bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequencing of SARS CoV2 in local transmission cases through oxford nanopore MinION platform from Karachi Pakistan
Authors: Mukry Samina Naz , Ahmed Shariq , Raza Ali , Shahni Aneeta , Sufaida Gul , Naz Arshi , Shamsi Tahir Sultan 
Published: January 2021

AbstractThe first case of severe acute respiratory syndrome 2 (SARS CoV2) was imported to Pakistan in February 2020 since then 10,258 deaths have been witnessed. The virus has been mutating and local transmission cases from different countries vary due to host dependent viral adaptation. Many distinct clusters of variant SARS CoV2 have been defined globally. In this study, the epidemiology of SARS CoV2 was studied and locally transmitted SARS CoV2 isolates from Karachi were sequenced to compared and identify any possible variants.The real time PCR was performed on nasopharyngeal specimen to confirm SARSCoV2 with Orf 1ab and E gene as targets. The viral sequencing was performed through oxford nanopore technology MinION platform. Isolates from first and second wave of COVID-19 outbreak in Karachi were compared. The overall positivity rate for PCR was 26.24% with highest number of positive cases in June. Approximately, 37.45% PCR positive subjects aged between 19-40 years. All the isolates belonged to GH clade and shared missense mutation D614G in spike protein linked to increased transmission rate worldwide. Another spike protein mutation A222V coexisted with D614G in the virus from second wave of COVID-19. Based on the present findings it is suggested that the locally transmitted virus from Karachi vary from those reported from other parts of Pakistan. Slight variability was also observed between viruses from first and second wave. Variability in any potential vaccine target may result in failed trials therefore information on any local viral variants is always useful for effective vaccine design and/or selection.Author’s summaryDespite precautionary measures the COVID-19 pandemic is causing deaths all over the world. The continuous mutations in viral genome is making it difficult to design vaccines. Variability in genome is host dependent and data sharing has revealed that variant for different geographical locations may harbor different mutations. Keeping this in mind the current study was focused on the epidemiology of SARS CoV2 in symptomatic and asymptomatic COVID –19 suspected cases with impact of age and gender. The locally transmitted SARS CoV2 isolates from Karachi were sequenced to compared and identify any possible variants. The sequenced viral genome varied from the already submitted sequences from Pakistan thereby confirming that slightly different viruses were causing infections during different time periods in Karachi. All belonged to GH clade with D614G, P323L and Q57H mutations. The virus from second wave had A222V mutation making it more different. This information can be useful in selecting or designing a vaccine.
Overexpression of a G-protein coupled receptor-like gene affects encystment ofAcanthamoeba castellanii
Authors: Rolland Steven , Mercier Anne , Mengue Luce , Héchard Yann , Samba-Louaka Ascel 
Published: January 2021

AbstractAcanthamoeba castellaniiis an amphizoïc free-living amoeba as it can be found in humans and in the environment. This amoeba represents an important reservoir of pathogenic microorganisms. Persistence ofA. castellaniiin the environment or in humans is allowed by the ability of the vegetative form to differentiate under cysts when surrounding conditions are unfavorable. In this study, we investigate the role of theACA1_383450gene during encystment ofA. castellanii.This gene encodes a putative G-protein coupled receptor, which shares homology with human GPR107 and murine GPR108. Expression of theACA1_383450gene is transiently repressed at the early phase of encystment and its overexpression affects encystment ofA. castellanii.This study reveals a newAcanthamoebagene which could affect the encystment process.HighlightsTheACA1_383450gene encodes for a putative G-protein coupled receptor (GPCR).TheACA1_383450mRNA levels are down-regulated during the early phase of encystment.Overexpression of theACA1_383450gene affects formation of cysts.
Immunoinformatic based analytics on T-cell epitope from spike protein of SARS-CoV-2 concerning Indian population
Authors: Devi Sreevidya S. , Dwivedi Manish 
Published: January 2021

AbstractThe whole world is drastically affected by the current pandemic due to severe virus, SARS-CoV-2 and scientists are rigorously looking for the efficient vaccine against it that become an emergent issue. Reverse vaccinology approach may provide us with significant therapeutic leads in this direction and further determination of T-cell / B-cell response to antigen. In the present study, we conducted population coverage analysis referring to the diverse Indian population. By using tools from Immune epitope database (IEDB), HLA- distribution analysis was performed to find the most promiscuous T-cell epitope out ofIn silicodetermined epitope of Spike protein from SARS-CoV-2. Selection of these epitopes have been conducted based on their binding affinity with the maximum number of HLA alleles belong to the highest population coverage rate values for the chosen geographical area in India. 404 cleavage sites within the 1288 amino acids sequence of spike glycoprotein were determined by NetChop proteasomal cleavage prediction suggesting that this protein has adequate sites in the protein sequence for cleaving into appropriate epitopes. For population coverage analysis, 221 selected epitopes are considered that shows the projected population coverage as 83.08% with 19.29 average hit (average number of epitope hits/HLA combinations recognized by the population) and 5.91 pc90 (minimum number of epitope hits/HLA combinations recognized by 90% of the population). 54 epitopes are found with the highest coverage among the Indian population and highly conserved within the given spike RBD domain sequence. Docking analysis of each epitope with their respective allele suggests that the epitope NSFTRGVYY represents highest binding affinity with docking score -7.6 kcal/mol with its allele HLA-C*07:01 among all the epitopes. Since the Covid-19 cases are still in progress and seem to remain like this until we find an effective vaccine, moreover in countries like India, vast diversity in the population may present a hindrance to particular vaccine efficiency. Outcomes from this study could be critical to design vaccine against SARS-CoV-2 for a different set of the population within the country.
Differential serotonin uptake mechanisms at the human maternal-fetal interface
Authors: Baković Petra , Kesić Maja , Horvatiček Marina , George Meekha , Perić Maja , Bečeheli Ivona , Čičin-Šain Lipa , Desoye Gernot , Wadsack Christian , Panzenboeck Ute , Štefulj Jasminka 
Published: January 2021

ABSTRACTMechanisms regulating serotonin (5-HT) homeostasis at the maternal-fetal interface are important for proper placental functioning and fetal (neuro)development. Here we studied 5-HT uptake mechanisms in human primary trophoblasts, feto-placental endothelial cells and cord blood platelets, all isolated directly after birth. Trophoblasts and cord blood platelets demonstrated high-affinity 5-HT uptake with similar Michaelis constant (Km) values (0.60±0.27 and 0.65±0.18 μM, respectively). In contrast, feto-placental endothelial cells displayed saturation kinetics only over the low-affinity range of 5-HT concentrations (Km=782±218 μM). 5-HT uptake into trophoblasts was inhibited by various psychotropic drugs targeting high-affinity serotonin transporter (SERT), and into feto-placental endothelial cells by an inhibitor of low-affinity transporters.SERTmRNAs were abundant in trophoblasts, but sparse in feto-placental endothelial cells; the opposite was found for transcripts of the low-affinity plasma membrane monoamine transporter (PMAT). These results show for the first time the presence of functional 5-HT uptake systems in feto-placental endothelial cells and fetal platelets, cells in direct contact with the fetal blood plasma. Data also emphasize sensitivity of 5-HT transport into trophoblasts, cells facing maternal blood, to various psychotropic drugs. The multiple, high- and low-affinity, systems present for cellular 5-HT uptake highlight the importance of maintaining 5-HT homeostasis at the maternal-fetal interface.
Protection against reinfection with D614- or G614-SARS-CoV-2 isolates in hamsters
Authors: Brustolin Marco , Rodon Jordi , de la Concepción María Luisa Rodríguez , Ávila-Nieto Carlos , Cantero Guillermo , Pérez Mónica , Te Nigeer , Noguera-Julián Marc , Guallar Víctor , Valencia Alfonso , Roca Núria , Izquierdo-Useros Nuria , Blanco Julià , Clotet Bonaventura , Bensaid Albert , Carrillo Jorge , Vergara-Alert Júlia , Segalés Joaquim 
Published: January 2021

AbstractReinfections with SARS-CoV-2 have already been documented in humans, although its real incidence is currently unknown. Besides having great impact on public health, this phenomenon raises the question if immunity generated by a single infection is sufficient to provide sterilizing/protective immunity to a subsequent SARS-CoV-2 re-exposure. The Golden Syrian hamster is a manageable animal model to explore immunological mechanisms able to counteract COVID-19, as it recapitulates pathological aspects of mild to moderately affected patients. Here, we report that SARS-CoV-2-inoculated hamsters resolve infection in the upper and lower respiratory tracts within seven days upon inoculation with the Cat01 (G614) SARS-CoV-2 isolate. Three weeks after primary challenge, and despite high titers of neutralizing antibodies, half of the animals were susceptible to reinfection by both identical (Cat01, G614) and variant (WA/1, D614) SARS-CoV-2 isolates. However, upon re-inoculation, only nasal tissues were transiently infected with much lower viral replication than those observed after the first inoculation. These data indicate that a primary SARS-CoV-2 infection is not sufficient to elicit a sterilizing immunity in hamster models but protects against lung disease.
Synchronous brain dynamics establish brief states of communality in distant neuronal populations
Authors: Seeber Martin , Michel Christoph M. 
Published: January 2021

AbstractIntrinsic brain dynamics co-fluctuate between distant regions in an organized manner during rest, establishing large-scale functional networks. We investigate these brain dynamics on a millisecond time scale by focusing on Electroencephalographic (EEG) source analyses. While synchrony is thought of as a neuronal mechanism grouping distant neuronal populations into assemblies, the relevance of simultaneous zero-lag synchronization between brain areas in humans remains largely unexplored. This negligence is due to the confound of volume conduction, leading inherently to temporal dependencies of source estimates derived from scalp EEG (and Magnetoencephalography, MEG), referred to as spatial leakage. Here, we focus on the analyses of simultaneous, i.e., quasi zero-lag related, synchronization that cannot be explained by spatial leakage phenomenon. In eighteen subjects during rest with eyes closed, we provide evidence that first, simultaneous synchronization is present between distant brain areas and second, that this long-range synchronization is occurring in brief epochs, i.e., 54-80 milliseconds. Simultaneous synchronization might signify the functional convergence of remote neuronal populations. Given the simultaneity of distant regions, these synchronization patterns might relate to the representation and maintenance, rather than processing of information. This long-range synchronization is briefly stable, not persistently, indicating flexible spatial reconfiguration pertaining to the establishment of particular, re-occurring states. Taken together, we suggest that the balance between temporal stability and spatial flexibility of long-range, simultaneous synchronization patterns is characteristic of the dynamic coordination of large-scale functional brain networks. As such, quasi zero-phase related EEG source fluctuations are physiologically meaningful if spatial leakage is considered appropriately.SignificanceSynchrony is suggested as a mechanism for coordinating distant neuronal populations. Yet, simultaneous (i.e., zero-lag) synchronization between remote brain regions in humans is difficult to demonstrate, because volume conduction in EEG/MEG recordings causes spurious zero-lag relations. Here, we investigate actual zero-lag relations and systematically compare them to the residual bias due to spatial smoothness of EEG source estimates. We indeed report simultaneous synchronization between distant brain regions. These synchronization patterns manifest variably in time. We suggest that simultaneous synchronization is relevant when studying the dynamic, large-scale functional architecture in humans.
Isolation of theBuchnera aphidicolaflagellum basal body from theBuchneramembrane
Authors: Schepers Matthew J. , Yelland James N. , Moran Nancy A. , Taylor David W. 
Published: January 2021

AbstractBuchnera aphidicolais an intracellular bacterial symbiont of aphids and maintains a small genome of only 600 kbps.Buchnerais thought to maintain only genes relevant to the symbiosis with its aphid host. Curiously, theBuchneragenome contains gene clusters coding for flagellum basal body structural proteins and for flagellum type III export machinery. These structures have been shown to be highly expressed and present in large numbers onBuchneracells. No recognizable pathogenicity factors or secreted proteins have been identified in theBuchneragenome, and the relevance of this protein complex to the symbiosis is unknown. Here, we show isolation ofBuchneraflagella from the cellular membrane ofBuchnera, confirming the enrichment of flagellum proteins relative to other proteins in theBuchneraproteome. This will facilitate studies of the structure and function of theBuchneraflagellum structure, and its role in this model symbiosis.
Ataxin-2 is essential for cytoskeletal dynamics and neurodevelopment in Drosophila
Authors: del Castillo Urko , Norkett Rosalind , Lu Wen , Serpinskaya Anna , Gelfand Vladimir I. 
Published: January 2021

SummaryAtaxin-2 (Atx2) is a highly conserved RNA binding protein. Atx2 undergoes polyglutamine expansion leading to Amyotrophic Lateral Sclerosis (ALS) or Spinocerebellar Ataxia type 2 (SCA2). However, the physiological functions of Atx2 in neurons remain unknown. Here, using the powerful genetics of Drosophila, we show that Atx2 is essential for normal neuronal cytoskeletal dynamics and organelle trafficking. Upon neuron-specific Atx2 loss, the microtubule and actin networks were abnormally stabilized and cargo transport was drastically inhibited. Depletion of Atx2 caused multiple morphological defects in the nervous system of 3rd instar larvae. These include reduced brain size, impaired optic lobe innervation and decreased dendrite outgrowth. Defects in the nervous system caused loss of the ability to crawl and lethality at the pupal stage. Taken together, these data mark Atx2 as a major regulator of cytoskeletal dynamics and denote Atx2 as an essential gene in neurodevelopment, as well as a neurodegenerative factor.
A simpleAgrobacterium-mediated stable transformation technique for the hornwort modelAnthoceros agrestis
Authors: Frangedakis Eftychios , Waller Manuel , Nishiyama Tomoaki , Tsukaya Hirokazu , Xu Xia , Yue Yuling , Tjahjadi Michelle , Gunadi Andika , Van Eck Joyce , Li Fay-Wei , Szövényi Péter , Sakakibara Keiko 
Published: January 2021

AbstractWe have developed a simpleAgrobacterium-mediatedmethod for the stable transformation of the hornwortAnthoceros agrestis, the fifth bryophyte species for which a genetic manipulation technique becomes available. High transformation efficiency was achieved by using thallus tissue grown under low-light conditions. We generated a total of 216 transgenicA. agrestislines expressing the β-Glucuronidase (GUS), cyan, green, and yellow fluorescent proteins under the control of the CaMV 35S promoter and several endogenous promoters. Nuclear and plasma membrane localization with multiple color fluorescent proteins was also confirmed. The transformation technique described here should pave the way for detailed molecular and genetic studies of hornwort biology, providing much needed insight into the molecular mechanisms underlying symbiosis, carbon-concentrating mechanism, RNA editing, and land plant evolution in general.
An endosome-associated actin network involved in directed apical plasma membrane growth
Authors: Rios-Barrera LD , Leptin M 
Published: January 2021

AbstractThe subcellular membrane-trafficking system plays many roles in cell growth and morphogenesis, from bulk membrane provision to targeted delivery of membrane proteins and other cargos. In tracheal terminal cells of the Drosophila respiratory system, endocytosis and trafficking through late endosomes balances membrane delivery between the basal plasma membrane and the apical membrane that forms a subcellular tube, but it has been unclear how the direction of growth of the subcellular tube with the overall growth of the cell is coordinated. We show here that endosomes are involved in this process as coordinators of F-actin. Actin assembles around late endocytic vesicles in the growth cone of the cell, reaching from the tip of the subcellular tube to the leading filopodia of the basal membrane. Preventing actin nucleation at late endosomes disturbs the directionality of tube growth, uncoupling it from the direction of cell elongation. Severing actin in this area affects tube integrity. Our findings show a new role for late endosomes in directing cell morphogenesis by organizing actin, in addition to their known role in membrane and protein trafficking.
A non-adaptive demographic mechanism for genome expansion inStreptomyces
Authors: Choudoir Mallory J , Järvenpää Marko J , Marttinen Pekka , Buckley Daniel H 
Published: January 2021

AbstractThe evolution of microbial genome size is driven by gene acquisition and loss events that occur at scales from individual genomes to entire pangenomes. The equilibrium between gene gain and loss is shaped by evolutionary forces, including selection and drift, which are in turn influenced by population demographics. There is a well-known bias towards deletion in microbial genomes, which promotes genome streamlining. Less well described are mechanisms that promote genome expansion, giving rise to the many microbes, such asStreptomyces, that have unusually large genomes. We find evidence of genome expansion inStreptomycessister-taxa, and we hypothesize that a recent demographic range expansion drove increases in genome size through a non-adaptive mechanism. TheseStreptomycessister-taxa, NDR (northern-derived) and SDR (southern-derived), represent recently diverged lineages that occupy distinct geographic ranges. Relative to SDR genomes, NDR genomes are larger, have more genes, and their genomes are enriched in intermediate frequency genes. We also find evidence of relaxed selection in NDR genomes relative to SDR genomes. We hypothesize that geographic range expansion, coupled with relaxed selection, facilitated the introgression of non-adaptive horizontally acquired genes, which accumulated at intermediate frequencies through a mechanism known as genome surfing. We show that similar patterns of pangenome structure and genome expansion occur in a simulation that models the effects of population expansion on genome dynamics. We show that non-adaptive evolutionary phenomena can explain expansion of microbial genome size, and suggest that this mechanism might explain why some bacteria with large genomes can be found in soil.
Potential possibility of using the DNA regions of the internal transcribed spacer ITS and the beta-tubulin gene TUB in the diagnosis of the pathogenMycosphaerella linicolaNaumov
Authors: Shchukovskaya A. , Skripka O. , Uvarova D. , Shipulin A. 
Published: January 2021

AbstractDuring the study, the suitability of the ITS and TUB DNA regions was shown for identifying the target species at the genetic level. However, these DNA regions do not reveal significant differences between the sequences of the target species from different geographic regions. However, when constructing dendrograms of similarities and differences, the sequential differentiation between isolates at the population level was found, which may further affect the results of identification of the target species.
The impacts of lean principles on the production of civil aircraft in Boeing
Authors: Agyeman Nana Emmanuel Samuel 
Published: January 2021

Purpose
The purpose of this paper is to review how lean through the Boeing Production System impacted the production of civil aircraft in Boeing.

Design/methodology/approach
The paper engages the usage of literature on lean from researchers, book authors and the Boeing Company. These literatures were studied to ascertain why Boeing pursued the lean journey and the transformations it attained.

Findings
The outcomes disclose lean offers Boeing an all-inclusive approach in managing the value-stream of a company. It further presents a sustainable business model that prioritizes customer and industry demands, births innovative ways of satisfying them and keeps Boeing in business.

Originality/value
This research is useful to upcoming aircraft manufacturers who seek to optimize their production as well as satisfy their customers.
Effects of different levels of salt and temperature on some physico-chemical and colour properties of microwave-dried beef round (M. semitendinosus)
Authors: Özbay Sena , Sariçoban Cemalettin 
Published: January 2021

PurposeThe aim of this work was to study the effect of the different levels of salt and the temperature on some physico-chemical and colour change properties of microwave-dried beef round (M. semitendinosus).Design/methodology/approachThe samples were pretreated with different temperatures (0°C, 40°C and 50°C) and salting (0, 1.5, 2.5%). Later these samples have been dried by the microwave energy at 540 W for seven minutes. Some physical properties (water activity, moisture content, change in diameter, change in thickness, change in shrinkage ratio) and texture, colour and microscopic surface structure analysis were conducted in dried beef round samples.FindingsAs a result, the colour and moisture were the most affected factors. Also, physical and microstructural characteristics were affected by salting and pre-drying. In addition, while the textural structure did not show a significant difference, meat weight and water activity varied.Research limitations/implicationsMeat obtained from a local butcher in Konya was used as the study material. In addition, only a special part of the meat (M. semitendinosus) was used in the study. In the drying process, the parameters were determined as 540 W and 7 min. These are the limitations of the research.Originality/valueAll changes that can occur in the physical properties of the meat after the drying process were examined. The structure of beef round samples formed by microwave drying was shown by using electron microscope. The effects of pretreatment such as salting and pre-drying have been examined on microwave drying.