bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maternal phylogenetic relationships and genetic variation among rare similar phenotype donkey breeds
Authors: Mazzatenta Andrea , Caputo Maurizio , De Sanctis Francesco , Mirò Roig Jordi , Robbe Domenico , Carluccio Augusto 
Published: April 2020

AbstractMaternal inheritance is an indispensable aspect in donkey rare breed population biodiversity management and breeding programs. It is a challenge to characterize breeds genetic inheritance using morphology and historical records, we study mtDNA, to overcome those limitations. The mitochondrial DNA (mtDNA) sequencing is a highly informative system to investigate maternal lineages and breed linkage such as molecular evolution and phylogenetic relationships. Martina Franca, Ragusano, Pantesco and Catalonian donkey mtDNA sequencing analyses were used to study intraspecific genetic diversity and population structure, and to reconstruct phylogenetic relations among these geographically isolated breeds.A wide lost in variability among all breeds emerged. In this scenario, the primeval haplotypes, higher haplogroups variability and larger number of maternal lineages are preserved in Martina Franca and Ragusano. Accordingly, a putative pivotal role in the phyletic relationship is likely for such breeds.Given the level of endangerment undergone by these breeds, some actions are necessary to ensure their longtime survival and conservation. Improving the reproduction and management of existing populations, clarifying their historic interactions by studying the genetic status of their populations, extending and improving monitoring maternal lineages represent valid options.
A single-cell gene regulatory network inference method for identifying complex regulatory dynamics across cell phenotypes
Authors: Peng Jianhao , Serrano Guillermo , Traniello Ian M. , Calleja-Cervantes Maria E. , Chembazhi Ullas V. , Bangru Sushant , Ezponda Teresa , Rodriguez-Madoz Juan Roberto , Kalsotra Auinash , Prosper Felipe , Ochoa Idoia , Hernaez Mikel 
Published: April 2020

AbstractSingle-cell RNA-Sequencing has made it possible to infer high-resolution gene regulatory networks (GRNs), providing deep biological insights by revealing regulatory interactions at single-cell resolution. However, current single-cell GRN analysis methods produce only a single GRN per input dataset, potentially missing relationships between cells from different phenotypes. To address this issue, we present SimiC, a single-cell GRN inference method that produces a GRN per phenotype while imposing a similarity constraint that forces a smooth transition between GRNs, allowing for a direct comparison between different states, treatments, or conditions. We show that jointly inferring GRNs can uncover variation in regulatory relationships across phenotypes that would have otherwise been missed. Moreover, SimiC can recapitulate complex regulatory dynamics across a range of systems, both model and non-model alike. Taken together, we establish a new approach to quantitating regulatory architectures between the GRNs of distinct cellular phenotypes, with far-reaching implications for systems biology.
Addition of Multiple Introns to a Cas9 Gene Results in Dramatic Improvement in Efficiency for Generation of Gene Knockouts in Plants
Authors: Grützner Ramona , Martin Patrick , Horn Claudia , Mortensen Samuel , Cram Erin J. , Lee-Parsons Carolyn W. T. , Stuttmann Johannes , Marillonnet Sylvestre 
Published: April 2020

AbstractThe recent discovery of the mode of action of the CRISPR/Cas9 system has provided biologists with a useful tool for generating site-specific mutations in genes of interest. In plants, site-targeted mutations are usually obtained by stably transforming a Cas9 expression construct into the plant genome. The efficiency with which mutations are obtained in genes of interest can vary considerably depending on specific features of the constructs, including the source and nature of the promoters and terminators used for expression of the Cas9 gene and the guide RNA, and the sequence of the Cas9 nuclease itself. To optimize the efficiency with which mutations could be obtained in target genes inArabidopsis thalianawith the Cas9 nuclease, we have investigated several features of its nucleotide and/or amino acid sequence, including the codon usage, the number of nuclear localization signals (NLS) and the presence or absence of introns. We found that the Cas9 gene codon usage had some effect on Cas9 activity and that two NLSs work better than one. However, the most important impact on the efficiency of the constructs was obtained by addition of 13 introns into the Cas9 coding sequence, which dramatically improved editing efficiencies of the constructs; none of the primary transformants obtained with a Cas9 lacking introns displayed a knockout mutant phenotype, whereas between 70% and 100% of primary transformants generated with intronized Cas9 displayed mutant phenotypes. The intronized Cas9 was also found to be effective in other plants such asNicotiana benthamianaandCatharanthus roseus.
Ratchetaxisin channels: cells move directionally by pushing walls asymmetrically
Authors: Le Maout Emilie , Vecchio Simon Lo , Korla Praveen Kumar , Sheu Jim Jinn-Chyuan , Riveline Daniel 
Published: April 2020

AbstractCell motility is essential in a variety of biological phenomena ranging from early development to organ homeostasis and diseases. This phenomenon was so far mainly studied and characterized on flat surfaces in vitro whereas this situation is rarely seen in vivo. Recently, cell motion in 3D microfabricated channels was reported to be possible, and it was shown that confined cells push on walls. However, rules setting cell directions in this context were not characterized yet. Here, we show by using assays that ratchetaxis operates in 3D ratchets on fibroblasts and on epithelial cancerous cells. Open ratchets rectify cell motion, whereas closed ratchets impose a direct cell migration along channels set by the cell orientation at the channel entry point. We also show that nuclei are pressed at constrictions zones through mechanisms involving dynamic asymmetries of focal contacts, stress fibers, and intermediate filaments. Interestingly, cells do not pass these constricting zones when defective in the keratin fusion implicated in squamous cancer. By combining ratchetaxis with chemical gradients, we finally report that cells are sensitive to local asymmetries in confinement and that topological and chemical cues may be encoded differently by cells. Altogether our ratchet channels could mimic small blood vessels where cells are confined: cells would probe local asymmetries which would determine their entry into tissues and direction. Our results could shed light on invasions mechanisms in cancer.
Phenotypic screening using synthetic CRISPR gRNAs reveals pro-regenerative genes in spinal cord injury
Authors: Keatinge Marcus , Tsarouchas Themistoklis M. , Munir Tahimina , Larraz Juan , Gianni Davide , Tsai Hui-Hsin , Becker Catherina G. , Lyons David A. , Becker Thomas 
Published: April 2020

ABSTRACTAcute CRISPR/Cas9 targeting offers the opportunity for scalable phenotypic genetic screening in zebrafish. However, the unpredictable efficiency of CRISPR gRNA (CrRNA) activity is a limiting factor. Here we describe how to resolve this by prescreening CrRNAs for high activity in vivo, using a simple standardised assay based on restriction fragment length polymorphism analysis (RFLP). We targeted 350 genomic sites with synthetic RNA Oligo guide RNAs (sCrRNAs) in zebrafish embryos and found that almost half exhibited > 90% efficiency in our RFLP assay. Having the ability to preselect highly active sCrRNAs (haCRs), we carried out a focussed phenotypic screen of 30 macrophage-related genes in spinal cord regeneration and found 10 genes whose disruption impaired axonal regeneration. Four (tgfb1a, tgfb3, tnfa, sparc) out of 5 stable mutants subsequently analysed retained the acute haCR phenotype, validating the efficiency of this approach. Mechanistically, lack of tgfb1a leads to a prolonged immune response after injury, which inhibits regeneration. Our rapid and scalable screening approach has identified functional regulators of spinal cord regeneration, and can be applied to study any biological function of interest.HIGHLIGHTS- Synthetic CRISPR gRNAs are highly active- in vivo pre-screening allows rapid assessment of CRISPR gRNA activity- Phenotypic CRISPR screen reveals crucial genes for spinal cord regeneration- tgfb1a promotes spinal regeneration by controlling inflammation
High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters
Authors: Egli Adrian , Goldman Nina , Müller Nicola F. , Brunner Myrta , Wüthrich Daniel , Tschudin-Sutter Sarah , Hodcroft Emma , Neher Richard , Saalfrank Claudia , Hadfield James , Bedford Trevor , Syedbasha Mohammedyaseen , Vogel Thomas , Augustin Noémie , Bauer Jan , Sailer Nadine , Amar-Sliwa Nadezhda , Lang Daniela , Seth-Smith Helena M.B. , Blaich Annette , Hollenstein Yvonne , Dubuis Olivier , Nägele Michael , Buser Andreas , Nickel Christian H. , Ritz Nicole , Zeller Andreas , Stadler Tanja , Battegay Manuel , Schneider-Sliwa Rita 
Published: April 2020

AbstractWith two-thirds of the global population projected to be living in urban areas by 2050, understanding the transmission patterns of viral pathogens within cities is crucial for effective prevention strategies. Here, in unprecedented spatial resolution, we analysed the socioeconomic determinants of influenza transmission in a European city. We combined geographical and epidemiological data with whole genome sequencing of influenza viruses at the scale of urban quarters and statistical blocks, the smallest geographic subdivisions within a city. We observed annually re-occurring geographic clusters of influenza incidences, mainly associated with net income, and independent of population density and living space. Vaccination against influenza was also mainly associated with household income and was linked to the likelihood of influenza-like illness within an urban quarter. Transmissions patterns within and between quarters were complex. High-resolution city-level epidemiological studies combined with social science surveys such as this will be essential for understanding seasonal and pandemic transmission chains and delivering tailored public health information and vaccination programs at the municipal level.
The effect of noise trauma and high-frequency stimulation on thalamic sensory gating in rodents
Authors: Zare Aryo , van Zwieten Gusta , Kotz Sonja A. , Temel Yasin , Schultz Benjamin G. , Schwartze Michael , Janssen Marcus L.F. 
Published: April 2020

AbstractBackgroundThe medial geniculate body (MGB) of the thalamus plays a central role in tinnitus pathophysiology. Breakdown of sensory gating in this part of the auditory thalamus is a potential mechanism underlying tinnitus. The alleviation of tinnitus-like behavior by high-frequency stimulation (HFS) of the MGB might mitigate dysfunctional sensory gating.ObjectiveThe study aims at exploring the role of the MGB in sensory gating as a mandatory relay area in auditory processing in noise-exposed and control subjects, and to assess the effect of MGB HFS on this function.MethodsNoise-exposed rats and controls were tested. Continuous auditory sequences were presented to allow assessment of sensory gating effects associated with pitch, binary grouping, and temporal regularity. Evoked potentials (EP) were recorded from the MGB and acquired before and after HFS (100 Hz).ResultsNoise-exposed rats showed differential modulation of MGB EP amplitudes, confirmed by significant main effects of stimulus type, pair position and temporal regularity. Noise-exposure selectively abolished the effect of temporal regularity on EP amplitudes. A significant three-way interaction between HFS phase, temporal regularity and rat condition (noise-exposed, control) revealed that only noise-exposed rats showed significantly reduced EP amplitudes following MGB HFS.ConclusionThis is the first report that shows thalamic filtering of incoming auditory signals based on different sound features. Noise-exposed rats further showed higher EP amplitudes in most conditions and did not differentiate the temporal regularity. Critically, MGB HFS was effective in reducing amplitudes of the EP responses in noise-exposed animals.HighlightsEP findings indicate sensory gating in the MGB in rats.Noise exposure alters EP amplitudes in the MGB.HFS selectively suppresses EP responses in noise-exposed animals.
Engineering of critical enzymes and pathways for improved triterpenoid biosynthesis in yeast
Authors: Guo Hao , Wang Huiyan , Huo Yi-xin 
Published: April 2020

AbstractTriterpenoids represent a diverse group of phytochemicals, widely distributed in the plant kingdom with many biological activities. Recently, the heterologous production of triterpenoids inSaccharomyces cerevisiaehas been successfully implemented by introducing various triterpenoids biosynthetic pathways. By engineering related enzymes as well as yeast metabolism, the yield of various triterpenoids is significantly improved from milligram-scale per liter to gram-scale level per liter. This achievement demonstrates that engineering of critical enzymes is considered as a potential strategy to overcome the main hurdles of translation of these potent natural products into industry. Here, we review strategies for designing enzymes to improve the yield of triterpenoids inS. cerevisiae, which is mainly separated into three aspects: 1. elevating the supply of the precursor—2,3-oxidosqualene, 2. optimizing triterpenoid-involved reactions, 3. lowering the competition of the native sterol pathway. And then we provide challenges and prospects on further enhancing the triterpenoid production inS. cerevisiae.
Direct Electrical Detection of sub-aM DNA Concentrations
Authors: Guo Maoxiang , Madaboosi Narayanan , Neumann Felix , Nilsson Mats , van der Wijngaart Wouter 
Published: April 2020

AbstractSensors for detecting ultra-low concentrations are limited by the efficient transport of target molecules from large sample volumes to small detection regions. We here report a small-format digital DNA sensor in the shape of a microporous membrane that electrically detects DNA substrates with a concentration as low as 790 zM. This ultra-high sensitivity follows from optimising the mass transport of target DNA to specific receptors on the membrane across multiple spatial scales. mm-sized membranes support the rapid convection of a large sample volume to the detection zone; µm-sized pores ensure that DNA diffusion to the surface-based receptors dominates over convective loss through the pores (low Péclet number), and; at the nm-scale, target-receptor binding dominates over diffusive transport (high Damköhler number). After their efficient capture, the DNA molecules are converted with high specificity into trans-membrane gold nanowires that are detected using a simple, high signal-to-noise, electrical resistance measurement. This sensor design is of interest for detecting low-abundant target molecules without the need for sample amplification or up-concentration, and the mass-transport strategy could be adapted to other surface-based sensing schemes.
Stimulation Artifact Source Separation (SASS) for assessing electric brain oscillations during transcranial alternating current stimulation (tACS)
Authors: Haslacher David , Nasr Khaled , Robinson Stephen E. , Braun Christoph , Soekadar Surjo R. 
Published: April 2020

AbstractBrain oscillations, e.g. measured by electro- or magnetoencephalography (EEG/MEG), are causally linked to brain functions that are fundamental for perception, cognition and learning. Recent advances in neurotechnology provide means to non-invasively target these oscillations using frequency-tuned amplitude-modulated transcranial alternating current stimulation (AM-tACS). However, online adaptation of stimulation parameters to ongoing brain oscillations remains an unsolved problem due to stimulation artifacts that impede such adaptation, particularly at the target frequency. Here, we introduce a real-time compatible artifact rejection algorithm (Stimulation Artifact Source Separation, SASS) that overcomes this limitation. SASS is a spatial filter (linear projection) removing EEG signal components that are maximally different in the presence versus absence of stimulation. This enables the reliable removal of stimulation-specific signal components, while leaving physiological signal components unaffected. For validation of SASS, we evoked brain activity with known phase and amplitude using 10 Hz visual flickers across 7 healthy human volunteers. 64-channel EEG was recorded during and in absence of 10 Hz AM-tACS targeting the visual cortex. Phase differences between AM-tACS and the visual stimuli were randomized, so that steady-state visually evoked potentials (SSVEPs) were phase-locked to the visual stimuli but not to the AM-tACS signal. For validation, distributions of single-trial amplitude and phase of EEG signals recorded during and in absence of AM-tACS were compared for each participant. When no artifact rejection method was applied, AM-tACS stimulation artifacts impeded assessment of single-trial SSVEP amplitude and phase. Using SASS, amplitude and phase of single trials recorded during and in absence of AM-tACS were comparable. These results indicate that SASS can be used to establish adaptive (closed-loop) AM-tACS, a potentially powerful tool to target various brain functions, and to investigate how AM-tACS interacts with electric brain oscillations.Highlights- Stimulation Artifact Source Separation (SASS), a real-time compatible signal decomposition algorithm for separating electric brain activity and stimulation signal artifacts related to amplitude-modulated transcranial alternating current stimulation (AM-tACS), is introduced- Employing SASS, phase and amplitude of single-trial steady state visual evoked potentials (SSVEPs) were reliably recovered from electroencephalography (EEG) recordings at the frequency targeted with AM-tACS- SASS enables assessment of single-trial oscillatory brain activity at the target frequency during stimulation and paves the way for online adaptation of stimulation parameters to ongoing brain oscillations
TINC - a method to dissect transcriptional complexes at single locus resolution - reveals novelNanogregulators in mouse embryonic stem cells
Authors: Knaupp AS , Mohenska M , Larcombe MR , Ford E , Lim SM , Wong K , Chen J , Firas J , Huang C , Liu X , Nguyen T , Sun YBY , Holmes ML , Tripathi P , Rossello FJ , Schröder J , Nefzger CM , Das PP , Haigh JJ , Lister R , Schittenhelm RB , Polo JM 
Published: April 2020

AbstractCellular identity is ultimately controlled by transcription factors (TFs), which bind to specific regulatory elements (REs) within the genome to regulate gene expression and cell fate changes. While recent advances in genome-wide epigenetic profiling techniques have significantly increased our understanding of which REs are utilized in which cell type, it remains largely unknown which TFs and cofactors interact with these REs to modulate gene expression. A major hurdle in dissecting the whole composition of a multi-protein complex formed at a specific RE is the shortage of appropriate techniques. We have developed a novel method termed TALE-mediated Isolation of Nuclear Chromatin (TINC). TINC utilizes epitope-tagged TALEs to isolate a specific genomic region from the mammalian genome and includes a nuclei isolation and chromatin enrichment step for increased specificity. Upon cross-linking of the cells and isolation of the chromatin, the target region is purified based on affinity purification of the TALE and associated nucleic acid and protein molecules can be subjected to further analyses. A key TF in the pluripotency network and therefore in embryonic stem cells (ESCs) is NANOG. It is currently not fully understood howNanogexpression is regulated and consequently it remains unclear how the ESC state is maintained. Using TINC we dissected the protein complex formed at theNanogpromoter in mouse ESCs and identified many known and numerous novel factors.
Degradation modeling of water environmental DNA: Experiments on multiple DNA sources in pond and seawater
Authors: Saito Tatsuya , Doi Hideyuki 
Published: April 2020

ABSTRACTEnvironmental DNA (eDNA) methods have been developed to detect organism distribution and abundance/biomass in various environments. eDNA degradation is critical for eDNA evaluation. However, the dynamics and mechanisms of eDNA degradation are largely unknown, especially when considering different eDNA sources, e.g., cells and fragmental DNA. We experimentally evaluated the degradation rates of eDNA derived from multiple sources, including fragmental DNA, free cells, and inhabiting species. We conducted the experiment with pond and seawater to evaluate the differences between freshwater and marine habitats. We quantified the eDNA copies of free cells, fragmental DNA, and inhabiting species (Cyprinus carpio in the pond and Trachurus japonicus in the sea). Our results show that eDNA derived from both cells and fragmental DNA decreased exponentially in both the sea and pond samples. The degradation of eDNA from inhabiting species showed similar behavior to the cell-derived eDNA. We evaluated three degradation models with different assumptions and degradation steps and found that a simple exponential model is effective in most cases. Our findings on cell- and fragmental DNA-derived eDNA provide fundamental information about the eDNA degradation process and can be applied to elucidate eDNA behavior in natural environments.
Codon usage bias in prokaryotic genomes and environmental adaptation
Authors: Arella Davide , Dilucca Maddalena , Giansanti Andrea 
Published: April 2020

AbstractIn each genome synonymous codons are used with different frequencies; this phenomenon is known as codon usage bias. The preferred codons tend to correspond to the most highly expressed tRNAs. It had been known that codon usage bias can influence the cellular fitness and that might be associated with the lifestyle of the organism. To test the impact of environments on genome evolution we studied the relationship between codon usage bias and the phenotypic traits of 615 prokaryotic organisms. Principal component analysis revealed that prokaryotes with a specific phenotypic characteristic and living in similar environmental conditions have similar codon preferences, accessed by the Relative Synonymous Codon Usage (RSCU), and a similar tRNA availability gauged by the tRNA gene copy number (tGCN). In addition, by measuring the average tRNA adaptation index (tAI) for each genome, we discovered that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, exhibit lower extents of translational efficiency, consistent with their need to adapt to different environments.This is the first large-scale study that examines the role of translational efficiency in the environmental adaptation of prokaryotes. Our results show that synonymous codon choices might be under strong translational selection, adapting the codons to the tRNA pool to different extents depending on the organism’s lifestyle needs.