bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of novel HPFH-like mutations by CRISPR base editing that elevates the expression of fetal hemoglobin
Authors: Ravi Nithin Sam , Wienert Beeke , Wyman Stacia K. , Vu Jonathan , Pai Aswin Anand , Balasubramanian Poonkuzhali , Nakamura Yukio , Kurita Ryo , Marepally Srujan , Thangavel Saravanabhavan , Velayudhan Shaji R. , Srivastava Alok , DeWitt Mark A. , Corn Jacob E. , Mohankumar Kumarasamypet M. 
Published: July 2020

ABSTRACTSwitching hemoglobin synthesis from defective adult beta-globin to fetal gamma-globin is an effective strategy for the treatment of beta-hemoglobinopathies. Fetal hemoglobin expression is down-regulated in the postnatal period due to the interplay of transcription regulators with theHBGpromoters. However, in the hereditary persistence of fetal hemoglobin (HPFH) condition, naturally occurring point mutations in theHBGpromoter causes continued expression of fetal globin even during adulthood. Inspired by this natural phenomenon, we screened the proximal promoter of humanHBGgenes using adenine and cytosine base editors to identify other nucleotide substitutions that could potentially lead to elevated levels of fetal globin. Both the base editors efficiently and precisely edited at the target sites with a minimal generation of indels and no deletion of one of the duplicatedHBGgenes. Through systematic tiling acrossthe HBGproximal promoter, we identified multiple novel target sites that resulted in a significant increase in fetal globin levels. Further, we individually validated the top eight potential target sites from both the base editors and observed robust elevation in the fetal globin levels up to 47 %, without any detrimental effects on erythroid differentiation. Our screening strategy resulted in the identification of multiple novel point mutations and also validated the known non-deletional HPFH mutations that could elevate the fetal globin expression at therapeutically relevant levels. Overall, our findings shed light on so far unknown regulatory elements within theHBGpromoter that normally mediates fetal globin silencing and identify additional targets for therapeutic upregulation of fetal hemoglobin.
Generation of stress fibers through myosin-driven re-organization of the actin cortex
Authors: Lehtimäki JI , Rajakylä EK , Tojkander S , Lappalainen P 
Published: July 2020

SummaryContractile actomyosin bundles, stress fibers, govern key cellular processes including migration, adhesion, and mechanosensing. Stress fibers are thus critical for developmental morphogenesis. The most prominent actomyosin bundles, ventral stress fibers, are generated through coalescence of pre-existing stress fiber precursors. However, whether stress fibers can assemble through other mechanisms has remained elusive. We report that stress fibers can also form without requirement of pre-existing actomyosin bundles. These structures, which we named cortical stress fibers, are embedded in the cell cortex and assemble preferentially underneath the nucleus. In this process, non-muscle myosin II pulses orchestrate the reorganization of cortical actin meshwork into regular bundles, which promote reinforcement of nascent focal adhesions, and subsequent stabilization of the cortical stress fibers. These results identify a new mechanism by which stress fibers can be generatedde novofrom the actin cortex, and establish role for stochastic myosin pulses in the assembly of functional actomyosin bundles.
Diversification of the restriction–modification system ofStreptococcus pyogenesthrough its acquisition of mobile elements
Authors: Ota Atsushi , Nishiuchi Yukiko , Nakanishi Noriko , Iijima Yoshio , Iwamoto Tomotada , Osaki Ken , Ogura Yoshitoshi , Toyoda Atsushi , Suzuki Yutaka , Hayashi Tetsuya , Ohge Hiroki , Mori Hirotada , Ato Manabu , Maruyama Fumito 
Published: July 2020

ABSTRACTRestriction–modification (RM) systems are typically regarded as “primitive immune systems” in bacteria. The roles of methylation in gene regulation, segregation, and mismatch repair are increasingly recognized. To analyze methyltransferase (MTase) diversity inStreptococcus pyogenes, we compared the RM system distribution in eight new complete genome sequences obtained here and in the database-deposited complete genome sequences of 51 strains. The MTase gene distribution showed that type I MTases often change DNA sequence specificity via switching target recognition domains between strains. The type II MTases in the included strains fell into two groups: a prophage-dominant one and a CRISPR-dominant one. Some highly variable type II MTases were found in the prophage region, suggesting that MTases acquired from phage DNA can generate methylome diversity. Additionally, to investigate the possible contribution of DNA methylation to phenotype, we compared the methylomes and transcriptomes from the four most closely related strains, the results of which suggest that phage-derived methylases possibly regulate the methylome, and, hence, regulate expression levels inS.pyogenes. Our findings will benefit further experimental work on the relationship between virulence genes and pathogenicity inS.pyogenes.
Decoding spontaneous pain from brain cellular calcium signals using deep learning
Authors: Yoon Heera , Bak Myeong Seong , Kim Seung Ha , Lee Ji Hwan , Chung Geehoon , Kim Sang Jeong , Kim Sun Kwang 
Published: July 2020

AbstractWe developed AI-bRNN (Average training, Individual test-bidirectional Recurrent Neural Network) to decipher spontaneous pain information from brain cellular calcium signals recorded by two-photon imaging in awake, head-fixed mice. The AI-bRNN determines the intensity and time point of spontaneous pain even during the chronic pain period and evaluates the efficacy of analgesics. Furthermore, it could be applied to different cell types and brain areas, and it distinguished between itch and pain, proving its versatility.
The effectiveness of prevention and early detection of tuberculosis in people living with HIV
Authors: Sinitsyn Mikhail , Belilovsky Evgeniy , Bogorodskaya Elena , Borisov Sergey , Kudlay Dmitry , Slogotskaya Liudmila 
Published: July 2020

AbstractBackgroundThe difficult epidemic situation caused by TB/HIV co-infection and, accordingly, the need to strengthen measures for the prevention of tuberculosis among HIV patients, identified the need to create a model of collaborating tuberculosis management facilities and AIDS centers.Study purposeanalysis of the effectiveness of measures used in Moscow to prevent the spread of HIV/tuberculosis co-infection based on the developed new algorithm.Materials and methodsThe design of the study – a full-design retrospective cohort study of all HIV patients in tuberculosis preventive care and early detection unit for HIV patients (PCED TB Unit), which was organized in 2014 as a subdivision of Moscow TB Center on the premises of the Moscow AIDS Center. The study was conducted from 2014 to 2017. 22,190 HIV-infected patients were examined. In order to detect tuberculosis infection, all HIV patients were referred for skin testing with preparation Diaskintest, which represents recombinant proteins CFP10-ESAT6 and persons with a positive and doubtful reaction were examined for the diagnosis of tuberculosis and latent tuberculosis infection (LTBI). Preventive therapy (PT) was prescribed to patients with LTBI, which was also received by those with CD4+count ≤350 cells/mm3, regardless of the results of a skin test.ResultsOver a period of 4 years, Diaskintest was performed in 19,777 people. Positive results were in 857 patients (4.3%) [95% CI 4.1-4.6]. 131 patients were diagnosed with tuberculosis, the rest - with LTBI. The effectiveness of PT was estimated by the number of TB cases detected among HIV patients who completed PT (1757) and those who did not receive it (5990). The notification rate of TB in the first group was 228 [95%CI 65-582] per 100,000 patients, in the second 1486 [95%CI 1195–1825], which is 6,5 times higher. To assess the effectiveness of early detection of TB, the proportion of severity forms of pulmonary TB diagnosed in 87 patients at the PCED TB Unit using a new algorithm in 2016-2017 were compared with 411patients detected in different medical organizations of Moscow using conventional methods. The proportion of disseminated TB was lower in the first group (23.0% versus 44.5%) (p<0.01).ConclusionThe study showed that the integration of the two services allows increases the accessibility of TB care and makes a significant contribution to improving the effectiveness of measures to prevent the TB spread among HIV patients. It supports the necessity of treating LTBI detected using the Diaskintest to prevent TB in HIV-infected patients. Significant effects that have been achieved include a reduction in the TB notification rate among HIV patients, improvement of the diagnostic structure of registered TB cases as a result of their timely detection.
Colonization of the murine oropharynx byStreptococcus pyogenesis governed by the Rgg2/3 quorum sensing system
Authors: Gogos Artemis , Federle Michael J. 
Published: July 2020

AbstractStreptococcus pyogenesis a human-restricted pathogen most often found in the human nasopharynx. Multiple bacterial factors are known to contribute to persistent colonization of this niche, and many are important in mucosal immunity and vaccine development. In this work, mice were infected intranasally with transcriptional regulator mutants of the Rgg2/3 quorum sensing (QS) system—a peptide-based signaling system conserved in sequenced isolates ofS. pyogenes. Deletion of the QS system’s transcriptional activator (Δrgg2) dramatically diminished the percentage of colonized mice while deletion of the transcriptional repressor (Δrgg3) increased the percentage of colonized mice compared to wild type. Stimulation of the QS system using synthetic pheromones prior to inoculation did not significantly increase the percentage of animals colonized, indicating that QS-dependent colonization is responsive to the intrinsic conditions within the host upper respiratory tract. Bacterial RNA extracted directly from oropharyngeal swabs and evaluated by quantitative RT-PCR subsequently confirmed QS upregulation within one hour of inoculation. In the nasal-associated lymphoid tissue (NALT), a muted inflammatory response to the Δrgg2bacteria suggests that their rapid elimination failed to elicit the previously characterized response to intranasal inoculation of GAS. This work identifies a new transcriptional regulatory system governing the ability ofS. pyogenesto colonize the nasopharynx and provides knowledge that could help lead to decolonization therapeutics.Author SummaryStreptococcus pyogenesis responsible for a wide spectrum of diseases ranging from common pharyngitis to infrequent invasive infections like necrotizing fasciitis. The ability of this microorganism to persist in the human oropharynx predisposes colonized individuals to a variety of superficial and invasive diseases which lead to significant morbidities and mortality. Identification of the regulatory systems that augment the bacteria’s ability to colonize the oropharynx provides potential targets against which molecular therapeutics can be designed. Here we show that the Rgg2/3 quorum sensing system, an interbacterial communication system, governs the ability ofS. pyogenesto colonize the murine oropharynx. Disruption of the system’s transcriptional activator reduced colonization dramatically, eliminated the transcription of two sets of genes known to be activated by the Rgg2/3 system, and tempered the innate immune response seen whenS. pyogenesis intranasally infected into the mouse.
Progression of the late-stage divisome is unaffected by the depletion of the cytoplasmic FtsZ pool
Authors: Silber Nadine , Mayer Christian , de Opitz Cruz L Matos , Sass Peter 
Published: July 2020

AbstractCell division is a central and essential process in most bacteria, and also due to its complexity and highly coordinated nature, it has emerged as a promising new antibiotic target pathway in recent years. We have previously shown that ADEP antibiotics preferably induce the degradation of the major cell division protein FtsZ, thereby primarily leading to a depletion of the cytoplasmic FtsZ pool that is needed for treadmilling FtsZ rings. To further investigate the physiological consequences of ADEP treatment, we here studied the effect of ADEP on the different stages of the FtsZ ring in rod-shaped bacteria. Our data reveal the disintegration of early FtsZ rings during ADEP treatment inBacillus subtilis, indicating an essential role of the cytoplasmic FtsZ pool and thus FtsZ ring dynamics during initiation and maturation of the divisome. However, progressed FtsZ rings finalized cytokinesis once the septal peptidoglycan synthase PBP2b, a late stage cell division protein, colocalized at the division site, thus implying that the concentration of the cytoplasmic FtsZ pool and FtsZ ring dynamics are less critical during the late stages of divisome assembly and progression.
The effect of delayed processing on ovarian tissue stored for fertility preservation
Authors: Zemyarska M S , Bjarkadottir B D , Wei X , Walker C A , Lane S M , Davies J , Williams S A 
Published: July 2020

AbstractBackgroundOvarian tissue cryopreservation (OTC) is important for fertility preservation and conservation. Delay in OTC may be required for transport or workflow management, however little is understood about the effect of processing delay on the tissue.ObjectiveTo determine whether a delay of 24-48 hours to OTC affects primordial follicle (PF) health.MethodsOvaries (n=6 sheep) were processed immediately or after storage at 4°C (24h, 48h). Tissue was fixed fresh, after cryopreservation or 10-day xenotransplantation. Morphological assessment of follicle health and development was performed.FindingsA total of 1541 follicles were analysed. A 24h processing delay did not impact PF health in fresh or cryopreserved tissue. In fresh tissue a 48h delay had an adverse effect on follicle health (OR=2.47, 95% CI 1.29-4.71). Interestingly, a 48h delay resulted in cryopreserved tissue being less likely to be graded as unhealthy compared to control (OR=0.56, 95% CI 0.36-0.87). There was no difference in PF health or development across groups following xenotransplantation.ConclusionOvarian tissue can be stored for up to 48 hours prior to cryopreservation with no net impact on PF health.
Multidrug-Resistant Avian PathogenicEscherichia coliStrains and Association of Their Virulence Genes in Bangladesh
Authors: Saha Otun , Hoque M. Nazmul , Islam Ovinu Kibria , Rahaman Md. Mizanur , Sultana Munawar , Hossain M. Anwar 
Published: July 2020

AbstractThe avian pathogenicEscherichia coli(APEC) strains are the chief etiology of avian colibacillosis worldwide. The present study investigated the circulating phylotypes, existence of virulence genes (VGs) and antimicrobial resistance (AMR) in 392 APEC isolates, obtained from 130 samples belonged to six farms using both phenotypic and PCR-based molecular approaches. Congo red binding (CRB) assay confirmed 174 APEC isolates which were segregated into 10, 9 and 8 distinctive genotypes by RAPD assay (discriminatory index, D=0.8707), BOX-PCR (D=0.8591) and ERIC-PCR (D=0.8371), respectively. The combination of three phylogenetic markers (chuA, yjaAand DNA fragment TspE4.C2) classified APEC isolates into B23(37.36%), A1 (33.91%), D2 (11.49%), B22(9.20%) and B1 (8.05%) phylotypes. Majority of the APEC isolates (75-100%) harbored VGs (ial, fimH,crl, papC andcjrC), and of them, VGs (papC andcjrC) and phylotypes (D2 and B2) of APEC had significant (p=0.004) association with colibacillosis. Phylogenetic analysis showed two distinct clades (Clade A and Clade B) of APEC where Clade A had 98-100.0% similarity withE. coliAPEC O78 andE. coliEHEC strains, and Clade B had closest relationship withE. coliO169:H41 strain. Interestingly, phylogroups B2 and D2 were found in the APEC strains of both clades while the strains from phylogroups A1 and B1 were found in clade A only. In this study, 81.71% of the isolates were biofilm formers and possessed plasmids of varying ranges (1.0 to 54 kb).In vitroantibiogram profiling revealed that 100.0% isolates were resistant to ≥3 antibiotics, of which61.96%, 55.24, 53.85, 51.16 and 45.58 % isolates in phylotypes B1, D2, B22, B23and A1, respectively were these antimicrobials. The resistance patterns varied among different phylotypes, notably in phylotype B22showing the highest resistance to ampicillin (90.91%), nalidixic acid (90.11%), tetracycline (83.72%) and nitrofurantoin (65.12%). Correspondence analysis also showed significant correlation of phylotypes with CRB (p=0.008), biofilm formation (p=0.02), drug resistance (p=0.03) and VGs (p=0.06). This report demonstrated that B2 and A1 phylotypes are dominantly circulating APEC phylotypes in Bangladesh; however, B2 and D2 are strongly associated with the pathogenicity. A high prevalence of antibiotic resistant APEC strains from different phylotypes suggest to use of organic antimicrobial compounds, and/or metals, and the rotational use of antibiotics in the poultry farms in Bangladesh.
A High Content Screen for Mucin-1-Reducing Compounds Identifies Fostamatinib as a Candidate for Rapid Repurposing for Acute Lung Injury during the COVID-19 pandemic
Authors: Alimova Maria , Sidhom Eriene-Heidi , Satyam Abhigyan , Dvela-Levitt Moran , Melanson Michelle , Chamberlain Brian T. , Alper Seth L. , Santos Jean , Gutierrez Juan , Subramanian Ayshwarya , Grinkevich Elizabeth , Bricio Estefania Reyes , Kim Choah , Clark Abbe , Watts Andrew , Thompson Rebecca , Marshall Jamie , Pablo Juan Lorenzo , Coraor Juliana , Roignot Julie , Vernon Katherine A. , Keller Keith , Campbell Alissa , Emani Maheswarareddy , Racette Matthew , Bazua-Valenti Silvana , Padovano Valeria , Weins Astrid , McAdoo Stephen P. , Tam Frederick W.K. , Ronco Lucienne , Wagner Florence , Tsokos George C. , Shaw Jillian L. , Greka Anna 
Published: July 2020

SummaryDrug repurposing is the only method capable of delivering treatments on the shortened time-scale required for patients afflicted with lung disease arising from SARS-CoV-2 infection. Mucin-1 (MUC1), a membrane-bound molecule expressed on the apical surfaces of most mucosal epithelial cells, is a biochemical marker whose elevated levels predict the development of acute lung injury (ALI) and respiratory distress syndrome (ARDS), and correlate with poor clinical outcomes. In response to the pandemic spread of SARS-CoV-2, we took advantage of a high content screen of 3,713 compounds at different stages of clinical development to identify FDA-approved compounds that reduce MUC1 protein abundance. Our screen identified Fostamatinib (R788), an inhibitor of spleen tyrosine kinase (SYK) approved for the treatment of chronic immune thrombocytopenia, as a repurposing candidate for the treatment of ALI.In vivo, Fostamatinib reduced MUC1 abundance in lung epithelial cells in a mouse model of ALI.In vitro, SYK inhibition by Fostamatinib promoted MUC1 removal from the cell surface. Our work reveals Fostamatinib as a repurposing drug candidate for ALI and provides the rationale for rapidly standing up clinical trials to test Fostamatinib efficacy in patients with COVID-19 lung injury.
Reconstitution of contractile actomyosin rings in vesicles
Authors: Litschel Thomas , Kelley Charlotte F. , Holz Danielle , Koudehi Maral Adeli , Vogel Sven Kenjiro , Burbaum Laura , Mizuno Naoko , Vavylonis Dimitrios , Schwille Petra 
Published: July 2020

AbstractOne of the grand challenges of bottom-up synthetic biology is the development of minimal machineries for cell division. The mechanical transformation of large-scale compartments, such as Giant Unilamellar Vesicles (GUVs), requires the geometry-specific coordination of active elements, several orders of magnitude larger than the molecular scale. Of all cytoskeletal structures, large-scale actomyosin rings appear to be the most promising cellular elements to accomplish this task. Here, we have adopted advanced encapsulation methods to study bundled actin filaments in GUVs and compare our results with theoretical modeling. By changing few key parameters, actin polymerization can be differentiated to resemble various types of networks in living cells. Importantly, we find membrane binding to be crucial for the robust condensation into a single actin ring in spherical vesicles, as predicted by theoretical considerations. Upon force generation by ATP-driven myosin motors, these ring-like actin structures contract and locally constrict the vesicle, forming furrow-like deformations. On the other hand, cortex-like actin networks are shown to induce and stabilize deformations from spherical shapes.
Saccharomycesspores are born prepolarized to outgrow away from spore-spore connections and penetrate the ascus wall
Authors: Heasley Lydia R. , Singer Emily , McMurray Michael A. 
Published: July 2020

1.AbstractHow non-spore haploidSaccharomycescells choose sites of budding and polarize towards pheromone signals in order to mate has been a subject of intense study. Unlike non-spore haploids, sibling spores produced via meiosis and sporulation by a diploid cell are physically interconnected and encased in a sac derived from the old cell wall of the diploid, called the ascus. Non-spore haploids bud adjacent to previous sites of budding, relying on stable cortical landmarks laid down during prior divisions, but since spore membranes are made de novo it was assumed that, as is known for fission yeast,Saccharomycesspores break symmetry and polarize at random locations. Here we show that this assumption is incorrect:Saccharomyces cerevisiaespores are born prepolarized to outgrow, prior to budding or mating, away from interspore bridges. Consequently, when spores bud within an intact ascus, their buds locally penetrate the ascus wall, and when they mate, the resulting zygotes adopt a unique morphology reflective of re-polarization towards pheromone, which we dub the derrière. Long-lived cortical foci containing the septin Cdc10 mark polarity sites, but the canonical bud site selection program is dispensable for spore polarity, thus the origin and molecular composition of these landmarks remain unknown. These findings demand further investigation of previously overlooked mechanisms of polarity establishment and local cell wall digestion, and highlight how a key step in theSaccharomyceslife cycle has been historically neglected.
Exploring attitudes of medical students towards intellectual disabilities
Authors: Abdi Rubab , Metcalf Elizabeth 
Published: July 2020

PurposeThis paper aims to determine whether an inclusive teaching session changes student attitudes towards people with intellectual disabilities (ID). To investigate the impact of an inclusive teaching session in terms of student perceptions.Design/methodology/approach66 years 4 students at Cardiff University completed the attitudes towards disabled people form B questionnaire (ATDP-B) before and after a communication skills session on ID. Before and after scores were collated and compared using a pairedt-test analysis. Common perceptions were identified using anonymised ATDP-B results to conduct five semi-structured interviews and one focus group with nine students. The common perceptions were discussed, alongside how the teaching session tackled them and suggestions for further improvements.FindingsMean ATDP-B score before the teaching session was 115 (SD = 14.5). Mean ATDP-B score after the teaching session was 122 (SD = 17.2). The teaching session improved scores in the ATDP-B by a mean of 6.92 (4.69, 9.16). A pairedt-test found this to be a statistically significant difference, t(65) = 6.20, p < 0.001. Qualitative data was thematically analysed and three main themes were identified: Student identity, patient contact and curriculum content.Originality/valueThis is the first study to investigate the origin of the negative attitudes of medical students, and found they stem from a lack of confidence in their abilities and failure to develop a professional identity. The impact of the teaching session stems from its focus on meaningful patient contact and identifying and overcoming communication barriers.