bluuebunny/crossref_metadata_2025 huggingface dataset:
Variation in root secondary metabolites is shaped by past climatic conditions
Authors: Bont Zoe , Züst Tobias , Huber Meret , Erb Matthias
Published: January 2020

Plants can adapt to changing environments by adjusting the production and maintenance of diverse sets of bioactive secondary metabolites. To date, the impact of past climatic conditions relative to other factors such as soil abiotic factors and herbivore pressure on the evolution of plant secondary metabolites is poorly understood, especially for plant roots.

We explored associations between root latex secondary metabolites in 63Taraxacum officinalepopulations across Switzerland and past climatic conditions, soil abiotic parameters, and root herbivore pressure. To assess the contribution of environmental effects, root secondary metabolites were measured in F0 plants in nature and F2 plants under controlled greenhouse conditions.

Concentrations of root latex secondary metabolites were most strongly associated with past climatic conditions, while current soil abiotic factors or root herbivore pressure did not show a clear association with root latex chemistry. Results were identical for natural and controlled conditions, suggesting heritable trait variation rather than environmental plasticity as underlying factor.

Synthesis.We conclude that climatic conditions likely play a major role in the evolution of root secondary metabolites. Direct abiotic effects are likely underlying this pattern, hinting at a novel role of root latex metabolites the tolerance of abiotic stress.
Quantitative and molecular differences distinguish adult human medullary and extramedullary haematopoietic stem and progenitor cell landscapes
Authors: Mende Nicole , Bastos Hugo P , Santoro Antonella , Sham Kendig , Mahbubani Krishnaa T. , Curd Abbie , Takizawa Hitoshi , Wilson Nicola K , Göttgens Bertie , Saeb-Parsy Kourosh , Laurenti Elisa
Published: January 2020

In adults, the bone marrow (BM) is the main site of haematopoietic stem and progenitor cells (HSPCs) maintenance and differentiation. It is known that other anatomical sites can contribute significantly to blood production under stress conditions. However limited tissue availability restricts our knowledge on the cellular, molecular and functional composition of extramedullary HSPC pools in humans at steady state or under stress. Here we describe the landscape of human HSPC differentiation across the three major haematopoietic anatomical sites: BM, spleen and peripheral blood (PB), using matched tissues isolated from the same individuals. Single cell RNA-seq of 30,000 HSPCs and 700 phenotypic haematopoietic stem cells and multipotent progenitors (HSC/MPP) demonstrates significantly different dynamics of haematopoiesis between BM and extramedullary tissues. Lineage-committed progenitors of spleen and PB do not actively divide, whereas BM is the primary site of progenitor proliferation. The balance of differentiation in spleen and PB is skewed towards the lymphoid and erythroid lineages, whereas in BM it is tilted towards megakaryocytic and myeloid progenitors. Extramedullary tissues also harbour a molecularly defined subset of HSC/MPP not found in the BM, which is marked by a specific acto-myosin cytoskeletal signature and transcriptional priming for division and lineage differentiation. Collectively, our findings define a unique cellular and molecular structure of the haematopoietic landscape in extramedullary organs, positioned for rapid lineage-primed demand-adapted haematopoiesis. These data also provide a framework for better understanding of human extramedullary haematopoiesis in health and disease.
Single-cell RNA expression profiling of ACE2, the receptor of SARS-CoV-2
Authors: Zhao Yu , Zhao Zixian , Wang Yujia , Zhou Yueqing , Ma Yu , Zuo Wei
Published: January 2020

A novel coronavirus SARS-CoV-2 was identified in Wuhan, Hubei Province, China in December of 2019. According to WHO report, this new coronavirus has resulted in 76,392 confirmed infections and 2,348 deaths in China by 22 February, 2020, with additional patients being identified in a rapidly growing number internationally. SARS-CoV-2 was reported to share the same receptor, Angiotensin-converting enzyme 2 (ACE2), with SARS-CoV. Here based on the public database and the state-of-the-art single-cell RNA-Seq technique, we analyzed the ACE2 RNA expression profile in the normal human lungs. The result indicates that the ACE2 virus receptor expression is concentrated in a small population of type II alveolar cells (AT2). Surprisingly, we found that this population of ACE2-expressing AT2 also highly expressed many other genes that positively regulating viral entry, reproduction and transmission. This study provides a biological background for the epidemic investigation of the COVID-19, and could be informative for future anti-ACE2 therapeutic strategy development.
“Patient-specific Alzheimer-like pathology in trisomy 21 cerebral organoids reveals BACE2 as a gene-dose-sensitive AD-suppressor in human brain”
Authors: Alić Ivan , Goh Pollyanna A , Murray Aoife , Portelius Erik , Gkanatsiou Eleni , Gough Gillian , Mok Kin Y , Koschut David , Brunmeir Reinhard , Yeap Yee Jie , O’Brien Niamh L , Groet Jurgen , Shao Xiaowei , Havlicek Steven , Dunn N Ray , Kvartsberg Hlin , Brinkmalm Gunnar , Hithersay Rosalyn , Startin Carla , Hamburg Sarah , Phillips Margaret , Pervushin Konstantin , Turmaine Mark , Wallon David , Rovelet-Lecrux Anne , Soininen Hilkka , Volpi Emanuela , Martin Joanne E , Foo Jia Nee , Becker David L , Rostagno Agueda , Ghiso Jorge , Krsnik Željka , Šimić Goran , Kostović Ivica , Mitrečić Dinko ,   LonDownS Consortium, Francis Paul T , Blennow Kaj , Strydom Andre , Hardy John , Zetterberg Henrik , Nižetić Dean
Published: January 2020

A population of >6 million people worldwide at high risk of Alzheimer’s disease (AD) are those with Down Syndrome (DS, caused by trisomy 21 (T21)), 70% of whom develop dementia during lifetime, caused by an extra copy of β-amyloid-(Aβ)-precursor-protein gene. We report AD-like pathology in cerebral organoids grownin vitrofrom non-invasively sampled strands of hair from 71% of DS donors. The pathology consisted of extracellular diffuse and fibrillar Aβ deposits, hyperphosphorylated/pathologically conformed Tau, and premature neuronal loss.

Presence/absence of AD-like pathology was donor-specific (reproducible between individual organoids/iPSC lines/experiments). Pathology could be triggered in pathology-negative T21 organoids by CRISPR/Cas9-mediated elimination of the third copy of chromosome-21-geneBACE2, but prevented by combined chemical β and γ-secretase inhibition. We found that T21-organoids secrete increased proportions of Aβ-preventing (Aβ1-19) and Aβ-degradation products (Aβ1-20 and Aβ1-34). We show these profiles mirror in cerebrospinal fluid of people with DS. We demonstrate that this protective mechanism is mediated by BACE2-trisomy and cross-inhibited by clinically trialled BACE1-inhibitors. Combined, our data prove the physiological role ofBACE2as a dose-sensitive AD-suppressor gene, potentially explaining the dementia delay in ∼30% of people with DS. We also show that DS cerebral organoids could be explored as pre-morbid AD-risk population detector and a system for hypothesis-free drug screens as well as identification of natural suppressor genes for neurodegenerative diseases.
Eating breakfast and avoiding the evening snack sustains lipid oxidation
Authors: Kelly Kevin Parsons , McGuinness Owen P. , Buchowski Maciej , Hughey Jacob J. , Chen Heidi , Powers James , Page Terry , Johnson Carl Hirschie
Published: January 2020

Circadian (daily) regulation of metabolic pathways implies that food may be metabolized differentially over the daily cycle. To test that hypothesis, we monitored the metabolism of older subjects in a whole-room respiratory chamber over two separate 56-h sessions in a random crossover design. In one session, one of the three daily meals was presented as breakfast whereas in the other session, a nutritionally equivalent meal was presented as a late-evening snack. The duration of the overnight fast was the same for both sessions. Whereas the two sessions did not differ in overall energy expenditure, the respiratory exchange ratio (RER) was different during sleep between the two sessions. Unexpectedly, this difference in RER due to daily meal timing was not due to daily differences in physical activity, sleep disruption, or core body temperature. Rather, we found that the daily timing of nutrient availability coupled with daily/circadian control of metabolism drives a switch in substrate preference such that the late-evening snack session resulted in significantly lower lipid oxidation compared to the breakfast session. Therefore, the timing of meals during the day/night cycle affects how ingested food is oxidized or stored in humans with important implications for optimal eating habits.
The activity of chloroplast NADH dehydrogenase-like complex influences the photosynthetic activity of the mossPhyscomitrella patens
Authors: Storti Mattia , Puggioni Maria Paola , Segalla Anna , Morosinotto Tomas , Alboresi Alessandro
Published: January 2020

Alternative electron pathways contribute to the regulation of photosynthetic light reactions to meet metabolic demands in a dynamic environment. Understanding the molecular mechanisms of their activity is seminal to decipher their role in response to environmental cues and in plant adaptation. The chloroplast NADH dehydrogenase-like (NDH) complex mediates cyclic electron transport pathway around photosystem I (PSI) in different organisms like cyanobacteria, algae and various plant species but has a discontinuous distribution in the green lineage. In order to assess how its activity and physiological role changed during plant evolution, we isolatedPhyscomitrella patenslines knocked out of the geneNDHMwhich encodes for a subunit fundamental for the stability and activity of the whole complex.P. patens ndhmKO mosses showed high PSI acceptor side limitation upon illumination leading to PSI photoinhibition. Flavodiiron proteins (FLV) have similar and particularly important role in preventing PSI overreduction when plants are exposed to light fluctuations. Theflva ndhmdouble KO mosses alteration in photosynthetic parameters leaded to a defect in plant growth under fluctuating light as compared to WT and single KO mutants. Results evidenced that, while FLV sustain strong electron transport after an abrupt change in light intensity, NDH contribution to electron transport is small. NDH still participate in modulating PSI activity and it is seminal to prevent PSI photoinhibition especially when FLV are inactive. In plants the functional overlap between NDH- and FLV-dependent electron transport systems sustains PSI activity and to prevent its photoinhibition.
Cortical surface alterations in cingulate and frontal regulatory areas underlie insensitive mothering
Authors: León Inmaculada , Rodrigo María José , Quiñones Ileana , Andrés Hernández-Cabrera Juan , García-Pentón Lorna
Published: January 2020

This study focuses on severe insensitive or neglectful mothering, the most prevalent type of child maltreatment, to examine cortical surface feature alterations underlying maternal functioning and their impact on mother-child interactive bonding. High-resolution 3D volumetric images were obtained on 24 neglectful (NM) and 21 non-neglectful control (CM) mothers. Using surface-based morphometry, we compared differences in cortical thickness and surface area. Mothers completed alexithymia and cortical integrity measures and participated with their children in a play task (Emotional Availability Scale). We found cortical thinning for NM in the right rostral middle frontal gyrus and the right anterior/medial cingulate cortex, and also increased surface area in the right occipital lingual and fusiform areas and the caudal middle frontal area. Mediation analyses showed that cognitive integrity and alexithymia mediated, respectively, the positive and negative effect of the rostral middle frontal gyrus on Emotional Availability. The findings suggest cortical thinning in the rostral frontal area underlying high-order regulatory functioning as being critical for poor maternal self-awareness of emotions and the organization of coordinated actions during mother-child interactive bonding.
Reconstituted Mining Effluent Reduces Neuronal Proliferation in the Developing Brain and Slows Growth of Body and Facial Features in Wild-Caught Wood Frog Tadpoles
Authors: Sturgeon Hannah G. , Kitchen Jeremy P. , Dahora Lara I. , Sweeten Sara E. , Thompson Christopher K.
Published: January 2020

Mining, whether current or inactive, generally increases salt concentrations in catchment watersheds due to precipitation on and through exposed rock surfaces. Practices like mountaintop removal mining have exacerbated this issue, with measurements of salt concentrations in nearby catchment systems well above normal levels. Nevertheless, the impact of the ionic composition of mining effluent on aquatic animal health is not well understood. This is a particularly important issue in Appalachia because it is home to an enormous diversity of organisms, including a huge array of amphibians that live in streams that receive mining effluent from operating and abandoned mines. To investigate this issue, we examined the effects of reconstituted mining effluent on the development of wild-caught wood frog (Lithobates sylvaticus) tadpoles. We collected day-old fertilized eggs from a creek near Blacksburg, VA in early March, 2018 and raised them to hatch. Tadpoles were then assigned to either sulfate or chloride-based reconstituted mining effluent diluted to six different conductivities (100 μS/cm - 2,400 μS/cm). After 7 or 14 days of treatment, tadpoles were euthanized and fixed in paraformaldehyde. We imaged the heads and bodies of tadpoles for morphometric analysis before dissecting out brains and immunostaining them for phospho-histone H3, which labels dividing progenitor cells in the brain. We found that sulfate-based reconstituted mining effluent significantly lowered progenitor cell division at 1200 μS/cm at Day 7 and at 600 μS/cm at Day 14 relative to control. Chloride-based reconstituted mining effluent was less impactful, with no significant differences observed at Day 7 and significantly lowered progenitor cell division at 2400 μS/cm at Day 14. In addition, both treatments slowed growth of some head morphological features, including head size and interocular distance. Chloride treatment slowed growth of body length at Day 14 at 600 μS/cm, whereas sulfate-based reconstituted mining effluent had no effect on body length. These data show that sulfate-based mining effluent has a substantial impact on aspects of neural development, whereas chloride-based reconstituted mining effluent had less effect. In contrast, chloride-based reconstituted mining effluent had a much greater impact than sulfate on body morphology and growth. These experiments demonstrate that the chemical composition of salts in mining effluent can have divergent effects on the development of amphibians.
Nucleolar disruption, activation of P53 and premature senescence in POLR3A-mutated Wiedemann-Rautenstrauch Syndrome fibroblasts
Authors: Báez-Becerra Cindy Tatiana , Valencia-Rincón Estefania , Velásquez-Méndez Karen , Ramírez-Suárez Nelson J. , Guevara Claudia , Sandoval-Hernandez Adrian , Arboleda-Bustos Carlos E. , Olivos-Cisneros Leonora , Gutiérrez-Ospina Gabriela , Arboleda Humberto , Arboleda Gonzalo
Published: January 2020

Recently, mutations in the RNA polymerase III subunit 3A (POLR3A) have been described as the cause of the neonatal progeria or Wiedemann-Rautenstrauch syndrome (WRS). POLR3A have important roles in the regulation of transcription of small RNAs, including tRNA, 5S rRNA and U6 snRNA. We aim to describe cellular and molecular features of WRS fibroblasts. Cultures of primary fibroblasts from one WRS patient [monoallelic POLR3A variant c.3772_3773delCT (p.Leu1258Glyfs*12)] and one control were grown. Mutation in POLR3A causes a decreased in the expression of POLR3A mRNA and protein and a sharp increased of mutant protein. In addition, there was an increased in its nuclear localization. These changes were associated to an increase number and area of nucleoli, a significantly larger nuclear area, and a high increased in the expression of pP53 and pH2AX. All these changes were associated to premature senescence. The present observations add to our understanding of the differences between HGPS and WRS, and opens new alternatives to study cell senesce and human aging.
Clustering of dispersal corridors in metapopulations leads to higher rates of recovery following subpopulation extinction
Authors: Kurkjian Helen M.
Published: January 2020

Understanding how spatially divided populations are affected by the physical characteristics of the landscapes they occupy is critical to their conservation. While some metapopulations have dispersal corridors spread relatively evenly through space in a homogeneous arrangement such that most subpopulations are connected to a few neighbors, others may have corridors clustered in a heterogeneous arrangement, creating a few highly connected subpopulations and leaving most subpopulations with only one or two neighbors. Graph theory and empirical data from other biological and non-biological networks suggest that heterogeneous metapopulations should be the most robust to subpopulation extinction. Here, I usedPseudomonas syringaepv.syringaeB728a in metapopulation microcosms to compare the recovery of metapopulations with homogeneous and heterogeneous corridor arrangements following small, medium, and large subpopulation extinction events. I found that while metapopulations with heterogeneous corridor arrangements had the fastest rates of recovery following extinction events of all sizes and had the shortest absolute time to recovery following medium-sized extinction events, metapopulations with homogeneous corridor arrangements had the shortest time to recovery following the smallest extinction events.
VARIATION AND SELECTION IN AXON NAVIGATION THROUGH MICROTUBULE-DEPENDENT STEPWISE GROWTH CONE ADVANCE
Authors: Turney Stephen G , Chandrasekar Indra , Ahmed Mostafa , Rioux Robert M , Whitesides George M , Bridgman Paul C
Published: January 2020

Myosin II (MII) activity is required for elongating mammalian sensory axons to change speed and direction in response to Nerve Growth Factor (NGF) and laminin-1 (LN). NGF signaling induces faster outgrowth on LN through regulation of actomyosin restraint of microtubule advance into the growth cone periphery. It remains unclear whether growth cone turning on LN works through the same mechanism and, if it does, how the mechanism produces directed advance. Using a novel method for substrate patterning, we tested how directed advance occurs on LN by creating a gap immediately in front of a growth cone advancing on a narrow LN path. The growth cone stopped until an actin-rich protrusion extended over the gap, adhered to LN, and became stabilized. Stepwise advance over the gap was triggered by microtubule +tip entry up to the adhesion site of the protrusion and was independent of traction force pulling. We found that the probability of microtubule entry is regulated at the level of the individual protrusion and is sensitive to the rate of microtubule polymerization and the rate of rearward actin flow as controlled by adhesion-cytoskeletal coupling and MII. We conclude that growth cone navigation is an iterative process of variation and selection. Growth cones extend leading edge actin-rich protrusions that adhere transiently (variation). Microtubule entry up to an adhesion site stabilizes a protrusion (selection) leading to engorgement, consolidation, protrusive activity distal to the adhesion site, and stepwise growth cone advance. The orientation of the protrusion determines the direction of advance.
Distribution and localization of phosphatidylinositol 5-phosphate, 4-kinase alpha and beta in the brain
Authors: Noch Evan K. , Yim Isaiah , Milner Teresa A. , Cantley Lewis C.
Published: January 2020

Phosphatidylinositol-4,5-bisphosphate (PI-4,5-P2) is critical for synaptic vesicle docking and fusion and generation of the second messengers, diacylglycerol and inositol-1,4,5-trisphosphate. PI-4,5-P2can be generated by two families of kinases: type 1 phosphatidylinositol-4-phosphate 5-kinases, encoded by PIP5K1A, PIP5K1B and PIP5K1C, and type 2 phosphatidylinositol-5-phosphate 4-kinases, encoded by PIP4K2A, PIP4K2B, and PIP4K2C. While the roles of the type 1 enzymes in brain function have been extensively studied, the roles of the type 2 enzymes are poorly understood. Using selective antibodies validated by genetic deletion of pip4k2a or pip4k2b in mouse brain, we characterized the location of the enzymes, PI5P4Kα and PI5P4Kß, encoded by these genes. In mice, we demonstrate that PI5P4Kα is expressed in adulthood, whereas PI5P4Kß is expressed early in development. PI5P4Kα localizes to white matter tracts, especially the corpus callosum, and at a low level in neurons, while PI5P4Kß is expressed in neuronal populations, especially hippocampus and cortex. Dual labeling studies demonstrate that PI5P4Kα co-localizes with the oligodendrocyte marker, Olig2, whereas PI5P4Kß co-localizes with the neuronal marker, NeuN. Immunohistochemical subcellular distribution studies demonstrate that PI5P4Kα and PI5P4Kß are expressed in the early endosome system. Ultrastructural analysis demonstrates that both kinases are contained in axon terminals and dendritic spines adjacent to the synaptic membrane, which support a potential role in synaptic transmission. Immunohistochemical analysis of macaque and human brain tissue demonstrate a conserved pattern for PI5P4Kα and PI5P4Kß. These results highlight the diverse cell-autonomous expression of PI5P4Kα and PI5P4Kß and support further exploration into their role in synaptic function in the brain.
Redundant and additive functions of the four Lef/Tcf transcription factors in lung epithelial progenitors
Authors: Gerner-Mauro Kamryn N. , Akiyama Haruhiko , Chen Jichao
Published: January 2020

In multicellular organisms, paralogs from gene duplication survive purifying selection by evolving tissue-specific expression and function. Whether this genetic redundancy is also selected for within a single cell type is unclear for multi-member paralogs, as exemplified by the 4 obligatory Lef/Tcf transcription factors of canonical Wnt signaling, mainly due to the dauntingly complex genetics involved. Using the developing mouse lung as a model system, we generate 2 quadruple conditional knockouts and myriad triple and double combinations, and show that the 4 Lef/Tcf genes function redundantly in the presence of at least 2 Lef/Tcf paralogs, but additively upon losing additional paralogs to specify and maintain lung epithelial progenitors. Pre-lung-specification, pan-epithelial double knockouts have no lung phenotype, triple knockouts have varying phenotypes, including defective branching and tracheoesophageal fistulas, and the quadruple knockout barely forms a lung, resembling theCtnnb1mutant. Post-lung-specification deletion of all 4 Lef/Tcf genes leads to branching defects, downregulation of progenitor genes, premature alveolar differentiation, and derepression of gastrointestinal genes, again phenocopying the correspondingCtnnb1mutant. Our study supports a monotonic, positive signaling relationship between CTNNB1 and Lef/Tcf in lung epithelial progenitors and represents, to our knowledge, the first in vivo analysis of cell-type-specific genetic redundancy among the 4 Lef/Tcf paralogs.

SIGNIFICANCE STATEMENT

Paralogs represent genetic redundancy and survive purifying selection by evolving overlapping and distinct functions. In multicellular organisms, such functional diversification can manifest as tissue and cell type specific expression, which masks possible selective pressure for genetic redundancy within a single cell type. Using in vivo genetic and genomic analyses, we show that although the 4 mammalian Lef/Tcf transcription factors have evolved organ-specific functions, they function additively and redundantly, depending on gene dosage, to promote lung epithelial progenitors and do so in a monotonic, positive manner with beta-Catenin in the canonical Wnt signaling pathway.
CopyMix: Mixture Model Based Single-Cell Clustering and Copy Number Profiling using Variational Inference
Authors: Safinianaini Negar , P. E. de Souza Camila , Roth Andrew , Koptagel Hazal , Toosi Hosein , Lagergren Jens
Published: January 2020

Investigating tumor heterogeneity using single-cell sequencing technologies is imperative to understand how tumors evolve since each cell subpopulation harbors a unique set of genomic features that yields a unique phenotype, which is bound to have clinical relevance. Clustering of cells based on copy number data obtained from single-cell DNA sequencing provides an opportunity to identify different tumor cell subpopulations. Accordingly, computational methods have emerged for single-cell copy number profiling and clustering; however, these two tasks have been handled sequentially by applying various ad-hoc pre- and post-processing steps; hence, a procedure vulnerable to introducing clustering artifacts. Moreover, clonal copy number profiling has been missing except for one method, CONET, which unfortunately computes it by a post-processing tool. Finally, a common copy number profiling tool, HMMcopy, requires parameter tuning. We avoid the clustering artifact issues and provide clonal copy number profiles without the labor of parameter tuning in our method, CopyMix, a Variational Inference for a novel mixture model, by jointly inferring cell clusters and their underlying copy number profile. We evaluate CopyMix using simulated data and published biological data from ovarian cancer. The results reveal high clustering performance and low errors in copy number profiling. These favorable results indicate a considerable potential to obtain clinical impact by using CopyMix in studies of cancer tumor heterogeneity.
Pdap1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification
Authors: Delgado-Benito Verónica , Berruezo-Llacuna Maria , Altwasser Robert , Winkler Wiebke , Balasubramanian Sandhya , Sundaravinayagam Devakumar , Graf Robin , Rahjouei Ali , Driesner Madlen , Keller Lisa , Janz Martin , Akalin Altuna , Virgilio Michela Di
Published: January 2020

The establishment of protective humoral immunity is dependent on the ability of mature B cells to undergo antibody gene diversification while adjusting to the physiological stressors induced by activation with the antigen. Mature B cells diversify their antibody genes by class switch recombination (CSR) and somatic hypermutation (SHM), which are both dependent on efficient induction of activation-induced cytidine deaminase (AID). Here, we identified PDGFA-associated protein 1 (Pdap1) as an essential regulator of cellular homeostasis in mature B cells. Pdap1 deficiency leads to sustained expression of the integrated stress response (ISR) effector activating transcription factor 4 (Atf4) and induction of the ISR transcriptional program, increased cell death, and defective AID expression. As a consequence, loss of Pdap1 reduces germinal center B cell formation and impairs CSR and SHM. Thus, Pdap1 protects mature B cells against chronic ISR activation and ensures efficient antibody diversification by promoting their survival and optimal function.
Transferability, development of Single Sequence Repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopumMart.) in Benin
Authors: Kpaténon Mariano Joly , Salako Valère Kolawolé , Santoni Sylvain , Zekraoui Leila , Latreille Muriel , Tollon-Cordet Christine , Mariac Cédric , Jaligot Estelle , Beulé Thierry , Adéoti Kifouli
Published: January 2020

In Sub-Saharan Africa, the fan palmBorassus aethiopumMart. is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource.

The present work is a first attempt at characterizing the genetic diversity of this palm species as well as its spatial structuration in Benin, West Africa. During a first phase we implemented a microsatellite markers-based approach relying on the reported transferability of primers developed in other palm species and found that, in disagreement with previously published results, only 22.5% of the 80 markers tested enabled amplification of African fan palm DNA and polymorphism detection was insufficient. During a second phase, we therefore generated aB. aethiopum-specific genomic dataset through high-throughput sequencing and used it for thede novodetection of potential microsatellite markers. Among these, 11 enabled polymorphism detection and were further used for analyzing genetic diversity in nineB. aethiopumpopulations.

Our results show that genetic diversity of Beninese fan palm populations is low, with an overall average expected heterozygosity (He) of 0.354. Moreover, the positive values of the fixation index (F) in populations from both the Central (Soudano-Guinean) and the Southern (Guinean) regions suggest limited gene flows. Our analysis show that sampledB. aethiopumpopulations are clustered into two groups, one spanning populations from both the Southern and most of the Central region, and the other including the Central population of Savè (which also has the highest He) and populations from the North.

In light of our results, we discuss the use of inter-species transfer vs.de novodevelopment of microsatellite markers in genetic diversity analyses targeting under-studied species. We also suggest future applications for the molecular resources generated through the present study.
Improving Heart disease risk through quality-focused diet logging: pre-post study of a diet quality tracking app
Authors: VanDam Courtland , Kwon Bum Chul , Chiuve Stephanie , Choi Hyung-Wook , Entler Paul , Tan Pang-Ning , Huh-Yoo Jina
Published: January 2020

Diet-tracking mobile apps have been effective in behavior change. At the same time, quantity-focused diet tracking (e.g., calorie counting) can be time-consuming and tedious, leading to unsustained adoption. Diet Quality—focusing on high-quality dietary patterns rather than quantifying diet into calories—has shown effectiveness in improving heart disease risk. Healthy Heart Score (HHS) predicts 20-year cardiovascular risks based on quality-focused food category consumptions, rather than detailed serving sizes. No studies have examined how mobile health apps focusing on diet quality can bring promising results on health outcomes and ease of adoption. We designed a mobile app to support the HHS informed quality-focused dietary approach by enabling users to log simplified diet quality and view its real-time impact on future heart disease risks. Users were asked to log food categories that are the main predictors of HHS. We measured the app’s feasibility and efficacy on improving individuals’ clinical and behavioral factors affecting future heart disease risks and app use. We recruited 38 overweight or obese participants at high heart disease risk, who used the app for 5 weeks and measured weight, blood sugar, and blood pressure, HHS, and Diet Score (DS) measuring diet quality at baseline and the fifth week of the intervention. The majority used the application every week (84%) and significantly improved DS and HHS at the fifth week (p<0.05), although only 10 participants (31%) checked their risk scores more than once. Other outcomes did not show significant changes. Our study showed logging simplified diet quality significantly improved dietary behavior. The participants were not interested in seeing HHS, and the participants perceived logging diet categories irrelevant to improving HHS as important. We discuss the complexities of addressing health risks, quantity vs. quality-based health monitoring, and incorporating secondary behavior change goals that matter to users when designing mobile health.
Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms
Authors: Pabis Anna , Rawle Robert J. , Kasson Peter M.
Published: January 2020

Enveloped viruses enter cells via a process of membrane fusion between the viral envelope and a cellular membrane. For influenza virus, mutational data have shown that the membrane-inserted portions of the hemagglutinin protein play a critical role in achieving fusion. In contrast to the relatively well-understood ectodomain, a predictive mechanistic understanding of the intramembrane mechanisms by which influenza hemagglutinin drives fusion has been elusive. We have used molecular dynamics simulations of fusion between a full-length hemagglutinin proteoliposome and a lipid bilayer to analyze these mechanisms. In our simulations, hemagglutinin first acts within the membrane to increase lipid tail protrusion and promote stalk formation and then acts to engage the distal leaflets of each membrane and promote stalk widening, curvature, and eventual fusion. These two sequential mechanisms, one occurring prior to stalk formation and one after, are consistent with experimental measurements we report of single-virus fusion kinetics to liposomes of different sizes. The resulting model also helps explain and integrate prior mutational and biophysical data, particularly the mutational sensitivity of the fusion peptide N-terminus and the length sensitivity of the transmembrane domain. We hypothesize that entry by other enveloped viruses may also utilize sequential processes of acyl tail exposure followed by membrane curvature and distal leaflet engagement.
Engineered unnatural ubiquitin for optimal detection of deubiquitinating enzymes
Authors: Rut Wioletta , Żmudziński Mikołaj , Snipas Scott J. , Bekes Miklos , Huang Tony T. , Drag Marcin
Published: January 2020

Deubiquitinating enzymes (DUBs) are responsible for removing ubiquitin (Ub) from its protein conjugates. DUBs have been implicated as attractive therapeutic targets in the treatment of viral diseases, neurodegenerative disorders and cancer. The lack of selective chemical tools for the exploration of these enzymes significantly impairs the determination of their roles in both normal and pathological states. Commercially available fluorogenic substrates are based on the C-terminal Ub motif or contain Ub coupled to a fluorophore (Z-LRGG-AMC, Ub-AMC); therefore, these substrates suffer from lack of selectivity. By using a hybrid combinatorial substrate library (HyCoSuL) and a defined P2 library containing a wide variety of nonproteinogenic amino acids, we established a full substrate specificity profile for two DUBs—MERS PLpro and human UCH-L3. Based on these results, we designed and synthesized Ub-based substrates and activity-based probes (ABPs) containing selected unnatural amino acids located in the C-terminal Ub motif. Biochemical analysis and cell-based experiments confirmed the activity and selectivity of engineered Ub-based substrates and probes. Using this approach, we propose that for any protease that recognizes Ub and Ub-like substrates, a highly active and selective unnatural substrate or probe can be engineered.
Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets
Authors: Erbe Rossin , Kessler Michael D. , Favorov Alexander V. , Easwaran Hariharan , Gaykalova Daria A. , Fertig Elana J.
Published: January 2020

While single-cell ATAC-seq analysis methods allow for robust clustering of cell types, the question of how to integrate multiple scATAC-seq data sets and/or sequencing modalities is still open. We present an analysis framework that enables such integration by applying the CoGAPS Matrix Factorization algorithm and the projectR transfer learning program to identify common regulatory patterns across scATAC-seq data sets. Using publicly available scATAC-seq data, we find patterns that accurately characterize cell types both within and across data sets. Furthermore, we demonstrate that these patterns are both consistent with current biological understanding and reflective of novel regulatory biology.
Excess crossovers impede faithful meiotic chromosome segregation inC. elegans
Authors: Hollis Jeremy A. , Glover Marissa L. , Schlientz Aleesa , Cahoon Cori K. , Bowerman Bruce , Wignall Sarah M. , Libuda Diana E.
Published: January 2020

During meiosis, at least one crossover must form between each pair of homologous chromosomes to ensure their proper partitioning. However, most organisms limit the number of crossovers by a phenomenon called crossover interference; why this occurs is not well understood. Here we investigate the functional consequences of extra crossovers inCaenorhabditis elegans. Using a fusion chromosome that exhibits a high frequency of supernumerary crossovers, we find that essential chromosomal structures are mispatterned, subjecting chromosomes to improper spindle forces and leading to congression and segregation defects. Moreover, we uncover mechanisms that counteract these errors; anaphase I chromosome bridges were often able to resolve in a LEM-3 nuclease dependent manner, and tethers between homologs that persisted were frequently resolved during Meiosis II by a second mechanism. This study thus provides evidence that excess crossovers impact chromosome patterning and segregation, and also sheds light on how these errors are corrected.
Effect of micro-arc oxidation coating on stress corrosion behavior of AA7050
Authors: Song R.G. , Hua T.S. , Zong Y. , Cai S.W.
Published: January 2020

Purpose

This paper aims to study the effect of Micro-arc oxidation (MAO) coating on stress corrosion and electrochemical behavior of aluminum alloy.

Design/methodology/approach

The stress corrosion cracking behavior of 7050 aluminum alloy (AA7050) after MAO treatment was investigated in 3.5 Wt.% NaCl solution using the constant load ring. Electrochemical impedance spectroscopy (EIS) was used to evaluate the change of corrosion resistance of MAO specimens in 3.5  Wt.% NaCl solution, and appropriate equivalent circuits were established.

Findings

The results demonstrated that the MAO coating can improve the corrosion resistance of the AA7050 and avoid the reduction of mechanical properties caused by corrosion. In the initial stage of corrosion, the corrosion resistance of coated specimen decreased at first and then increased. In the middle and final stage of corrosion, the corrosion resistance of coated specimen decreased at first and then stabilized.

Originality/value

The long-term corrosion behavior of MAO specimens under stress was studied by constant load experiment and EIS. It has guiding significance for the application of MAO technology on aluminum alloy.
Simulation of bipolar charge transport in graphene on h-BN
Authors: Coco Marco , Nastasi Giovanni
Published: January 2020

Purpose

The purpose of this paper is to simulate charge transport in monolayer graphene on a substrate made of hexagonal boron nitride (h-BN). This choice is motivated by the fact that h-BN is one of the most promising substrates on account of the reduced degradation of the velocity due to the remote impurities.

Design/methodology/approach

The semiclassical Boltzmann equations for electrons in the monolayer graphene are numerically solved by an approach based on a discontinuous Galerkin (DG) method. Both the conduction and valence bands are included, and the inter-band scatterings are taken into account as well.

Findings

The importance of the inter-band scatterings is accurately evaluated for several values of the Fermi energy, addressing the issue related to the validity of neglecting the generation-recombination terms. It is found out that the inclusion of the inter-band scatterings produces sizable variations in the average values, like the current density, at zero Fermi energy, whereas, as expected, the effect of the inter-band scattering becomes negligible by increasing the absolute value of the Fermi energy.

Research limitations/implications

The correct evaluation of the influence of the inter-band scatterings on the electronic performances is deeply important not only from a theoretical point of view but also for the applications. In particular, it will be shown that the time necessary to reach the steady state is greatly affected by the inter-band scatterings, with not negligible consequences on the switching on/off processes of realistic devices. As a limitation of the present work, the proposed approach refers to the spatially homogeneous case. For the simulation of electron devices, non-homogenous numerical solutions are required. This last case will be tackled in a forthcoming paper.

Originality/value

As observed in Majorana et al. (2019), the use of a Direct Simulation Monte Carlo (DSMC) approach, which properly describes the inter-band scatterings, is computationally very expensive because the valence band is highly populated and a huge number of particles is needed. Even by simulating holes instead of electrons does not overcome the problem because there is a certain degree of ambiguity in the generation and recombination terms of electron-hole pairs. The DG approach, used in this paper, does not suffer from the previous drawbacks and requires a reasonable computing effort.
Logics behind evading overnight taxes: a configurational analysis
Authors: Beritelli Pietro , Reinhold Stephan , Laesser Christian
Published: January 2020

Purpose

Overnight taxes are controversial. They affect tourists’ consumption behavior and hotels’ profits. This potentially generates undesirable industry practices such as underreporting overnights to evade overnight taxes. The aim of the paper is to understand the conditions and outcomes of underreporting. This is important because underreporting affects destinations’ tax income, which in turn may have further effects on tourism or other public services.

Design/methodology/approach

This study uses qualitative comparative analysis to identify what specific combinations of conditions motivate managers of hospitality businesses to evade overnight taxes.

Findings

While potential economic gain seems to be the obvious answer, this study finds that different configurations of causal conditions account for non-compliance. Four different configurations combining six conditions explain the logics behind hotel overnight tax evasion behavior. The conditions refer to both utilitarian affordances and the individual tax morale of hospitality managers. Certain utilitarian conditions in combination can overrule moral objections to non-compliance.

Originality/value

The study provides a nuanced understanding of overnight tax evasion motives and suggests how to connect work on tourism taxes with destination governance issues and destination management organization funding.
Effects of African local food consumption experiences on post-tasting behavior
Authors: Kim Seongseop (Sam) , Badu-Baiden Frank , Oh Munhyang (Moon) , Kim Jungkeun
Published: January 2020

Purpose

The purpose of this paper is to investigate the effects of experiences with local food in Ghana on satisfaction, favorability and behavioral intention.

Design/methodology/approach

Unlike previous studies that have used multiple regression analysis or structural equation modeling, this study adopts impact-range performance analysis (IRPA) and impact asymmetry analysis (IAA). A total of 336 questionnaires were used in the data analyses.

Findings

Factor analysis generates five domains of experience of consuming local food. Socialization and boasting and experience with various menus and quality of food contribute most to explaining the three dependent variables.

Originality/value

This study has significant value because it extends the study of local food consumption experience to the understudied area of African food tourism, particularly Ghanaian food and tourists to Ghana.
Multiple identities of a festival
Authors: Masiello Barbara , Bonetti Enrico , Izzo Francesco
Published: January 2020

Purpose

This paper aims to understand how festival brand personality is built and managed in the social media environment by explaining the intended (by the organizers) festival brand personality and how this concept is communicated and perceived by social media users.

Design/methodology/approach

A multi-method research design was used. Initially, a qualitative analysis based on the free-listing psychological meaning approach was adopted. Then, a content analysis of 23,717 Facebook posts and tweets was performed through NVivo11. Finally, the resulting data were examined through a non-parametric statistical analysis.

Findings

The results show an “internal brand personality gap” (between the intended and communicated brand personality) and an “external brand personality gap” (between the communicated and perceived brand personality). The findings also highlight the existence of an “ultimate brand personality on social media,” which represents a collective and dynamic construct that is co-created by the organization and its customers through interaction and the key role of the customers’ experiences.

Research limitations/implications

The findings contribute to a theory of event brand personality and its management on social media by showing a case with multiple identities.

Practical implications

Implications for the organizers of festivals and non-sport events are discussed to reduce internal and external gaps and better understand the “fit/unfit problem” when dealing with brand personality on social media.

Originality/value

This paper contributes to a research area that is in its infancy because it is one of the first attempts to analyze festival brand personality and its relationship with social media.
Contexts and gender – looking back and thinking forward
Authors: Welter Friederike
Published: January 2020

Purpose

This paper aims to illustrate the main contributions of the context-gender discussion in entrepreneurship research and its main developments over time to identify promising future research avenues.

Design/methodology/approach

This paper builds on the author’s extensive knowledge of the context-gender debate and on several recent overviews and reviews of the debate. It is written as essay, introducing its main themes through a personal reflection and complemented by a selective review of research on gendered contexts and women’s entrepreneurship.

Findings

The context-gender discussion has moved forward. The first wave of context-gender studies contextualized gender, considering the impact of contexts on women’s entrepreneurship. Nowadays, studies are conducted on how contexts are gendered and how they are constructed in gendered ways through, for example, words, images, cognitions, as well as how women entrepreneurs can impact on and enact their contexts.

Originality/value

This paper contributes novel insights into contextualizing gender and gendering contexts. It is unique in suggesting that a perspective on gendering contexts will allow to explore the diversity of entrepreneurship and further develop theories related to contexts and gender.