bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ambient temperature effects on stress-induced hyperthermia in Svalbard ptarmigan
Authors: Nord Andreas , Folkow Lars P. 
Published: April 2019

ABSTRACTStress-induced hyperthermia (SIH) is commonly observed during handling in homeotherms. However, in birds, handling in cold environments typically elicits hypothermia. It is unclear whether this indicates that SIH is differently regulated in this taxon or if it is due to size, because body temperatures changes during handling in low temperature have only been measured in small birds ≤ 0.03 kg (that are more likely to suffer high heat loss when handled). We have, therefore, studied thermal responses to handling stress in the intermediate-sized (0.5-1.0 kg) Svalbard ptarmigan (Lagopus muta hyperborea) in 0°C and −20°C, in winter and spring. Handling caused elevated core body temperature, and peripheral vasoconstriction that reduced back skin temperature. Core temperature increased less and back skin temperature decreased more in −20°C than in 0°C, probably because of higher heat loss rate at the lower temperature. Responses were qualitatively consistent between seasons, despite higher body condition/insulation in winter and dramatic seasonal changes in photoperiod, possibly affecting stress responsiveness. Our study supports the notion that SIH is a general thermoregulatory reaction to acute stressors in endotherms, but also suggests that body size and thermal environment should be taken into account when evaluating this response in birds.
Limiting-stress-elimination hypothesis: approach to increase savanna cowpea productivity by stress reduction
Authors: Atta-Boateng Acheampong , Berlyn Graeme P. 
Published: April 2019

AbstractWe propose and test the Limiting-Stress-Elimination Hypothesis (LSEH), as a decision axiom to guide in determining the optimal intervention strategy towards yield allocation in a savanna legume. We considered osmotic stress and soil nitrogen (N) limitation, which both characterize Guinea savanna agro-ecozone. We hypothesized that biomass allocation will increase when the limiting stress is eliminated at least until the next limiting stress impacts yield. We assessed responses ofVigna unguiculata(L.) Walp (cowpea) to osmotic stress treatments (non-hormonal biostimulant and exogenous metabolite) and N input by leaf level physiology, N-fixing capacity and biomass. The relative increase in biomass (%), and pod yields reveal that osmotic stress (45%) more than nitrogen (13%) is limiting to cowpea growth under Guinea savanna conditions, although N fertilization increased nodulation and maximized PSII quantum yield. In the Sprengel-Liebig’s decrement from the maximum concept, the decrement from the maximum for each stressor must be minimized in order to produce the absolute maximum production. However, this may not be economically feasible in many situations. Conversely, LSEH demonstrates that significant productivity is attainable by eliminating a relatively more limiting stress, osmotic stress, regardless of the limitation and natural demand for the relatively less limiting N in leguminous cowpea in the savanna.
Behavioural analysis of single-cell aneural ciliate,Stentor roeselii, using machine learning approaches
Authors: Trịnh Kiều Mi , Wayland Matthew T. , Prabakaran Sudhakaran 
Published: April 2019

AbstractThere is still a significant gap between our understanding of neural circuits and the behaviours they compute – i.e. the computations performed by these neural networks (Carandini 2012). Learning, behaviour, and memory formation, what used to only be associated with animals with neural systems, have been observed in many unicellular aneural species, namely Physarum, Paramecium, and Stentor (Tang & Marshall 2018). As these are fully functioning organisms, yet being unicellular, there is a much better chance to elucidate the detailed mechanisms underlying these learning processes in these organisms without the complications of highly interconnected neural circuits. An intriguing learning behaviour observed inStentor roeselii(Jennings 1902) when stimulated with carmine has left scientists puzzled for more than a century. So far, none of the existing learning paradigm can fully encapsulate this particular series of five characteristic avoidant reactions. Although we were able to observe all responses described in literature and in a previous study (Dexter et al. 2019, manuscript in preparation), they do not conform to any particular learning model. We then investigated whether models based on machine learning approaches, including decision tree, random forest, and feed-forward neural networks could infer and predict the behavior ofS. roeselii. Our results showed that an artificial neural network with multiple ‘computational’ neurons is inefficient at modelling the single-celled ciliate’s avoidant reactions. This has highlighted the complexity of behaviours in aneural organisms. Additionally, this report will also discuss the significance of elucidating molecular details underlying learning and decision-making processes in these unicellular organisms, which could offer valuable insights that are applicable to higher animals.
Antagonistic and auxin-dependent phosphoregulation of columella PIN proteins controls lateral root gravitropic setpoint angle in Arabidopsis
Authors: Roychoudhry Suruchi , Sageman-Furnas Katelyn , Wolverton Chris , Goodman Heather L. , Grones Peter , Mullen Jack , Hangarter Roger , Friml Jiří , Kepinski Stefan 
Published: April 2019

AbstractLateral roots of many species are maintained at non-vertical angles with respect to gravity. These gravitropic setpoint angles (GSAs) are intriguing because their maintenance requires that roots are able to effect gravitropic response both with and against the gravity vector. Here we have used the Arabidopsis lateral root in order to investigate the molecular basis of the maintenance of non-vertical GSAs. We show that gravitropism in the lateral root is angle-dependent and that both upward and downward graviresponse requires auxin transport and the generation of auxin asymmetries consistent with the Cholodny-Went model. We show that the symmetry in auxin distribution in lateral roots growing at GSA can be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters in the columella cells. Further, upward and downward graviresponse in lateral roots correlates with corresponding changes in PIN3 and PIN7 polar localisation. Finally, we show that auxin, in addition to driving tropic growth in the lateral root, acts within the columella to regulate GSA via the PIN phosphatase subunit RCN1 in a PIN3-dependent and PIN7-independent manner. Together, these findings provide a molecular framework for understanding gravity-dependent nonvertical growth in Arabidopsis lateral roots.
Opposing contributions of GABAergic and glutamatergic ventral pallidal neurons to motivational behaviours
Authors: Stephenson-Jones Marcus , Bravo-Rivera Christian , Ahrens Sandra , Furlan Alessandro , Fernandes-Henriques Carolina , Li Bo 
Published: April 2019

ABSTRACTThe ventral pallidum (VP) is critical for invigorating reward seeking and is also involved in punishment avoidance, but how it contributes to such opposing behavioural actions remains unclear. Here we show that GABAergic and glutamatergic VP neurons selectively control behaviour in opposing motivational contexts. In vivo recording combined with optogenetics in mice revealed that these two populations oppositely encode positive and negative motivational value, are differentially modulated by animal’s internal state and determine the behavioural response during motivational conflict. Furthermore, GABAergic VP neurons are essential for movements towards reward in a positive motivational context, but suppress movements in an aversive context. In contrast, glutamatergic VP neurons are essential for movements to avoid a threat but suppress movements in an appetitive context. Our results indicate that GABAergic and glutamatergic VP neurons encode the drive for approach and avoidance, respectively, with the balance between their activities determining the type of motivational behaviour.
Evolution of neuronal anatomy and circuitry in two highly divergent nematode species
Authors: Hong Ray L. , Riebesell Metta , Bumbarger Daniel J. , Cook Steven J. , Carstensen Heather R. , Sarpolaki Tahmineh , Cochella Luisa , Castrejon Jessica , Moreno Eduardo , Sieriebriennikov Bogdan , Hobert Oliver , Sommer Ralf J. 
Published: April 2019

AbstractThe nematodesC. elegansandP. pacificuspopulate diverse habitats and display distinct patterns of behavior. To understand how their nervous systems have diverged, we undertook a detailed examination of the neuroanatomy of the chemosensory system ofP. pacificus. Using independent features such as cell body position, axon projections and lipophilic dye uptake, we have assigned homologies between the amphid neurons, their first-layer interneurons, and several internal receptor neurons ofP. pacificusandC. elegans.We found that neuronal number and soma position are highly conserved. However, the morphological elaborations of several amphid cilia are different between them, most notably in the absence of ‘winged’ cilia morphology inP. pacificus. We established a synaptic wiring diagram of amphid sensory neurons and amphid interneurons inP. pacificusand found striking patterns of conservation and divergence in connectivity relative toC. elegans, but very little changes in relative neighborhood of neuronal processes.Impact StatementThe substrate for evolutionary divergence does not lie in changes in neuronal cell number or targeting, but rather in sensory perception and synaptic partner choice within invariant, prepatterned neuronal processes.
FGF signalling regulates enhancer activation during ear progenitor induction
Authors: Tambalo Monica , Anwar Maryam , Ahmed Mohi , Streit Andrea 
Published: April 2019

ABSTRACTThe fibroblast growth factor pathway is essential for inner ear induction in many vertebrates, however how it regulates the chromatin landscape to coordinate the activation of otic genes remains unclear. Here we show that FGF exposure of sensory progenitors leads to rapid deposition of active chromatin marks H3K27ac near hundreds of FGF-responsive, otic-epibranchial progenitor (OEP) genes, while H3K27ac is depleted in the vicinity of non-otic genes. Genomic regions that gain H3K27ac act as cis-regulatory elements controlling OEP gene expression in time and space and define a unique transcription factor signature likely to control their activity. Finally, we provide evidence that in response to FGF signalling the transcription factor dimer AP1 recruits the histone acetyl transferase p300 to OEP enhancers and that de novo acetylation is required for subsequent expression of OEP genes. Thus, during ear induction FGF signalling modifies the chromatin landscape to promote enhancer activation and chromatin accessibility.
Complete genome sequence and annotation of the laboratory reference strainShigella flexneriserotype 5a M90T and genome-wide transcriptional start site determination
Authors: Cervantes-Rivera Ramón , Tronnet Sophie , Puhar Andrea 
Published: April 2019

AbstractBackgroundShigellais a Gram-negative facultative intracellular bacterium that causes bacillary dysentery in humans.Shigellainvades cells of the colonic mucosa owing to its virulence plasmid-encoded Type 3 Secretion System (T3SS), and multiplies in the target cell cytosol. Although the laboratory reference strainS. flexneriserotype 5a M90T has been extensively used to understand the molecular mechanisms of pathogenesis, its complete genome sequence is not available, thereby greatly limiting studies employing high-throughput sequencing and systems biology approaches.ResultsWe have sequenced, assembled, annotated and manually curated the full genome ofS. flexneri5a M90T. This yielded two complete circular contigs, the chromosome and the virulence plasmid (pWR100). To obtain the genome sequence, we have employed long-read PacBio DNA sequencing followed by polishing with Illumina RNA-seq data. This provides a new pipeline to prepare gapless, highly accurate genome sequences. Furthermore, we have performed genome-wide analysis of transcriptional start sites and determined the length of 5’ untranslated regions (5’-UTRs) at typical culture conditions for the inoculum ofin vitroinfection experiments. We identified 6,723 primary TSS (pTSS) and 7,328 secondary TSS (sTSS). TheS. flexneri5a M90T annotated genome sequence and the transcriptional start sites are integrated into RegulonDB (http://regulondb.ccg.unam.mx) and RSAT (http://embnet.ccg.unam.mx/rsat/) to use its analysis tools inS. flexneri5a M90T genome.ConclusionsWe provide the first complete genome forS. flexneriserotype 5a, specifically the laboratory reference strain M90T. Our work opens the possibility of employingS. flexneriM90T in high-quality systems biology studies such as transcriptomic and differential expression analyses or in genome evolution studies. Moreover, the catalogue of TSS that we report here can be used in molecular pathogenesis studies as a resource to know which genes are transcribed before infection of host cells. The genome sequence, together with the analysis of transcriptional start sites, is also a valuable tool for precise genetic manipulation ofS. flexneri5a M90T. The hybrid pipeline that we report here combining genome sequencing with long-reads technology and polishing with RNAseq data defines a powerful strategy for genome assembly, polishing and annotation in any type of organism.
Gene expression heterogeneity during brain development and aging: temporal changes and functional consequences
Authors: Işıldak Ulaş , Somel Mehmet , Thornton Janet M. , Dönertaş Handan Melike 
Published: April 2019

AbstractCells in largely non-mitotic tissues such as the brain are prone to stochastic (epi-)genetic alterations that may cause increased variability between cells and individuals over time. Although increased inter-individual heterogeneity in gene expression was previously reported, whether this process starts during development or if it is restricted to the aging period has not yet been studied. The regulatory dynamics and functional significance of putative aging-related heterogeneity are also unknown. Here we address these by a meta-analysis of 19 transcriptome datasets from diverse human brain regions. We observed a significant increase in inter-individual heterogeneity during aging (20+ years) compared to postnatal development (0 to 20 years). Increased heterogeneity during aging was consistent among different brain regions at the gene level and associated with lifespan regulation and neuronal functions. Overall, our results show that increased expression heterogeneity is a characteristic of aging human brain, and may influence aging-related changes in brain functions.
Optimal decoding of NFkB signaling dynamic
Authors: Maity Alok , Wollman Roy 
Published: April 2019

AbstractThe encoder/decoder paradigm suggests that signaling networks transform information about the extracellular environment into specific signaling patterns that are then read by downstream effectors to control cellular behavior. Previous work used information theoretical tools to analyze the fidelity of encoding using dynamic signaling patterns. However, as the overall fidelity depends on both encoding and decoding, it is important to consider information loss during signal decoding. Here we used NFkB signaling as a model to understand the accuracy of signal decoding. Using a detailed mathematical model we simulated realistic NFkB signaling patterns with different degrees of variability. The NFkB patterns were used as an input to a simple gene expression model. Analysis of information transmission between ligand and NFkB and ligand and gene expression allow us to determine information loss in both encoding and decoding steps. Information loss could occur due to biochemical noise or due to lack of specificity in decoding response. We found that noise free decoding has very little information loss suggesting that decoding through gene expression can preserve specificity in NFkB patterns. As expected, information transmission through a noisy decoder suffers from information loss. Interestingly, this effect can be mitigated by a specific choice of decoding parameters that can substantially reduce information loss due to biochemical noise during signal decoding. Overall our results show that optimal decoding of dynamic patterns can preserve ligand specificity to maximize the accuracy of cellular response to environmental cues.SynopsisThe fidelity of signal transduction depends on the accurate encoding of ligand information in specific signaling patterns and the reliable decoding of these patterns by downstream gene expression machinery. We present an analysis of the accuracy of decoding processes in the case of the transcription factor NFkB. We show that noiseless decoding can preserve ligand identity with minimal information loss. Noisy decoding does result in information loss, an effect that can be largely mitigated by choice of optimal decoding parameter values.Decoding of dynamic signaling patterns by a simple gene model can preserve most of the information about ligand identity.Noisy decoding will result in information loss, but this effect can be mitigated by the optimal choice of decoding parameters.Improvement in decoding is a result of decreased variability in gene expression patterns.
Mask family proteins ANKHD1 and ANKRD17 regulate YAP nuclear import, stability and phase separation
Authors: Sidor Clara , Borreguero-Munoz Nerea , Fletcher Georgina C , Elbediwy Ahmed , Vanyai Hannah , Guillermin Oriane , Thompson Barry J 
Published: April 2019

AbstractThe Mask family of multiple ankyrin repeat and KH domain proteins were discovered in Drosophila to promote the activity of the transcriptional coactivator Yorkie (Yki), the sole fly homolog of mammalian YAP (YAP1) and TAZ (WWTR1). The molecular function of Mask, or its mammalian homologs Mask1 (ANKHD1) and Mask2 (ANKRD17), remains unclear. Mask family proteins contain two Ankyrin repeat domains that bind Yki/YAP as well as a conserved nuclear localisation sequence (NLS) and nuclear export sequence (NES), suggesting a role in nucleo-cytoplasmic transport. Here we show that Mask acts to promote nuclear import of Yki, and that addition of an ectopic NLS to Yki is sufficient to bypass the requirement for Mask in Yki-driven tissue growth. Mammalian Mask1/2 proteins also promote nuclear import of YAP, as well as stabilising YAP and driving colloidal phase separation into large liquid droplets. Mask1/2 and YAP normally colocalise in a granular fashion in both nucleus and cytoplasm, and are co-regulated during mechanotransduction. Our results suggest that Mask family proteins promote YAP nuclear import and phase separation to regulate YAP stability and transcriptional activity.
Complementary roles for parvalbumin and somatostatin interneurons in the generation of hippocampal gamma oscillations
Authors: Antonoudiou Pantelis , Tan Yu Lin , Kontou Georgina , Upton A. Louise , Mann Edward O. 
Published: April 2019

AbstractGamma-frequency oscillations (30-120 Hz) can be separated into fast (>60 Hz) and slow oscillations, with different roles in neuronal encoding and information transfer. While synaptic inhibition is important for synchronization across the gamma-frequency range, the role of distinct interneuronal subtypes in fast and slow gamma states remains unclear. Here, we used optogenetics to examine the involvement of parvalbumin (PV+) and somatostatin (SST+) expressing interneurons in gamma oscillations in the mouse hippocampal CA3 ex vivo. Disrupting either PV+ or STT+ interneuron activity, via either photo-inhibition or photo-excitation, led to a decrease in the power of cholinergically-induced slow gamma oscillations. Furthermore, photo-excitation of SST+ interneurons induced fast gamma oscillations, which depended on both synaptic excitation and inhibition. Our findings support a critical role for both PV+ and SST+ interneurons in slow hippocampal gamma oscillations, and further suggest that STT+ interneurons are capable of switching the network between slow and fast gamma states.
Optimization of a Modular Steroid-Inducible Gene Expression System for Use in Rice
Authors: Vlad Daniela , Samalova Marketa , Abu-Jamous Basel , Wang Peng , Moore Ian R. , Langdale Jane A. 
Published: April 2019

SUMMARYChemically inducible systems that provide both spatial and temporal control of gene expression are essential tools, with many applications in plant biology. Using Golden Gate modular cloning, we have created a monocot-optimized dexamethasone (DEX)-induciblepOp6/LhGR system and tested its efficacy in rice using the reporter enzyme β-glucuronidase (GUS). The system is tightly regulated and highly sensitive to DEX application, with six hours of induction sufficient to induce high levels of GUS activity in transgenic callus. In seedlings, GUS activity was detectable in the root afterin vitroapplication of just 0.01μM DEX. However, transgenic plants manifested severe developmental perturbations when grown on higher concentrations of DEX. The direct cause of these growth defects is not known, but the rice genome contains sequences with high similarity to the LhGR target sequencelacO, suggesting non-specific activation of endogenous genes by DEX induction. These off-target effects can be minimized by quenching with isopropyl β-D-1-thiogalactopyranoside (IPTG). The system is thus suitable for general use in rice, when the method of DEX application and relevant controls are tailored appropriately for each specific application.
TLR-induced reorganization of the IgM-BCR complex regulates B-1 cell responses to infections
Authors: Savage Hannah P. , Kläsener Kathrin , Smith Fauna L. , Luo Zheng , Reth Michael , Baumgarth Nicole 
Published: April 2019

AbstractNeonatally-developing, self-reactive B-1 cells generate steady levels natural antibodies throughout life. They can, however, also rapidly respond to infections with increased local antibody production. The mechanisms regulating these two seemingly very distinct functions are poorly understood, but have been linked to expression of CD5, an inhibitor of BCR-signaling. Here we demonstrate that TLR-mediated activation of CD5+ B-1 cells induced the rapid reorganization of the IgM-BCR complex, leading to the eventual loss of CD5 expression, and a concomitant increase in BCR-downstream signaling, bothin vitroandin vivoafter infections with influenza virus andSalmonella typhimurium. Both, initial CD5 expression and TLR-mediated stimulation, were required for the differentiation of B-1 cells to IgM-producing plasmablasts after infections. Thus, TLR-mediated signals support participation of B-1 cells in immune defense via BCR-complex reorganization.