bluuebunny/crossref_metadata_2025 huggingface dataset:
Cancer cells induce hepatocytes apoptosis in co-opted colorectal cancer liver metastatic lesions
Authors: Rada Miran , Tsamchoe Migmar , Kapelanski-Lamoureux Audrey , Bloom Jessica , Petrillo Stephanie , Kim Diane H , Lazaris Anthoula , Metrakos Peter
Published: February 2021

Vessel co-option in colorectal cancer liver metastases (CRCLM) has been recognized as one of the mechanistic pathways that contribute to resistance against anti-angiogenic therapy. In vessel co-opted CRCLM lesions, the cancer cells are highly motile that move toward and along the pre-existing sinusoidal vessels and hijack them to gain access to nutrient. The movement of cancer cells is accompanied by replacement of the hepatocytes. However, the molecular mechanisms by which this replacement occurs are unclear yet. To examine the involvement of apoptosis in hepatocytes replacement by cancer cells in co-opted lesions, we conducted immunohistochemical staining for chemonaïve CRCLM specimens using pro-apoptotic markers antibody, such as cleaved caspase-3 and cleaved poly (ADP-ribose) polymerase-1 (PARP-1). The results suggested overexpression of pro-apoptotic markers in liver parenchyma of co-opted lesions compared to angiogenic lesions, specifically the hepatocytes that are in close proximity to the cancer cells. Importantly, co-culturing hepatocytes with colorectal cancer cells induced overexpression of pro-apoptotic markers in the hepatocytes. Altogether, these results propose that cancer cells could exploit apoptosis to replace the hepatocytes and establish vessel co-option in CRCLM.
The C. elegans Notch proteins LIN-12 and GLP-1 are tuned to lower force thresholds for activation than Drosophila Notch
Authors: Langridge Paul D. , Chan Jessica Yu , Garcia-Diaz Alejandro , Greenwald Iva , Struhl Gary
Published: February 2021

The conserved transmembrane receptor Notch mediates cell fate decisions in all animals. In the absence of ligand, a Negative Regulatory Region (NRR) in the Notch ectodomain adopts an autoinhibited confirmation, masking an ADAM protease cleavage site [1, 2]; ligand binding makes the cleavage site accessible, leading to shedding of the Notch ectodomain as the first step of signal transduction [3, 4]. In Drosophila and vertebrates, the ligands are all single-pass transmembrane Delta/Serrate/LAG-2 (DSL) proteins; the endocytic adaptor Epsin binds to the ubiquitinated intracellular domain, and the resulting Clathrin-mediated endocytosis exerts a “pulling force” that exposes the cleavage site in the NRR [4–6]. However, inC. elegans, the presence of natural secreted DSL proteins [7] and other observations suggested that Epsin-mediated endocytosis may not be required to activate the Notch proteins LIN-12 and GLP-1. Here, we confirm that neither Epsin nor the cytosolic domains of DSL proteins are required for Notch signaling in C. elegans. Furthermore, we provide evidence that the NRRs of LIN-12 and GLP-1 are tuned to a lower force level than the NRR of Drosophila Notch. Finally, we show that adding a Leucine “plug” that occludes the cleavage site in vertebrate and Drosophila Notch proteins but is absent in theC. elegansNotch proteins [1, 2] renders the LIN-12 and GLP-1 NRRs dependent on Epsin-mediated ligand endocytosis, indicating that greater force is now required to expose the cleavage site. Thus, the NRRs of LIN-12 and GLP-1 appear to be tuned to a lower force threshold, accounting for the different requirements for signaling inC. elegans.
Multi-channel 4D parametrized Atlas of Macro- and Microstructural Neonatal Brain Development
Authors: Uus Alena , Grigorescu Irina , Pietsch Maximillian , Batalle Dafnis , Christiaens Daan , Hughes Emer , Hutter Jana , Grande Lucilio Cordero , Price Anthony N. , Turnier Jacques-Donald , Rutherford Mary A. , Counsell Serena J. , Hajnal Joseph V. , Edwards A. David , Deprez Maria
Published: February 2021

Structural and diffusion MRI provide complimentary anatomical and microstructural characterization of early brain maturation. The existing models of the developing brain in time include only either structural or diffusion channels. Furthermore, there is a lack of tools for combined analysis of structural and diffusion MRI in the same reference space.

In this work we propose methodology to generate multi-channel (MC) continuous spatio-temporal parametrized atlas of brain development based on MC registration driven by both T2-weighted and orientation distribution functions (ODF) channels along with the Gompertz model (GM) fitting of the signals and spatial transformations in time. We construct a 4D MC atlas of neonatal brain development during 38 to 44 week PMA range from 170 normal term subjects from developing Human Connectomme Project. The resulting atlas consists of fourteen spatio-temporal microstructural indices and two parcellation maps delineating white matter tracts and neonatal transient structures. We demonstrate applicability of the atlas for quantitative region-specific comparison of 140 term and 40 preterm subjects scanned at the term-equivalent age. We show multi-parametric microstructural differences in multiple white matter regions, including the transient compartments. The atlas and software will be available after publication of the article.
Different trajectories of polyploidization shape the genomic landscape of theBrettanomyces bruxellensisyeast species
Authors: Eberlein Chris , Saada Omar Abou , Friedrich Anne , Albertin Warren , Schacherer Joseph
Published: February 2021

Polyploidization events are observed across the tree of life and occurred in many fungi, plant and animal species. Polyploidy is thought to be an important source of speciation and tumorigenesis. However, the origins of polyploid populations are not always clear and little is known about the precise nature and structure of their complex genome. Using a long-read sequencing strategy, we sequenced a large number of isolates from theBrettanomyces bruxellensisyeast species, which is found in anthropized environments (e.g.beer, contaminant of wine, kombucha and ethanol production) and characterized by several polyploid subpopulations. To reconstruct the polyploid genomes, we phased them by using different strategies and we found that each subpopulation had a unique polyploidization history with distinct trajectories. The polyploid genomes contain either genetically closely related (with a genetic divergence < 1%) or diverged copies (> 3%), indicating auto- as well as allopolyploidization events. These latest events have occurred independently with a specific and unique donor in each of the polyploid subpopulations, and exclude the knownBrettanomycessister species as possible donors. Finally, loss of heterozygosity events have shaped the structure of these polyploid genomes and underline their dynamic. Overall, our study highlights the multiplicity of the trajectories leading to polyploid genomes within a same species.
Mapping global shifts inSaccharomyces cerevisiaegene expression across asynchronous time trajectories with diffusion maps
Authors: Reiter Taylor , Montpetit Rachel , Runnebaum Ron , Brown C. Titus , Montpetit Ben
Published: February 2021

Grapes grown in a particular geographic region often produce wines with consistent characteristics, suggesting there are site-specific factors driving recurrent fermentation outcomes. However, our understanding of the relationship between site-specific factors, microbial metabolism, and wine fermentation outcomes are not well understood. Here, we used differences inSaccharomyces cerevisiaegene expression as a biosensor for differences among Pinot noir fermentations from 15 vineyard sites. We profiled time series gene expression patterns of primary fermentations, but fermentations proceeded at different rates, making analyzes of these data with conventional differential expression tools difficult. This led us to develop a novel approach that combines diffusion mapping with continuous differential expression analysis. Using this method, we identified vineyard specific deviations in gene expression, including changes in gene expression correlated with the activity of thenon-SaccharomycesyeastHanseniaspora uvarum, as well as with initial nitrogen concentrations in grape musts. These results highlight novel relationships between site-specific variables andSaccharomyces cerevisiaegene expression that are linked to repeated wine fermentation outcomes. In addition, we demonstrate that our analysis approach can extract biologically relevant gene expression patterns in other contexts (e.g., hypoxic response ofSaccharomyces cerevisiae), indicating that this approach offers a general method for investigating asynchronous time series gene expression data.

Importance

While it is generally accepted that foods, in particular wine, possess sensory characteristics associated with or derived from their place of origin, we lack knowledge of the biotic and abiotic factors central to this phenomenon. We have usedSaccharomyces cerevisiaegene expression as a biosensor to capture differences in fermentations of Pinot noir grapes from 15 vineyards across two vintages. We find that gene expression by non-Saccharomycesyeasts and initial nitrogen content in the grape must correlates with differences in gene expression among fermentations from these vintages. These findings highlight important relationships between site-specific variables and gene expression that can be used to understand, or possibly modify, wine fermentation outcomes. Our work also provides a novel analysis method for investigating asynchronous gene expression data sets that is able to reveal both global shifts and subtle differences in gene expression due to varied cell – environment interactions.
Development and validation of a mouse model of contemporary cannabis smoke exposure
Authors: Fantauzzi Matthew F. , Cass Steven P. , McGrath Joshua J.C. , Thayaparan Danya , Wang Peiyao , Stampfli Martin R. , Hirota Jeremy A.
Published: February 2021

Cannabis is widely used for both recreational and medicinal purposes. Inhalation of combusted cannabis smoke is the most common mode of drug consumption, exposing the lungs to the pharmacologically active ingredients, including tetrahydrocannabinol (THC) and cannabidiol (CBD). While the relationship between cannabis smoke exposure and compromised respiratory health has yet to be sufficiently defined, previous investigations suggest that cannabis smoke may dysregulate pulmonary immunity. Presently, there exists few pre-clinical animal models that have been extensively validated for contemporary cannabis smoke exposure. To address this need, we developed a mouse model with readouts of total particular matter, serum cannabinoid and carboxyhemoglobin levels, lung cellular responses, and immune mediator production.

Using a commercially available smoke exposure system and a cannabis source material of documented THC/CBD composition, we exposed mice to a total particulate matter of 698.89 (SD = 66.09) µg/L and demonstrate increases in serum cannabinoids and carboxyhemoglobin. We demonstrate that cannabis smoke modulates immune cell populations and mediators in both male and female BALB/c mice. This modulation is highlighted by increases in airway and lung tissue macrophage populations, including tissue-resident alveolar macrophages, monocyte-derived alveolar macrophages, and interstitial macrophage subpopulations. No changes in airway or lung tissue infiltration of neutrophils were observed. Immune mediator analysis indicated significant upregulation of MDC, TARC, and VEGF within the lung tissue of cannabis smoke exposed mice. This accessible and reproducible smoke exposure model provides a foundation to explore the impact of chronic cannabis exposures and/or co-exposures with pathogens of clinical relevance, such as influenza.
The making of cauliflowers: the story of unsuccessful flowers
Authors: Azpeitia Eugenio , Tichtinsky Gabrielle , Le Masson Marie , Serrano-Mislata Antonio , Gregis Veronica , Gimenez Carlos , Prunet Nathanaёl , Lucas Jérémy , Farcot Etienne , Kater Martin M. , Bradley Desmond , Madueño Francisco , Godin Christophe , Parcy Francois
Published: February 2021

The arrangement of plant organs, called phyllotaxis, produce remarkable spiral or whorled patterns. Cauliflowers present a unique phyllotaxis with a multitude of spirals over a wide range of scales. How such a self-similar fractal organization emerges from developmental mechanisms has remained elusive. Combining experimental assays with modeling, we found that cauliflowers arise due to the hysteresis of the bistable floral network that generates inflorescences imprinted by a transient floral state. We further show how additional mutations affecting meristem growth dynamics can induce the production of conical phyllotactic structures reminiscent of the conspicuous fractal Romanesco shape. This study reveals how the spectacular morphological modification of the inflorescences in cauliflower and Romanesco shape arises from the hysteresis of the genetic programs controlling inflorescence development.

One Sentence Summary

The molecular making of cauliflowers
The Evolution of Chunks in Sequence Learning
Authors: Tosatto Laure , Fagot Joël , Nemeth Dezso , Rey Arnaud
Published: February 2021

Chunking mechanisms are central to several cognitive processes and notably to the acquisition of visuo-motor sequences. Individuals segment sequences into chunks of items to perform visuo-motor tasks more fluidly, rapidly, and accurately. However, the exact dynamics of chunking processes in the case of extended practice remain unclear. Using an operant conditioning device, eighteen Guinea baboons (Papio papio) produced a fixed sequence of nine movements during 1,000 trials by pointing to a moving target on a touch screen. Response times analyses revealed a specific chunking pattern of the sequence for each baboon. More importantly, we found that these patterns evolved during the course of the experiment, with chunks becoming progressively fewer and longer. We identified two chunk reorganization mechanisms: therecombinationof preexisting chunks and theconcatenationof two distinct chunks into a single one. These results provide new evidence on chunking mechanisms in sequence learning and challenge current models of associative and statistical learning.
Dynamics of primary productivity in relation to submerged vegetation of a shallow, eutrophic lagoon: a field and mesocosm study
Authors: Berthold Maximilian , Paar Martin
Published: February 2021

Aquatic ecosystems nowadays are under constant pressure, either from recent or historical events. In most systems with increased nutrient supply, submerged macrophytes got replaced by another stable state, dominated by phytoplankton as main primary producer. Yet, reducing the nutrient supply did not yield the aimed goal of restored habitats for submerged macrophytes in systems worldwide. The question arises, why submerged macrophytes do not re-colonize, and if they are actually competitive. Therefore, primary production assays were conducted inex-situbentho-pelagic mesocosms and compared to the actual ecosystem, a turbid brackish lagoon of the southern Baltic Sea. Mesocosm were either manipulated to be colonized by macrophytes, or stayed phytoplankton dominated. Oxygen evolution was monitored over a period of five months in 5 min (mesocosms) to 10 min (ecosystem) intervals. Surface and depth-integrated production was calculated to analyse seasonal and areal resolved production patterns. It was found that macrophyte mesocosms were more stable, when considering only surface O2production. However, calculating depth-integrated production resulted in net-heterotrophy in both shallow mesocosms approaches and the actual ecosystem. This heterotrophy is likely mediated by sediment respiration and POC accumulation in mesocosms, and a low share of productive to respiring water column in the actual ecosystem. Therefore, it seems unlikely that macrophytes will re-settle, as constant net-heterotrophy may allow for high-nutrient turnover at sediment-water interfaces and within the water column, favouring phytoplankton. Changes within the ecosystem cannot be expected without further restoration measures within and in the systems proximity.
KCTD19 associates with ZFP541 and HDAC1 and is required for meiotic exit in male mice
Authors: Oura Seiya , Koyano Takayuki , Kodera Chisato , Horisawa-Takada Yuki , Matsuyama Makoto , Ishiguro Kei-ichiro , Ikawa Masahito
Published: February 2021

Meiosis is a cell division process with complex chromosome events where various molecules must work in tandem. To find meiosis-related genes, we screened evolutionarily conserved and reproductive tract-enriched genes using the CRISPR/Cas9 system and identified potassium channel tetramerization domain containing 19 (Kctd19) as an essential factor for meiosis. In prophase I,Kctd19deficiency did not affect synapsis or the DNA damage response, and chiasma structures were also observed in metaphase I spermatocytes ofKctd19KO mice. However, spermatocytes underwent apoptotic elimination during the metaphase-anaphase transition. We were able to rescue theKctd19KO phenotype with an epitope-taggedKctd19transgene. Immunoprecipitation-mass spectrometry identified zinc finger protein 541 (ZFP541) and histone deacetylase 1 (HDAC1) as binding partners of KCTD19, indicating that KCTD19 is involved in chromatin modification. Phenotyping ofZfp541KO spermatocytes demonstrated XY chromosome asynapsis and recurrent DNA damage in the late pachytene stage, leading to apoptosis. In summary, our study reveals that KCTD19 associates with ZFP541 and HDAC1, and that both KCTD19 and ZFP541 were essential for meiotic exit in male mice.

Author summary

Meiosis is a fundamental process that consisting of one round of genomic DNA replication and two rounds of chromosome segregation producing four haploid cells. To properly distribute their genetic material, cells need to undergo complex chromosome events such as a physical linkage of homologous chromosomes (termed synapsis) and meiotic recombination. The molecules involved in these events have not been fully characterized yet, especially in mammals. Using a CRISPR/Cas9-screening system, we identified the potassium channel tetramerization domain containing 19 (Kctd19) as an essential factor for meiosis in male mice. Further, we identified zinc finger protein 541 (ZFP541) and histone deacetylase 1 (HDAC1) as binding partners of KCTD19. By observing meiosis ofZfp541knockout germ cells, we found thatZfp541was also essential for meiotic completion. These results show that the KCTD19/ZFP541 complex plays a critical role and is indispensable for male meiosis and fertility.
Integration of electric, calcium, reactive oxygen species and hydraulic signals during rapid systemic signaling in plants
Authors: Fichman Yosef , Mittler Ron
Published: February 2021

The sensing of abiotic stress, mechanical injury, or pathogen attack by a single plant tissue results in the activation of systemic signals that travel from the affected tissue to the entire plant, alerting it of an impending stress or pathogen attack. This process is essential for plant survival during stress and is termed systemic signaling. Among the different signals triggered during this process are calcium, electric, reactive oxygen species (ROS) and hydraulic signals. These are thought to propagate at rapid rates through the plant vascular bundles and to regulate many of the systemic processes essential for plant survival. Although the different signals activated during systemic signaling are thought to be interlinked, their coordination and hierarchy remain to be determined. Here, using a combination of advanced whole-plant imaging and hydraulic pressure measurements, we studied the activation of all four systemic signals in wild type and differentArabidopsis thalianamutants subjected to a local high light (HL) stress or wounding. Our findings reveal that in response to wounding systemic changes in membrane potential, calcium, ROS, and hydraulic pressure are coordinated by glutamate receptor-like (GLR) proteins 3.3 and 3.6, while in response to HL the respiratory burst oxidase homolog D-driven systemic ROS signal could be separated from systemic changes in membrane potential and calcium levels. We further determine that plasmodesmata functions are required for systemic changes in membrane potential, calcium, and ROS during systemic signaling. Our findings shed new light on the different mechanisms that integrate different systemic signals in plants during stress.

Significance statement

The ability of plants to transmit a signal from a stressed or wounded tissue to the entire plant, termed systemic signaling, is key to plant survival during conditions of environmental stress. At least four different systemic signals are thought to be involved in this process: electric, calcium, reactive oxygen and hydraulic. However, how are they coordinated and whether they can be stress-specific is mostly unknown. Here we report that different types of stimuli can induce different types of systemic signals that may or may not be linked with each other. We further reveal that hydraulic waves can be actively regulated in plants in response to wounding, and that proteins that regulate plasmodesmata pores play a key role in systemic signaling.
Photoperiod shapes aluminium tolerance in plants
Authors: Siqueira João Antonio , Wakin Thiago , Batista-Silva Willian , Silva José Cleydson F. , Vicente Matheus H. , Silva Jéssica C. , Clarindo Wellington R. , Zsögön Agustin , Peres Lazaro E. P. , De Veylder Lieven , Fernie Alisdair R. , Nunes-Nesi Adriano , Araújo Wagner L.
Published: February 2021

Aluminium is a limiting factor for crop productivity in acidic soils (pH ≤ 5.5). Since acid soil distribution on Earth cannot adequately explain the differential Al tolerance across the plant kingdom, we investigated photoperiod effects on plant Al tolerance. We observed that with increasing distance from the equator, Al tolerance disappears, suggesting a relationship with the photoperiod. Long-day (LD) species are generally more Al-sensitive than short-day (SD) species, whereas genetic conversion of tomato for SD growth boosts Al tolerance. Reduced Al tolerance correlates with DNA-checkpoint activation under LD. DNA-checkpoint-related genes are under positive selection inArabidopsisaccessions from regions with shorter days, suggesting photoperiod acts as a selective barrier for Al tolerance. Our findings revealed that diel regulation and genetic diversity affect Al tolerance, suggesting that day-length orchestrates Al tolerance.

One-Sentence Summary

Aluminum is a major constraint for crop yield worldwide. We reveal that photoperiod acts as a barrier for Al tolerance in plants.
Single-cell sequencing of plasma cells from COVID-19 patients reveals highly expanded clonal lineages produce specific and neutralizing antibodies to SARS-CoV-2
Authors: Ehling Roy A. , Weber Cédric R. , Mason Derek M. , Friedensohn Simon , Wagner Bastian , Bieberich Florian , Kapetanovic Edo , Vazquez-Lombardi Rodrigo , Di Roberto Raphaël B. , Hong Kai-Lin , Wagner Camille , Sheward Daniel J. , Murrell Ben , Yermanos Alexander , Cuny Andreas P. , Savic Miodrag , Rudolf Fabian , Reddy Sai T.
Published: February 2021

Isolation and characterization of antibodies in COVID-19 patients has largely focused on memory B cells, however it is the antibody-secreting plasma cells that are directly responsible for the production of serum antibodies, which play a critical role in controlling and resolving SARS-CoV-2 infection. To date there is little known about the specificity of plasma cells in COVID-19 patients. This is largely because plasma cells lack surface antibody expression, which complicates their screening. Here, we describe a technology pipeline that integrates single-cell antibody repertoire sequencing and high-throughput mammalian display screening to interrogate the specificity of plasma cells from 16 convalescent COVID-19 patients. Single-cell sequencing allows us to profile antibody repertoire features in these patients and identify highly expanded clonal lineages. Mammalian display screening is employed to reveal that 37 antibodies (out of 132 candidates) derived from expanded plasma cell clonal lineages are specific for SARS-CoV-2 antigens, including antibodies that target the receptor binding domain (RBD) with high affinity and exhibit potent neutralization of SARS-CoV-2.

One Sentence Summary

Single-cell antibody repertoire sequencing and high-throughput screening identifies highly expanded plasma cells from convalescent COVID-19 patients that produce SARS-CoV-2-specific antibodies capable of potent neutralization.
GRK2/3/5/6 knockout: The impact of individual GRKs on arrestin-binding and GPCR regulation
Authors: Drube J. , Haider R.S. , Matthees E.S.F. , Reichel M. , Zeiner J. , Fritzwanker S. , Ziegler C. , Barz S. , Klement L. , Kliewer A. , Miess E. , Kostenis E. , Schulz S. , Hoffmann C.
Published: February 2021

G protein-coupled receptors (GPCRs) comprise the largest family of transmembrane receptors and represent major drug targets. Upon ligand stimulation, GPCRs activate G proteins and undergo a complex regulation by interaction with GPCR kinases (GRKs) and formation of receptor–arrestin complexes. For many GPCRs, this mechanism triggers receptor desensitisation, internalisation, and possibly a second intracellular signalling wave. Here we created eleven different HEK293 knockout cell clones for GRK2, 3, 5, and 6 individually and in combination. These include four single, two double, four triple, and the quadruple GRK knockout. The statistical evaluation of β-arrestin1/2 interactions for twelve different receptors grouped the tested GPCRs into two main subsets: those for which β-arrestin interaction was mediated by either GRK2, 3, 5, or 6 and those that are mediated by GRK2 or 3 only. Interestingly, the overexpression of specific GRKs was found to induce a robust, ligand-independent β-arrestin interaction with the V2R and AT1R. Finally, using GRK knockout cells, PKC inhibitors, and β-arrestin mutants, we present evidence for differential AT1R–β-arrestin2 complex configurations mediated by selective engagement of PKC, GRK2, or GRK6. We anticipate our novel GRK-knockout platform to facilitate the elucidation of previously unappreciated details of GRK-specific GPCR regulation and β-arrestin complex formation.
The role of auxin and sugar signaling in dominance inhibition of inflorescence growth by fruit load
Authors: Goetz Marc , Rabinovich Maia , Smith Harley M.
Published: February 2021

Dominance inhibition of shoot growth by fruit load is a major factor that regulates shoot architecture and limits yield in agriculture and horticulture crops. In annual plants, the inhibition of inflorescence growth by fruit load occurs at a late stage of inflorescence development termed the end of flowering transition. Physiological studies show that this transition is mediated by production and export of auxin from developing fruits in close proximity to the inflorescence apex. In the meristem, cessation of inflorescence growth is controlled in part by the age dependent pathway, which regulates the timing of arrest. Here, results show that the end of flowering transition is a two-step process in which the first stage is characterized by a cessation of inflorescence growth, while immature fruit continue to develop. At this stage, dominance inhibition of inflorescence growth by fruit load correlates with a selective dampening of auxin transport in the apical region of the stem. Subsequently, an increase in auxin response in the vascular tissues of the apical stem where developing fruits are attached marks the second stage for the end of flowering transition. Similar to the vegetative and floral transition, the end of flowering transition correlates with a change in sugar signaling and metabolism in the inflorescence apex. Taken together, our results suggest that during the end of flowering transition, dominance inhibition of inflorescence shoot growth by fruit load is mediated by auxin and sugar signaling.

One-sentence summary

Dominance inhibition of inflorescence shoot growth by fruit load is involves auxin and sugar signaling during the end of flowering transition.
Non-invasive sex genotyping of paicheArapaima gigasby qPCR: An applied bioinformatic approach to identify sex differences
Authors: López-Landavery Edgar A. , Corona-Herrera Guillermo A. , Santos-Rojas Luis E. , Herrera-Castillo Nadhia M. , Delgadin Tomás H. , Tapia-Morales Sandra , González-Martinez Sophia , Reyes-Flores Lorenzo E. , Marín Alan , Yzásiga-Barrera Carmen G. , Fernandino Juan I. , Zelada-Mázmela Eliana
Published: February 2021

Arapaima gigas, one of the largest freshwater fish in the world, is suffering from high fishing pressure and habitat loss, which threaten the conservation status of its natural populations. Of great cultural importance to Amazonian people, the paiche or pirarucuA. gigasis in high demand for its meat, ornamental uses and other byproducts such as scales. Aquaculture is a feasible solution to this dilemma. However, the fact thatA. gigaspresents no sexual dimorphism until it is 5 years old and its long period to sexual maturity are major obstacles for brood-stock management and fingerling production. Thus, the aim of this study was to develop a molecular tool for non-invasive genotypic sexing of paiche throughout its life cycle. We collected samples from gonads, fins and gill mucus of juvenile specimens from local facilities for histological and molecular analysis. Based on the recently available genome sequence of the paiche and making use of current NGS method, we implemented a novel approach, called Genome Differences by Unmapped Reads, to identify DNA sex markers. We found a Male-Specific Region (MSR), identified as MSR_3728, to be present only in males. Next, we designed two specific sets of primers on this region to identify genotypic sex by qPCR assays. Both primer sets, MSR_107 and MSR_129, detected males with 100% accuracy. Then we developed a duplex qPCR reaction for each primer set along a reference gene, analyzed the melting curves and detected males by observing two distinct peaks, one for MSR_107 or MSR_129 and one for the reference, while females only presented the reference peak. The same results were obtained for gonads, fins and interestingly, a non-invasive source from gill mucus samples. Finally, the gonads were evaluated histologically in a double-blind test, showing 100% accuracy with qPCR assay for identifying males and females. Data clearly demonstrated a novel pipeline approach for identifying DNA sex markers, followed by a quick, non-invasive, cost-effective duplex qPCR method for sexing A.gigas. These results may be valuable to efficient paiche aquaculture and conservation studies, helping to reduce the fishing pressure on its natural populations.

Highlights of the manuscript

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Implementation of a novel approach, called Genome Differences by Unmapped Reads, to identify DNA sex markers.

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Finding of a Male-Specific Region (MSR), present only in males.

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Development of a duplex qPCR to identify genotypic sex through non-invasive sampling.
SalmonellaTyphimurium outer membrane protein A (OmpA) renders protection against nitrosative stress by promoting SCV stability in murine macrophages
Authors: Roy Chowdhury Atish , Sah Shivjee , Varshney Umesh , Chakravortty Dipshikha
Published: February 2021

Porins are highly conserved bacterial outer membrane proteins involved in the selective transport of charged molecules across the membrane. Despite their significant contributions to the pathogenesis of Gram-negative bacteria, their precise role in salmonellosis remains elusive. In this study, we investigated the role of porins (OmpA, OmpC, OmpD, and OmpF) inSalmonellaTyphimurium (STM) pathogenesis. OmpA played a multifaceted role in STM pathogenesis, and a strain deleted forompA(STMΔompA) showed enhanced proneness to phagocytosis and compromised proliferation in macrophages. However, in the epithelial cells, despite being invasion deficient, it was hyper-proliferative. The poor colocalization of STMΔompAwith LAMP-1 confirmed impaired stability of SCV membrane around the intracellular bacteria, resulting in its (STMΔompA) release into the cytosol of macrophages where it is assaulted with reactive nitrogen intermediates (RNI). The cytosolic localization of STMΔompAwas responsible for the downregulation of SPI-2 encoded virulence factor SpiC, which is required to suppress the activity of iNOS. The reduced recruitment of nitrotyrosine on STM in the macrophage cytosol upon ectopically expressing Listeriolysin O (LLO) explicitly supported the pro-bacterial role of OmpA against the host nitrosative stress. Further, we show that the generation of time-dependent redox burst could be responsible for the enhanced sensitivity of STMΔompAtowards nitrosative stress. The absence of OmpA in STMΔompAresulted in the loss of integrity and enhanced porosity of the bacterial outer membrane, which was attributed to the upregulated expression ofompC,ompD,andompF. We showed the involvement of OmpF in the entry of excess nitrite in STMΔompA,thus increasing the susceptibility of the bacteria towardsin vitroandin vivonitrosative stress. In conclusion, we illustrated a mechanism of strategic utilization of OmpA compared to other porins by wildtypeSalmonellafor combating the nitrosative stress in macrophages.
Benchmarking Association Analyses of Continuous Exposures with RNA-seq in Observational Studies
Authors: Sofer Tamar , Kurniansyah Nuzulul , Aguet François , Ardlie Kristin , Durda Peter , Nickerson Deborah A. , Smith Joshua D. , Liu Yongmei , Gharib Sina A. , Redline Susan , Rich Stephen S. , Rotter Jerome I. , Taylor Kent D.
Published: February 2021

Large datasets of hundreds to thousands of individuals measuring RNA-seq in observational studies are becoming available. Many popular software packages for analysis of RNA-seq data were constructed to study differences in expression signatures in an experimental design with well-defined conditions (exposures). In contrast, observational studies may have varying levels of confounding of the transcript-exposure associations; further, exposure measures may vary from discrete (exposed, yes/no) to continuous (levels of exposure), with non-normal distributions of exposure. We compare popular software for gene expression -DESeq2, edgeR, andlimma- as well as linear regression-based analyses for studying the association of continuous exposures with RNA-seq. We developed a computation pipeline that includes transformation, filtering, and generation of empirical null distribution of association p-values, and we apply the pipeline to compute empirical p-values with multiple testing correction. We employ a resampling approach that allows for assessment of false positive detection across methods, power comparison, and the computation of quantile empirical p-values. The results suggest that linear regression methods are substantially faster with better control of false detections than other methods, even with the resampling method to compute empirical p-values. We provide the proposed pipeline with fast algorithms in R.
TPR1, a novel rifampin derivative demonstrates efficacy alone and in combination with doxycycline against the NIAID Category A Priority PathogenF. tularensis
Authors: Cummings Jason E. , Slayden Keaton W. , Slayden Richard A.
Published: February 2021

Objectives

Francisella tularensisis a highly virulent and contagious gram-negative intracellular bacterium that causes the disease tularemia in mammals and is classified as a Category A priority pathogen. The high infectivity, difficulty of obtaining a durable cure of disseminated disease and the emergence of drug resistance warrants investigation of new drugs that can be used alone and in combination with existing standard of care clinical drugs.

Methods

We utilized a systematic analysis of antibacterial potency, extent of dissemination by analysis of bacterial burden in a secondary vital organ, and survival rates to assess the efficacy of a novel rifampicin derivative, TPR1. The efficacy of TPR1 was evaluated alone and in combination with the standard of care drug, doxycycline, against Type AF. tularensisSchu S4 using a lethal pulmonary model of infection in mice.

Results

TPR1 has an MIC value range of 0.125-4 mg/L against reference laboratory strain SchuS4 and a panel of clinical strains. TPR1 alone reduced the bacterial burden in the lungs and spleen at 40 mg/kg and 80 mg/kg, and no antagonism was observed when co-administered with doxycycline. Dosing at 40 mg/kg doxycycline reduced the bacterial burden by 1 Log10CFU in the lungs and 4 Log10CFU spleen in comparison to untreated controls. Co-administration of TPR1 and doxycycline demonstrated efficacy upon treatment withdrawal after 4 days of treatment, and 100% survival.

Conclusions

Significantly, TPR1 demonstrated efficacy when delivered alone and in combination with doxycycline, which provides compelling evidence of a superior treatment strategy that would normally rely on a single chemotherapeutic for efficacy. In addition, this work substantiates the use of rifampicin derivatives as a platform for the development of novel treatments to other bacterial agents in addition to tularemia.
Computational anatomy and geometric shape analysis enables analysis of complex craniofacial phenotypes in zebrafish
Authors: Diamond Kelly M. , Rolfe Sara M. , Kwon Ronald Y. , Maga A. Murat
Published: February 2021

Due to the complexity of fish skulls, previous attempts to classify craniofacial phenotypes have relied on qualitative features or 2D landmarks. In this work we aim to identify and quantify differences in 3D craniofacial phenotypes in adult zebrafish mutants. We first estimate a synthetic ‘normative’ zebrafish template using microCT scans from a sample pool of wildtype animals using the Advanced Normalization Tools (ANTs). We apply a computational anatomy (CA) approach to quantify the phenotype of zebrafish with disruptions inbmp1a, a gene implicated in later skeletal development and whose human ortholog when disrupted is associated with Osteogenesis Imperfecta. Compared to controls, thebmp1afish have larger otoliths and exhibit shape differences concentrated around the operculum, anterior frontal, and posterior parietal bones. Moreover,bmp1afish differ in the degree of asymmetry. Our CA approach offers a potential pipeline for high throughput screening of complex fish craniofacial phenotypes, especially those of zebrafish which are an important model system for testing genome to phenome relationships in the study of development, evolution, and human diseases.

Summary statement

A computational anatomy approach offers a potential pipeline for high throughput screening of complex zebrafish craniofacial phenotypes, an important model system for the study of development, evolution, and human diseases.
The impacts of interest rate changes on US Midwest farmland values
Authors: Basha Albulena , Zhang Wendong , Hart Chad
Published: February 2021

Purpose

This paper quantifies the effects of recent Federal Reserve interest rate changes, specifically recent hikes and cuts in the federal funds rate since 2015, on Midwest farmland values.

Design/methodology/approach

The authors apply three autoregressive distributed lag (ARDL) models to a panel data of state-level farmland values from 1963 to 2018 to estimate the dynamic effects of interest rate changes on the US farmland market. We focus on the I-states, Lakes states and Great Plains states. The models in the study capture both short-term and long-term impacts of policy changes on land values.

Findings

The authors find that changes in the federal funds rate have long-lasting impacts on farmland values, as it takes at least a decade for the full effects of an interest rate change to be capitalized in farmland values. The results show that the three recent federal funds rate cuts in 2019 were not sufficient to offset the downward pressures from the 2015–2018 interest rate hikes, but the 2020 cut is. The combined effect of the Federal Reserve's recent interest rate moves on farmland values will be positive for some time starting in 2022.

Originality/value

This paper provides the first empirical quantification of the immediate and long-run impacts of recent Federal Reserve interest rate moves on farmland values. The authors demonstrate the long-lasting repercussions of Federal Reserve's policy choices in the farmland market.
Enhancing the social networks of adults with ASD: a low level community intervention
Authors: McConkey Roy , Cassin Marie-Therese , McNaughton Rosie , Armstrong Elaine
Published: February 2021

Purpose

This paper aims to design and evaluate an innovative community-based service for adults with autism in a rural region of Northern Ireland. The goal was to reduce their social isolation through gaining social skills and building social networks.

Design/methodology/approach

Over three years, 54 persons with a median age of 21 years received 12 months of one-to-one, personalised support and opportunities to participate in peer groups and social activities which are detailed in the paper. Quantitative and qualitative information about the impact of the service was obtained from its users, their relatives, as well as service personnel.

Findings

Service users rated themselves to have changed in more ways than did their relatives and staff although there was a consensus that the changes were most marked in terms of spending more time out of the house, engaging in more community activities, being more independent and increased confidence. The main benefits they perceived from participation in the project were socialising, new experiences and learning new things.

Research limitations/implications

As with many service projects, a longer term follow-up of service users was not possible due to resource constraints.

Practical implications

The service could be replicated with suitable staff although current constraints on social care budgets have limited its expansion to more users and extension to other areas in Northern Ireland.

Social implications

Reducing the social isolation of adult persons with autism spectrum disorders needs to be personalised to the person, their living circumstances and the community in which they live. Family carers also stand to gain from community support services.

Originality/value

This low level, low cost service was implemented in a predominantly rural area with a majority of users from socially deprived areas.
How might we best support the effective and meaningful employment of autistic people and improve outcomes?
Authors: Cameron Carl , Townend Abbey
Published: February 2021

Purpose

To determine the most appropriate and effective support to enable autistic people to gain and maintain employment in their chosen field. This paper aims to determine this and by which methods are most suitable for this kind of support, with a focus on mentoring.

Design/methodology/approach

Mentoring is an intervention that has shown promise in assisting people who encounter barriers in finding work (for example, Roycroft, 2014). This research was conducted to determine whether the mentoring of autistic adults is effective in helping them to gain and maintain employment. The study examined the mentoring records of 90 autistic adults who were in receipt of funded mentoring with 18 separate organisations across England.

Findings

The authors found that the nationally recognised statistic of autistic people in full-time employment as 16% (National Autistic Society, 2016) was ambitious and subject to regional variation. Based on the results of a programme providing employment and mentoring support that is available and accessible to autistic people, however, outcomes improve and employment is more likely to be achieved and maintained – including in areas of, especially low employment. It was found that 48% of autistic job seekers who were supported by specialist mentors found paid employment (full-time or part-time), demonstrating a 16% increase in paid employment between those who received mentoring support and those who did not.

Research limitations/implications

A wider study across the UK would first determine if the nationally recognised figure is incorrect and also highlight those areas of the country which perform particularly well or badly.

Originality/value

This paper believes that this is the only research of it is kind in the UK and that it is a springboard for others who have greater resources available to them. This study is two very early-career academics on the autism spectrum with limited resources available to us.
Architectural design and consumer experience: an investigation of shopping malls throughout the design process
Authors: Yuan Ye , Liu Gang , Dang Rui , Lau Stephen Siu Yu , Qu Guanhua
Published: February 2021

Purpose

The purpose of this paper is to identify the design elements of environmental features that affect consumer experience in shopping malls and develop a comprehensive understanding of the relationship between architectural design and consumer experience.

Design/methodology/approach

Through the systematic literature review, 13 design elements were obtained and then verified through interviews of 30 professional designers. The obtained elements were made into a questionnaire to collect data across China from 1,016 consumers of different groups. Data were analyzed using cluster analysis, principal component analysis and difference analysis.

Findings

The results show that design elements that influence consumer experience in shopping malls are a four-dimensional construct: visual atmosphere, physical environment comfort, space structure and business planning, among which space structure and business planning play a larger role in the consumer experience. In addition, the perception differences of consumers for those elements are significant due to the individual differences.

Originality/value

This paper comprehensively investigates the architectural design elements affecting consumer experience in the Chinese mall context. Moreover, it provides unique insights about the relationship between architectural design and consumer experience by exploring the categories, weights and perception differences of those elements.
Proximity to broad bond rating change and annual report readability
Authors: Bradley Wray , Sun Li
Published: February 2021

Purpose

The purpose of this study is to examine the impact of proximity to broad bond rating change on annual report reading difficulty.

Design/methodology/approach

We use regression analysis to examine the association between proximity to broad bond rating change and reading difficulty of annual report.

Findings

Using a large panel sample with 11,767 firm-year observations representing 1,474 unique US companies from 1994 to 2016, we find a significant positive relation between proximity to broad bond rating change and annual report reading difficulty, which suggests that the annual reports of borderline firms are difficult for stakeholders to read and understand.

Originality/value

By investigating whether and how borderline firms manipulate readability of annual reports, our study contributes to bond rating research in finance literature and disclosure quality research in accounting literature. To the best of our knowledge, this study is perhaps the first empirical study that directly tests the link between proximity to broad bond rating change and annual report readability. In particular, the majority of prior studies concentrate on the economic consequences of annual report readability, but few studies investigate the determinants of readability. Therefore, examining the impact of proximity to broad bond rating change on readability contributes to a more comprehensive understanding of annual report readability.