bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational identification of human biological processes and protein sequence motifs putatively targeted by SARS-CoV-2 proteins using protein-protein interaction networks
Authors: Nadeau Rachel , Fard Soroush Shahryari , Scheer Amit , Roth Emily , Nygard Dallas , Abramchuk Iryna , Chung Yun-En , Bennett Steffany A. L. , Lavallée-Adam Mathieu 
Published: October 2020

AbstractWhile the COVID-19 pandemic is causing important loss of life, knowledge of the effects of the causative SARS-CoV-2 virus on human cells is currently limited. Investigating protein-protein interactions (PPIs) between viral and host proteins can provide a better understanding of the mechanisms exploited by the virus and enable the identification of potential drug targets. We therefore performed an in-depth computational analysis of the interactome of SARS-CoV-2 and human proteins in infected HEK293 cells published by Gordon et al. to reveal processes that are potentially affected by the virus and putative protein binding sites. Specifically, we performed a set of network-based functional and sequence motif enrichment analyses on SARS-CoV-2-interacting human proteins and on a PPI network generated by supplementing viral-host PPIs with known interactions. Using a novel implementation of our GoNet algorithm, we identified 329 Gene Ontology terms for which the SARS-CoV-2-interacting human proteins are significantly clustered in the network. Furthermore, we present a novel protein sequence motif discovery approach, LESMoN-Pro, that identified 9 amino acid motifs for which the associated proteins are clustered in the network. Together, these results provide insights into the processes and sequence motifs that are putatively implicated in SARS-CoV-2 infection and could lead to potential therapeutic targets.
BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response
Authors: Baray Juwel Chandra , Khan Md. Maksudur Rahman , Mahmud Asif , Islam Md. Jikrul , Myti Sanat , Ali Md. Rostum , Sarker Md. Enamul Haq , Kumar Samir , Chowdhury Md. Mobarak Hossain , Roy Rony , Islam Faqrul , Barman Uttam , Khan Habiba , Chakraborty Sourav , Hossain Md. Manik , Chowdhury Md. Mashfiqur Rahman , Ghosh Polash , Mohiuddin Mohammad , Sultana Naznin , Nag Kakon 
Published: October 2020

AbstractEffective vaccine against SARS-CoV-2 is the utmost importance in the current world. More than 1 million deaths are accounted for relevant pandemic disease COVID-19. Recent data showed that D614G genotype of the virus is highly infectious and responsible for almost all infection for 2ndwave. Despite of multiple vaccine development initiatives, there are currently no report that has addressed this critical variant D614G as vaccine candidate. Here we report the development of an mRNA-LNP vaccine considering the D614G variant and characterization of the vaccine in preclinical trial. The surface plasmon resonance (SPR) data with spike protein as probe and competitive neutralization with RBD and S2 domain revealed that immunization generated specific antibody pools against the whole extracellular domain (RBD and S2) of the spike protein. The anti-sera and purified IgGs from immunized mice on day 7 and 14 neutralized SARS-CoV-2 pseudovirus in ACE2-expressing HEK293 cells in a dose dependent manner. Importantly, immunization protected mice lungs from pseudovirus entry and cytopathy. The immunologic responses have been implicated by a balanced and stable population of CD4+cells with a Th1 bias. The IgG2a to IgG1 and (IgG2a+IgG2b) to (IgG1+IgG3) ratios were found 1±0.2 and 1.24±0.1, respectively. These values are comparatively higher than relevant values for other published SARS-CoV-2 vaccine in development,1, 2and suggesting higher viral clearance capacity for our vaccine. The data suggested great promise for immediate translation of the technology to the clinic.
Reengineering the Specificity of the Highly SelectiveClostridium botulinumProtease via Directed Evolution
Authors: Dyer Rebekah P. , Isoda Hariny M. , Salcedo Gabriela S. , Speciale Gaetano , Fletcher Madison H. , Le Linh Q. , Liu Yi , Malik Shiazah Z. , Vazquez-Cintron Edwin J. , Chu Andrew C. , Rupp David C. , Jacky Birgitte P.S. , Nguyen Thu T.M. , Steward Lance E. , Majumdar Sudipta , Brideau-Andersen Amy D. , Weiss Gregory A. 
Published: October 2020

AbstractThe botulinum neurotoxin serotype A (BoNT/A) cuts a single peptide bond in SNAP25, an activity used to treat a wide range of diseases. Reengineering the substrate specificity of BoNT/A’s protease domain (LC/A) could expand its therapeutic applications; however, LC/A’s extended substrate recognition (≈60 residues) challenges conventional approaches. We report a directed evolution method for retargeting LC/A’s substrate and retaining its exquisite specificity. The resultant eight-mutation LC/A (omLC/A) has improved cleavage specificity and catalytic efficiency (1300- and 120-fold, respectively) for SNAP23 versus SNAP25 compared to a previously reported LC/A variant. Importantly, the BoNT/A holotoxin equipped with omLC/A infiltrates neurons and retains its SNAP23 activity. The identification of substrate control loops outside BoNT/A’s active site could guide the design of improved BoNT proteases and inhibitors.One Sentence SummaryDirected evolution of the BoNT/A protease targets a new cellular protein, SNAP23, expanding its therapeutic potential.
Development of a 16S metabarcoding assay for the environmental DNA (eDNA) detection of aquatic reptiles across northern Australia
Authors: West Katrina , Heydenrych Matthew , Lines Rose , Tucker Tony , Fossette Sabrina , Whiting Scott , Bunce Michael 
Published: October 2020

AbstractA severe lack of distribution data for aquatic reptiles in northern Australia leaves many taxa vulnerable to extirpation and extinction. Environmental DNA (eDNA) technologies offer sensitive and non-invasive genetic alternatives to trapping and visual surveys and are increasingly employed for the detection of aquatic and semi-aquatic reptiles. However, at present, these studies have largely applied species-specific primers which do not provide a cost-effective avenue for the simultaneous detection of multiple reptilian taxa. Here, we present a 16S rRNA metabarcoding assay for the broad detection of aquatic and semi-aquatic reptile species. This assay is tested on water samples collected at multiple sampling sites at two tropical locations: 12 marine/estuarine sites in Roebuck Bay, Western Australia, and 4 estuarine sites in Cooktown, Queensland, Australia. A total of nine reptile taxa were detected from 10 of the 16 sampled sites, including marine and freshwater turtles, aquatic and semi-aquatic/terrestrial snakes, and terrestrial skinks. However, inconsistencies in the detection of previously observed aquatic reptiles at our sampled sites, such as saltwater crocodile and sea snakes, indicates that further research is required to assess the reliability, strengths and limitations of eDNA methods for aquatic reptile detection before it can be integrated as a broad-scale bioassessment tool.
Consolidation and maintenance ofDrosophilalong-term memory require LIM homeodomain protein Apterous in distinct brain neurons
Authors: Inami Show , Sato Tomohito , Suzuki Yuki , Kitamoto Toshihiro , Sakai Takaomi 
Published: October 2020

AbstractThe LIM-homeodomain (LIM-HD) transcription factor Apterous (Ap) and its cofactor Chip (Chi) form a complex that regulates various developmental events inDrosophila. Although Ap continues to be expressed in the adult brain, the functions of the centrally expressed Ap remain incompletely understood. Here, we show that Ap and Chi in theDrosophilamemory center, the mushroom bodies (MBs), are indispensable for long-term memory (LTM) maintenance, whereas Ap in a subset of clock neurons [large ventral-lateral neurons (l-LNvs)] plays a crucial role in memory consolidation in a Chi-independent manner.Ex vivoimaging revealed that Ap, but not Chi, in l-LNvs is essential for the appropriate Cl−responses to GABA. Furthermore, knockdown of GABAAreceptor in l-LNvs compensated for the impairment of memory consolidation inapnull mutant flies. Our results indicate thatDrosophilaAp functions differently in l-LNvs and MBs, and it contributes to the consolidation and maintenance of LTM.
Mitochondria fragment and reassemble to initiate the formation and development of the nucleus
Authors: Jiang Xuejun , Hou Bolin , Xu Yang , Li Erwei , Cao Pei , Liu Shuchun , Xi Zhijun , Yang Huaiyi , Huo Yuqing , Che Yongsheng 
Published: October 2020

AbstractThe function of nuclear-localized mitochondria remains unknown. We found that mitochondria assembled dense particles to fragment and disperse into the particles, which reassembled to initiate nuclear formation and development. Individually-formed nuclei in one single cell were joined together by mitochondrial fragmentation concurrently partitioning cytoplasm to form an intranuclear inclusion (INC), whose creation was not related to herniation or invagination of the cytoplasm. Along with the nuclear transition of a mitochondrion and its neighboring counterparts, the organelle included itself in the nucleus to become nuclear mitochondrion through peripherally assembling of dense particles. New medium reversed the nuclear formation of the organelles to recovery and re-establishment via the return of the particles, which consisted of dense microvesicles (MIVs).
Randomized Controlled Trials of Early Ambulatory Hydroxychloroquine in the Prevention of COVID-19 Infection, Hospitalization, and Death: Meta-Analysis
Authors: Ladapo Joseph A. , McKinnon John E. , McCullough Peter A. , Risch Harvey A. 
Published: October 2020

AbstractObjectiveTo determine if hydroxychloroquine (HCQ) reduces the incidence of new illness, hospitalization or death among outpatients at risk for or infected with SARS-CoV-2 (COVID-19).DesignSystematic review and meta-analysis of randomized clinical trials.Data sourcesSearch of MEDLINE, EMBASE, PubMed, medRxiv, PROSPERO, and the Cochrane Central Register of Controlled Trials. Also review of reference lists from recent meta-analyses.Study selectionRandomized clinical trials in which participants were treated with HCQ or placebo/standard-of-care for pre-exposure prophylaxis, post-exposure prophylaxis, or outpatient therapy for COVID-19.MethodsTwo investigators independently extracted data on trial design and outcomes. Medication side effects and adverse reactions were also assessed. The primary outcome was COVID-19 hospitalization or death. When unavailable, new COVID-19 infection was used. We calculated random effects meta-analysis according to the method of DerSimonian and Laird. Heterogeneity between the studies was evaluated by calculation of Cochran Q and I2parameters. An Egger funnel plot was drawn to investigate publication bias. We also calculated the fixed effects meta-analysis summary of the five studies. All calculations were done in Excel, and results were considered to be statistically significant at a two-sided threshold of P=.05.ResultsFive randomized controlled clinical trials enrolling 5,577 patients were included. HCQ was associated with a 24% reduction in COVID-19 infection, hospitalization or death, P=.025 (RR, 0.76 [95% CI, 0.59 to 0.97]). No serious adverse cardiac events were reported. The most common side effects were gastrointestinal.ConclusionHydroxychloroquine use in outpatients reduces the incidence of the composite outcome of COVID-19 infection, hospitalization, and death. Serious adverse events were not reported and cardiac arrhythmia was rare.Systematic review registrationThis review was not registered.
Modified Harvard Step Testing within a Clinic Setting Enables Exercise Prescription for Cancer Survivors
Authors: White Katherine R. , Lu Jana , Ibrahim Zara , Furth Priscilla A. 
Published: October 2020

ABSTRACTPurposeTo evaluate the utility of modified Harvard Step tests within the context of a comprehensive physical examination for fitness evaluation and exercise prescription for cancer survivors.MethodsA retrospective chart review of initial cancer survivor clinic visits over a ten-year period (n=169) was conducted to evaluate correlations between demographic factors, clinical characteristics, step and strength test performance, and exercise prescriptions.ResultsClinic population was 94% female, aged 27-79 years, predominantly breast cancer (87%), presenting within two years of cancer diagnosis with current exercise history significantly less vigorous than past exercise (p=0.00; 34% sedentary). Fifty-two percent completed a 3-minute-9-inch step test at pace (96 steps per minute). Fourteen percent required slower self-pacing, 12% both a slower pace and shortened time, and 5% a flat test. Younger age (p=0.04) and more vigorous exercise histories (p<0.04) correlated with ability to complete the at pace test but all formats led to exercise prescriptions more vigorous than current activity (p<0.0002). Stratified fitness ratings using YMCA normative data yielded associations between higher fitness levels and lower BMI (F(1,86)=4.149,p<0.05), office pulse (F(1,87)=7.677,p<0.05), and systolic blood pressure (F(1,18)=6.58,p<0.05).ConclusionsOffice-based fitness evaluation with a panel of modified step test options accommodating different baseline fitness levels enabled personalized exercise prescriptions more vigorous than current activity.Implications for Cancer SurvivorsCancer patients frequently engage in less vigorous activity as they enter into survivorship. Modified step tests are a means for office-based evaluation of cardiovascular fitness within the context of a comprehensive physical examination.
Transgenic pyrimethamine resistantPlasmodium bergheias a model forin vivoanti-DHFR drug testing
Authors: Koonyosying Pongpisid , Jupatanakul Natapong , Vanichtanankul Jarunee , Saeyang Thanaya , Pethrak Chatpong , Pengon Jutharat , Tipsuwan Wachiraporn , Yuthavong Yongyuth , Kamchonwongpaisan Sumalee , Uthaipibull Chairat 
Published: October 2020

AbstractInhibitors forPlasmodium falciparumdihydrofolate reductase (DHFR) form an important class of antimalarial drugs widely used for malaria treatment, but have been compromised by development of resistance to the drugs. Mutations in DHFR are the main contributing factors to the resistance. Although new, rationally designed antifolates active against resistantP. falciparum, such as P218, have been developed, the activity against the quadruple mutantP. falciparum(V1/S) has only been demonstratedin vitro, andin vivoactivity has only been shown in SCID mice. A convenientin vivomodel for antifolate testing is desirable. In this study, the endogenousP. bergheidihydrofolate reductase-thymidylate synthase (Pbdhfr-ts) gene was successfully replaced by quadrupledhfr-tsmutant gene fromP. falciparum(N51I+C59R+S108N+I164L). The transgenic parasite gained resistance to pyrimethamine but not to other class of antimalarial drugs. While 30 mg/kg of pyrimethamine could not inhibit the transgenic parasite, P218 could inhibit the transgenic parasite with the ED50of 0.11±0.02 mg/kg, a level similar to theP. falciparumin SCID mice model. These results demonstrated the validity of our model and showed that P218 was very potent against quadruplePfdhfr-tsmutant parasite,in vivo.
Disturbance Triggers Non-Linear Microbe-Environment Feedbacks
Authors: Sengupta Aditi , Fansler Sarah J. , Chu Rosalie K. , Danczak Robert E. , Garayburu-Caruso Vanessa A. , Renteria Lupita , Song Hyun-Seob , Toyoda Jason , Wells Jacqueline , Stegen James C. 
Published: October 2020

AbstractConceptual frameworks linking microbial community membership, properties, and processes with the environment and emergent function have been proposed but remain untested. Here we refine and test a recent conceptual framework using hyporheic zone sediments exposed to wetting/drying transitions. Throughout the system we found threshold-like responses to the duration of desiccation. Membership of the putatively active community--but not the whole community--responded due to enhanced deterministic selection (an emergent community property). Concurrently, the thermodynamic properties of organic matter became less favorable for oxidation (an environmental component) and respiration decreased (a microbial process). While these responses were step functions of desiccation, we observed continuous monotonic relationships among community assembly, respiration, and organic matter thermodynamics. Placing the results in context of our conceptual framework points to previously unrecognized internal feedbacks that are initiated by disturbance, mediated by thermodynamics, and that cause the impacts of disturbance to be dependent on the history of disturbance.
Combining epiGBS markers with long read transcriptome sequencing to assess differentiation associated with habitat inReynoutria(akaFallopia)
Authors: Robertson Marta , Alvarez Mariano , van Gurp Thomas , Wagemaker Cornelis A. M. , Yu Fahong , Amador David Moraga , Farmerie William G. , Verhoeven Koen J. F. , Richards Christina L. 
Published: October 2020

SummaryDespite the limitations of genetic bottlenecks, several invasive species appear to thrive in non-native ranges with extremely low levels of sequence-based genetic variation. We previously demonstrated differentiation of DNA methylation to habitat types of the highly clonal, genetically depauperate Japanese knotweeds using anonymous markers, but the functional relevance of this DNA methylation variation is unknown. Here, we sequenced the full transcriptome combined with a reduced representation bisulfite sequencing approach, epigenotyping by sequencing (epiGBS), to characterize the association among DNA methylation, functional transcripts and the diverse habitat types occupied by the invasiveReynoutriaspecies. We identified 50,435 putative transcripts overall, of which 48,866 were annotated with the NCBI NR database. Of these 17,872 (35%) and 16,122 (32%) transcripts shared sequence identity withArabidopsis thalianaandBeta vulgaris, respectively. We found genetic differentiation by habitat type suggesting the action of selection and a marginal pattern of differentiation of DNA methylation among habitats, which appears to be associated with sequence differences. However, we found no individual methylation loci associated with habitat, limiting our ability to make functional interpretations. Regardless of the source of variation in DNA methylation, these changes may represent an important component of the response to environmental conditions, particularly in highly clonal plants, but more fine scale genomics analysis is required to test if DNA methylation variation in this system is responsible for functional divergence.
The Role of DOT1L Methyltransferase Activity in Fetal Hematopoiesis
Authors: Malcom Carrie A. , Piaseka-Srader Joanna , Chakravarthi V. Praveen , Borosha Shaon , Ratri Anamika , Alvarez Nehemiah , Vivian Jay L. , Fields Timothy A. , Rumi M.A. Karim , Fields Patrick E. 
Published: October 2020

ABSTRACTEarly mammalian erythropoiesis requires the DOT1L methyltransferase. We demonstrated that loss of DOT1L in mutant mice resulted in lethal anemia during midgestation. The molecular mechanisms by which DOT1L regulates embryonic erythropoiesis have not yet been elucidated. In this study, a methyltransferase mutant mouse line (Dot1L-MM) was generated to determine whether the methyltransferase activity of DOT1L is essential for erythropoiesis.Dot1L-MM mice displayed embryonic lethality between embryonic days 10.5 and 13.5, similar toDot1lLknockout (Dot1L-KO) mice. However, when examined at E10.5, unlike theDot1L-KO,Dot1L-MM embryos did not exhibit evidence of anemia. Inex vivohematopoietic differentiation cultures,Dot1L-KO andDot1L-MM yolk sac (YS) cells both formed reduced numbers of myeloid, and mixed hematopoietic colonies. Erythroid colonies were able to be formed in numbers equal to wildtype embryos. Extensively self-renewing erythroblast (ESRE) cultures were established using YS cells from E10.5 embryos.Dot1L-KO andDot1L-MM cells expanded significantly less than wild-type cells and exhibited increased cell death. Strikingly,Dot1L-KO andDot1L-MM cells of YS origin exhibited profound genomic instability, implicating DOT1L methyltransferase activity in maintenance of the genome as well as viability of hematopoietic progenitors. Our results indicate that the methyltransferase activity of DOT1L plays an important role early murine hematopoiesis.
Estimating the extrinsic incubation period of malaria using a mechanistic model of sporogony
Authors: Stopard Isaac J. , Churcher Thomas S. , Lambert Ben 
Published: October 2020

AbstractDuring sporogony, malaria-causing parasites infect a mosquito, reproduce and migrate to the mosquito salivary glands where they can be transmitted the next time blood-feeding occurs. The time required for sporogony, or extrinsic incubation period (EIP), is a crucial determinant of malaria transmission intensity. The EIP is typically estimated as the time for a given percentile of infected mosquitoes to have salivary gland sporozoites (the infectious parasite life stage). Many mechanisms, however, affect the observed sporozoite prevalence including the human-to-mosquito transmission probability and possibly differences in mosquito mortality according to infection status. To account for these various mechanisms, we present a mechanistic mathematical model (“mSOS”), which explicitly models key processes at the parasite, mosquito and observational scales. Fitting this model to experimental data, we find greater variation in EIP than previously thought: we estimated the range between two percentiles of the distribution, EIP10–EIP90(at 27°C), as 4.5 days, compared to 0.9 days using existing methods. This pattern holds over the range of study temperatures included in the dataset. Increasing temperature from 21°C to 34°C decreased the EIP50from 16.1 to 8.8 days and the human-to-mosquito transmission probability from 84% to 42%. Our work highlights the importance of mechanistic modelling of sporogony to (1) improve estimates of malaria transmission under different environmental conditions or disease control programs and (2) evaluate novel interventions that target the mosquito life stages of the parasite.Author summaryAnophelesmosquitoes become infected with malaria-causing parasites when blood feeding on an infectious human host. The parasites then process through a number of life stages, which begin in the mosquito gut and end in the salivary glands, where the newly formed infectious parasites can be transmitted to another host the next time a mosquito blood-feeds. The large variability in parasite numbers and development times that exists between mosquitoes, environments and parasites, mean that understanding parasite population dynamics from individual mosquito dissections is difficult. Here, we introduce a mathematical model of the mosquito life stages of parasites that mimics key characteristics of the biology. We show that the model’s parameters can be chosen so that its predictions correspond with experimental observations. In doing so, we estimate key system characteristics that are crucial determinants of malaria transmission intensity. Our work is a step towards a realistic model of within-mosquito parasite dynamics, which is increasingly important given that many recently proposed disease interventions specifically target mosquito life stages of the parasite.