bluuebunny/crossref_metadata_2025 huggingface dataset:
Systemic Brain Tumor Delivery of Synthetic Protein Nanoparticles for Glioblastoma Therapy
Authors: Gregory Jason V. , Kadiyala Padma , Doherty Robert , Cadena Melissa , Habeel Samer , Ruoslahti Erkki , Lowenstein Pedro R. , Castro Maria G. , Lahann Joerg
Published: December 2019

Glioblastoma multiforme (GBM), the most aggressive form of brain cancer, has witnessed very little clinical progress over the last decades, in parts, due to the absence of effective drug delivery strategies. Intravenous injection is the least invasive delivery route to the brain, but has been severely limited by the blood-brain barrier (BBB). Inspired by the capacity of natural proteins and viral particulates to cross the BBB, we engineered a synthetic protein nanoparticle (SPNP) based on polymerized human serum albumin (HSA) equipped with the cell-penetrating peptide iRGD. SPNPs containing siRNA against Signal Transducer and Activation of Transcription 3 factor (STAT3i) result inin vitroandin vivodownregulation of STAT3, a central hub associated with GBM progression. When combined with the standard of care, ionized radiation, STAT3iSPNPs result in tumor regression and long-term survival in 87.5% of GBM bearing mice and primes the immune system to develop anti-GBM immunological memory.
Neural Fragility as an EEG Marker of the Seizure Onset Zone
Authors: Li Adam , Huynh Chester , Fitzgerald Zachary , Cajigas Iahn , Brusko Damian , Jagid Jonathan , Claudio Angel , Kanner Andres , Hopp Jennifer , Chen Stephanie , Haagensen Jennifer , Johnson Emily , Anderson William , Crone Nathan , Inati Sara , Zaghloul Kareem , Bulacio Juan , Gonzalez-Martinez Jorge , Sarma Sridevi V.
Published: December 2019

Over 15 million epilepsy patients worldwide do not respond to drugs. Successful surgical treatment requires complete removal, or disconnection of the seizure onset zone (SOZ), brain region(s) where seizures originate. Unfortunately, surgical success rates vary between 30%-70% because no clinically validated biological marker of the SOZ exists. We develop and retrospectively validate a new EEG marker - neural fragility - in a retrospective analysis of 91 patients by using neural fragility of the annotated SOZ as a metric to predict surgical outcomes. Fragility predicts 43/47 surgical failures with an overall prediction accuracy of 76%, compared to the accuracy of clinicians being 48% (successful outcomes). In failed outcomes, we identify fragile regions that were untreated. When compared to 20 EEG features proposed as SOZ markers, fragility outperformed in predictive power and interpretability suggesting neural fragility as an EEG biomarker of the SOZ.
QAlign: Aligning nanopore reads accurately using current-level modeling
Authors: Joshi Dhaivat , Mao Shunfu , Kannan Sreeram , Diggavi Suhas
Published: December 2019

Motivation

Efficient and accurate alignment of DNA / RNA sequence reads to each other or to a reference genome / transcriptome is an important problem in genomic analysis. Nanopore sequencing has emerged as a major sequencing technology and many long-read aligners have been designed for aligning nanopore reads. However, the high error rate makes accurate and efficient alignment difficult. Utilizing the noise and error characteristics inherent in the sequencing process properly can play a vital role in constructing a robust aligner. In this paper, we design QAlign, a pre-processor that can be used with any long-read aligner for aligning long reads to a genome / transcriptome or to other long reads. The key idea in QAlign is to convert the nucleotide reads into discretized current levels that capture the error modes of the nanopore sequencer before running it through a sequence aligner.

Results

We show that QAlign is able to improve alignment rates from around 80% up to 90% with nanopore reads when aligning to the genome. We also show that QAlign improves the average overlap quality by 9.2%, 2.5% and 10.8% in three real datasets for read-to-read alignment. Read-to-transcriptome alignment rates are improved from 51.6% to 75.4% and 82.6% to 90% in two real datasets.

Availability

https://github.com/joshidhaivat/QAlign.git
WHISKiT Physics: A three-dimensional mechanical model of the rat vibrissal array
Authors: Zweifel Nadina O. , Bush Nicholas E. , Abraham Ian , Murphey Todd D. , Hartmann Mitra J.Z.
Published: December 2019

Rodents tactually explore the environment using ~62 whiskers (vibrissae), regularly arranged in arrays on both sides of the face. The rat vibrissal system is one of the most commonly used models to study how the brain encodes and processes somatosensory information. To date, however, researchers have been unable to quantify the mechanosensory input at the base of each whisker, because the field lacks accurate models of three-dimensional whisker dynamics. To close this gap, we developed WHISKiT Physics, a simulation framework that incorporates realistic morphology of the full rat whisker array to predict time-varying mechanical signals for all whiskers. The dynamics of single whiskers were optimized based on experimental data, and then validated against free tip oscillations and the dynamic response to collision. The model is then extrapolated to include all whiskers in the array, taking into account each whisker’s individual geometry. Simulations of first mode resonances across the array approximately match previous experimental results and fall well within the range expected from biological variability. Finally, we use WHISKiT Physics to simulate mechanical signals across the array during three distinct behavioral conditions: passive whisker stimulation, active whisking against two pegs, and active whisking in a natural environment. The results demonstrate that the simulation system can be used to predict input signals during a variety of behaviors, something that would be difficult or impossible in the biological animal. In all behavioral conditions, interactions between array morphology and individual whisker geometry shape the tactile input to the whisker system.
DomainScope: A disease network based on protein domain connections
Authors: Voskanian-kordi Alin , Funai Ashley , Kann Maricel G.
Published: December 2019

Protein domains are highly conserved functional units of proteins. Because they carry functionally significant information, the majority of the coding disease variants are located on domains. Additionally, domains are specific units of the proteins that can be targeted for drug delivery purposes. Here, using information about variants sites associated with diseases, a disease network was built, based on their sharing the same domain and domain variation site. The result was 49,990 disease pairs linked by domain variant site and 533,687 disease pairs that share the same mutated domain. These pairs were compared to disease pairs made using previous methods such as gene identity and gene variant site identity, which revealed that over 8,000 of these pairs were not only missing from the gene pairings but also not found commonly together in literature. The disease network was analyzed from their disease subject categories, which when compared to the gene-based disease network revealed that the domain method results in higher number of connections across disease categories versus within a disease category. Further, a study into the drug repurposing possibilities of the disease network created using domain revealed that 16,902 of the disease pairs had a drug reported for one disease but not the other, highlighting the drug repurposing potential of this new methodology.
Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago
Authors: Morgan Andrew P , Brazeau Nicholas F , Ngasala Billy , Mhamilawa Lwidiko E. , Denton Madeline , Msellem Mwinyi , Morris Ulrika , Filer Dayne L , Aydemir Ozkan , Bailey Jeffrey A. , Parr Jonathan , Mårtensson Andreas , Bjorkman Anders , Juliano Jonathan J
Published: December 2019

Background

Tanzania’s Zanzibar archipelago has made significant gains in malaria control over the last decade and is a target for malaria elimination. Despite consistent implementation of effective tools since 2002, elimination has not been achieved. Importation of parasites from outside of the archipelago is thought to be an important cause of malaria’s persistence, but this paradigm has not been studied using modern genetic tools.

Methods

We used whole-genome sequencing (WGS) to investigate the impact of importation, employing population genetic analyses of Plasmodium falciparum isolates from both the archipelago and mainland Tanzania. We assessed ancestry, levels of genetic diversity and differentiation, patterns of relatedness, and patterns of selection between these two populations by leveraging recent advances in deconvolution of genomes from polyclonal malaria infections.

Results

We identified significant decreases in the effective population sizes in both populations in the timeframe of decreasing malaria transmission in Tanzania. Identity by descent analysis showed that parasites in the two populations shared large sections of their genomes, on the order of 5 cM, suggesting shared ancestry within the last 10 generations. Even with limited sampling,, we demonstrate a pair of isolates between the mainland and Zanzibar that are related at the expected level of half-siblings, consistent with recent importation

Conclusions

These findings suggest that importation plays an increasing role for malaria incidence on Zanzibar and demonstrate the value of genomic approaches for identifying corridors of parasite movement to the island.
Gene expression pattern of vacuolar-iron transporter-like (VTL) genes in hexaploid wheat during metal stress
Authors: Sharma Shivani , Kaur Gazaldeep , Kumar Anil , Meena Varsha , Ram Hasthi , Kaur Jaspreet , Pandey Ajay Kumar
Published: December 2019

Iron is one of the important micronutrients that is not just essential for the human body, but also required for crop productivity and yield-related traits. To address the Fe homeostasis in crop plants, multiple transporters belonging to the category of Major facilitator superfamily are being explored. In this direction, Vacuolar iron transporters (VIT) are being reported and have been characterized functionally as an important candidate to address biofortification in cereal crops. In the present study, the identification and characterization of new members of Vacuolar iron transporters-like proteins (VTL) was performed. Phylogenetic analyses demonstrated distinct clustering of all the VTL genes from the previously known VIT genes. Our analysis identifies multiple VTL genes from hexaploid wheat with the highest number of this gene family localized on chromosome 2. Quantitative expression analysis suggests that most of the VTL genes are induced only during the Fe surplus condition, thereby reinforcing their role metal homeostasis. Interestingly, most of the wheat VTL genes were significantly up-regulated in a tissue-specific manner under Zn, Mn and Cu deficiency conditions. Although, no significant changes in expression of wheat VTL genes were observed in roots under heavy metals, but TaVTL2, TaVTL3 and TaVTL5 were upregulated in the presence of cobalt stress. Overall, this work deals with the characterization of wheat VTL genes that could provide an important genetic resource for addressing metal homeostasis in bread wheat.
Multiplexing information flow through dynamic signalling systems
Authors: Minas Giorgos , Woodcock Dan J. , Ashall Louise , Harper Claire V. , White Michael R. H. , Rand David A
Published: December 2019

We consider how a signalling system can act as an information hub by multiplexing information arising from multiple signals. We formally define multiplexing, mathematically characterise which systems can multiplex and how well they can do it. While the results of this paper are theoretical, to motivate the idea of multiplexing, we provide experimental evidence that tentatively suggests that the NF-κB transcription factor can multiplex information about changes in multiple signals. We believe that our theoretical results may resolve the apparent paradox of how a system like NF-κB that regulates cell fate and inflammatory signalling in response to diverse stimuli can appear to have the low information carrying capacity suggested by recent studies on scalar signals. In carrying out our study, we introduce new methods for the analysis of large, nonlinear stochastic dynamic models, and develop computational algorithms that facilitate the calculation of fundamental constructs of information theory such as Kullback–Leibler divergences and sensitivity matrices, and link these methods to new theory about multiplexing information. We show that many current models such as those of the NF-κB system cannot multiplex effectively and provide models that overcome this limitation using post-transcriptional modifications.
Genome resequencing, improvement of variant calling, and population genomic analyses provide insights into the seedlessness in the genusVitis
Authors: Kim Myung-Shin , Hur Youn Young , Kim Ji Hong , Jeong Soon-Chun
Published: December 2019

The seedlessness of grape derived from stenospermocarpy is one of the most prized traits of table or raisin grapes. It is controlled by a complex genetic system containing one major dominant gene and multiple minor recessive genes. Here, we collected dense variation data from high-depth resequencing data of seeded, seedless, and wild relative grape genomes sequenced to > 37x mean depth. Variant calls were made using a modified variant calling pipeline that was suitable for highly diverse interspecific grape accessions. The modified pipeline enabled us to call several million more variants than the commonly recommended pipeline. The quality was validated by Sanger sequencing data and subsequently supported by the genetic population structure and the phylogenetic tree constructed using the obtained variation data, results of which were generally consistent with known pedigree and taxonomic classifications. Variation data enabled us to confirm a major dominant gene and identify minor recessive loci for seedlessness. Incidentally, we found that grape cultivar Rizamat contains an ancestral chromosomal region of the major gene in Sultanina, a predominant seedlessness donor cultivar. Furthermore, we predicted new candidate causal genes includingVitvi01g00455,Vitvi08g01528, and Vitvi18g01237associated with the minor seedless-regulating loci, which showed high homology with genes that regulate seed development inArabidopsis. This study provides fundamental insights relevant to variant calling from genome resequencing data of diverse interspecific hybrid germplasms such as grape and will accelerate future efforts aimed at crop improvement.
Late life metformin treatment limits cell survival and shortens lifespan by triggering an aging-associated failure of energy metabolism
Authors: Espada Lilia , Dakhovnik Alexander , Chaudhari Prerana , Martirosyan Asya , Miek Laura , Poliezhaieva Tetiana , Schaub Yvonne , Nair Ashish , Döring Nadia , Rahnis Norman , Werz Oliver , Koeberle Andreas , Kirkpatrick Joanna , Ori Alessandro , Ermolaeva Maria A.
Published: December 2019

The diabetes drug metformin is to be clinically tested in aged humans to achieve health span extension, but little is known about responses of old non-diabetic individuals to this drug. Byin vitroandin vivotests we found that metformin shortens life span and limits cell survival when provided in late life, contrary to its positive early life effects. Mechanistically, metformin exacerbates aging-associated mitochondrial dysfunction towards respiratory failure, aggravated by the inability of old cells to upregulate glycolysis in response to metformin, leading to ATP exhaustion. The beneficial dietary restriction effect of metformin on lipid reserves is abrogated in old animals, contributing to metabolic failure, while ectopic stabilization of cellular ATP levels alleviates late life metformin toxicityin vitroandin vivo. The toxicity is also suspended in nematodes carrying diabetes-like insulin receptor insufficiency and showing prolonged resilience to metabolic stress induced by metformin. In sum, we uncovered an alarming metabolic decay triggered by metformin in late life which may limit its benefits for non-diabetic elderly patients. Novel regulators of life extension by metformin are also presented.

Highlights

Late life metformin treatment limits cell survival and shortens lifespan.

Metformin exacerbates aging-associated mitochondrial dysfunction causing fatal ATP exhaustion.

Old cells fail to upregulate glycolysis as a compensatory response to metformin.

The dietary restriction (DR) mimetic response to metformin is abrogated in old animals.

PKA and not AMPK pathway instigates the early life DR response to metformin.

Stabilization of cellular ATP levels alleviates late life metformin toxicityin vitroandin vivo.
Spike-timing-dependent plasticity rewards synchrony rather than causality
Authors: Anisimova Margarita , van Bommel Bas , Mikhaylova Marina , Wiegert J. Simon , Oertner Thomas G. , Gee Christine E.
Published: December 2019

Spike-timing-dependent plasticity (STDP) is a candidate mechanism for information storage in the brain, but the whole-cell recordings required for the experimental induction of STDP are typically limited to one hour. This mismatch of time scales is a long-standing weakness in synaptic theories of memory. Here we use spectrally separated optogenetic stimulation to fire precisely timed action potentials (spikes) in CA3 and CA1 pyramidal cells. Twenty minutes after optogenetic induction of STDP (oSTDP), we observed timing-dependent depression (tLTD) and timing-dependent potentiation (tLTP), depending on the sequence of spiking. As oSTDP does not require electrodes, we could also assess the strength of these paired connections three days later. At this late time point, late tLTP was observed for both causal (CA3 before CA1) and anti-causal (CA1 before CA3) timing, but not for asynchronous activity patterns (Δt = 50 ms). Blocking activity after induction of oSTDP prevented stable potentiation. Our results confirm that neurons wire together if they fire together, but suggest that synaptic depression after anti-causal activation (tLTD) is a transient phenomenon.

Highlights

Optogenetic induction of spike-timing-dependent plasticity at Schaffer collateral synapses

Causal pairing induces potentiation whereas anti-causal pairing induces depression during patch-clamp recordings.

Three days after optogenetic induction, the consequence of STDP is potentiation (tLTP) irrespective of spiking order.

Late tLTP requires ongoing activity in the days following oSTDP.

Graphical Abstract
Chromosome segregation is driven by joint microtubule sliding action of kinesins KIF4A and EG5
Authors: Vukušić Kruno , Buđa Renata , Ponjavić Ivana , Risteski Patrik , Tolić Iva M.
Published: December 2019

Successful cell division requires proper chromosome segregation during anaphase. Forces required for chromosome segregation in human cells are linked to sliding of antiparallel microtubules and sliding capacity has been demonstrated in vitro for multiple motor proteins, but the molecular mechanism of sliding in the spindle of human cells remains unknown. Using combined depletion and inactivation assays to explore redundancy between multiple targets together with CRISPR technology, we found that PRC1-dependent motor KIF4A/kinesin-4, together with EG5/kinesin-5 motor is essential for spindle elongation in human cells. Photoactivation of tubulin and super-resolution microscopy show that perturbation of both proteins impairs sliding, while decreased midzone microtubule stability cannot explain the observed anaphase arrest. Thus, two independent sliding modules power sliding mechanism that drives spindle elongation in human cells.
Extracting the GEMs: Genotype, Environment and Microbiome interactions shaping host phenotypes
Authors: Oyserman Ben O. , Cordovez Viviane , Sarango Flores Stalin W. , Nijveen Harm , Medema Marnix H. , Raaijmakers Jos M.
Published: December 2019

One of the fundamental tenets of biology is that the phenotype of an organism (Y) is determined by its genotype (G), the environment (E) and their interaction (GE). Quantitative phenotypes can then be modeled as Y=G+E+GE+e, where e is the biological variance. This simple and tractable model has long served as the basis for studies investigating the heritability of traits and decomposing the variability in fitness. Increasingly, the importance of microbe interactions on organismal phenotypes is being recognized, but it is currently unclear what the relative contribution of microbiomes to a given host phenotype is and how this translates into the traditional GE model. Here we address this fundamental question and propose an expansion of the original model, referred to as GEM, which explicitly incorporates the contribution of the microbiome (M) to the host phenotype, while maintaining the simplicity and tractability of the original GE model. We show that by keeping host, environment and microbiome as separate but interacting variables, the GEM model can capture the nuanced ecological interactions between these variables. Finally, we demonstrate with an in vitro experiment how the GEM model can be used to statistically disentangle the relative contributions of each component on specific host phenotypes.
CD4+T cells persist for years in the human small intestine and mediate robust TH1 immunity
Authors: Casado Raquel Bartolomé , Landsverk Ole J.B. , Chauhan Sudhir Kumar , Sætre Frank , Hagen Kjersti Thorvaldsen , Yaqub Sheraz , Øyen Ole , Horneland Rune , Aandahl Einar Martin , Aabakken Lars , Bækkevold Espen S. , Jahnsen Frode L.
Published: December 2019

Studies in mice and humans have shown that CD8+T cell immunosurveillance in non-lymphoid tissues is dominated by resident populations. Whether CD4+T cells use the same strategies to survey peripheral tissues is less clear. Here, examining the turnover of CD4+T cells in transplanted duodenum in humans, we demonstrate that the majority of CD4+T cells were still donor-derived one year after transplantation. In contrast to memory CD4+T cells in peripheral blood, intestinal CD4+TRMcells expressed CD69 and CD161, but only a minor fraction expressed CD103. Functionally, intestinal CD4+TRMcells were very potent cytokine producers; the vast majority being polyfunctional TH1 cells, whereas a minor fraction produced IL-17. Interestingly, a fraction of intestinal CD4+T cells produced granzyme-B and perforin after activation. Together, we show that the intestinal CD4+T-cell compartment is dominated by resident populations that survive for more than 1 year. This finding is of high relevance for the development of oral vaccines and therapies for diseases in the gut.
The apparent requirement for protein synthesis during G2 phase is due to checkpoint activation
Authors: Lockhead Sarah , Moskaleva Alisa , Kamenz Julia , Chen Yuxin , Kang Minjung , Reddy Anay , Santos Silvia , Ferrell James E.
Published: December 2019

Protein synthesis inhibitors (e.g. cycloheximide) prevent cells from entering mitosis, suggesting that cell cycle progression requires protein synthesis until right before mitotic entry. However, cycloheximide is also known to activate p38 MAPK, which can delay mitotic entry through a G2/M checkpoint. Here we asked whether checkpoint activation or a requirement for protein synthesis is responsible for the cycloheximide effect. We found that p38 inhibitors prevent cycloheximide-treated cells from arresting in G2 phase, and that G2 duration is normal in about half of these cells. The Wee1/Myt1 inhibitor PD0166285 also prevents cycloheximide from blocking mitotic entry, raising the possibility that Wee1 and/or Myt1 mediate the cycloheximide-induced G2 arrest. Thus, the ultimate trigger for mitotic entry appears not to be the continued synthesis of mitotic cyclins or other proteins. However, M-phase progression was delayed in cycloheximide-plus-kinase-inhibitor-treated cells, emphasizing the different requirements of protein synthesis for timely entry and completion of mitosis.

Impact statement

Cycloheximide arrests cells in G2 phase due to activation of p38 MAPK, not inhibition of protein synthesis, arguing that protein synthesis in G2 phase is not required for mitotic entry.
Evaluating the data quality of iNaturalist termite records
Authors: Hochmair Hartwig H. , Scheffrahn Rudolf H. , Basille Mathieu , Boone Matthew
Published: December 2019

Citizen science (CS) contributes to the combined knowledge about species distributions, which is a critical foundation in the studies of invasive species, biological conservation, and response to climatic change. In this study, we assessed the value of CS for termites worldwide. First, we compared the abundance and species diversity of geo-tagged termite records in iNaturalist to that of the University of Florida termite collection (UFTC) and the Global Biodiversity Information Facility (GBIF). Second, we quantified how the combination of these data sources affected the number of genera that satisfy data requirements for ecological niche modeling. Third, we assessed the taxonomic correctness of iNaturalist termite records in the Americas at the genus and family level through expert review based on photo identification. Results showed that iNaturalist records were less abundant than those in UFTC and in GBIF, although they complemented the latter two in selected world regions. A combination of GBIF and UFTC led to a significant increase in the number of termite genera satisfying the abundance criterion for niche modeling compared to either of those two sources alone, whereas adding iNaturalist observations as a third source only had a moderate effect on the number of termite genera satisfying that criterion. Although research grade observations in iNaturalist require a community-supported and agreed upon ID below the family taxonomic rank, our results indicated that iNaturalist data do not exhibit a higher taxonomic classification accuracy when they are designated research grade. This means that non-research grade observations can be used to more completely map the presence of termite locations in certain geographic locations without significantly jeopardizing data quality. We concluded that CS termite observation records can, to some extent, complement expert termite collections in terms of geographic coverage and species diversity. Based on recent data contribution patterns in CS data, the role of CS termite contributions is expected to grow significantly in the near future.
Host targets of effectors of the lettuce downy mildew Bremia lactucae from cDNA-based yeast two-hybrid screening
Authors: Pelgrom Alexandra J.E. , Meisrimler Claudia-Nicole , Elberse Joyce , Koorman Thijs , Boxem Mike , Van den Ackerveken Guido
Published: December 2019

Plant pathogenic bacteria, fungi and oomycetes secrete effector proteins to manipulate host cell processes to establish a successful infection. Over the last decade the genomes and transcriptomes of many agriculturally important plant pathogens have been sequenced and vast candidate effector repertoires were identified using bioinformatic analyses. Elucidating the contribution of individual effectors to pathogenicity is the next major hurdle. To advance our understanding of the molecular mechanisms underlying lettuce susceptibility to the downy mildew Bremia lactucae, we mapped a network of physical interactions between B. lactucae effectors and lettuce target proteins. Using a lettuce cDNA library-based yeast-two-hybrid system, 61 protein-protein interactions were identified, involving 21 B. lactucae effectors and 46 unique lettuce proteins. The top ten targets based on the number of independent colonies identified in the Y2H and two targets that belong to gene families involved in plant immunity, were further characterized. We determined the subcellular localization of the fluorescently tagged target proteins and their interacting effectors. Importantly, relocalization of effectors or targets to the nucleus was observed for four effector-target pairs upon their co-expression, supporting their interaction in planta.
Inferring Chromosome Radial Organization from Hi-C Data
Authors: Das Priyojit , Shen Tongye , McCord Rachel Patton
Published: December 2019

Background

The nonrandom radial organization of eukaryotic chromosome territories (CTs) inside the nucleus plays an important role in nuclear functional compartmentalization. Increasingly, chromosome conformation capture (Hi-C) based approaches are being used to characterize the genome structure of many cell types and conditions. Computational methods to extract 3D arrangements of CTs from this type of pairwise contact data will thus increase our ability to analyze CT organization in a wider variety of biological situations.

Results

A number of full-scale polymer models have successfully reconstructed the 3D structure of chromosome territories from Hi-C. To supplement such methods, we explore alternative, direct, and less computationally intensive approaches to capture radial CT organization from Hi-C data. We show that we can infer relative chromo-some ordering using PCA on a thresholded inter-chromosomal contact matrix. We simulate an ensemble of possible CT arrangements using a force-directed network layout algorithm and propose an approach to integrate additional chromosome properties into our predictions. Our CT radial organization predictions have a high correlation with microscopy imaging data for various cell nucleus geometries (lymphoblastoid, skin fibroblast, and breast epithelial cells), and we can capture previously documented changes in senescent and progeria cells.

Conclusions

Our analysis approaches provide rapid and modular approaches to screen for alterations in CT organization across widely available Hi-C data. We demon-strate which stages of the approach can extract meaningful information, and also de-scribe limitations of pairwise contacts alone to predict absolute 3D positions.
Polynuclear ruthenium amines inhibit K2P channels via a ‘finger in the dam’ mechanism
Authors: Pope Lianne , Lolicato Marco , Minor Daniel L.
Published: December 2019

The trinuclear ruthenium amine Ruthenium Red (RuR) inhibits diverse ion channels including K2P potassium channels, TRPs, the mitochondrial calcium uniporter, CALHMs, ryanodine receptors, and Piezos. Despite this extraordinary array, there is very limited information for how RuR engages its targets. Here, using X-ray crystallographic and electrophysiological studies of an RuR-sensitive K2P, K2P2.1 (TREK-1) I110D, we show that RuR acts by binding an acidic residue pair comprising the ‘Keystone inhibitor site’ under the K2P CAP domain archway above the channel pore. We further establish that Ru360, a dinuclear ruthenium amine not known to affect K2Ps, inhibits RuR-sensitive K2Ps using the same mechanism. Structural knowledge enabled a generalizable RuR ‘super-responder’ design strategy for creating K2Ps having nanomolar sensitivity. Together, the data define a ‘finger in the dam’ inhibition mechanism acting at a novel K2P inhibitor binding site. These findings highlight the polysite nature of K2P pharmacology and provide a new framework for K2P inhibitor development.
MicroRNA function transitions from regulating developmental genes to transposable elements during the maturation of pollen
Authors: Oliver Cecilia , Annacondia Maria Luz , Wang Zhenxing , Slotkin R Keith , Köhler Claudia , Martinez German
Published: December 2019

microRNAs play important roles to control the development of eukaryotic organisms. Both animal and plant microRNAs are essential for the spatio-temporal regulation of development but together with this role, plant microRNAs also control transposable elements and stimulate the production of epigenetically-active small interfering RNAs. This last role is evident in the plant male gamete containing structure, the male gametophyte or pollen grain, but how the dual role of plant microRNAs is integrated during its development is unknown. Here, we provide a detailed analysis of microRNA dynamics during pollen development and their genic and transposable element targets using small RNA and mRNA cleavage (PARE) high-throughput sequencing. Furthermore we uncover the microRNAs loaded in the two main Argonaute proteins in the mature pollen grain, AGO1 and AGO5. Our results indicate that the developmental progression from microspore to mature pollen grain is characterized by a reprogramming from microRNAs focused on the control of development to microRNAs regulating transposable element control.
Reliable method for high quality His-tagged and untaggedE. coliphosphoribosyl phosphate synthase (Prs) purification
Authors: Maria Walter Beata , Aneta Szulc , Monika Glinkowska
Published: December 2019

Prs (phosphoribosyl pyrophosphate synthase) is a broadly conserved protein that synthesises 5-phosphoribosyl 1-pyrophospate (PRPP); a substrate for biosynthesis of at least 10 enzymatic pathways including biosynthesis of DNA building blocks – purines and pyrimidines. InEscherichia coli, it is a protein of homo-hexameric quaternary structure, which can be challenging to work with, due to frequent aggregation and activity loss. Several studies showed brief purification protocols for various bacterial PRPP synthases, in most cases involving ammonium sulfate precipitation.

Here, we provide a protocol for expression ofE. coliPrs protein in Rosetta (DE3) and BL21 (DE3) pLysE strains and a detailed method for His-Prs and untagged Prs purification on nickel affinity chromatography columns. This protocol allows purification of proteins with high yield, purity and activity. We report here N-terminally His-tagged protein fusions, stable and active, providing that the temperature around 20 °C is maintained at all stages, including centrifugation. Moreover, we successfully applied this method to purify two enzyme variants with K194A and G9S alterations. The K194A mutation in conserved lysine residue results in protein variant unable to synthetize PRPP, while the G9S alteration originates fromprs-2allele variant which was previously related to thermo-sensitive growth. His-PrsG9S protein purified here, exhibited comparable activity as previously observedin-vivosuggesting the proteins purified with our protocol resemble their physiological state.

The protocol for Prs purification showed here indicates guidance to improve stability and quality of the protein and to ensure more reliable results in further assaysin-vitro.
Cell shape changes during larval body plan development in Clytia hemisphaerica
Authors: Kraus Yulia , Chevalier Sandra , Houliston Evelyn
Published: December 2019

The cnidarian “planula” larva shows radial symmetry around a polarized, oral-aboral, body axis and comprises two epithelia cell layers, ectodermal and endodermal. This simple body plan is set up during gastrulation, a process which proceeds by a variety of modes amongst the diverse cnidarian species. In the hydrozoan laboratory model Clytia hemisphaerica, gastrulation involves a process termed unipolar cell ingression, in which the endoderm derives from mass ingression of individual cells via a process of epithelial-mesenchymal transition (EMT) around the future oral pole of an epithelial embryo. This contrasts markedly from the gastrulation mode in the anthozoan cnidarian Nematostella vectensis, in which endoderm formation primarily relies on cell sheet invagination. To understand the cellular basis of gastrulation in Clytia we have characterized in detail successive cell morphology changes during planula formation by Scanning and Transmission Electron Microscopy combined with confocal imaging. These changes successively accompany epithialization of the blastoderm, EMT occurring in the oral domain through the bottle cell formation and ingression, cohesive migration and intercalation of ingressed cells with mesenchymal morphology, and their epithelialization to form the endoderm. From our data, we have reconstructed the cascade of morphogenetic events leading to the formation of planula larva. We also matched the domains of cell morphology changes to the expression of selected regulatory and marker genes expressed during gastrulation. We propose that cell ingression in Clytia not only provides the endoderm, but generates internal forces that shape the embryo in the course of gastrulation. These observations help build a more complete understanding of the cellular basis of morphogenesis and of the evolutionary plasticity of cnidarian gastrulation modes.
Mutation of an L-Type Calcium Channel Gene Leads to a Novel Human Primary Cellular Immunodeficiency
Authors: Fenninger Franz , Stanwood Shawna R. , Lu Chieh-Ju , Pfeifer Cheryl G. , Henrickson Sarah E. , Khan Omar , O’Boyle Kaitlin C. , Maurer Kelly , Ruffner Melanie , Herati Ramin S. , Romberg Neil D. , John Wherry E. , Sullivan Kathleen E. , Jefferies Wilfred A.
Published: December 2019

Human primary immunodeficiencies are inherited diseases that can provide valuable insight into the immune system. Calcium (Ca2+) is a vital secondary messenger in T lymphocytes regulating a vast array of important events including maturation, homeostasis, activation, and apoptosis and can enter the cell through CRAC, TRP, and Cav channels. Here we describe three Cav1.4-deficient siblings presenting with X-linked incomplete congenital stationary night blindness as well as an immune phenotype characterized by several recurrent infections. Complete exome sequencing demonstrated that the patients share only a single pathogenic allele; a R625X (p.Arg625Ter) point mutation that leads to a premature stop codon in theCACNA1Fgene encoding the L-type Ca2+channel Cav1.4. The subjects uniformly exhibited an expansion of central and effector memory T lymphocytes, and evidence of T lymphocytes exhaustion with corresponding upregulation of inhibitory receptors. Moreover, the sustained elevated levels of activation markers on B lymphocytes suggest that they are in a chronic state of activation. Finally, the T lymphocytes from patients andCACNA1Fknockdown Jurkat T lymphocytes exhibited a reduced Ca2+flux, compared to controls. This is the first example where the mutation of any Cav channel causes a primary immunodeficiency in humans and establishes the physiological importance of Cav channels in the human immune system.
Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data
Authors: Wagner Natascha D. , He Li , Hörandl Elvira
Published: December 2019

Abstract

Despite the general progress in using next generation sequencing techniques for evolutionary research questions, the analysis of polyploid species is still hampered by the lack of suitable analytical tools and the statistical difficulties of dealing with more than two alleles per locus. Polyploidization and especially allopolyploidy leads to new combinations of traits by combining genomes of two or more parental species. This enhances the adaptive potential and often results in speciation. However, multiple origins of polyploids, backcrossing to the parental species and post-origin evolution can strongly influence the genome composition of polyploid species. Here, we used RAD sequencing, which revealed 23,393 loci and 320,010 high quality SNPs, to analyze the relationships and origin of seven polyploid species of the diverse genus Salix by utilizing a phylogenomic and a network approach, as well as analyzing the genetic structure and composition of the polyploid genome in comparison to putative parental species. We adapted the SNiPloid pipeline that was originally developed to analyse SNP composition of recently established allotetraploid crop lineages to RAD sequencing data by using concatenated RAD loci as reference. Our results revealed a well-resolved phylogeny of 35 species of Eurasian shrub willows (Salix subg. Chamaetia/Vetrix), including 28 diploid and 7 polyploid species. Polyploidization in willows appears to be predominantly connected to hybridization, i.e. to an allopolyploid origin of species. More ancient allopolyploidization events involving hybridization of more distantly related, ancestral lineages were observed for two hexaploid and one octoploid species. Our data suggested a more recent allopolyploid origin for the included tetraploids within the major subclades and identified putative parental taxa that appear to be plausible in the context of geographical, morphological and ecological patterns. SNiPloid and HyDe analyses disentangled the different genomic signatures resulting from hybrid origin, backcrossing, and secondary post-origin evolution in the polyploid species. All tetraploids showed a considerable post-origin, species-specific proportion of SNPs. The amount of extant hybridization appears to be related to the degree of geographical and ecological isolation of species. Our data demonstrate that high-quality RAD sequencing data are suitable and highly informative for the analysis of the origin and relationships of polyploid species. The combination of the traditional tools RAxML, STRUCTURE, SplitsTree and recently developed programs like SNAPP, HyDe and SNiPloid established a bioinformatic pipeline for unraveling the complexity of polyploid genomes.
Food authenticity as one of the stimuli to world heritage sites
Authors: Latiff Khairunnisak , Ng Siew Imm , Aziz Yuhanis Abdul , Kamal Basha Norazlyn
Published: December 2019

Purpose

The purpose of this paper is to discover authenticity dimensions that draw tourists to Melaka and George Town World Heritage Site. It also examined the mediating effect of attachment and the moderating effect of cultural motivation.

Design/methodology/approach

A mixed-method design was used. Qualitative approach was conducted to discover authenticity dimensions followed by a quantitative approach to explore the dimensions’ ability in predicting attachment and intention to recommend.

Findings

Findings revealed that objective, existential and food authenticity were significant stimuli of recommend intention. The mediating effect of attachment on constructive authenticity-intention and existential authenticity-intention were also supported. Cultural motivation indeed moderated the relationship between objective authenticity-attachment, constructive authenticity-attachment and existential authenticity-attachment.

Originality/value

Knowing that authenticity can be perceived differently, therefore, a mixed-method study design offers more insight on discovering authenticity elements. Using a qualitative approach, the study began by exploring important authenticity dimensions from both supply and demand groups, and subsequently, these dimensions were verified using quantitative approach. As expected, food authenticity was found as a standalone dimension.
Double-edged effects of ethical leadership in the development of Greater China salespeople's emotional exhaustion and long-term customer relationships
Authors: Lee Chih-Jen , Huang Stanley Y.B.
Published: December 2019

Purpose

The purpose of this paper is to present how ethical leadership has a double-edged effect to influence emotional exhaustion and long-term customer relationship developments of employees in a sales management context through a latent growth model (LGM).

Design/methodology/approach

To test the LGM, data were collected by surveying 407 salespeople of a retail travel agency with 814 customers in Greater China at multiple points over an eight-month period.

Findings

This study found that, as salespeople perceived more ethical leadership at Time 1, they were more likely to show increases in the work engagement development that increased the service performance development and increased the work–family conflict development over time. In addition, increases in service performance development influenced increases in customer relationship development and increases in work–family conflict development also influenced the emotional exhaustion development.

Originality/value

These findings help managers understand that enabling salespeople to use their full capabilities to their work by ethical leadership may bring not only high service performance but also negative factors that erode salespeople’s well-being.
Modern Public School – technical procurement
Authors: Shaikh Abdul Rehman , Qazi Asad Ali
Published: December 2019

Learning outcomes

Understand the process of purchasing and procurement in a commercial organization; describe the process of tendering, evaluation of bids, and the selection of the supplier; describe the commercial, technical and financial bids; understand the importance of vendor selection criteria and develop the same; and identify the parameters for the procurement of assets.

Case overview/synopsis

Mr Shaikh, working as Procurement Manager at Modern Public School Sukkur (MPSS), is facing the challenge of procuring the bunk beds for recently inducted students. He was asked by the management of the school and his financiers to procure the best quality bunk beds. These beds shall be used at hostels for the students of Class VI. Director academics had already rejected his initial proposal and requested him to source out some cheaper solution keeping in view the budgets. Mr Shaikh then arranged a sample, which was well within the budget, however, this sample was rejected by the owner of the school on the basis of quality. Mr Shaikh now had to source out not only the best quality product but also a budget-friendly solution. He visited the markets and finalized the best quality of pipes to be used for bunk beds. With limited funds, and very short time, shall he be able to select the vendor of his choice and arrange the best quality products? Shall he be able to motivate his key stakeholders and gain procurement committee approval this time?

Complexity academic level

Bachelor of Business Administration and Master of Business Administration.

Supplementary materials

Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code

CSS 11: Strategy
Thematic analysis of short-term renter preferences for housing market in Kuala Lumpur, Malaysia
Authors: Ho Pui-Yee , Low Sheau-Ting , Wee Siaw-Chui , Choong Weng-Wai
Published: December 2019

Purpose

The purpose of this paper is to propose a short-term renters’ preference profile for peer-to-peer (P2P) accommodation selection in the housing market in Kuala Lumpur, Malaysia. The emergence of P2P accommodation was initiated by the concept of a sharing economy, allowing the peer provider to share personal properties with the peer end-users. As the housing market has become more competitive, understanding the preference profile among short-term renters is advantageous to offer a matching marketing mix to the targeted customers.

Design/methodology/approach

This study uses qualitative method associated with thematic analysis. A total of 10,509 reviews on Airbnb were gathered from 377 properties in Kuala Lumpur Federal Territory from 2013 to 2017. Thematic analysis assisted by NVivo software was applied to analyse the empirical data. In total, 14 attributes were identified which could be categorised into 5Ps. The concept of 5Ps adopted from modern marketing is commonly used to categorise the strategies in the marketing process. In the current context, 5Ps is used to categorise the preference of the short-term renter in their selection of P2P accommodation including product, price, promotion, process and people.

Findings

This paper has developed a preference profile for P2P accommodation selection in Malaysia’s housing market. In total, 14 attributes were identified and categorised into the 5Ps of marketing mix. The results showed that the majority of short-term renters were concerned mostly with product (73.2 per cent), followed by people (14.5 per cent), process (10.1 per cent), price (2.0 per cent) and promotion (0.2 per cent).

Originality/value

This study contributes to existing literature with a novel case in Malaysia’s housing market by identifying the short-term renter’s preference in the P2P accommodation selection in the Malaysian housing market, specifically in Kuala Lumpur. The preference profile provides guidance for property owners and developers in the housing market to offer the right product in enhancing the marketability and rentability of the property.