bluuebunny/crossref_metadata_2025_split huggingface dataset:
Production and control of a Brazilian tailor-made meningococcal B vaccine
Authors: Jessouroun E , Santos AP , Figueira ES , Correa MB , Leal ML 
Published: August 2021

AbstractMeningococcal disease has been a public health problem in Brazil since the serogroups A and C epidemics occurred in the 1970s. The Oswaldo Cruz Foundation in Brazil has been working to develop a serogroup B meningococcal vaccine composed of detergent-treated outer membrane vesicles (OMV) and detoxified endotoxin (dLOS) from Neisseria meningitidis serogroup B prevalent strains. Experimental vaccine were produced in a pilot-scale under Good Manufacturing Practice condition (GMP). Physicochemical and biological controls were established based on what has been reported previously for OMV vaccines. The developed vaccine contained the main class 1, 2, 3, and 5 proteins, some minor iron-regulated proteins, and 5–10% residual lipopolysaccharide related to total protein content. The dLOS was added, as a vaccine component, in half of the total protein amount. The pyrogenicity of the final products, based on the residual LOS in OMVs, varied from 1.01 to 2.24 ng LOS/kg rabbit. Three experimental vaccines, were highly immunogenic in mice with better performance using higher antigen concentrations.
In vitro reconstitution demonstrates the amyloid-beta mediated myelin membrane deformation
Authors: Tiwari Anuj , Pradhan Sweta , Sannigrahi Achinta , Jha Suman , Chattopadhyay Krishnananda , Biswas Mithun , Saleem Mohammed 
Published: August 2021

ABSTRACTAmyloid-beta (Aβ) aggregation mediated neuronal membrane deformation, although poorly understood, is implicated in Alzheimer’s Disease (AD). Particularly, whether Aβ aggregation can induce neuronal demyelination remains unknown. Here we show that Aβ-40 binds and induces extensive tubulation in the myelin membrane in vitro. The binding of Aβ-40 depends predominantly on the lipid packing defect densities and electrostatic interactions and results in rigidification of the myelin membrane in the early time scales. Furthermore, elongation of Aβ-40 into higher oligomeric and fibrillar species leads to eventual fluidization of the myelin membrane followed by extensive membrane tubulation observed in the late phase. Taken together, our results capture mechanistic insights into snapshots of temporal dynamics of Aβ-40 - myelin membrane interaction and demonstrate how short timescale, local phenomena of binding, and fibril mediated load generation manifests into long timescale, global phenomena of myelin tubulation and demonstrates the ability of Aβ-40 to demyelinate.
Structural transitions in the GTP cap visualized by cryo-EM of catalytically inactive microtubules
Authors: LaFrance Benjamin J , Roostalu Johanna , Henkin Gil , Greber Basil J , Zhang Rui , Normanno Davide , McCollum Chloe , Surrey Thomas , Nogales Eva 
Published: August 2021

AbstractMicrotubules (MTs) are polymers of α/β-tubulin heterodimers that stochastically switch between growth and shrinkage phases. This dynamic instability is critically important for MT function. It is believed that GTP hydrolysis within the MT lattice is accompanied by destabilizing conformational changes, and that MT stability depends on a transiently existing GTP cap at the growing MT end. Here we use cryo-EM and TIRF microscopy of GTP hydrolysis-deficient MTs assembled from mutant recombinant human tubulin to investigate the structure of a GTP-bound MT lattice. We find that the GTP-MT lattice of two mutants in which the catalytically active glutamate in α-tubulin was substituted by inactive amino acids (E254A and E254N) is remarkably plastic. Undecorated E254A and E254N MTs with 13 protofilaments both have an expanded lattice, but display opposite protofilament twists, making these lattices distinct from the compacted lattice of wildtype GDP-MTs. End binding proteins of the EB family have the ability to compact both mutant GTP-lattices and to stabilize a negative twist, suggesting that they promote this transition also in the GTP cap of wildtype MTs, thereby contributing to the maturation of the MT structure. We also find that the MT seam appears to be stabilized in mutant GTP-MTs and destabilized in GDP-MTs, supporting the proposal that the seam plays an important role in MT stability. Together, these first high-resolution structures of truly GTP-bound MTs add mechanistic insight to our understanding of MT dynamic instability.Significance StatementMicrotubules (MTs) are non-equilibrium polymers that switch between states of growth and shrinkage. This property is critical for their function and is a consequence of GTP hydrolysis in the MT. The structure of the stable GTP part of the MT (the GTP cap) has previously been inferred from MTs polymerized with non-hydrolyzable GTP analogs. Here, we report the first high-resolution structures of MTs truly containing GTP, polymerized from mutated, hydrolysis-deficient tubulins. We find that GTP-MTs have an “expanded lattice” and a “closed seam”, structural characteristics possibly responsible for stabilizing the GTP cap. These results provide new insight into the structural transitions at growing MT ends, furthering our understanding of the bistable nature of MTs.
Mapping the genetic landscape of biomineralization in Magnetospirillum magneticum AMB-1 with RB-Tnseq
Authors: McCausland Hayley C. , Wetmore Kelly M. , Arkin Adam P. , Komeili Arash 
Published: August 2021

AbstractMagnetotactic bacteria (MTB) are a phylogenetically diverse group of bacteria remarkable for their ability to biomineralize magnetite (Fe3O4) or greigite (Fe3S4) in organelles called magnetosomes. The majority of genes required for magnetosome formation are encoded by a magnetosome gene island (MAI). Most previous genetic studies in MTB have focused on the MAI, using screens to identify key MAI genes or targeted genetics to isolate specific genes and their function in one specific growth condition. Here, we conducted random barcoded transposon mutagenesis (RB-TnSeq) in Magnetospirillum magneticum AMB-1 to identify the global genetic requirements for magnetosome formation under different growth conditions. We generated a library of 184,710 unique strains in a wild-type background, generating ~34 mutant strains for each gene. RB-TnSeq also allowed us to determine the essential gene set of AMB-1 under standard laboratory growth conditions. To pinpoint novel genes that are important for magnetosome formation, we subjected the library to magnetic selection screens in varied growth conditions. We compared biomineralization in standard growth conditions to biomineralization in high iron and anaerobic conditions, respectively. Strains with transposon insertions in the MAI gene mamT had an exacerbated biomineralization defect under both high iron and anerobic conditions compared to standard conditions, adding to our knowledge of the role of MamT in magnetosome formation. Mutants in amb4151, a gene outside of the MAI, are more magnetic than wild-type cells under anaerobic conditions. All three of these phenotypes were validated by creating a markerless deletion strain of the gene and evaluating with TEM imaging. Overall, our results indicate that growth conditions affect which genes are required for biomineralization and that some MAI genes may have more nuanced functions than was previously understood.
Identification and targeting of G-quadruplex structures inMALAT1long non-coding RNA
Authors: Mou Xi , Liew Shiau Wei , Kwok Chun Kit 
Published: August 2021

ABSTRACTRNA G-quadruplexes (rG4s) have functional roles in many cellular processes in diverse organisms. While a number of rG4 examples have been reported in coding messenger RNAs (mRNA), so far only limited works have studied rG4s in non-coding RNAs (ncRNAs), especially in long non-coding RNAs (lncRNAs) that are of emerging interest and significance in biology. Herein, we report thatMALAT1lncRNA contains conserved rG4 motifs, forming thermostable rG4 structures with parallel topology. We also show that rG4s inMALAT1lncRNA can interact with NONO protein with high specificity and affinityin vitroand in nuclear cell lysate, and we providein vivodata to support that NONO protein recognizesMALAT1lncRNA via rG4 motifs. Notably, we demonstrate that rG4s inMALAT1lncRNA can be targeted by rG4-specific small molecule, peptide, and L-aptamer, leading to the dissociation ofMALAT1rG4-NONO protein interaction. Altogether, this study uncovers new and important rG4s inMALAT1lncRNAs, reveals their specific interactions with NONO protein, offers multiple strategies for targetingMALAT1and its RNA-protein complex via its rG4 structure, and illustrates the prevalence and significance of rG4s in ncRNAs.
Mycorrhizal inoculation and treatment with biochar and compost from pruning waste improve the qualitative properties of a calcareous soil under wheat cultivation
Authors: Vahedi Roghayeh , Rasouli-Sadaghiani MirHassan , Barin Mohsen , Vetukuri Ramesh Raju 
Published: August 2021

AbstractMost calcareous soils have relatively low levels of organic matter. To address this issue and improve the qualitative properties of calcareous soils, soils can be treated with mycorrhizal fungi and/or exogenous organic material such as biochar or compost derived from tree pruning waste. To evaluate the effect of pruning waste biochar (PWB) and pruning waste compost (PWC) derived from apple and grape trees combined with arbuscular mycorrhizal fungi (AMF) on the biological indices of calcareous soils, a rhizobox study on wheat plants using a completely randomized design was conducted under greenhouse conditions. The studied factors included the source of the type of organic material applied (PWB, PWC, and control), the nature of the microbial inoculation (inoculation with AMF or no inoculation), and the zone to which the treatments were applied (rhizosphere and non-rhizosphere soil). At the end of the plant growth period, organic carbon (OC), microbial biomass carbon (MBC), microbial biomass phosphorous (MBP), microbial respiration (BR), substrate-induced respiration (SIR), alkaline (ALP), acid (ACP) phosphatase enzyme activities in the rhizosphere and non-rhizosphere soils, and root mycorrhizal colonization were determined. Simultaneous application of a source of organic matter and AMF inoculation significantly increased the OC and biological indices of soil relative to those observed when applying organic matter without AMF inoculation. Additionally, MBC, MBP, ACP and ALP - enzymes activities in the rhizosphere zone were significantly higher than in the non-rhizosphere. AMF increased BR and SIR levels in the rhizosphere by 13.06% and 7.95% compared to non-rhizosphere, respectively. It can be concluded that in calcareous soils with low organic carbon contents, organic amendments such as PWC and PWB can improve soil biological properties by increasing microbial activity and changing the properties of the rhizosphere.
Target Enrichment Enhances the Sensitivity of Sanger Sequencing for BRAF V600 Mutation Detection
Authors: Gan Qiang , Fu Andrew , Liu Fang , Shen Shuo , Jamba Maidar , Liu Wei , Powell Mike , Zhang Aiguo , Sha Michael 
Published: August 2021

AbstractBRAF is a serine/threonine protein kinase whose mutations lead to unregulated cell growth and cause different types of cancers. Since V600E is a major BRAF mutation and V600E detection as a companion diagnostic test (CDx) is stipulated in the labeling of the BRAF V600 inhibitors. Traditional Sanger sequencing cannot accurately detect mutations lower than 15% variant allele frequency (VAF) due to its limited sensitivity. Here we applied our patented XNA molecular clamping technology to modify Sanger sequencing template preparation by enriching the mutation population. We found that the use of our mutation-enriched template enhanced the analytical sensitivity of Sanger sequencing to 0.04% VAF. The method is verified to detect V600E, V600K, and V600R mutants and is validated for the known BRAF mutation status in clinical samples. Our streamlined protocol can be used for easy validation of the highly sensitive target-enrichment method for detecting BRAF V600 mutations using Sanger sequencing in clinical labs. In addition to BRAF V600 mutations, this method can be extended to the detection of other clinically important actionable mutations for cancer diagnostics.
Host cell amplification of nutritional stress contributes to persistence inChlamydia trachomatis
Authors: Pokorzynski Nick D. , Alla Monisha R. , Carabeo Rey A. 
Published: August 2021

Persistence, a viable but non-replicating growth state, has been implicated in diseases caused byChlamydia trachomatis. Starvation of distinct nutrients produce a superficially similar persistent state, implying convergence on a common intracellular environment. We employed host-pathogen dual RNA-sequencing under both iron- and tryptophan-starved conditions to systematically characterize the persistent chlamydial transcriptome and to define common contributions of the host cell transcriptional stress response in shaping the intracellular environment. The transcriptome of the infected host cells was highly specific to each nutritional stress, despite comparable effects on chlamydial growth and development in each condition. In contrast, the chlamydial transcriptomes between nutritional conditions were highly similar, suggesting some overlap in host cell responses to iron limitation and tryptophan starvation that contribute to a common persistent phenotype. We demonstrate that a commonality in the host cell responses is the suppression of guanosine triphosphate (GTP) biosynthesis, a nucleotide for whichChlamydiaare auxotrophic. Pharmacological inhibition of host inosine monophosphate dehydrogenase (IMPDH1), which catalyzes the rate-limiting step inde novoguanine nucleotide synthesis, resulted in comparable GTP depletion to both iron and tryptophan starvation and induced chlamydial persistence. Moreover, IMPDH1 inhibition and iron starvation acted synergistically to control chlamydial growth. Thus, host cell reduction in GTP levels amplifies the nutritional stress to intracellular chlamydiae in infection-relevant models of persistence, illustrating the determinative role the infected host cell plays in bacterial stress responses.IMPORTANCEBacteria respond to nutritional stress through universal and unique mechanisms. Genome reduction in theChlamydiaceae, a consequence of coevolution with their obligate eukaryotic hosts, has reduced their repertoire of stress response mechanisms. Here we demonstrate that the infected host cell may provide the context within which universal stress responses emerge forChlamydia trachomatis. We report that during starvation of the essential nutrients iron or tryptophan, a common response of the infected epithelial cell is the suppression of GTP biosynthesis, which induces a persistent developmental state in the pathogen. Thus, chlamydial persistence results from the combined effects of primary stresses on the pathogen and the host, with the latter eliciting a secondary host cell response that intensifies the inhospitable intracellular environment.
Corrosion inhibition of aluminium in hydrochloric acid medium using cimetidine as inhibitor: empirical and optimization studies
Authors: Onukwuli Okechukwu Okechukwu , Udeh Benson Chinweuba , Omotioma Monday , Nnanwube Ikechukwu Abuchi 
Published: August 2021

PurposeThe purpose of this study was to investigate cimetidine as corrosion inhibitor of aluminium in hydrochloric acid medium.Design/methodology/approachCimetidine was characterized by gas chromatography mass spectrophotometer and Fourier transform infrared spectroscopy to determine its chemical composition and functional groups, respectively. Gravimetric, potentiodynamic polarization and electrochemical impedance spectroscopic techniques were used in the corrosion inhibition process. Thermodynamic and adsorption parameters were evaluated. And response surface methodology was used to optimize the corrosion inhibition process.FindingsAnalysis of the results revealed that major constituents of cimetidine include metronidazole, n-hexadecanoic acid cyclohexane and methyl ester. It has C-H stretch, C = N stretch, CH3C-H bend, ring C = C stretch, -C-O-O stretch, N-H bend, C-O stretch and C-H bend as predominant functional groups. Adsorption of molecules of the inhibitor on the aluminium surface was spontaneous, and it followed mechanism of physical adsorption. Response surface methodology revealed that quadratic model adequately described the inhibition efficiency of cimetidine as function of inhibitor concentration, temperature and time. Chemical and electrochemical results are in agreement that the cimetidine is a viable corrosion inhibitor. Cimetidine was revealed as mixed-type inhibitor because it controlled both cathodic and anodic reactions.Originality/valueEmpirical and optimization studies of cimetidine drug as corrosion inhibitor of aluminium in hydrochloric acid medium were carried out. The research results can provide the basis for deploying drugs (with mucosal protective and antacid properties) for corrosion control of metallic structures.
Behavioural errors and stock market investment decisions: recent evidence from Pakistan
Authors: Rashid Kashif , Tariq Yasir Bin , Rehman Mamoon Ur 
Published: August 2021

PurposeThis study examines the role of behavioural factors, such as confidence, optimism, pessimism and rational expectation, in affecting investment decisions in the Pakistani stock market.Design/methodology/approachUsing daily trading data of Karachi Stock Exchange-100 index from January 2012 to December 2015, different regression models, including descriptive statistics and stationarity tests, are performed.FindingsResults indicate that stock market trading has suffered from pessimistic behaviour of investors. In the first model, the authors find a positive sign of confidence and negative sign of optimism with the trading volume. The second model shows a positive role of confidence and rational expectations in affecting the trading volume in daily, Monday and Friday samples. The results of the third model show a negative sign of both optimism and rational expectation with the trading volume. Furthermore, the next model shows a negative sign of confidence combined with pessimism while testing their relationship with the trading volume. Finally, results of the final model suggest that optimism negatively affects the trading volume, and on the other hand, pessimism has a positive impact on the trading volume.Research limitations/implicationsThe method and empirical testing of behavioural biases and their relationship with economic variable used in this study seem to be a promising way to better understand the role of psychology in deriving financial decisions for academics and policymakers.Originality/valueThis study uses secondary data for measuring behavioural biases and decomposes the effect between rational expectation and behavioural biases.
Finish your plate! Food disposition behaviour among late adolescents
Authors: Lim Tze-Yin , Lim Bibiana , Leong Choi-Meng , Le Andrea 
Published: August 2021

PurposeThis study explores the disposition behaviour of late adolescents towards unfinished food. Specifically, this paper identifies and discusses the manner (the how's) and the reasons (the why's) of food disposition.Design/methodology/approachThis study adopted a taxonomy of decisions pertaining to consumer disposition processes. A generic qualitative approach based on personal interviews and focus group discussions was used to collect data from late adolescents. Data was subsequently analysed using content and thematic analyses.FindingsThe findings revealed five manners (the how's) of food disposition among late adolescents, namely keeping it for original purposes, leaving it for other people to dispose of, converting it for another purpose, trying to finish it and getting rid of it permanently. Additionally, there are three reasons (the why's) for food disposition among late adolescents, namely food-related factors, socio-cultural factors and personal factors.Originality/valueFood waste has continually impacted food production, supply and consumption in a profound way. Responsible food disposition behaviour among individuals has become essential to improve food sustainability. Proper food disposition requires a behavioural change among individuals, including late adolescents, who are growing into adulthood. This study contributes to the body of knowledge of food systems by identifying how and why food is disposed of among late adolescents during their formative years. The findings can be utilised to raise awareness of food disposition behaviour and design food responsibility initiatives.
Conceptual framework of value management adoption in the Nigerian construction industry
Authors: Ojo Lekan Damilola , Ogunsemi Deji Rufus , Ogunsina Olusola 
Published: August 2021

PurposeThe Nigerian construction industry is bedeviled with poor project performance and outcomes which value management (VM) could address if applied. The application of VM on Nigerian construction projects is very minimal due to certain obstacles, namely, lack of VM experts, paucity of knowledge on the techniques, etc., which inhibits the adoption into the construction industry. Therefore, this study aims to develop a conceptual framework of the adoption of VM on construction projects in a typical developing economy.Design/methodology/approachThis study engaged 15 selected VM experts in two rounds of Delphi survey to develop a conceptual framework of VM adoption. The method of data analysis includes mean score, standard deviation, Kendall’s coefficient of concordance, chi-square (χ2) test, interrater agreement analysis and significant level analysis. The developed conceptual framework was sent to a team of local and international VM experts for validation.FindingsThis study reveals that the adoption of VM requires the collective effort of relevant stakeholders in the construction industry. The framework developed presents individual and collective activities to be undertaken by the stakeholders. The activities include training, legislation, government-funded research, etc. Thus, the adoption of innovative management methodology like VM requires the collaboration of academics, construction professional bodies and government parastatals. This will assist in the judicious use of limited construction resources and boost the relevance of the Nigerian construction industry among developing nations and in the global construction market.Originality/valueThis study used the opinions of few construction professionals that can be regarded as VM experts in Nigeria, as against engaging a pool of construction professionals who may not be knowledgeable in VM process. Engaging the few VM experts in the Nigerian construction industry is important to have a valid basis for drawing conclusion, as large questionnaire survey could be possibly filled by inexperienced or unqualified respondents if stringent criteria are not considered at the outset of this study.