bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractAspartic 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.ImportanceThe 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

ABSTRACTFor 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.ImportanceAll 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

ABSTRACTCytotoxic 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.IMPORTANCEA 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

AbstractMathematical 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

AbstractCase 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 statementThere 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

ABSTRACTIntroductionThe 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.MethodsWe 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.ResultsA 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%.ConclusionThis 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

ABSTRACTNaegleria 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

AbstractOncogenic 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

AbstractCentromeres 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

AbstractFlexible 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

SummaryEstablishing 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

AbstractIn 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.