of transcriptional profiles in total CD8+cells from ECs, treated, and untreated progressors. We found distinct groups of ECs, which may have different mechanisms governing HIV nonprogression, and we identified related pathways and cellular processes that are dissimilar from those in progressors. We also identified master regulators, key proteins in the signaling network that can be responsible for observed transcriptional changes in CD8+cells from ECs and may be essential for disease nonprogression. These proteins may represent potential targets for therapeutic interventions.
Analytical solution of equivalent SEIR and agent-based model of COVID-19; showing the bounds of contact tracing
Authors: Tunc Huseyin , Sari Fatma Zehra , Darendeli Busra Nur , Nashebi Ramin , Sari Murat , Kotil Seyfullah
Published: October 2020

Mathematical models not only forecast the possible future but also is used to find hidden parameters of the COVID-19 pandemic. Numerical estimates can inform us of both goals. Still, the interdependencies of parameters stay obscure. Many numerical solutions have been proposed so far; however, the analytical relationship between the outbreak growth, decay and equilibrium are much less studied. In this study, we have employed both an equivalent agent-based model and a Susceptible-Exposed-Infected-Recovered (SEIR)-like model to prove that the growth rate can be determined analytically in terms of other model parameters, including contact tracing rate. We identify the most sensitive parameters as undocumented transmission rate and documentation ratio. Unfortunately, these are the parameters we have the least knowledge. We derived an identity that predicts the effectiveness of contact tracing in a country from observable parameters. We underline an unavoidable dilemma: that even in the case of high contact tracing, we cannot bring the outbreak to stalemate without applying substantial quarantine; however, some countries are benefiting from contact tracing. Besides, we have shown that the seemingly same parameters of the SEIR models and agent-based models are not equivalent. We propose a correction to bridge both models.
Cognitive deficits in people who have recovered from COVID-19 relative to controls: An N=84,285 online study
Authors: Hampshire Adam , Trender William , Chamberlain Samuel R , Jolly Amy , Grant Jon E. , Patrick Fiona , Mazibuko Ndaba , Williams Steve , Barnby Joseph M , Hellyer Peter , Mehta Mitul A
Published: October 2020

Case studies have revealed neurological problems in severely affected COVID-19 patients. However, there is little information regarding the nature and broader prevalence of cognitive problems post-infection or across the full spread of severity. We analysed cognitive test data from 84,285 Great British Intelligence Test participants who completed a questionnaire regarding suspected and biologically confirmed COVID-19 infection. People who had recovered, including those no longer reporting symptoms, exhibited significant cognitive deficits when controlling for age, gender, education level, income, racial-ethnic group and pre-existing medical disorders. They were of substantial effect size for people who had been hospitalised, but also for mild but biologically confirmed cases who reported no breathing difficulty. Finer grained analyses of performance support the hypothesis that COVID-19 has a multi-system impact on human cognition.

Significance statement

There is evidence that COVID-19 may cause long term health changes past acute symptoms, termed ‘long COVID’. Our analyses of detailed cognitive assessment and questionnaire data from tens thousands of datasets, collected in collaboration with BBC2 Horizon, align with the view that there are chronic cognitive consequences of having COVID-19. Individuals who recovered from suspected or confirmed COVID-19 perform worse on cognitive tests in multiple domains than would be expected given their detailed age and demographic profiles. This deficit scales with symptom severity and is evident amongst those without hospital treatment. These results should act as a clarion call for more detailed research investigating the basis of cognitive deficits in people who have survived SARS-COV-2 infection.
Clinical characteristics of 4490 COVID-19 patients in Africa: A meta-analysis
Authors: Olumade Testimony Jesupamilerin , Uzairue Leonard Ighodalo
Published: October 2020

Introduction

The novel coronavirus disease-2019 (COVID-19) pandemic that started in December 2019 has affected over 39 million people and killed over 1.1 million people. While more studies are published to help us understand the virus, there is a dearth of studies on the clinical characteristics and associated outcomes of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on the African continent.

Methods

We evaluated evidence from previous studies in Africa available in six databases between January 1 and October 6, 2020. Meta-analysis was then performed using Open-Meta Analyst software.

Results

A total of seven studies including 4490 COVID-19 patients were included. The result of the meta-analysis showed 68.8% of infected patients were male. Common symptoms presented (with their incidences) were fever (42.8%), cough (33.3%), headache (11.3%), breathing problems (16.8%). Other minor occurring symptoms included diarrhea (7.5%), and rhinorrhea (9.4%). Fatality rate was 5.6%.

Conclusion

This study presents the first description and analysis of the clinical characteristics of COVID-19 patients in Africa. The most common symptoms are fever, cough and breathing problems.
Naegleria fowleri:protein structures to facilitate drug discovery for the deadly, pathogenic free-living amoeba
Authors: Barrett Kayleigh , Tillery Logan , Goldstein Jenna , Lassner Jared W. , Osterhout Bram , Tran Nathan L. , Xu Lily , Young Ryan M. , Craig Justin , Chun Ian , Dranow David M. , Abendroth Jan , Delker Silvia L. , Davies Douglas R. , Mayclin Stephen J. , Calhoun Brandy , Bolejack Madison J. , Staker Bart , Subramanian Sandhya , Phan Isabelle , Lorimer Donald D. , Myler Peter J. , Edwards Thomas E. , Kyle Dennis E. , Rice Christopher A. , Morris James C. , Leahy James W. , Manetsch Roman , Barrett Lynn K. , Smith Craig L. , Van Voorhis Wesley C.
Published: October 2020

Naegleria fowleriis a pathogenic, thermophilic, free-living amoeba which causes primary amebic meningoencephalitis (PAM). Penetrating the olfactory mucosa, the brain-eating amoeba travels along the olfactory nerves, burrowing through the cribriform plate to its destination: the brain’s frontal lobes. The amoeba thrives in warm, freshwater environments, with peak infection rates in the summer months and has a mortality rate of approximately 97%. A major contributor to the pathogen’s high mortality is the lack of sensitivity ofN. fowlerito current drug therapies, even in the face of combination-drug therapy. To enable rational drug discovery and design efforts we have pursued protein production and crystallography-based structure determination efforts for likely drug targets fromN. fowleri. N. fowlerigenes were selected if they had homology to drug targets listed in Drug Bank or were nominated by primary investigators engaged inN. fowleriresearch. In 2017, 178N. fowleriprotein targets were queued to the Seattle Structural Genomics Center of Infectious Disease (SSGCID) pipeline, and to date 89 soluble recombinant proteins and 19 unique target structures have been produced. Many of the new protein structures are potential drug targets and contain structural differences compared to their human homologs, which could allow for the development of pathogen-specific inhibitors. Five of the structures were analyzed in more detail, and four of five show promise that selective inhibitors of the active site could be found. The 19 solved crystal structures build a foundation for future work in combating this devastating disease by encouraging further investigation to stimulate drug discovery for this neglected pathogen.
Live-cell imaging shows uneven segregation of extrachromosomal DNA elements and transcriptionally active extrachromosomal DNA clusters in cancer
Authors: Yi Eunhee , Gujar Amit D. , Guthrie Molly , Kim Hoon , Johnson Kevin C. , Amin Samirkumar B. , Das Sunit , Clow Patricia A. , Cheng Albert W. , Verhaak Roel GW
Published: October 2020

Oncogenic extrachromosomal DNA elements (ecDNAs) promote intratumoral heterogeneity, creating a barrier for successful cancer treatments. The underlying mechanisms are poorly understood and studies are hampered in part by a lack of adequate tools enabling studies of ecDNA behavior. Here, we show that single-cell ecDNA copy numbers follow a Gaussian distribution across tumor cells in vitro and in patient glioblastoma specimens, suggesting uneven ecDNA segregation during mitosis. We established a CRISPR-based approach which leverages unique ecDNA breakpoint sequences to tag ecDNA with fluorescent markers in living cells. Applying this method during mitosis revealed disjointed ecDNA inheritance patterns, providing an explanation for rapid ecDNA accumulation in cancer. Post-mitosis, ecDNAs tended to cluster and clustered ecDNAs colocalized with RNA polymerase II, promoting transcription of cargo oncogenes. Our observations provide direct evidence for uneven segregation of ecDNA and shed new lights of mechanisms through which ecDNAs contribute to oncogenesis.
Population and species diversity at mouse centromere satellites
Authors: Arora Uma P. , Charlebois Caleigh , Lawal Raman Akinyanju , Dumont Beth L.
Published: October 2020

Centromeres are satellite-rich chromatin domains that are essential for chromosome segregation. Centromere satellites evolve rapidly between species but little is known about population-level diversity across these loci. We developed ak-mer based method to quantify centromere copy number and sequence variation from whole genome sequencing data. We applied this method to diverse inbred and wild house mouse (genusMus) genomes and uncover pronounced variation in centromere architecture between strains and populations. We show that patterns of centromere diversity do not mirror the known ancestry of inbred strains, revealing a remarkably rapid rate of centromere sequence evolution. We document increased satellite homogeneity and copy number in inbred compared to wild mice, suggesting that inbreeding remodels mouse centromere architecture. Our results highlight the power ofk-mer based approaches for probing variation across repetitive regions and provide the first in-depth, phylogenetic portrait of centromere variation acrossMus musculus.
Hippocampal place cells encode global location but not changes in environmental connectivity in a 4-room navigation task
Authors: Duvelle Éléonore , Grieves Roddy M , Liu Anyi , Jedidi-Ayoub Selim , Holeniewska Joanna , Harris Adam , Nyberg Nils , Donnarumma Francesco , Lefort Julie M. , Jeffery Kate J. , Summerfield Christopher , Pezzulo Giovanni , Spiers Hugo J.
Published: October 2020

Flexible navigation relies on a cognitive map of space, thought to be implemented by hippocampal place cells: neurons that exhibit location-specific firing. In connected environments, optimal navigation requires keeping track of one’s location and of the available connections between subspaces. We examined whether the dorsal CA1 place cells of rats encode environmental connectivity in four geometrically-identical boxes arranged in a square. Rats moved between boxes by pushing saloon-type doors that could be locked in one or both directions. While rats demonstrated knowledge of environmental connectivity, their place cells did not respond to connectivity changes, nor did they represent doorways differently from other locations. Importantly, place cells coded the space in a global frame, expressing minimal repetitive fields despite the repetitive geometry (global coding). These results suggest that CA1 place cells provide a spatial map that does not explicitly include connectivity.
Zebrafish studies on the vaccine candidate to COVID-19, the Spike protein: Production of antibody and adverse reaction
Authors: Ventura Fernandes Bianca H , Feitosa Natália Martins , Barbosa Ana Paula , Bomfim Camila Gasque , Garnique Anali M. B. , Gomes Francisco I. F. , Nakajima Rafael T. , Belo Marco A. A. , Eto Silas Fernandes , Fernandes Dayanne Carla , Malafaia Guilherme , Manrique Wilson G. , Conde Gabriel , Rosales Roberta R. C. , Todeschini Iris , Rivero Ilo , Llontop Edgar , Sgro German G. , Oka Gabriel Umaji , Bueno Natalia F , Ferraris Fausto K. , de Magalhaes Mariana T. Q. , Medeiros Renata J. , Gomes Juliana M. M , de Souza Junqueira Mara , Conceição Katia , Pontes Letícia G. , Condino-Neto Antonio , Perez Andrea C. , Barcellos Leonardo J. G. , Correa junior Jose Dias , Dorlass Erick G. , Camara Niels O. S , Durigon Edison Luiz , Cunha Fernando Q. , Nóbrega Rafael H. , Machado-Santelli Glaucia M. , Farah Chuck , Veras Flávio P , Galindo-Villegas Jorge , Costa-Lotufo Leticia , Cunha Thiago M. , Chammas Roger , Guzzo Cristiane R. , Carvalho Luciani R , Charlie-Silva Ives
Published: October 2020

Establishing new experimental animal models to assess the safety and immune response to the antigen used in the development of COVID-19 vaccine is an imperative issue. Based on the advantages of using zebrafish as a model in research, herein we suggest doing this to test the safety of the putative vaccine candidates and to study immune response against the virus. We produced a recombinant N-terminal fraction of the Spike SARS-CoV-2 protein and injected it into adult female zebrafish. The specimens generated humoral immunity and passed the antibodies to the eggs. However, they presented adverse reactions and inflammatory responses similar to severe cases of human COVID-19. The analysis of the structure and function of zebrafish and human Angiotensin-converting enzyme 2, the main human receptor for virus infection, presented remarkable sequence similarities. Moreover, bioinformatic analysis predicted protein-protein interaction of the Spike SARS-CoV-2 fragment and the Toll-like receptor pathway. It might help in the choice of future therapeutic pharmaceutical drugs to be studied. Based on thein vivoandin silicoresults presented here, we propose the zebrafish as a model for translational research into the safety of the vaccine and the immune response of the vertebrate organism to the SARS-CoV-2 virus.
Visuomotor anomalies in achiasmatic mice expressing a transfer-defective Vax1 mutant
Authors: Min Kwang Wook , Kim Namsuk , Lee Jae Hoon , Sung Younghoon , Kim Museong , Lee Eun Jung , Kim Jong-Myeong , Kim Jae-Hyun , Lee Jaeyoung , Cho Wonjin , Yang Jee Myung , Kim Nury , Kim Jaehoon , Lee C. Justin , Park Young-Gyun , Lee Seung-Hee , Lee Han-Woong , Kim Jin Woo
Published: October 2020

In binocular animals that exhibit stereoscopic visual responses, the axons of retinal ganglion cells (RGCs) connect to brain areas bilaterally by forming a commissure called the optic chiasm (OC). Ventral anterior homeobox 1 (Vax1) contributes to formation of the OC, acting endogenously in optic pathway cells and exogenously in growing RGC axons. Here, we generatedVax1AA/AAmice expressing the Vax1AAmutant, which is incapable of intercellular transfer. We found that RGC axons cannot take up Vax1AAprotein fromVax1AA/AAmouse optic stalk (OS) cells, of which maturation is delayed, and fail to access the midline. Consequently, RGC axons ofVax1AA/AAmice connect exclusively to ipsilateral brain areas, resulting in the reduced visual acuity and the abnormal oculomotor responses. Together, our study provides physiological evidences for the necessity of intercellular transfer of Vax1 and the importance of the bilateral RGC axon projection in visuomotor responses.
Mammalian-unique eIF4E2 maintains GSK3β proline kinase activity to resist senescence against hypoxia
Authors: zhang Min , Sun Lei , He Dong , Chen Jian , Dong Zhiqiang , Liang Huiting , Cao Yu , Cai Bingcheng , Yang He
Published: October 2020

Cellular senescence is a stable state of cell cycle arrest elicited by various stresses. Hypoxia modulates senescence, but its consequences and implications in living organisms remains unknown. Here we identified the eIF4E2-GSK3β pathway regulated by hypoxia to maintain p53 proline-directed phosphorylation (S/T-P) to prevent senescence. We previously knew that GSK3β activates p53 translation through phosphorylation of RBM38 Ser195 (-Pro196). Unexpectedly, eIF4E2 directly binds to GSK3β via a conserved motif, mediating Ser195 phosphorylation. Phosphoproteomics revealed that eIF4E2-GSK3β specifically regulates proline-directed phosphorylation. Peptide e2-I or G3-I that disrupts this pathway dephosphorylates p53 at multiple S/T-P, which accelerate senescence by transcriptional suppressing TOPBP1 and TRX1. Consistently, peptides induce liver senescence that is rescued by TOPBP1 expression, and mediate senescence-dependent tumor regression. Furthermore, hypoxia inhibits eIF4E2-GSK3β. Inspiringly, eIF4E2-GSK3β is unique to mammals, which maintains mice viability and prevents liver senescence against physiological hypoxia. Interestingly, this mammalian eIF4E2 protects heart of zebrafish against hypoxia. Together, we identified a mammalian -unique eIF4E2-GSK3β pathway preventing senescence and guarding against hypoxia in vivo.
Droplet printing reveals the importance of micron-scale structure for bacterial ecology
Authors: Kumar Ravinash Krishna , Meiller-Legrand Thomas A. , Alcinesio Alessandro , Gonzalez Diego , Mavridou Despoina A. I. , Meacock Oliver J. , Smith William P. J. , Zhou Linna , Kim Wook , Su Pulcu Gökçe , Bayley Hagan , Foster Kevin R.
Published: October 2020

Bacteria often live in diverse communities where the spatial arrangement of strains and species is considered critical for their ecology, including whether strains can coexist, which are ecologically dominant, and how productive they are as a community1,2. However, a test of the importance of spatial structure requires manipulation at the fine scales at which this structure naturally occurs3–8. Here we develop a droplet-based printing method to arrange different bacterial genotypes across a sub-millimetre array. We use this to test the importance of fine-scale spatial structure by printing strains of the gut bacteriumEscherichia colithat naturally compete with one another using protein toxins9,10. This reveals that the spatial arrangement of bacterial genotypes is important for ecological outcomes. Toxin-producing strains largely eliminate susceptible non-producers when genotypes are well-mixed. However, printing strains side-by-side creates an ecological refuge such that susceptible strains can coexist with toxin producers, even to the extent that a susceptible strain outnumbers the toxin producer. Head-to-head competitions between toxin producers also reveals strong effects, where spatial structure can make the difference between one strain winning and mutual destruction. Finally, we print different potential barriers between two competing strains to understand why space is so important. This reveals the importance of processes that limit the free diffusion of molecules. Specifically, we show that cells closest to a toxin producer bind to and capture toxin molecules, which creates a refuge for their clonemates. Our work provides a new method to generate customised bacterial communities with defined spatial distributions, and reveals that micron-scale changes in these distributions can drive major shifts in their ecology.
Ribosome exit tunnel electrostatics
Authors: Joiret Marc , Rapino Francesca , Close Pierre , Geris Liesbet
Published: October 2020

The impact of the ribosome exit tunnel electrostatics on the protein elongation rate or on the forces acting upon the nascent polypeptide chain are currently not fully elucidated. In the past, researchers have measured the electrostatic potential inside the ribosome polypeptide exit tunnel at a limited number of spatial points, at least in prokaryotes. Here, we present a basic electrostatic model of the exit tunnel of the ribosome, providing a quantitative physical description of the tunnel interaction with the nascent proteins at all centro-axial points inside the tunnel. We show how the tunnel geometry causes a positive potential difference between the tunnel exit and entry points which impedes positively charged amino acid residues from progressing through the tunnel, affecting the elongation rate in a range of minus 40% to plus 85% when compared to the average elongation rate. The time spent by the ribosome to decode the genetic encrypted message is constrained accordingly. We quantitatively derived, at single residue resolution, the axial forces acting on the nascent peptide from its particular sequence embedded in the tunnel. The model sheds light on how the experimental data point measurements of the potential are linked to the local structural chemistry of the inner wall and the shape and size of the tunnel. The model consistently connects experimental observations coming from different fields in molecular biology, structural and physical chemistry, biomechanics, synthetic and multi-omics biology. Our model should be a valuable tool to gain insight into protein synthesis dynamics, translational control and into the role of the ribosome’s mechanochemistry in the co-translational protein folding.
The domain-within-domain packing of euchromatin can be described as multiplicative cascades
Authors: Noa Amra , Kuan Hui-Shun , Aschmann Vera , Zaburdaev Vasily , Hilbert Lennart
Published: October 2020

The genome is packed into the cell nucleus in the form of chromatin. Biochemical approaches have revealed that chromatin is packed within domains, which group into larger domains, and so forth. Such domain-within-domain packing, also called hierarchical packing, is equally visible in super-resolution microscopy images of large-scale chromatin organization. While previous work has suggested that chromatin is partitioned into distinct domains via microphase separation, it is unclear how these domains organize into a hierarchical packing. A particular challenge is to find an image analysis approach that fully incorporates such hierarchical packing, so that hypothetical governing mechanisms of euchromatin packing can be compared against the results of such an analysis. Here, we obtain 3D STED super-resolution images from pluripotent zebrafish embryos labeled with improved DNA fluorescence stains, and demonstrate how the hierarchical packing of euchromatin in these images can be described as multiplicative cascades. Multiplicative cascades are an established theoretical concept to describe the placement of ever-smaller structures within bigger structures. Importantly, these cascades can generate artificial image data by applying a single rule again and again, and can be fully specified using only four parameters. Here, we show how the typical patterns of euchromatin organization are reflected in the values of these four parameters. In particular, we can pinpoint the values required to mimic a microphase-separated configuration of euchromatin. We suspect that the concept of multiplicative cascades can also be applied to images of other types of chromatin. In particular, cascade parameters could serve as test quantities to assess whether microphase separation or other theoretical models accurately reproduce the hierarchical packing of chromatin.

SIGNIFICANCE

DNA is stored inside the cell nucleus in the form of chromatin. Chromatin exhibits a striking three-dimensional organization, where small domains group into larger domains, which again group into larger domains, and so forth. While this hierarchical domain-within-domain organization is obvious from microscopy images, it is still not entirely clear how it is established, or how it should be properly characterized. Here, we demonstrate that multiplicative cascades – a concept from theoretical physics used to characterize for example cloud patterns, galaxy locations, or soil patterns – are also ideally suited to describe the domain-within-domain organization of chromatin. This description is rather simple, using only four numbers, and can thus facilitate testing of competing theories for the domain-within-domain organization of chromatin.
Satellite subgenomic particles are key regulators of adeno-associated virus life cycle
Authors: Zhang Junping , Guo Ping , Yu Xiangping , Lee Kiwon , Firrman Jenni , Chrzanowski Matthew , Chen Kuntao , Chen Xiongwen , Pouchnik Derek , Diao Yong , Samulski Richard Jude , Xiao Weidong
Published: October 2020

Historically, AAV defective interfering particles (DI) were known as abnormal virions arising from natural replication and encapsidation errors. Through single virion genome analysis, we revealed that a major category of DI particles contains a double stranded DNA genome in a “snapback” configuration (SBG). The 5’-SBGs include the P5 promoters and partial rep gene sequences. The 3’-SBGs contains the capsid region. The molecular configuration of 5’-SBGs allowed double stranded RNA transcription in their dimer configuration, which in turn regulate AAV rep expression and may improve AAV packaging. In contrast, 3’-SBGs at its dimer configuration increased levels of cap protein. The generation and accumulation of 5’-SBGs and 3’-SBGs appears to be coordinated to balance the viral gene expression level. Therefore, the functions of 5’-SBGs and 3’-SBGs may help maximize the yield of AAV progenies. We postulate that AAV virus population behaved as a colony and utilizes its subgenomic particles to overcome the size limit of viral genome and encodes additional essential functions.