bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synchronization of mammalian motile cilia in the brain with hydrodynamic forces
Authors: Pellicciotta Nicola , Hamilton Evelyn , Kotar Jurij , Faucourt Marion , Degehyr Nathalie , Spassky Nathalie , Cicuta Pietro 
Published: June 2019

Motile cilia are widespread across the animal and plant kingdoms, displaying complex collective dynamics central to their physiology. Their coordination mechanism is not generally understood, with pre-vious work mainly focusing on algae and protists. We study here the synchronization of cilia beat in multiciliated cells from brain ven-tricles. The response to controlled oscillatory external flows shows that strong flows at a similar frequency to the actively beating cilia can entrain cilia oscillations. We find that the hydrodynamic forces required for this entrainment strongly depend on the number of cilia per cell. Cells with few cilia (up to five) can be entrained at flows comparable to the cilia-driven flows reported in vivo. Simulations of a minimal model of cilia interacting hydrodynamically show the same trends observed in cilia. Our results suggest that hydrody-namic forces between cilia are sufficient to be the mechanism behind the synchronization of mammalian brain cilia dynamics.Significance StatementIt is shown experimentally, and also reproducing key qualitative results in a minimal mechanistic model simulated numerically, that in the motile cilia of the brain hydrodynamic forces of the magnitude that cilia themselves can generate are sufficient to establish the coordination of dynamics which is so crucial phys-iologically. This is the first experiment of its kind on multicilated cells, the key result is the unexpected importance of cilia num-ber per cell, with cells with fewer cilia much more susceptible to external flows. This finding changes the way in which we think about the question of collective cilia beating - it is not correct to simply examine isolated cilia and draw conclusions about the behaviour of cilia assemblies in multiciliated cells.
β-blockers augment L-type Ca2+channel activity by target-selective spatially restricted β2AR-cAMP-PKA signaling in neurons
Authors: Shen Ao , Chen Dana , Kaur Manpreet , Xu Bing , Shi Qian , Martinez Joseph M. , Man Kwun-nok Mimi , Hell Johannes W. , Navedo Manuel F. , Yu Xi-Yong , Xiang Yang K. 
Published: June 2019

AbstractG protein-coupled receptors (GPCRs) transduce pleiotropic intracellular signals in mammalian cells. Here, we report that some antagonists of β adrenergic receptors (βARs) such as β-blocker carvedilol and alprenolol activate β2AR at nanomolar concentrations, which promote G protein signaling and cAMP/PKA activity without action of G protein receptor kinases (GRKs). The cAMP/PKA signal is restricted within the local plasma membrane domain, leading to selectively enhance PKA-dependent augment of endogenous L-type calcium channel (LTCC) activity but not AMPA receptor in hippocampal neurons. Moreover, we have engineered a mutant β2AR that lacks serine 204 and 207 in the catecholamine binding pocket. This mutant can be preferentially activated by carvedilol but not the orthosteric agonist isoproterenol. Carvedilol activates the mutant β2AR in hippocampal neurons augmenting LTCC activity through cAMP/PKA signaling. Together, our study identifies a mechanism by which β-blocker-dependent activation of GPCRs at low ligand concentrations promotes local cAMP/PKA signaling to selectively target membrane downstream effectors such as LTCC in neurons.
The inter-dimeric interface controls function and stability ofUreaplasma urealiticummethionine S-adenosyltransferase
Authors: Kleiner Daniel , Shmulevich Fannia , Zarivach Raz , Shahar Anat , Sharon Michal , Ben-Nissan Gili , Bershtein Shimon 
Published: June 2019

SummaryMethionine S-adenosyltransferases (MATs) are predominantly homotetramers, comprised of dimers of dimers. The highly conserved dimeric interface harbors two active sites, making the dimer the obligatory functional unit. Yet, functionality of the recently evolved inter-dimeric interface remains unknown. Here, we show that the inter-dimeric interface ofU. urealiticumMAT has evolved to control the catalytic activity and structural integrity of the homotetramer in response to product accumulation. When all four active sites are occupied with the product, S-adenosylmethionine (SAM), binding of four additional SAM molecules to the inter-dimeric interface prompts a ∼45° shift in the dimer orientation and a concomitant ∼60% increase in the interface area. This rearrangement inhibits the enzymatic activity by locking the flexible active site loops in a closed state and renders the tetramer resistant to proteolytic degradation. Our findings suggest that the inter-dimeric interfaces of MATs are recruited by evolution to tune the molecular properties of the entire homotetramer.
BAMscale: quantification of DNA sequencing peaks and generation of scaled coverage tracks
Authors: Pongor Lorinc S. , Gross Jacob M. , Alvarez Roberto Vera , Murai Junko , Jang Sang-Min , Zhang Hongliang , Redon Christophe , Fu Haiqing , Huang Shar-Yin , Thakur Bhushan , Baris Adrian , Marino-Ramirez Leonardo , Landsman David , Aladjem Mirit I. , Pommier Yves 
Published: June 2019

AbstractBAMscale is a one-step tool that processes DNA sequencing datasets from chromatin binding (ChIP-seq) and chromatin state changes (ATAC-seq, END-seq) experiments to DNA replication data (OK-seq, NS-seq and replication timing). The outputs include normalized peak scores in text format and scaled coverage tracks (BigWig) which are directly accessible to data visualization programs. BAMscale (available at https://github.com/ncbi/BAMscale) effectively processes large sequencing datasets (~100Gb size) in minutes, outperforming currently available tools.
A Synthetic Peptide Encoded by a Random DNA Sequence Inhibits Discrete Red Light Responses
Authors: Shuipys Tautvydas , Carvalho Raquel F. , Clancy Maureen A. , Bao Zhilong , Folta Kevin M. 
Published: June 2019

AbstractWe have identified a synthetic peptide that interrupts discrete aspects of seedling development under red light. Previous reports have demonstrated that plants transformed with random DNA sequences produce synthetic peptides that affect plant biology. In this report one specific peptide is characterized that inhibits discrete aspects of red-light-mediated Arabidopsis thaliana development during photomorphogenesis. Seedlings expressing the PEP6-32 peptide presented longer hypocotyls and diminished cotyledon expansion when grown under red light. Other red-light-mediated seedling processes such as induction of Lhcb (cab) transcripts or loss of vertical growth remained unaffected. Long-term responses to red light in PEP6-32 expressing plants, such as repression of flowering time, did not show defects in red light signaling or integration. A synthesized peptide applied exogenously induced the long-hypocotyl phenotype under red light in non-transformed seedlings. The results indicate that the PEP6-32 peptide causes discrete cell expansion defects during early seedling development in red light, mimicking weak phyB alleles in some aspects of seedling photomorphogenesis. The findings demonstrate that new chemistries derived from random peptide expression can modulate specific facets of plant growth and development.One Sentence SummaryA plant line expressing random DNA sequence expresses a synthetic peptide that affects specific red-light responses in a developing seedling.
Stimulation augments spike sequence replay and memory consolidation during slow-wave sleep
Authors: Wei Yina , Krishnan Giri P , Marshall Lisa , Martinetz Thomas , Bazhenov Maxim 
Published: June 2019

AbstractNewly acquired memory traces are spontaneously reactivated during slow-wave sleep (SWS), leading to the consolidation of recent memories. Empirical studies found that sensory stimulation during SWS selectively enhances memory consolidation and the effect depends on the phase of stimulation. In this new study, we aimed to understand the mechanisms behind the role of sensory stimulation on memory consolidation using computational models implementing effects of neuromodulators to simulate transitions between awake and SWS sleep, and synaptic plasticity to allow the change of synaptic connections due to the training in awake or replay during sleep. We found that when closed-loop stimulation was applied during the Down states (900-2700) of sleep slow oscillation, particularly right before transition from Down to Up state, it significantly affected the spatio-temporal pattern of the slow-waves and maximized memory replay. In contrast, when the stimulation was presented during the Up states (2700-3600 and 00-900), it did not have a significant impact on the slow-waves or memory performance after sleep. For multiple memories trained in awake, presenting stimulation cues associated with specific memory trace could selectively augment replay and enhance consolidation of that memory and interfere with consolidation of the others (particularly weak) memories. Our study proposes a synaptic level mechanism of how memory consolidation is affected by sensory stimulation during sleep.Significance statementStimulation, such as training-associated cues or auditory stimulation, during sleep can augment consolidation of the newly encoded memories. In this study, we used a computational model of the thalamocortical system to describe the mechanisms behind the role of stimulation in memory consolidation during slow-wave sleep. Our study suggested that stimulation preferentially strengthens the memory traces when delivered at specific phase of slow oscillations just before Down to Up state transition when it makes the largest impact on the spatio-temporal pattern of sleep slow waves. In the presence of multiple memories, presenting sensory cues during sleep could selectively strengthen selected memories. Our study proposes a synaptic level mechanism of how memory consolidation is affected by sensory stimulation during sleep.
Anti-oxidant, anti-apoptotic, anti-hypoxic and anti-inflammatory conditions induced by PTY-2 against STZ-induced stress in islets
Authors: Srivastava Shivani , Pandey Harsh , Singh Surya Kumar , Tripathi Yamini Bhusan 
Published: June 2019

AbstractBackground and AimEarlier assessment of Pueraria tuberosa tubers has shown anti-diabetic effects through incretin mimetic action and DPP-IV inhibition. The aim of this work was to further explore the protective role of aqueous extract of Pueraria tuberosa against streptozotocin (STZ)-induced pancreatic stress in rats.MethodsDiabetes was induced with STZ (65 mg/kg body weight) in Charles foster male rats. After 60 days of STZ administration, animals with blood glucose levels > 200 g/dL were considered as diabetic. All the rats were later divided into three groups: Group-1 (STZ untreated normal rats), Group-2 (Diabetic control), and Group-3 (PTY-2 [50 mg/100 g bw treatment for next 10 days to diabetic rats). The rats were then sacrificed at the 10th day of treatment accordingly.ResultsSTZ treatment led to an increase in expression of MMP-9, Tnf α, HIF-1α, VEGF, IL-6, PKC ε, NF-kB, and Caspase-3. Reverse transcriptase Polymerase Chain Reaction (PCR), IHC and western blot analysis showed an increase in the expressions of superoxide dismutase (SOD) and Nephrin, and a decrease in the expressions of NF-kB, PKC ε, TNF-α MMP-9, HIF-1α, VEGF, Caspase 3 and IL-6 after 10 days of PTY-2 treatment.ConclusionThe results show that PTY-2 favorably changed the expression of NF-kB, PKC ε, TNF α, MMP 9, HIF-1α, VEGF, IL-6, Caspase3, Nephrin and SOD in cases of STZ-induced pancreatic stress. Further evaluation of PTY-2 might be helpful in establishing its role in the management of diabetes mellitus.HighlightsPTY 2 act as a protective herbal drug against STZ induced islet stress.PTY 2 upregulates protective and downregulates harmful markers.This study composed of four pathway through which PTY 2 acts on pancreas.GRAPHICAL ABSTRACTMechanism of action of PTY 2 against STZ induced islet stress.
Efficient depletion of ribosomal RNA for RNA sequencing in planarians
Authors: Kim Iana V. , Ross Eric J. , Dietrich Sascha , Döring Kristina , Sánchez Alvarado Alejandro , Kuhn Claus-D. 
Published: June 2019

AbstractBackgroundThe astounding regenerative abilities of planarian flatworms prompt a steadily growing interest in examining their molecular foundation. Planarian regeneration was found to require hundreds of genes and is hence a complex process. Thus, RNA interference followed by transcriptome-wide gene expression analysis by RNA-seq is a popular technique to study the impact of any particular planarian gene on regeneration. Typically, the removal of ribosomal RNA (rRNA) is the first step of all RNA-Seq library preparation protocols. To date, rRNA removal in planarians was primarily achieved by the enrichment of polyadenylated (poly(A)) transcripts. However, to better reflect transcriptome dynamics and to cover also non-poly(A) transcripts, a procedure for the targeted removal of rRNA in planarians is needed.ResultsIn this study, we describe a workflow for the efficient depletion of rRNA in the planarian model species S. mediterranea. Our protocol is based on subtractive hybridization using organism-specific probes. Importantly, the designed probes also deplete rRNA of other freshwater triclad families, a fact that considerably broadens the applicability of our protocol. We tested our approach on total RNA isolated stem cells (termed neoblasts) of S. mediterranea and compared ribodepleted libraries with publicly available poly(A)-enriched ones. Overall, mRNA levels after ribodepletion were consisted with poly(A) libraries. However, ribodepleted libraries revealed higher transcript levels for transposable elements and histone mRNAs that remained underrepresented in poly(A) libraries. As neoblasts experience high transposon activity this suggests that ribodepleted libraries better reflect the transcriptional dynamics of planarian stem cells. Furthermore, the presented ribodepletion procedure was successfully expanded to the removal of ribosomal RNA from the gram-negative bacterium Salmonella typhimurium.ConclusionsThe ribodepletion protocol presented here ensures the efficient rRNA removal from low input total planarian RNA, which can be further processed for RNA-Seq applications. Resulting libraries contain less than 2% rRNA. Moreover, for a cost-effective and efficient removal of rRNA prior to sequencing applications our procedure might be adapted to any prokaryotic or eukaryotic species of choice.
Antibiotic resistant bacteria and commensal fungi are common and conserved in the mosquito microbiome
Authors: Hyde Josephine , Gorham Courtney , Brackney Doug E. , Steven Blaire 
Published: June 2019

AbstractThe emerging and increasing prevalence of bacterial antibiotic resistance is a significant public health challenge. To begin to tackle this problem, it will be critical to not only understand the origins of this resistance but also document environmental reservoirs of antibiotic resistance. In this study we investigated the possibility that both colony and field caught mosquitoes could harbor antibiotic resistant bacteria. Specifically, we characterized the antibiotic resistant bacterial populations from colony-reared Aedes aegypti larvae and adults and two field caught mosquito species Coquillettidia perturbans and Ochlerotatus canadensis. The cultured bacterial populations were dominated by isolates belonging to the class Gammaproteobacteria. Among the antibiotic resistant populations, we found bacteria resistant to carbenicillin, kanamycin, and tetracycline, including bacteria resistant to a cocktail of all three antibiotics in combination. The antibiotic resistant bacteria were numerically rare, at most 5% of total cell counts. Isolates were characterized by 16S rRNA gene sequencing, and clustering into Operational Taxonomic Units (OTUs; 99% sequence identity). 27 antibiotic resistant OTUs were identified, although members of an OTU did not always share the same resistance profile. This suggests the clustering was either not sensitive enough to distinguish different bacteria taxa or different antibiotic resistant sub-populations exist within an OTU. Finally, the antibiotic selection opened up a niche to culture mosquito-associated fungi, and 10 fungal OTUs (28S rRNA gene sequencing) were identified. Two fungal OTUs both classified to the class Microbotryomycetes were commonly identified in the field-caught mosquitoes. Thus, in this study we demonstrate that antibiotic resistant bacteria and certain fungi are common and conserved mosquito microbiome members. These observations highlight the potential of invertebrates to serve as vehicles for the spread of antibiotic resistance throughout the environment.
Mechanization services, farm productivity and institutional innovation in China
Authors: Qing Yi , Chen Moyu , Sheng Yu , Huang Jikun 
Published: June 2019

Purpose
The purpose of this paper is to investigate the impact of mechanization services on farm productivity in Northern China from an empirical perspective, with the aim to identify the underlying market and institutional barriers.

Design/methodology/approach
The authors apply the regression method with the control of village fixed effects to examining the relationship between capital–labor ratio, mechanization service ratio and farm productivity, using the panel data collected in 2013 and 2015 by CCAP.

Findings
Mechanization services improve farm productivity through substituting labor, but it may generate a less positive impact on farms who do not have self-owned capital equipment.

Originality/value
It is the first study to investigate how mechanization services affect farm productivity for grain producers in Northern China.
Natural convection in differentially heated enclosures subjected to variable temperature boundaries
Authors: Mohamad Abdulmajeed , Sheremet Mikhail A. , Taler Jan , Ocłoń Paweł 
Published: June 2019

Purpose
Natural convection in differentially heated enclosures has been extensively investigated due to its importance in many industrial applications and has been used as a benchmark solution for testing numerical schemes. However, most of the published works considered uniform heating and cooling of the vertical boundaries. This paper aims to examine non-uniform heating and cooling of the mentioned boundaries. The mentioned case is very common in many electronic cooling devices, thermal storage systems, energy managements in buildings, material processing, etc.

Design/methodology/approach
Four cases are considered, the left-hand wall’s temperature linearly decreases along the wall, while the right-hand wall’s temperature is kept at a constant, cold temperature. In the second case, the left-hand wall’s temperature linearly increases along the wall, while the right-hand wall’s temperature is kept a constant, cold temperature. The third case, the left-hand wall’s temperature linearly decreases along the wall, while the right-hand wall’s temperature linearly increases along the wall. In the fourth case, the left-hand and the right-hand walls’ temperatures decrease along the wall, symmetry condition. Hence, four scenarios of natural convection in enclosures were covered.

Findings
It has been found that the average Nusselt number of the mentioned cases is less than the average Nusselt number of the uniformly heated and cooled enclosure, which reflects the physics of the problem. The work quantifies the deficiency in the rate of the heat transfer. Interestingly one of the mentioned cases showed two counter-rotating horizontal circulations. Such a flow structure can be considered for passively, highly controlled mechanism for species mixing processes application.

Originality/value
Previous works assumed that the vertical boundary is subjected to a constant temperature or to a sinusoidal varying temperature. The subject of the work is to examine the effect of non-uniformly heating and/or cooling vertical boundaries on the rate of heat transfer and flow structure for natural convection in a square enclosure. The temperature either linearly increases or decreases along the vertical coordinate at the boundary. Four scenarios are explored.
Capital market development and bank efficiency: a cross-country analysis
Authors: Ngo Thanh , Le Tu 
Published: June 2019

PurposeThe purpose of this paper is to empirically investigate the causal relationship between banking efficiency and capital market development in 86 countries between 2006 and 2011.Design/methodology/approachThe authors follow the two-stage framework: data envelopment analysis (DEA) with the use of financial ratios is used to arrive at efficiency scores of the banks in the first stage. Thereafter, those efficiency scores will be linked with the development level of the capital markets of the corresponding country in the second stage using the generalised method of moments in a simultaneous equations model.FindingsThe authors found that banking systems around the world were still inefficient, suggesting that it would take time for the global banking system to recover after the global financial crisis 2007/2008. More importantly, the findings demonstrated that the larger the capital market is, the less efficient its banking system would be. In contrast, banking efficiency can positively influence the development of the capital market.Research limitations/implicationsThe data are unbalanced and limited to 86 countries; the study did not analyse the productivity change over time of those banking systems; and it would be useful to test the first-stage DEA with different sets of variables as well as different assumptions.Practical implicationsThe paper suggests that for any economy around the world, an improvement in banking performance and efficiency rather than capital market development should be a priority, alongside with monitoring inflation.Originality/valueThe paper provides an unbiased analysis of the causal relationship between the banking sector and the capital market.
Retail strategies for rosé wines in Italy: a hedonic price analysis
Authors: Rossetto Luca , Galletto Luigi 
Published: June 2019

Purpose
The purpose of this paper is to analyze the market of rosé wines in Italy, to outline retail strategies and to investigate to what extent the price is affected by branding these wines.

Design/methodology/approach
A survey has been carried out on retailers by collecting data about wines as intrinsic attributes (grape variety, blending, origin, alcohol content, etc.) and extrinsic attributes (brand, price, packaging, etc.) and about outlet and retail environment. The hedonic analysis required a rearrangement of data survey, while a Box-Cox transformation allowed to control the strong heteroskedasticity detected of the data.

Findings
Results provide strategies for still, semi-sparkling and sparkling rosé market segments. Still rosé wines are strongly differentiated, while the price is affected by the appellation, grape variety, blending, brand and outlet features. Two main strategies are suggested: the first focuses on appellations endorsing consumer’s brand loyalty; the second is driven by retailers while involving weaker brands. Different pictures emerged for semi-sparkling and sparkling wines, as producers and retailers tend to follow consumer’s preferences for fresh and easy drinking wines as well as to extend the product assortment.

Research limitations/implications
Results for sparkling rosé wines cannot be generalized. The high fragmentation hinders the hedonic model performance in capturing the price effects of brands, appellations, grape variety and wine blend.

Practical implications
The hedonic analysis provides suggestions for rosé wine producers that should reinforce their brand through associations among intrinsic attributes, such as appellation, and extrinsic ones, such as price, while satisfying retailer requirements.

Originality/value
The paper contributes to the knowledge base about the Italian rosé wine market, which is mostly export-oriented. Model results help to understand why the domestic consumption is stagnant with respect to other countries such as France or the USA.