bluuebunny/crossref_metadata_2025_split huggingface dataset:
TaqMan quantitative real-time PCR for detectingAvipoxvirusDNA in various sample types from hummingbirds
Authors: Baek Hanna E. , Sehgal Ravinder N. , Bandivadekar Ruta R. , Pandit Pranav , Mah Michelle , Tell Lisa A. 
Published: March 2020

AbstractBackgroundAvian pox is a viral disease documented in a wide range of bird species. Disease related detrimental effects can cause dyspnea and dysphagia, therefore birds with high metabolic requirements, such as hummingbirds, are especially vulnerable. Hummingbirds have a strong presence in California, especially in urban environments; however, little is understood regarding the impact of pox virus on hummingbird populations. Diagnosing pox infections relies on obtaining a tissue biopsy that poses significant bird risks and field challenges. Understanding the ecology of hummingbird pox viral infections could be advanced by a minimally invasive ante-mortem diagnostic method. This study’s goal was to address this gap in understanding if pox infections can be diagnosed using integumentary system samples besides tissue biopsies. To meet this goal, we tested multiple integumentary sample types and tested them using a quantitative real-time PCR assay. A secondary study goal was to determine which sample types (ranging from minimally to highly invasive sampling) were optimal for identifying infected birds.Methodology/Principal FindingsLesion tissue, pectoral muscle, feathers, toenail, blood, and swabs (both lesion tissue and non-lesion tissues) were taken from live birds and carcasses of two species of hummingbirds found in California. To maximize successful diagnosis, especially for samples with low viral load, a real-time quantitative PCR assay was developed for detecting the hummingbird-specificAvipoxvirus4b core protein gene.AvipoxvirusDNA was successfully amplified from all sample types across 27 individuals. Our results were then compared to those of conventional PCR. Comparisons were also made between sample types utilizing lesion tissue samples as the gold standard.Conclusions/SignificanceHummingbird avian pox can be diagnosed without relying on tissue biopsies. Feather samples can be used for diagnosing infected birds and reduces sampling risk. A real-time PCR assay detected viral DNA in various integumentary system sample types and could be used for studying hummingbird disease ecology in the future.
Rhamnolipid production from waste cooking oil using newly isolated halotolerantPseudomonas aeruginosaM4
Authors: Shi Juan , Chen Yichao , Liu Xiaofeng , Ran Yi , Li Dong 
Published: March 2020

AbstractThis study isolated a novel halotolerantPseudomonas aeruginosaM4, that was able to degrade oil and produce rhamnolipids. Various carbon sources, nitrogen sources, inoculum ratio, pH, and temperature were tested to optimize the oil degradation conditions. The highest oil degradation rate of 85.20 % and lipase activity of 23.86 U/mL were obtained under the optimal conditions (5% inoculum at 35 °C and pH 8). The components of degradation products at different times were analyzed to explore the mechanism of oil degradation by GC-MS. Short chain fatty acid of acetic and n-butyric acids were the primary degradation intermediates.P. aeruginosaM4 had good salt tolerance up to 70 g/L. The maximum rhamnolipid concentration of 1119.87 mg/L was produced whenP. aeruginosaM4 used waste cooking oil as the sole carbon source. Rhamnose precursors were synthesized from glycerol, a hydrolysis product of waste cooking oil. R-3-hydroxyalkanoate precursors were synthesized de novo using acetyl-CoA produced from β-oxidation of fatty acids. The findings show thatP. aeruginosaM4 is a valuable biosurfactant producer in the treatment of waste cooking oil.Key PointsP. aeruginosaisolation, oil degradation mechanism, rhamnolipid production from WCO
Reprogramming the endogenous type III-A CRISPR-Cas system for genome editing, RNA interference and CRISPRi screening inMycobacterium tuberculosis
Authors: Rahman Khaista , Jamal Muhammad , Chen Xi , Zhou Wei , Yang Bin , Zou Yanyan , Xu Weize , Lei Yingying , Wu Chengchao , Cao Xiaojian , Tyagi Rohit , Naeem Muhammad Ahsan , Lin Da , Habib Zeshan , Peng Nan , Fu Zhen F. , Cao Gang 
Published: March 2020

AbstractMycobacterium tuberculosis(M.tb) causes the current leading infectious disease. Examination of the functional genomics ofM.tband development of drugs and vaccines are hampered by the complicated and time-consuming genetic manipulation techniques forM.tb.Here, we reprogrammedM.tbendogenous type III-A CRISPR-Cas10 system for simple and efficient gene editing, RNA interference and screeningviasimple delivery of a plasmid harboring a mini-CRISPR array, thereby avoiding the introduction of exogenous proteins and minimizing proteotoxicity. We demonstrated thatM.tbgenes were efficiently and specifically knocked-in/out by this system, which was confirmed by whole-genome sequencing. This system was further employed for single and simultaneous multiple-gene RNA interference. Moreover, we successfully applied this system for genome-wide CRISPR interference screening to identify thein-vitroand intracellular growth-regulating genes. This system can be extensively used to explore the functional genomics ofM.tband facilitate the development of new anti-Mycobacterialdrugs and vaccines.SummaryTuberculosis caused byMycobacterium tuberculosis(M.tb) is the current leading infectious disease affecting more than ten million people annually. To dissect the functional genomics and understand its virulence, persistence, and antibiotics resistance, a powerful genome editing tool and high-throughput screening methods are desperately wanted. Our study developed an efficient and a robust tool for genome editing and RNA interference inM.tbusing its endogenous CRISPR cas10 system. Moreover, the system has been successfully applied for genome-wide CRISPR interference screening. This tool could be employed to explore the functional genomics ofM.tband facilitate the development of anti-M.tbdrugs and vaccines.
Remyelination alters the pattern of myelin in the cerebral cortex
Authors: Orthmann-Murphy Jennifer , Call Cody L. , Molina-Castro Gian Carlo , Hsieh Yu Chen , Rasband Matthew N. , Calabresi Peter A. , Bergles Dwight E. 
Published: March 2020

ABSTRACTDestruction of oligodendrocytes and myelin sheaths in cortical gray matter profoundly alters neural activity and is associated with cognitive disability in multiple sclerosis (MS). Myelin can be restored by regenerating oligodendrocytes from resident progenitors; however, it is not known whether regeneration restores the complex myelination patterns in cortical circuits. Here we performed time lapsein vivotwo photon imaging in somatosensory cortex of adult mice to define the kinetics and specificity of myelin regeneration after acute oligodendrocyte ablation. These longitudinal studies revealed that the pattern of myelination in cortex changed dramatically after regeneration, as new oligodendrocytes were formed in different locations and new sheaths were often established along axon segments previously lacking myelin. Despite the dramatic increase in axonal territory available, oligodendrogenesis was persistently impaired in deeper cortical layers that experienced higher gliosis. The repeated reorganization of myelin patterns in MS may alter circuit function and contribute to cognitive decline.
Language modelling for biological sequences – curated datasets and baselines
Authors: Almagro Armenteros Jose Juan , Johansen Alexander Rosenberg , Winther Ole , Nielsen Henrik 
Published: March 2020

AbstractMotivationLanguage modelling (LM) on biological sequences is an emergent topic in the field of bioinformatics. Current research has shown that language modelling of proteins can create context-dependent representations that can be applied to improve performance on different protein prediction tasks. However, little effort has been directed towards analyzing the properties of the datasets used to train language models. Additionally, only the performance of cherry-picked downstream tasks are used to assess the capacity of LMs.ResultsWe analyze the entire UniProt database and investigate the different properties that can bias or hinder the performance of LMs such as homology, domain of origin, quality of the data, and completeness of the sequence. We evaluate n-gram and Recurrent Neural Network (RNN) LMs to assess the impact of these properties on performance. To our knowledge, this is the first protein dataset with an emphasis on language modelling. Our inclusion of properties specific to proteins gives a detailed analysis of how well natural language processing methods work on biological sequences. We find that organism domain and quality of data have an impact on the performance, while the completeness of the proteins has little influence. The RNN based LM can learn to model Bacteria, Eukarya, and Archaea; but struggles with Viruses. By using the LM we can also generate novel proteins that are shown to be similar to real proteins.Availability and implementationhttps://github.com/alrojo/UniLanguage
Microbiota–modulated enteric neuron translational profiling uncovers a CART+ glucoregulatory subset
Authors: Muller Paul A , Schneeberger Marc , Matheis Fanny , Kerner Zachary , Mucida Daniel 
Published: March 2020

AbstractMicrobial density and diversity increase towards the distal intestine, affecting tissue physiology, metabolism, and function of both immune and nervous systems. Intrinsic enteric–associated neurons (iEAN) continuously monitor and modulate intestinal functions, including nutrient absorption and motility. Through molecular, anatomic and functional approaches, we characterized the influence of the microbiota on iEAN. We found that iEAN are functionally adapted to the intestinal segment they occupy, with a stronger microbiota influence on distal intestine neurons. Chemogenetic characterization of microbiota-influenced iEAN identified a subset of viscerofugal CART+ neurons, enriched in the distal intestine, able to modulate feeding through insulin-glucose levels. Retro- and anterograde tracing revealed that CART+ viscerofugal neurons send axons to the gut sympathetic ganglion and are synaptically connected to the liver and pancreas. Our results demonstrate a region-specific adaptation of enteric neurons and indicate that specific iEAN subsets are capable of regulating host physiology independently from the central nervous system.One Sentence SummaryMicrobes impact regionally defined intrinsic enteric neuron translatomes, including a novel CART+ glucoregulatory viscerofugal population.
sideRETRO: a pipeline for identifying somatic and dimorphic insertions of processed pseudogenes or retrocopies
Authors: Miller Thiago L A , Orpinelli Fernanda , Buzzo José Leonel L , Galante Pedro A F 
Published: March 2020

ABSTRACTRetrocopies or processed pseudogenes are gene copies resulting from mRNA retrotransposition. These gene duplicates can be fixed, somatically inserted or dimorphic in the genome. However, knowledge regarding unfixed retrocopies (retroCNVs) is still limited, and the development of computational tools for effectively identifying and genotyping them is an urgent need. Here, we present sideRETRO, a pipeline dedicated not only to detecting retroCNVs in whole-genome or whole-exome sequencing data but also to revealing their insertion sites, zygosity, and genomic context and classifying them as somatic or dimorphic events. We show that sideRETRO can identify novel retroCNVs and genotype them (93.2% accuracy), in addition to identifying dimorphic retroCNVs in whole-genome and whole-exome data. Therefore, sideRETRO fills a gap in the literature and presents an efficient and straightforward algorithm to accelerate the study of retroCNVs.AvailabilitysideRETRO is available athttps://github.com/galantelab/sideRETRO
Quantitating denaturation by formic acid: Imperfect repeats are essential to the stability of the functional amyloid protein FapC
Authors: Christensen Line Friis Bakmann , Nowak Jan Stanislaw , Sønderby Thorbjørn Vincent , Frank Signe Andrea , Otzen Daniel Erik 
Published: March 2020

ABSTRACTBacterial functional amyloids are evolutionarily optimized to aggregate to help them fulfil their biological functions,e.g.to provide mechanical stability to biofilm. Amyloid is formed inPseudomonassp. by the protein FapC which contains 3 imperfect repeats connected by long linkers. Stepwise removal of these repeats slows down aggregation and increases the propensity of amyloids to fragment during the fibrillation process, but how these mechanistic properties link to fibril stability is unclear. Here we address this question. The extreme robustness of functional amyloid makes them resistant to conventional chemical denaturants, but they dissolve in formic acid (FA) at high concentrations. To quantify this, we first measured the denaturing potency of FA using 3 small acid-resistant proteins (S6, lysozyme and ubiquitin). This revealed a linear relationship between [FA] and the free energy of unfolding with a slope ofmFA, as well as a robust correlation between protein residue size andmFA. We then measured the solubilisation of fibrils formed from different FapC variants (with varying number of repeats) as a function of [FA]. The resultingmFAvalues revealed a decline in the number of residues driving amyloid formation when at least 2 repeats were deleted. The midpoint of denaturation declined monotonically with progressive removal of repeats and correlated with solubility in SDS. Complete removal of all repeats led to fibrils which were solubilized at FA concentrations 2-3 orders of magnitude lower than the repeat-containing variants, showing that at least one imperfect repeat is required for the stability of functional amyloid.
Diminished ventral oligodendrocyte precursor generation results in the subsequent over-production of dorsal oligodendrocyte precursors of aberrant morphology and function
Authors: Starikov Lev , Kottmann Andreas H. 
Published: March 2020

AbstractOligodendrocyte precursor cells (OPCs) arise sequentially first from a ventral and then from a dorsal precursor domain at the end of neurogenesis during spinal cord development. Whether the sequential production of OPCs is of physiological significance has not been examined. Here we show that ablating Shh signaling from nascent ventricular zone derivatives and partially from the floor plate results in a severe diminishment of ventral derived OPCs but normal numbers of motor neurons in the postnatal spinal cord. In the absence of ventral vOPCs, dorsal dOPCs populate the entire spinal cord resulting in an increased OPC density in the ventral horns. These OPCs take on an altered morphology, do not participate in the removal of excitatory vGlut1 synapses from injured motor neurons, and exhibit morphological features similar to those found in the vicinity of motor neurons in the SOD1 mouse model of Amyotrophic Lateral Sclerosis (ALS). Our data indicates that vOPCs prevent dOPCs from invading ventral spinal cord laminae and suggests that vOPCs have a unique ability to communicate with injured motor neurons.
Deficiency of cyclin-dependent kinase-like 5 causes spontaneous epileptic seizures in neonatal mice
Authors: Liao Wenlin , Lee Kun-Ze , Su San-Hua , Luo Yuju 
Published: March 2020

AbstractCyclin-dependent kinase-like 5 (CDKL5), an X-linked gene encoding a serine-threonine kinase, is enriched in the mammalian forebrain and critical for neuronal maturation and synaptic function. Mutations in this gene cause CDKL5 deficiency disorder (CDD) that is characterized by early-onset epileptic seizures, autistic behaviors and intellectual disability. Although numerous CDD symptoms have been recapitulated in mouse models, spontaneous seizures have not been reported in mice with CDKL5 deficiency. Here, we present the first systematic study of spontaneous seizures in a mouse model of CDD. Through wireless electroencephalographic (EEG) recording and simultaneous videotaping, we observed epileptiform discharges accompanied with ictal behaviors in pups lacking CDKL5 at a selective time window during the pre-weaning period. The seizure-like patterns of EEG showed robust increase in total number of spike events, the total number and duration of bursts inCdkl5null pups compared to wild-type littermate controls at the age of postnatal day 12 (P12). The mutants displayed not only jerky and spasm-like movements during the prolonged bursts of discharges at P12, but also strengthened ictal grasping in both juvenile stage and adulthood. In addition, loss of CDKL5 remarkably reduced the phosphorylation of K+/Cl-co-transporter 2, which may impede GABA-mediated inhibition, in the cortex of P12 mouse pups. Our study reveals previously unidentified phenotypes of early-onset seizures in CDKL5-deficient mice, highlights the translational value of mouse models of CDD and provides a potential molecular target for early diagnosis and treatment for CDD.Significance StatementCyclin-dependent kinase-like 5 (CDKL5) is an X-linked gene encoding a serine-threonine kinase. Mutations in this gene cause CDKL5 deficiency disorder (CDD), a rare disease characterized by developmental delays, autistic behaviors and early-onset epilepsy. Even though many symptoms of CDD patients have been phenocopied in mice, spontaneous seizures are yet to be reported in mouse models of CDD. Here, for the first time, we identified early-onset seizures and ictal behaviors in neonatal pups of CDKL5-deficient mice. Loss of CDKL5 also selectively reduced protein levels of phosphorylated K+/Cl-cotransporter 2 in neonatal cortex of mice. Our study reveals an indispensible role of CDKL5 in regulating neuronal excitability in developing brains and highlights the translational significance of the CDD mouse models.
Appraisal of stakeholders' willingness to adopt construction 4.0 technologies for construction projects
Authors: Osunsanmi Temidayo Oluwasola , Aigbavboa Clinton Ohis , Emmanuel Oke Ayodeji , Liphadzi Muredini 
Published: March 2020

PurposeConstruction 4.0 technology has the capabilities for improving the design, management, operations and decision making of construction projects. Therefore, this study aimed at examining the willingness of construction professionals towards adopting construction 4.0 technologies.Design/methodology/approachThe study adopts a survey design, and construction professionals in South Africa are assessed using a convenience sampling technique through a structured questionnaire. The questionnaire was analysed with SPSS while statistical test like; mean score, t-test and principal component analysis was used to present the data.FindingsThe findings, from the analysis, revealed that the construction professionals are willing to adopt construction 4.0 technologies for construction project. However, the possibility of fully integrating the technologies into the construction industry is low. This is because the major technologies such as; Internet of things, robotics, human-computer interaction and cyber-physical systems that encourage smart construction site are rated as not important by the construction professionals.Practical implicationsIt is believed that the findings emanating from this study will serve as an indicator for investors that are interested in procuring construction 4.0 technologies for the construction industry.Originality/valueThis paper presents a framework for the application of construction 4.0 technologies for the construction industry. It also contributes to the development of digitalising construction industry in South Africa.
Environmental practices in the wine industry: an overview of the Italian market
Authors: Bandinelli Romeo , Acuti Diletta , Fani Virginia , Bindi Bianca , Aiello Gaetano 
Published: March 2020

PurposeThe present research expands the debate on environmental sustainability in the wine industry. Since the literature on sustainability and wine is relatively recent, current results do not cover all the practices that can be implemented along the wine supply chain. Thus, the paper presents a classification of environmental practices specific for the wine industry, according to the increased attention that has been paid to this topic in recent years. Moreover, it investigates the adoption level of these practices with reference to Italian wine producers.Design/methodology/approachThe research presents a systematic literature review including papers published in academic journals during the past 30 years and in Italian specialised magazines. This methodology is useful to provide a clear overview of sustainable practices that can be adopted along the wine supply chain. Therefore, an empirical study based on the results of an online survey shows how wineries approach environmental sustainability.FindingsThe literature review provides a definition and classification of environmental practices in the wine industry, as well as identification of those that require further attention in the literature, suggesting future research paths. The results of the online survey give an overview of the adoption level of environmental practices and highlight widespread attention to all the listed environmental practices, including those not adopted.Originality/valueFrom a theoretical point of view, this paper fills a literature gap in terms of the definition and classification of environmental practices that cover all wine supply chain processes, also providing a useful instrument for wine companies' managers. Moreover, the results of the empirical research give an overview of the adoption level of environmental practices in one of the most relevant countries in terms of wine production and highlight widespread attention to all the listed environmental practices, including those not adopted.
An activity theory approach to information security non-compliance
Authors: Khatib Rima , Barki Henri 
Published: March 2020

PurposeThe purpose of this paper is to introduce activity theory (AT) as a new theoretical lens to the field of information security non-compliance by explaining how research in that field can benefit from AT and to suggest eight propositions for future research.Design/methodology/approachBased on AT, the paper suggests that employees, IT systems, task characteristics, information security policies (ISPs), community and division of labor can be viewed to form an ensemble that is labeled activity. Their characteristics and/or the relationships that exist between them in organizational contexts are hypothesized to influence non-compliance behaviors.FindingsThe paper suggests that AT provides a broad lens that can be useful for explaining a large variety of non-compliant behaviors related to information security.Research limitations/implicationsThe paper focuses only on non-compliant behaviors that employees undertake with non-malicious intentions and offers avenues for future research based on the propositions that are developed in the paper.Originality/valueThe paper provides a useful step toward a better understanding of non-compliant ISP behaviors. In addition, it proposes and explains new research areas in the non-compliance field.