bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes
Authors: Ward Michelle C. , Banovich Nicholas E. , Sarkar Abhishek , Stephens Matthew , Gilad Yoav
Published: March 2020

One life-threatening outcome of cardiovascular disease is myocardial infarction, where cardiomyocytes are deprived of oxygen. To study inter-individual differences in response to hypoxia, we established anin vitromodel of induced pluripotent stem cell-derived cardiomyocytes from 15 individuals. We measured gene expression levels, chromatin accessibility, and methylation levels in four culturing conditions that correspond to normoxia, hypoxia and short or long-term re-oxygenation. We characterized thousands of gene regulatory changes as the cells transition between conditions. Using available genotypes, we identified 1,573 genes with acisexpression quantitative locus (eQTL) in at least one condition, as well as 367 dynamic eQTLs, which are classified as eQTLs in at least one, but not in all conditions. A subset of genes with dynamic eQTLs is associated with complex traits and disease. Our data demonstrate how dynamic genetic effects on gene expression, which are likely relevant for disease, can be uncovered under stress.
Cryo-EM structures of SERCA2b reveal the mechanism of regulation by the luminal extension tail
Authors: Zhang Yuxia , Inoue Michio , Tsutsumi Akihisa , Watanabe Satoshi , Nishizawa Tomohiro , Nagata Kazuhiro , Kikkawa Masahide , Inaba Kenji
Published: March 2020

SERCA2b is a Ca2+-ATPase that pumps Ca2+from the cytosol into the ER and maintains the cellular calcium homeostasis. Herein, we present cryo-EM structures of human SERCA2b in E1·2Ca2+-AMPPCP and E2-BeF3-states at 2.9 and 2.8 Å resolutions, respectively. The structures revealed that the luminal extension tail (LE) characteristic of SERCA2b runs parallel to the lipid-water boundary near the luminal ends of transmembrane (TM) helices TM10 and TM7, and approaches the luminal loop flanked by TM7 and TM8. Upon deletion of the LE, the cytosolic- and TM-domain arrangement of SERCA2b resembled that of SERCA1a, resulting in multiple conformations. The LE regulates the conformational transition between the E1·2Ca2+-ATP and E2P states, explaining the different kinetic properties of SERCA2b from other isoforms lacking the LE.

One sentence summary

Cryo-EM structures of SERCA2b at 2.8-2.9 Å resolutions reveal how the luminal extension tail regulates its activity.
Focusing on human haplotype diversity in numerous individual genomes demonstrates an evolutional feature of each locus
Authors: Shimada Makoto K. , Nishida Tsunetoshi
Published: March 2020

The application of current genome-wide sequencing techniques on human populations helps elucidate the considerable gene flow among genusHomo, which includes modern and archaic humans. Gene flow among current human populations has been studied using frequencies of single nucleotide polymorphisms. Unlike single nucleotide polymorphism frequency data, haplotype data are suitable for identifying and tracing rare evolutionary events. Haplotype data can also conveniently detect genomic location and estimate molecular function that may be a target of selection. We analyzed eight loci of the human genome using the same procedure for each locus to infer human haplotype diversity and reevaluate past explanations of the evolutionary mechanisms that affected these loci. These loci have been recognized by separate studies because of their unusual gene genealogy and geographic distributions that are inconsistent with the recent out-of-Africa model. For each locus, we constructed genealogies for haplotypes using sequence data of the 1000 Genomes Project. Then, we performed S* analysis to estimate distinct gene flow events other than out-of-Africa events. Furthermore, we also estimated unevenness of selective pressure between haplotypes by Extended Haplotype Homozygosity analysis. Based on the patterns of results obtained by this combination of analyses, we classified the examined loci without using a specific population model. This simple method helped clarify evolutionary events for each locus, including rare evolutionary events such as introgression, incomplete lineage sorting, selection, and haplotype recombination that may be hard to discriminate from each other.
Genetic exploration of a nuclear receptor transcriptional regulatory complex
Authors: Asahina Masako , Thurtle-Schmidt Deborah , Yamamoto Keith R.
Published: March 2020

Metazoan transcriptional regulatory factors (TFs) bind to genomic response elements and assemble with co-regulators into transcriptional regulatory complexes (TRCs) whose composition, structure and activities are gene-, cell- and physiological-context specific. Each TRC is a “regulatory logic module,” integrating incoming signaling information, which defines context and thereby recruits a distinct combination of co-regulators that together specify outgoing regulatory activity. Analyzing TRCs unique to every context is daunting, yet justified by their properties as self-contained regulatory modules. As proof-of-concept, we performed a forward genetic screen inC. eleganscarrying a synthetic simple response element for nuclear receptor NHR-25 upstream of a fluorescent reporter gene. We isolated independent mutations inuba-2, a component of the sumoylation signaling machinery, and inlir-2, which we demonstrated to be a novel co-regulator, interacting with NHR-25 through LxxLL motifs and modulating target gene expression. Our studies establish that an unbiased genetic screen readily identifies both afferent and efferent components that specify TRC function, and suggest that screening natural response elements of interest could illuminate molecular mechanisms of both context-specificity and transcriptional regulation.
Imperative role of particulate matter in innate immunity during RNA virus infection
Authors: Mishra Richa , Pandikannan K , Gangamma S , Raut Ashwin Ashok , Kumar Himanshu
Published: March 2020

Sensing of pathogens by specialized receptors is the hallmark of the innate immune response. Innate immune response also mounts a defense response against various allergens and pollutants including particulate matter present in the atmosphere. Air pollution has been included as the top threat to global health declared by WHO which aims to cover more than three billion people against health emergencies from 2019-2023. Particulate matter (PM), one of the major components of air pollution, is a significant risk factor for many human diseases and its adverse effects include morbidity and premature deaths throughout the world. Several clinical and epidemiological studies have identified a key link between the PM composition and the prevalence of respiratory and inflammatory disorders. However, the underlying molecular mechanism is not well understood. Here, we investigated the influence of air pollutant, PM10during RNA virus infections using highly pathogenic avian influenza (HPAI). We thus characterized the transcriptomic profile of lung epithelial cell line, A549 treated with PM10prior to infection with (HPAI) H5N1 influenza virus, which is known to severely affect the lung and cause respiratory damage. We found that PM10regulates virus infectivity and enhances overall pathogenic burden in the lung cells. Additionally, the transcriptomic profile highlights the connection of host factors related to various metabolic pathways and immune responses which were dysregulated during virus infection. Overall our findings suggest a strong link between the prevalence of respiratory illness and the air quality.
Genomic evidence for recurrent genetic admixture during domestication mediterranean olive trees (Olea europaea)
Authors: Julca Irene , Marcet-Houben Marina , Cruz Fernando , Gómez-Garrido Jèssica , Gaut Brandon S. , Díez Concepción M. , Gut Ivo G. , Alioto Tyler S. , Vargas Pablo , Gabaldón Toni
Published: March 2020

Background

The olive tree (Olea europaeaL. subsp.europaea, Oleaceae) has been the most economic perennial crop for Mediterranean countries since its domestication around 6,000 years ago. Two taxonomic varieties are currently recognized: cultivated (var.europaea) and wild (var.sylvestris) trees. To shed light into the recent evolution and domestication of the olive tree, we sequenced the genomes of twelve individuals: ten var.europaea, one var.sylvestris, and one outgroup taxon (subsp.cuspidata). All of them were analysed together with an improved assembly of var.europaeareference genome and the available assembly of var.sylvestris.

Results

Our analyses show that cultivated olives exhibit slightly lower levels of overall genetic diversity than wild forms, and that this can be partially explained by the occurrence of a mild population bottleneck 5000-7000 years ago during the primary domestication period. We also provide the first phylogenetic analysis of genome-wide sequences, which supports a continuous process of domestication of the olive tree. This, together with population structure and introgression analyses highlights genetic admixture with wild populations across the Mediterranean Basin in the course of domestication.

Conclusions

Altogether, our results suggest that a primary domestication area in the eastern Mediterranean basin was followed by numerous secondary events across most countries of southern Europe and northern Africa, often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin. Based on selection tests and a search for selective sweeps, we found that genes associated with stress response and developmental processes were positively selected in cultivars. However, we did not find evidence that genes involved in fruit size or oil content were under positive selection.
A unified mechanism for spatiotemporal patterns in somitogenesis
Authors: Kuyyamudi Chandrashekar , Menon Shakti N. , Sinha Sitabhra
Published: March 2020

Somitogenesis, the process of body segmentation during embryonic development, exhibits a key set of features that is conserved across all vertebrate species despite differences in the detailed mechanisms. Prior to the formation of somites along the pre-somitic mesoderm (PSM), periodic expression of clock genes is observed in its constituent cells. As the PSM expands through the addition of new cells at its posterior, the oscillations in the cells closer to the anterior cease and eventually lead to formation of rostral and caudal halves of the somites. This pattern formation is believed to be coordinated by interactions between neighboring cells via receptor-ligand coupling. However, the mechanism underlying the transition from synchronized oscillations to traveling waves and subsequent arrest of activity, followed by the appearance of polarized somites, has not yet been established. In this paper we have proposed a unified mechanism that reproduces the sequence of dynamical transitions observed during somitogenesis by combining the local interactions mediated via Notch-Delta intercellular coupling with global spatial heterogeneity introduced through a morphogen gradient that is known to occur along the anteroposterior axis of the growing PSM. Our model provides a framework that integrates a boundary-organized pattern formation mechanism, which uses positional information provided by a morphogen gradient, with the coupling-mediated self-organized emergence of collective dynamics, to explain the processes that lead to segmentation.
Conserved luminal C-terminal domain dynamically controls interdomain communication in sarcolipin
Authors: Aguayo-Ortiz Rodrigo , Fernández-de Gortari Eli , Espinoza-Fonseca L. Michel
Published: March 2020

Sarcolipin (SLN) mediates Ca2+ transport and metabolism in muscle by regulating the activity of the Ca2+ pump SERCA. SLN has a conserved luminal C-terminal domain that contributes to the its functional divergence among homologous SERCA regulators, but the precise mechanistic role of this domain remains poorly understood. We used all-atom molecular dynamics (MD) simulations of SLN totaling 77.5 μs to show that the N- (NT) and C-terminal (CT) domains function in concert. Analysis of the MD simulations showed that serial deletions of SLN C-terminus does not affect the stability of the peptide nor induce dissociation of SLN from the membrane but promotes a gradual decrease in both tilt angle of the transmembrane helix and the local thickness of the lipid bilayer. Mutual information analysis showed that the NT and CT domains communicate with each other in SLN, and that interdomain communication is partially or completely abolished upon deletion of the conserved segment Tyr29-Tyr31 as well as by serial deletions beyond this domain. Phosphorylation of SLN at residue Thr5 also induces changes in the communication between the CT and NT domains, thus providing additional evidence for interdomain communication within SLN. We found that interdomain communication is independent of the force field used and lipid composition, thus demonstrating that communication between the NT and CT domains is an intrinsic functional feature of SLN. We propose the novel hypothesis that the conserved C-terminus is an essential element required for dynamic control of SLN regulatory function.

Abstract Figure
Identification and characterization of diverse OTU deubiquitinases in bacteria
Authors: Schubert Alexander F. , Nguyen Justine V. , Franklin Tyler G. , Geurink Paul P. , Roberts Cameron G. , Sanderson Daniel J. , Miller Lauren N. , Ovaa Huib , Hofmann Kay , Pruneda Jonathan N. , Komander David
Published: March 2020

Manipulation of host ubiquitin signaling is becoming an increasingly apparent evolutionary strategy among bacterial and viral pathogens. By removing host ubiquitin signals, for example, invading pathogens can inactivate immune response pathways and evade detection. The Ovarian Tumor (OTU) family of deubiquitinases regulates diverse ubiquitin signals in humans. Viral pathogens have also extensively co-opted the OTU fold to subvert host signaling, but the extent to which bacteria utilize the OTU fold was unknown. We have predicted and validated a set of OTU deubiquitinases encoded by several classes of pathogenic bacteria. Biochemical assays highlight the ubiquitin and polyubiquitin linkage specificities of these bacterial deubiquitinases. By determining the ubiquitin-bound structures of two examples, we demonstrate the novel strategies that have evolved to both thread an OTU fold and to recognize a ubiquitin substrate. With these new examples, we perform the first cross-kingdom structural analysis of the OTU fold that highlights commonalities among distantly-related OTU deubiquitinases.
Differential diffusional properties in loose and tight docking prior to membrane fusion
Authors: Witkowska Agata , Spindler Susann , Mahmoodabadi Reza Gholami , Sandoghdar Vahid , Jahn Reinhard
Published: March 2020

Fusion of biological membranes, although mediated by divergent proteins, is believed to follow a common pathway. It proceeds through distinct steps including docking, merger of proximal leaflets (stalk formation), and formation of a fusion pore. However, the structure of these intermediates is difficult to study due to their short lifetime. Previously, we observed a loosely and tightly docked state preceding leaflet merger using arresting point mutations in SNARE proteins, but the nature of these states remained elusive. Here we used interferometric scattering (iSCAT) microscopy to monitor diffusion of single vesicles across the surface of giant unilamellar vesicles (GUVs). We observed that the diffusion coefficients of arrested vesicles decreased during progression through the intermediate states. Modeling allowed for predicting the number of tethering SNARE complexes upon loose docking and the size of the interacting membrane patches upon tight docking. These results shed new light on the nature of membrane-membrane interactions immediately before fusion.
An optogenetic switch for the Set2 methyltransferase provides evidence for rapid transcription-dependent and independent dynamics of H3K36 methylation
Authors: Lerner Andrew M. , Hepperla Austin J. , Keele Gregory R. , Meriesh Hashem , Yumerefendi Hayretin , Restrepo David , Zimmerman Seth , Bear James , Kuhlman Brian , Davis Ian J. , Strahl Brian D.
Published: March 2020

Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification associated with transcription and DNA repair. Although the effects of H3K36 methylation have been studied, the short-term genome-wide dynamics of H3K36me deposition and removal are not known. We established rapid and reversible optogenetic control for Set2, the sole H3K36 methyltransferase in yeast, by fusing the enzyme with the light activated nuclear shuttle (LANS) domain. Early H3K36me3 dynamics identified rapid methylationin vivo, with total H3K36me3 levels correlating with RNA abundance. Although genes exhibited disparate levels of H3K36 methylation, relative rates of H3K36me3 accumulation were largely linear and consistent across genes, suggesting a rate-limiting mechanism for H3K36me3 deposition. Removal H3K36me2/3 was also rapid and highly dependent on the demethylase Rph1. However, the per-gene rate of H3K36me3 loss weakly correlated with RNA abundance and followed exponential decay, suggesting H3K36 demethylases act in a global, stochastic manner.
New and improved GRAB fluorescent sensors for monitoring dopaminergic activityin vivo
Authors: Sun Fangmiao , Zhou Jingheng , Dai Bing , Qian Tongrui , Zeng Jianzhi , Li Xuelin , Zhuo Yizhou , Zhang Yajun , Tan Ke , Feng Jiesi , Dong Hui , Qian Cheng , Lin Dayu , Cui Guohong , Li Yulong
Published: March 2020

The monoamine neuromodulator dopamine (DA) plays a critical role in the brain, and the ability to directly measure dopaminergic activity is essential for understanding its physiological functions. We therefore developed the first red fluorescent GPCR-activation–based DA (GRABDA) sensors and optimized versions of green fluorescent GRABDAsensors following our previous studies. In response to extracellular DA, both the red and green GRABDAsensors have a large increase in fluorescence (ΔF/F0values of 150% and 340%, respectively), with subcellular resolution, subsecond kinetics, and nanomolar to submicromolar affinity. Moreover, both the red and green GRABDAsensors readily resolve evoked DA release in mouse brain slices, detect compartmental DA release in live flies with single-cell resolution, and report optogenetically elicited nigrostriatal DA release as well as mesoaccumbens dopaminergic activity during sexual behavior in freely behaving mice. Importantly, co-expressing red GRABDAwith either green GRABDAor the calcium indicator GCaMP6s provides a robust tool for simultaneously tracking neuronal activity and dopaminergic signaling in distinct circuitsin vivo.
Population structure and pharmacogenomic risk stratification in the United States
Authors: Nagar Shashwat Deepali , Conley Andrew B. , King Jordan I.
Published: March 2020

Pharmacogenomic (PGx) variants mediate how individuals respond to medication, and response differences among racial/ethnic groups have been attributed to patterns of PGx diversity. We hypothesized that genetic ancestry (GA) would provide higher resolution for stratifying PGx risk, since it serves as a more reliable surrogate for genetic diversity than self-identified race/ethnicity (SIRE), which includes a substantial social component. We analyzed a cohort of 8,628 individuals from the United States (US), for whom we had both SIRE information and whole genome genotypes, with a focus on the three largest SIRE groups in the US: White, Black, and Hispanic. Whole genome genotypes were used to characterize individuals’ continental ancestry fractions – European, African, and Native American – and individuals were grouped according to their GA profiles. SIRE and GA groups were found to be highly concordant. Continental ancestry predicts individuals’ SIRE with >96% accuracy, and accordingly GA provides only a marginal increase in resolution for PGx risk stratification. PGx variants are highly diverged compared to the genomic background; 82 variants show significant frequency differences among SIRE groups, and genome-wide patterns of PGx variation are almost entirely concordant with SIRE. Nevertheless, 97% of PGx variation is found within rather than between groups. Examples of highly differentiated PGx variants illustrate how SIRE partitions PGx variation based on group-specific ancestry patterns and contains valuable information for risk stratification. Finally, we show that individuals who identify as Black or Hispanic benefit more when SIRE is considered for treatment decisions than individuals from the majority White population.
Predicting Molecular Fingerprint from Electron−Ionization Mass Spectrum with Deep Neural Networks
Authors: Ji Hongchao , Lu Hongmei , Zhang Zhimin
Published: April 2020

Electron−ionization mass spectrometry (EI-MS) hyphenated gas chromatography (GC) is the workhorse to analyze volatile compounds in complex samples. The spectral matching method can only identify compounds within spectral database. In response, we present a deep-learning-based approach (DeepEI) for structure elucidation of unknown compound with its EI-MS spectrum. DeepEI employs deep neural networks to predict molecular fingerprint from EI-MS spectrum, and searches molecular structure database with the predicted fingerprints. In addition, a convolutional neural network was also trained to filter the structures in database and improve the identification performance. Our method shows improvement on the competing method NEIMS in identification accuracy on both NIST test dataset and MassBank dataset. Furthermore, DeepEI (spectrum to fingerprint) and NEIMS (fingerprint to spectrum) can be combined to improve identification accuracy.
Host-dependent differences in replication strategy of theSulfolobusSpindle-shaped Virus strain SSV9 (a.k.a., SSVK1): Lytic replication in hosts of the family Sulfolobaceae
Authors: Ceballos Ruben Michael , Drummond Coyne , Stacy Carson Len , Crespo Elizabeth Padilla , Stedman Kenneth
Published: April 2020

TheSulfolobusSpindle-shaped Virus (SSV) system has become a model for studying thermophilic virus biology, including archaeal host-virus interactions and biogeography. Several factors make the SSV system amenable to studying archaeal genetic mechanisms (e.g., CRISPRs) as well as virus-host interactions in high temperature acidic environments. First, it has been shown that endemic populations ofSulfolobus, the reported SSV host, exhibit biogeographic structure. Second, the acidic (pH<4.5) high temperature (65-88°C) SSV habitats have low biodiversity, thus, diminishing opportunities forhost switching. Third, SSVs and their hosts are readily cultured in liquid media and on gellan gum plates. Fourth, given the wide geographic separation between the variousSSV-Sulfolobushabitats, the system is amenable for studying allopatric versus sympatric virus-host interactions. Previously, we reported that SSVs exhibit differential infectivity on allopatric and sympatric hosts. We also noticed a wide host range for virus strain SSV9 (a.k.a., SSVK1). For decades, SSVs have been described as “non-lytic” dsDNA viruses that infect species of the genusSulfolobusand release virions via “blebbing” or “budding” as a preferred strategy over host lysis. Here, we show that SSVs infect more than one genus of the family Sulfolobaceae and, in allopatric hosts, SSV9 does not appear to release virions by blebbing. Instead, SSV9 appears to lyse all susceptible allopatric hosts tested, while exhibiting canonical non-lytic viral release via “blebbing” (historically reported for all other SSVs), on a single sympatric host. Lytic versus non-lytic virion release does not appear to be driven by multiplicity of infection (MOI). Greater relative stability of SSV9 compared to other SSVs (i.e., SSV1) in high temperature, low pH environments may contribute to higher transmission rates. However, neither higher transmission rate nor relative virulence in SSV9 infection drives replication profile (i.e., lytic versus non-lytic) in susceptible hosts. Although it is known that CRISPR-Cas systems offer protection against viral infection in prokaryotes, CRISPRS are not reported to be a determinant virus replication strategy. Thus, the genetic/molecular mechanisms underlying SSV9-induced lysis are unknown. These results suggest that there are unknown genetic elements, resulting from allopatric evolution, that drive virion release strategy in specific host strain-SSV strain pairings.
Fast Cell Parasites Detection with Neural Networks
Authors: Xu X. F. , Talbot S. , Lu S. B. , Selvaraja T.
Published: April 2020

Deep learning has dramatically improved the performance in many application areas such as image classification, object detection, speech recognition, drug discovery and etc since 2012. Where deep learning algorithms promise to discover the intricate hidden information inside the data by leveraging the large dataset, advanced model and computing power. Although deep learning techniques show medical expert level performance in a lot of medical applications, but some of the applications are still not explored or under explored due to the variation of the species. In this work, we studied the bright field based cell level Cryptosporidium and Giardia detection in the drink water with deep learning. Our experimental demonstrates that the new developed deep learning-based algorithm surpassed the handcrafted SVM based algorithm with above 97 percentage in accuracy and 700+fps in speed on embedded Jetson TX2 platform. Our research will lead to real-time and high accuracy label-free cell level Cryptosporidium and Giardia detection system in the future.
Analysis of the Worldwide Corona Virus (COVID-19) Pandemic Trend; A Modelling Study to Predict Its Spread
Authors: Qasim Muhammad , Ahmad Waqas , Yoshida Minami , Gould Maree , Yasir Muhammad
Published: April 2020

Objective

The Coronavirus (COVID-19) has advanced into 197 countries and territories leaving behind a total of 372,757 confirmed cases and 16231 deaths.

Methods

One the basis of WHO situation reports data of COVID-19 along with daily official reports from the Japan, China and the Kore we modelled the spread of COVID19 by using the Successive Approximation Method. We defined the two state of data to find the mean ratio (η) of the present cases count to the sum of previous and present cases. This ratio further predicts the future state of COVID-19 pandemic.

Results

The mean ratio (η) of expected cases were found 0.485, while the mean ratio for deaths was found to be 0.49. We calculated worldwide expected lower bound value for confirmed cases 247007 cases with maximum limit of 1667719 cases and minimum deaths count 8660 with upper limit of 117397 deaths in next 30 days. While in the case of Iran, a large increase in the number of deaths are expected in the upcoming 30 days with lower bound value of 1140 deaths and maximum value of 598478 deaths.

Interpretation

Iran whole population is on risk.
Collapse of the hepatic gene regulatory network in the absence of FoxA factors
Authors: Reizel Yitzhak , Morgan Ashleigh , Gao Long , Lan Yemin , Manduchi Elisabetta , Waite Eric L. , Wang Amber W. , Wells Andrew , Kaestner Klaus H.
Published: April 2020

The FoxA transcription factors are critical for liver development through their pioneering activity, which initiates a highly complex regulatory network thought to become progressively resistant to the loss of any individual hepatic transcription factor via mutual redundancy. To investigate the dispensability of FoxA factors for maintaining this regulatory network, we ablated all FoxA genes in the adult mouse liver. Remarkably, loss of FoxA caused rapid hepatocyte dedifferentiation manifested by a massive reduction in the expression of key liver genes. Interestingly, expression of these genes was reduced back to the low levels of the fetal prehepatic endoderm stage, leading to necrosis and lethality within days. Mechanistically, we found FoxA proteins to be required for maintaining enhancer activity, chromatin accessibility, nucleosome positioning and binding by HNF4α. Thus, the FoxA factors act continuously, guarding hepatic enhancer activity throughout life.
Glucosylhydroxyceramides Modulate Secretion Machinery of a Subset of Plasmodesmata Proteins and a Change in the Callose Accumulation
Authors: Iswanto Arya Bagus Boedi , Shon Jong Cheol , Vu Minh Huy , Kumar Ritesh , Liu Kwang Hyeon , Kim Jae-Yean
Published: April 2020

The plasma membranes encapsulated in the plasmodesmata (PDs) with symplasmic nano-channels contain abundant lipid rafts, which are enriched by sphingolipids and sterols. The attenuation of sterol compositions has demonstrated the role played by lipid raft integrity in the intercellular trafficking of glycosylphosphatidylinositol (GPI)-anchored PD proteins, particularly affecting in the callose enhancement. The presence of callose at PD is tightly attributed to the callose metabolic enzymes, callose synthases (CalSs) and β-1,3-glucanases (BGs) in regulating callose accumulation and callose degradation, respectively. Sphingolipids have been implicated in signaling and membrane protein trafficking, however the underlying processes linking sphingolipid compositions to the control of symplasmic apertures remain unknown. A wide variety of sphingolipids in plants prompts us to investigate which sphingolipid molecules are important in regulating symplasmic apertures. Here, we demonstrate that perturbations of sphingolipid metabolism by introducing several potential sphingolipid (SL) pathway inhibitors and genetically modifying SL contents from two independent SL pathway mutants are able to modulate callose deposition to control symplasmic connectivity. Our data from pharmacological and genetic approaches show that the alteration in glucosylhydroxyceramides (GlcHCers) particularly disturb the secretory machinery for GPI-anchored PdBG2 protein, resulting in an over accumulated callose. Moreover, our results reveal that SL-enriched lipid rafts link symplasmic channeling to PD callose homeostasis by controlling the targeting of GPI-anchored PdBG2. This study elevates our understanding of the molecular linkage underlying intracellular trafficking and precise targeting to specific destination of GPI-anchored PD proteins incorporated with GlcHCers contents.
The influence of training-induced sarcomerogenesis on the history dependence of force
Authors: Chen Jackey , Mashouri Parastoo , Fontyn Stephanie , Valvano Mikella , Elliott-Mohamed Shakeap , Noonan Alex M. , Brown Stephen H. M. , Power Geoffrey A.
Published: April 2020

The increase or decrease in isometric force following active muscle lengthening or shortening, relative to a reference isometric contraction at the same muscle length and level of activation, are referred to as residual force enhancement (rFE) and residual force depression (rFD), respectively. The purpose of these experiments was to gain further mechanistic insight into the trainability of rFE and rFD, on the basis of serial sarcomere number (SSN) alterations to length-dependent properties. Maximal rFE/rFD measures from the soleus and extensor digitorum longus (EDL) of rats were compared after 4 weeks of uphill/downhill running and a no running control. Serial sarcomere numbers adapted to the training: soleus serial sarcomere number was greater with downhill compared to uphill running, while EDL demonstrated a trend towards more serial sarcomeres for downhill compared to no running. In contrast, absolute and normalized rFE/rFD did not differ across training groups for either muscle. As such, it appears that training-induced SSN adaptations do not modify rFE/rFD at the whole-muscle level.

Summary Statement

The addition and subtraction of serial sarcomeres induced by downhill and uphill running, respectively, did not influence the magnitude of stretch-induced force enhancement and shortening-induced force depression.
Persister state-directed transitioning and vulnerability in melanoma
Authors: Chauvistré Heike , Shannan Batool , Daignault Sheena M. , Ju Robert J. , Picard Daniel , Egetemaier Stefanie , Váraljai Renáta , Sechi Antonio , Kaschani Farnusch , Keminer Oliver , Stehbens Samantha J. , Liu Qin , Yin Xiangfan , Jeyakumar Kirujan , Vogel Felix C. E. , Krepler Clemens , Rebecca Vito W. , Kubat Linda , Lueong Smiths S , Forster Jan , Horn Susanne , Remke Marc , Ehrmann Michael , Paschen Annette , Becker Jürgen C. , Helfrich Iris , Rauh Daniel , Kaiser Markus , Gul Sheraz , Herlyn Meenhard , Rodríguez-López José Neptuno , Haass Nikolas K. , Schadendorf Dirk , Roesch Alexander
Published: April 2020

Melanoma is a highly plastic tumor characterized by dynamic interconversion of different cell identities depending on the biological context. For example, melanoma cells with high expression of the H3K4 demethylase KDM5B (JARID1B) rest in a slow-cycling, yet reversible persister state. Over time, KDM5Bhighcells can promote rapid tumor repopulation with equilibrated KDM5B expression heterogeneity. The cellular identity of KDM5Bhighpersister cells has not been studied so far, missing an important cell state-directed treatment opportunity in melanoma. Here, we have established a doxycycline-titratable system for genetic induction of permanent intratumor expression of KDM5B and screened for chemical agents that phenocopy this effect. Transcriptional profiling and cell functional assays confirmed that the dihydropyridine phenoxyethyl 4-(2-fluorophenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxylate (termed Cpd1) supports high KDM5B expression and directs melanoma cells towards differentiation along the melanocytic lineage and to cell cycle-arrest. The high KDM5B state additionally prevents cell proliferation through negative regulation of cytokinetic abscission. Moreover, treatment with Cpd1 promoted the expression of the melanocyte-specific tyrosinase gene specifically sensitizing melanoma cells for the tyrosinase-processed antifolate prodrug 3-O-(3,4,5-trimethoxybenzoyl)-(-)-epicatechin (TMECG). In summary, our study provides proof-of-concept for a new dual hit strategy in melanoma, in which persister state-directed transitioning limits tumor growth and plasticity and primes melanoma cells towards lineage-specific elimination.
Seismic vulnerability evaluation of educational buildings of Mymensingh city, Bangladesh using rapid visual screening and index based approach
Authors: Alam Md. Shaharier , Haque Shamim Mahabubul
Published: April 2020

Purpose

Seismic vulnerability evaluation of various public structures, especially school buildings, is very crucial for designing hazard mitigation initiatives in seismic prone areas. The city of Mymensingh is at great risk of earthquake because of its geographical location, geological structure and proximity to active faults. The city is famous for its ancient and renowned educational institutes that need to be evaluated for understanding the seismic performance of the building during an earthquake. This study aims to evaluate the seismic vulnerability of educational buildings of Mymensingh city using rapid visual screening (RVS) and index based approach.

Design/methodology/approach

RVS procedure includes field survey and secondary source assessment for evaluating structural vulnerability attributes. Analytical hierarchy process is applied to develop an index focusing on systematic attributes of vulnerability based on expert opinions. Then, a composite vulnerability map is developed combining both structural and systematic vulnerability score providing an equal weight.

Findings

This study evaluates the seismic vulnerability of 458 educational buildings of Mymensingh city and the result shows that 23.14% educational building has high, 46.29% has moderate and 26.86% has moderately low and only 3.71% buildings has the low seismic vulnerability. This study expected to be helpful in resource targeting and prioritizing seismic hazard mitigation activities for education buildings of Mymensingh city.

Originality/value

This study endeavors to present a comprehensive vulnerability assessment method by integrating RVS and index based approach that incorporates both structural and systematic dimensions of vulnerability. The result is expected to be helpful in the formulation of disaster prevention policy for vulnerable educational buildings and development of the earthquake-resistant building codes for the new building construction in Mymensingh city.
Brand-related feelings and sponsor attitude formation
Authors: Boronczyk Felix , Breuer Christoph
Published: April 2020

Purpose

This study examines how brand attitude formation with respect to sport event sponsors is affected by feelings related to the sponsor brand, the sponsored event, and concurrent sponsors.

Design/methodology/approach

Using systematically manipulated press releases, 216 sport-interested participants were presented with different sponsorships of a major sport event. Sponsor information was systematically manipulated both within the stimulus text and the accompanying photo, which contained clearly visible sponsor signage. Participants' brand-related feelings and attitudes toward the stimulus brands were assessed through an online questionnaire following the treatment and analyzed using structural equation modeling.

Findings

The results show that sponsor brand-related feelings represent an important step in the creation of brand attitudes. Sponsor brand attitudes are further revealed to be in part determined by event- and co-sponsor-related feelings through several indirect pathways.

Practical implications

The findings presented in this study suggest that managers who seek to create favorable brand responses need to consider the feelings associated with their brands, the event and concurrent sponsors. Brands may experience both beneficial and detrimental effects, depending on whether the feelings involved are positive or negative.

Originality/value

To date, no research has investigated the relationships between brand-related feelings and brand attitudes in event sponsorship while accounting for the influence of the sponsored event and concurrent sponsors. Therefore, this study contributes to a better understanding of the role of feelings in sponsor brand attitude formation.
Determination of pharmacokinetic parameters of vitamin K1 in rats after an intravenous infusion
Authors: Mi Yan‐ni , Yan Ping‐ping , Yu Rui‐hong , Li Qiong‐ge , Wang Cui‐cui , Hui Ming‐quan , Cao Lei , Cao Yong‐xiao
Published: March 2020

Pharmacokinetic parameters of vitamin K1 have a large range of values in different literature. The aim of this study was to determine the pharmacokinetic parameters of vitamin K1 following post‐constant speed intravenous infusion (PCSII) to provide rational pharmacokinetic parameters of vitamin K1 and compare these with results of noncompartmental analysis following intravenous injection (IV). After 15 hours intravenous infusion of vitamin K1 in rats, the logarithmic concentration–time curve of vitamin K1 was fit to a linear equation following PCSII (R2 = 0.9599 ± 0.0096). Then, half‐time (T1/2), apparent volume of distribution (Vd), and clearance rate (CL) were estimated successively. T1/2 of vitamin K1 was 4.07 ± 0.41 hour, CL was 89.47 ± 3.60 mL/h, and Vd was 525.38 ± 54.45 mL in rats following PCSII. There was no significant difference in pharmacokinetic parameters of vitamin K1 among different sampling times. For noncompartmental analysis, T1/2 and mean residence time (MRTINF) for a sampling duration of 6h were shorter than those of 12 hours or 24 hours sampling duration following IV (P < .05, P < .01). In addition, T1/2 of vitamin K1 was obviously different from MRT‐equated half‐time (T1/2, MRT)(P < .05). Vd and CL of vitamin K1 following PCSII were larger than those following IV based on noncompartmental analysis (P < .01). The results demonstrated that drug distribution in the body was balanced and the Napierian logarithmic concentration–time curve of vitamin K1 fit to a linear equation following PCSII. Vitamin K1 has a long T1/2 and a relatively large Vd following PCSII.
Long‐term outcomes and risk factors of recurrent biliary obstruction after permanent endoscopic biliary stenting for choledocholithiasis in high‐risk patients
Authors: Sugiura Ryo , Naruse Hirohito , Yamato Hiroaki , Kudo Taiki , Yamamoto Yoshiya , Hatanaka Kazuteru , Ito Jun , Kinoshita Kenji , Miyamoto Shuichi , Higashino Masayuki , Hayasaka Shuhei , Sakamoto Naoya
Published: March 2020

Objective

To elucidate the long‐term outcomes of permanent endoscopic biliary stenting (EBS) and risk factors for recurrent biliary obstruction (RBO) in high‐risk or elderly patients with common bile duct (CBD) stones.

Methods

The electronic database of Hakodate Municipal Hospital was searched to identify elderly or high‐risk patients with CBD stones who had undergone permanent EBS using a plastic stent without stone removal and were followed up between April 2011 and May 2019, with no further intervention until symptoms occurred.

Results

We analyzed a total of 47 patients, of whom 19 (40.4%) were men, with a median age of 86 years (interquartile range 80‐90 years). RBO and death without biliary disease occurred in 14 (29.8%) and 19 (40.4%) patients, respectively. The cumulative RBO rates at 20, 40, and 60 months were 22.1%, 31.8%, and 35.5%, respectively. The median time to RBO was 13.0 and 38.0 months in the group with CBD stone  ≥15 mm and 11‐14 mm in diameter, respectively. The cumulative RBO incidence rate in the group with CBD stone ≤10 mm in diameter did not reach 50%. The cumulative RBO incidence rates were significantly different among the three groups based on the CBD stone diameter (competing risk analysis, P < 0.01). Multivariate analysis showed that an increase in CBD stone diameter predicted the increased risk of RBO (hazard ratio 1.26, P = 0.01).

Conclusions

Permanent EBS is a feasible option for high‐risk patients with small CBD stones.
Marked thickening of muscularis mucosae and submucosa in the gastric cardia: A histopathological study of 110 surgical resection cases
Authors: Huang Qin , Shi Jiong , Liu Tian Yun , Cheng Yu Qing , Wang Yao Hui , Du Ming Zhan , Li Lin , Fan Xiang Shan , Zhou Xiao Li , Zhang Yi Fen , Guo Ling Chuan , Xu Gui Fang , Zou Xiao Ping
Published: March 2020

Objective

To investigate histopathologic changes of muscularis mucosae (MM) and submucosa in the gastric cardia.

Methods

We performed a histopathology study of 50 distal esophagectomies with proximal gastrectomies for esophageal squamous cell carcinoma as the study (non‐cancerous cardiac) group and 60 gastrectomies for early gastric cardiac carcinoma as the cancer group. The gastroesophageal junction was defined as the distal end of squamous epithelium, multilayered epithelium, or deep esophageal glands or ducts. Gastric cardia (n = 110) was defined as the presence of cardiac and cardio‐oxyntic mucosae distal to the gastroesophageal junction.

Results

The average thickness of MM and submucosa in the cardia was 1.04 and 1.41 mm, respectively, which was significantly thicker than that in distal stomach (n = 34) (0.22 and 0.99 mm) or distal esophagus (n = 92) (0.60 and 1.15 mm). In the cardia, thickened MM displayed frayed muscle fibers (93.3%) with a significantly higher prevalence of entrapped glands, cysts, and lymphoid follicles than in the distal stomach or distal esophagus. In the submucosa fatty changes, cysts, and abnormal arteries were significantly more common in the cardia than in the distal stomach or distal esophagus. Compared with the study group, the cardia in the cancer group showed significantly thicker MM (average 1.31 vs 0.72 mm) and submucosa (average 1.61 vs 1.16 mm), more frequent frayed MM (93.3% vs 60.0%), prolapse‐like changes (50.0% vs 2.0%), and cysts (26.7% vs 4.0%).

Conclusion

MM and submucosa of the cardia were significantly thickened, especially in early gastric cardiac carcinomas.
Assessing the contribution of alcohol‐specific causes to socio‐economic inequalities in mortality in England and Wales 2001–16
Authors: Angus Colin , Pryce Rob , Holmes John , de Vocht Frank , Hickman Matthew , Meier Petra , Brennan Alan , Gillespie Duncan
Published: April 2020

Background and Aims

When measuring inequalities in health, public health and addiction research has tended to focus on differences in average life‐span between socio‐economic groups. This does not account for the extent to which age of death varies between individuals within socio‐economic groups or whether this variation differs between groups. This study assesses (1) socio‐economic inequalities in both average life‐span and variation in age at death, (2) the extent to which these inequalities can be attributed to alcohol‐specific causes (i.e. those attributable only to alcohol) and (3) how this contribution has changed over time.

Design

Cause‐deleted life table analysis of national mortality records.

Setting

England and Wales, 2001–16.

Cases

All‐cause and alcohol‐specific deaths for all adults aged 18+, stratified by sex, age and quintiles of the index of multiple deprivation (IMD).

Measurements

Life expectancy at age 18 yearss and standard deviation in age at death within IMD quintiles and the contribution of alcohol to overall differences in both measures between the highest and lowest IMD quintiles by comparing observed and cause‐deleted inequality ‘gaps’.

Findings

In 2016, alcohol‐specific causes reduced life expectancy for men and women by 0.26 and 0.14 years, respectively, and increased the standard deviation in age at death. These causes also increased the inequality gap in life expectancy by 0.33 years for men and 0.17 years for women, and variation in age at death by 0.14 years and 0.13 years, respectively. For both measures, the contribution of alcohol to mortality inequalities rose after 2001 and subsequently fell back. For women, alcohol accounted for 3.6% of inequality in age at death and 6.0% of life‐span uncertainty, suggesting that using only the former may underestimate alcohol‐induced inequalities. There was no comparable difference for men.

Conclusions

Deaths from alcohol‐specific causes increase inequalities in both life expectancy and variation in age of death between socio‐economic groups. Using both measures can provide a fuller picture of overall inequalities in health.
Polyunsaturated fatty acid‐derived IKs channel activators shorten the QT interval ex‐vivo and in‐vivo
Authors: Skarsfeldt Mark A. , Liin Sara I. , Larsson Hans P. , Bentzen Bo H.
Published: March 2020

Aim

We aimed to assess the ability of natural and modified polyunsaturated fatty acids (PUFAs) to shorten QT interval in ex‐vivo and in‐vivo guinea pig hearts.

Methods

The effect of one natural (docosahexaenoic acid [DHA]) and three modified (linoleoyl glycine [Lin‐GLY], docosahexaenoyl glycine [DHA‐GLY], N‐arachidonoyl taurine [N‐AT]) PUFAs on ventricular action potential duration (APD) and QT interval was studied in a E4031 drug‐induced long QT2 model of ex‐vivo guinea pig hearts. The effect of DHA‐GLY on QT interval was also studied in in‐vivo guinea pig hearts upon intravenous administration. The effect of modified PUFAs on IKs was studied using Xenopus laevis oocytes expressing human KCNQ1 and KCNE1.

Results

All tested PUFAs shortened ADP and QT interval in ex‐vivo guinea pig hearts, however, with different ability in restoring baseline APD/QT interval with specific modified PUFAs being most efficacious. Despite comparable ability in activating the human KCNQ1/KCNE1 channel, Lin‐GLY was not as effective in shortening APD/QT interval as DHA‐GLY in ex‐vivo hearts. By constructing a guinea pig‐like KCNE1, we found Lin‐GLY to induce less activating effect compared with DHA‐GLY on human KCNQ1 co‐expressed with guinea pig‐like KCNE1. Docosahexaenoyl glycine was studied in more detail and was found to shorten QT interval in in‐vivo guinea pig hearts.

Conclusion

Our results show that specific PUFAs shorten QT interval in guinea pig hearts. The tendency of modified PUFAs with pronounced IKs channel activating effect to better restore QT interval suggests that modifying PUFAs to target the IKs channel is a means to improve the QT‐shortening effect.