bluuebunny/crossref_metadata_2025 huggingface dataset:
Integration of Diverse Transcriptomics Datasets using Random Forest to Predict Universal Functional Pathways in Tfr Cells
Authors: Diallo Alos , Cavazzoni Cecilia B , Sun Jiaoyuan E , Sage Peter T
Published: December 2021

Motivation

T follicular regulatory (Tfr) cells are a specialized cell subset that controls humoral immunity. Despite a number of individual transcriptomic studies on these cells, core functional pathways have been difficult to uncover due to the substantial transcriptional overlap of these cells with other effector cell types, as well as transcriptional changes occurring due to disease settings. Developing a core transcriptional module for Tfr cells that integrates multiple cell type comparisons as well as diverse disease settings will allow a more accurate prediction of functional pathways. Researchers studying allergic reactions, immune responses to vaccines, autoimmunity and cancer could use this gene set to better understand the roles of Tfr cells in controlling disease progression.

Additional cell types beyond Tfr cells that have similar features of transcriptomic complexity within diverse disease settings may also be studied using similar approaches. High-throughput sequencing technologies allow the generation of large datasets that require specific tools to best interpret the data. The development of a core transcriptional module for Tfr cells will allow investigators to determine if Tfr cells may have functional roles within their biological systems with little knowledge of Tfr biology. With this work, we have addressed the need of core gene modules to define specific subsets of immune cells.

Results

We introduce an integrated “core Tfr cell gene module” that can be incorporated into GSEA analysis using various input sizes. The integrated core Tfr gene module was built using transcriptomic studies in Tfr cells from several different tissues, disease settings, and cell type comparisons. Random forest was used to integrate the transcriptomic studies to generate the core gene module. A GSEA gene set was formulated from the integrated core Tfr gene module for incorporation into end-user friendly GSEA. The gene sets are presented along with random genes taken from the GTEX data set and are presented as GMT files. The user can upload the gene set to the GSEA website or any gene set tool which takes GMT files. We also present the full results of the model including p-values calculated by random forest. This provides users with more flexibility in choosing a p-value cutoff that is most appropriate for the experimental setting.

Availability

The core Tfr gene sets are freely available at:https://github.com/alosdiallo/TFR_Model. We have also included all of the code and data used in developing these gene sets. The code and results are released under an MIT license.

Supplementary information

Supplementary data are available at Bioinformatics online.
Density-by-diet interactions during larval development shape adult life-history trait expression and fitness in a polyphagous fly
Authors: Morimoto Juliano , Than Anh The , Nguyen Binh , Lundbäck Ida , Dinh Hue , Ponton Fleur
Published: December 2021

Habitat quality early in life determines individual fitness, with possible long-term evolutionary effects on groups and populations. In holometabolous insects, larval ecology plays a major role in determining the expression of traits in adulthood, but how ecological conditions during larval stage interact to shape adult life-history and fitness, particularly in non-model organisms, remains subject to scrutiny. Consequently, our knowledge of the interactive effects of ecological factors on insect development is limited. Here, using the polyphagous fly Bactrocera tryoni, we conducted a fully-factorial design where we manipulated larval density and larval diet (protein-rich, standard, and sugar-rich) to gain insights into how these ecological factors interact to modulate adult fitness. As expected, a protein-rich diet resulted in faster larval development, heavier and leaner adults that were more fecund compared with standard and sugar-rich diets, irrespective of larval density. Females from the protein-rich larval diet had overall higher reproductive rate (i.e., eggs per day) than females from other diets, and reproductive rate decreased linearly with density for females from the protein-rich but non-linearly for females from the standard and sugar-rich diets over time. Surprisingly, adult lipid reserve increased with larval density for adults from the sugar-rich diet (as opposed to decreasing, as in other diets), possibly due to a stress-response to an extremely adverse condition during development (i.e., high intraspecific competition and poor nutrition). Together, our results provide insights into how ecological factors early in life interact and shape the fate of individuals through life-stages in holometabolous insects.
PhyloHerb: A phylogenomic pipeline for processing genome skimming data for plants
Authors: Cai Liming , Zhang Hongrui , DAVIS CHARLES C
Published: December 2021

Premise of the study: The application of high throughput sequencing, especially to herbarium specimens, is greatly accelerating biodiversity research. Among various techniques, low coverage Illumina sequencing of total genomic DNA (genome skimming) can simultaneously recover the plastid, mitochondrial, and nuclear ribosomal regions across hundreds of species. Here, we introduce PhyloHerb -- a bioinformatic pipeline to efficiently and effectively assemble phylogenomic datasets derived from genome skimming.
Methods and Results: PhyloHerb uses either a built-in database or user-specified references to extract orthologous sequences using BLAST search. It outputs FASTA files and offers a suite of utility functions to assist with alignment, data partitioning, concatenation, and phylogeny inference. The program is freely available at https://github.com/lmcai/PhyloHerb/.
Conclusions: Using published data from Clusiaceae, we demonstrated that PhyloHerb can accurately identify genes using highly fragmented assemblies derived from sequencing older herbarium specimens. Our approach is effective at all taxonomic depths and is scalable to thousands of species.
Fractional Laser Treatment Boosts Systemic Anti-Tumor Immunity in Combination with OX40 Agonist and PD-1 Blockade
Authors: Kawakubo Masayoshi , Glahn Joshua , Tao Zhipeng , Demehri Shadmehr , Manstein Dieter
Published: December 2021

While ablative fractional photothermolysis (aFP) with a 10,600 nm CO2laser is employed for a wide variety of dermatologic conditions, its applications in oncology are relatively unexplored. Building off our previous work, we investigated the effect of unilateral aFP treatment in combination with anti-PD-1 blocking antibody and OX40 agonist on bilateral tumor growth and remission. A CT26 wild type (CT26WT) colon carcinoma cell line was established bilaterally on the hind flanks of a standardized mouse model and tumor characteristics were investigated on aFP treated and untreated sides. Remarkably, triple therapy with fractional CO2laser in combination with anti-PD-1 antibodies and OX40 agonists resulted in significantly slower tumor growth and complete remissions on bilateral tumors. Flow cytometric analysis showed the triple treatments elicited an increase of granzyme B+ CD8+T cells due to synergistic effect of aFP treatment and the checkpoint molecules, including the induction of CD103+ CCR7+ dendritic cells (DCs) in aFP-treated tumor by aFP treatment, XCR1+ DCs in drainage lymph node by anti-PD-1 inhibitor and OX40+ Ki67+ CD8+ T cells in the lymph node by OX40 agonist. Triple therapy-mediated tumor regression and survival was abrogated upon CD8+ T cell depletion. Importantly, when two mismatched cancer cells were implanted into mice, the effect of the triple therapy on distant tumor was abrogated, showing antigen specificity of the T cell immunity induced by triple therapy. This study highlights the efficacy of aFP a novel adjuvant for current cancer immunotherapeutics.
Site-specificity of streptococci in the oral microbiome
Authors: McLean Anthony R. , Torres-Morales Julian , Borisy Gary G. , Mark Welch Jessica L.
Published: December 2021

Patterns of microbial distribution are determined by as-yet poorly understood rules governing where microbes can grow and thrive. Therefore, a detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely-related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here we assess whether individual species within this genus are generalists using publicly available genomic sequence data that provides species-level resolution. We chose a set of high-quality representative genomes for Streptococcus species from the human oral microbiome. Onto these genomes, we mapped short-read metagenomic sequences from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every reliably detectable Streptococcus species in the human oral cavity was a site-specialist and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. These three species also share substantially the same species-specific core genes indicating that neither taxonomy nor gene content are clear predictors of site-specialization. Site-specificity may instead be influenced by subtle characteristics such as nucleotide-level divergences within conserved genes.
How do spike collisions affect spike sorting performance?
Authors: Garcia Samuel , Buccino Alessio P. , Yger Pierre
Published: December 2021

Recently, a new generation of devices have been developed to record neural activity simultaneously from hundreds of electrodes with a very high spatial density, both for in vitro and in vivo applications. While these advances enable to record from many more cells, they also dramatically increase the amount overlapping “synchronous” spikes (colliding in space and/or in time), challenging the already complicated process of spike sorting (i.e. extracting isolated single-neuron activity from extracellular signals). In this work, we used synthetic ground-truth recordings to quantitatively benchmark the performance of state-of-the-art spike sorters focusing specifically on spike collisions. Our results show that while modern template-matching based algorithms are more accurate than density-based approaches, all methods, to some extent, failed to detect synchronous spike events of neurons with similar extracellular signals. Interestingly, the performance of the sorters is not largely affected by the the spiking activity in the recordings, with respect to average firing rates and spike-train correlation levels.
Can we use anti-predator behavior theory to predict wildlife responses to high-speed vehicles?
Authors: Lunn Ryan B. , Blackwel Bradley F. , DeVault Travis L. , Fernández-Juricic Esteban
Published: December 2021

Animals seem to rely on antipredator behavior to avoid vehicle collisions. There is an extensive body of antipredator behavior theory that have been used to predict the distance/time animals should escape from predators. These models have also been used to guide empirical research on escape behavior from vehicles. However, little is known as to whether antipredator behavior models are appropriate to apply to an approaching high-speed vehicle. We addressed this gap by (a) providing an overview of the main hypothesis and predictions of different antipredator behavior models via a literature review, (b) exploring whether these models can generatequantitativepredictions on escape distance when parameterized with empirical data from the literature, and (c) evaluating their sensitivity to vehicle approach speed via a simulation approach where we assessed model performance based on changes in effect size with variations in the slope of the flight initiation distance (FID) vs. approach speed relationship. We used literature on birds for goals (b) and (c). We considered the following eight models: the economic escape model, Blumstein’s economic escape model, the optimal escape model, the perceptual limit hypothesis, the visual cue model, the flush early and avoid the rush (FEAR) hypothesis, the looming stimulus hypothesis, and the Bayesian model of escape behavior. We were able to generatequantitativepredictions about escape distances with the last five models. However, we were only able to assess sensitivity to vehicle approach speed for the last three models. The FEAR hypothesis is most sensitive to high-speed vehicles when the species follows the spatial (FID remains constant as speed increases) and the temporal margin of safety (FID increases with an increase in speed) rules of escape. The looming stimulus effect hypothesis reached small to intermediate levels of sensitivity to high-speed vehicles when a species follows the delayed margin of safety (FID decreases with an increase in speed). The Bayesian optimal escape model reached intermediate levels of sensitivity to approach speed across all escape rules (spatial, temporal, delayed margins of safety) but only for larger (> 1 kg) species, but was not sensitive to speed for smaller species. Overall, no single antipredator behavior model could characterize all different types of escape responses relative to vehicle approach speed but some models showed some levels of sensitivity for certain rules of escape. We derive some applied applications of our finding by suggesting the estimation of critical vehicle approach speeds for managing populations that are especially susceptible to road mortality. Overall, we recommend that new escape behavior models specifically tailored to high- speeds vehicles should be developed to better predict quantitatively the responses of animals to an increase in the frequency of cars, airplanes, drones, etc. they will be facing in the next decade.
Panzootic chytrid fungus exploits diverse amphibian host environments through plastic infection strategies
Authors: Torres-Sánchez María , Villate Jennifer , McGrath-Blaser Sarah , Longo Ana V.
Published: December 2021

While many pathogens are limited to a single host, others can jump from host to host, which likely contributes to the emergence of infectious diseases. Despite this threat to biodiversity, traits associated with overcoming eco-evolutionary barriers to achieve host niche expansions are not well understood. Here, we examined the case of Batrachochytrium dendrobatidis (Bd), a multi-host pathogen that infects the skin of hundreds of amphibian species worldwide. To uncover functional machinery driving multi-host invasion, we analyzed Bd transcriptomic landscapes across 14 amphibian hosts and inferred the origin and evolutionary history of pathogenic genes under a phylogenetic framework comprising 12 other early-divergent zoosporic fungi. Our results not only revealed a conserved basal genetic machinery, but also highlighted the ability of Bd to display plastic infection strategies when challenged under suboptimal host environments. We found that genes related to amphibian skin exploitation have arisen mainly via gene duplications. We argue that plastic gene expression can drive variation in Bd lifecycles with different mode and tempo of development. Our findings support the idea that host skin environments exert contrasting selective pressures, such that gene expression plasticity constitutes one of the evolutionary keys leading to the success of this panzootic multi-host pathogen.
Synapse-associated astrocyte mitochondria stabilize motor circuits to prevent excitotoxicity
Authors: Zolnoski Sonja A. , Heckman Emily L. , Doe Chris Q. , Ackerman Sarah D.
Published: December 2021

Early stages of the devastating neurodegenerative disease amyotrophic lateral sclerosis (ALS) are characterized by motor neuron hyperexcitability. During this phase, peri-synaptic astrocytes are neuroprotective. When reactive, loss of wild-type astrocyte functions results in excitotoxicity. How astrocytes stabilize motor circuit function in early-stage ALS is poorly understood. Here, we used Drosophila motor neurons to define the role of astrocyte-motor neuron metabolic coupling in a model of ALS: astrocyte knockdown of the ALS-causing gene tbph/TARDBP. In wild-type, astrocyte mitochondria were dynamically trafficked towards active motor dendrites/synapses to meet local metabolic demand. Knockdown of tbph in astrocytes resulted in motor neuron hyperexcitability, reminiscent of early-stage ALS, which was met with a compensatory accumulation of astrocyte mitochondria near motor dendrites/synapses. Finally, we blocked mitochondria-synapse association in tbph knockdown animals and observed locomotor deficits and synapse loss. Thus, synapse-associated astrocyte mitochondria stabilize motor circuits to prevent the transition from hyperexcitability to excitotoxicity.
Mapping consistent, reproducible, and transcriptionally relevant functional connectome hubs of the human brain
Authors: Xu Zhilei , Xia Mingrui , Wang Xindi , Liao Xuhong , Zhao Tengda , He Yong
Published: December 2021

Human brain connectomes include sets of densely connected regions, known as connectome hubs, which play a vital role in understanding global brain communication, cognitive processing, and brain disorders. However, the consistency and reproducibility of functional connectome hubs’ anatomical localization have not been established to date and the genetic signatures underlying robust connectome hubs remain unknown. Here, we conduct the first worldwide, harmonized meta-connectomic analysis by pooling resting-state functional MRI data of 5,212 healthy young adults across 61 independent cohorts. We identify highly consistent and reproducible functional connectome hubs in heteromodal and unimodal regions both across cohorts and across individuals. These connectome hubs show heterogeneous connectivity profiles and are critical for both intra- and inter-network communications. Using post-mortem gene expression data, we show that these connectome hubs have a spatiotemporally distinctive transcriptomic pattern dominated by genes involved in the neuropeptide signaling pathway, neurodevelopmental processes, and metabolic processes. These results highlight the robustness of macroscopic connectome hubs and their potential cellular and molecular underpinnings.
Mutation, selection, and the prevalence of the C. elegans heat-sensitive mortal germline phenotype
Authors: Saber Sayran , Snyder Michael , Rajaei Moein , Baer Charles F.
Published: December 2021

C. elegans strains with the heat-sensitive mortal germline (Mrt) phenotype become progressively sterile over the course of a few tens of generations when maintained at temperatures near the upper range of C. elegans’ tolerance. Mrt is transgenerationally-heritable, and proximately under epigenetic control. Previous studies have suggested that Mrt presents a relatively large mutational target, and that Mrt is not uncommon in natural populations of C. elegans. The Mrt phenotype is not monolithic. Some strains exhibit a strong Mrt phenotype, in which individuals invariably become sterile over a few generations, whereas other strains show a weaker (less penetrant) phenotype in which the onset of sterility is slower and more stochastic. We present results in which we (1) quantify the rate of mutation to the Mrt phenotype, and (2) quantify the frequency of Mrt in a collection of 95 wild isolates. Over the course of ~16,000 meioses, we detected one mutation to a strong Mrt phenotype, resulting in a point estimate of the mutation rate UMrt≈ 6×10−5/genome/generation. We detected no mutations to a weak Mrt phenotype. 6/95 wild isolates have a strong Mrt phenotype, and although quantification of the weak Mrt phenotype is inexact, the weak Mrt phenotype is not rare in nature. We estimate a strength of selection against mutations conferring the strong Mrt phenotype , similar to selection against mutations affecting competitive fitness. The appreciable frequency of weak Mrt variants in nature combined with the low mutation rate suggests that Mrt may be maintained by balancing selection.
Reemployment of Kupffer’s vesicle cells into axial and paraxial mesoderm via transdifferentiation
Authors: Ikeda Takafumi , Inamori Kiichi , Kawanishi Toru , Takeda Hiroyuki
Published: December 2021

Kupffer’s vesicle (KV) in the teleost embryo is a fluid-filled vesicle surrounded by a layer of epithelial cells with rotating primary cilia. KV transiently acts as the left-right organizer but degenerates after the establishment of left-right asymmetric gene expression. Previous labelling experiments indicated that descendants of KV-epithelial cells are incorporated into mesodermal tissues after KV collapses (KV-collapse) in zebrafish embryos. However, the overall picture of their differentiation potency had been unclear due to the lack of suitable genetic tools and molecular analyses. In the present study, we established a novel zebrafish transgenic line with a promoter of charon, in which all KV-epithelial cells and their descendants are specifically labelled until the larval stage. We found that KV-epithelial cells underwent epithelial-mesenchymal transition upon KV-collapse and infiltrate into adjacent mesodermal progenitors, the presomitic mesoderm and chordoneural hinge. Once incorporated, the descendants of KV-epithelial cells expressed distinct mesodermal differentiation markers and contributed to the mature populations such as the axial muscles and notochordal sheath through normal developmental process. These results indicate that fully differentiated KV-epithelial cells possess unique plasticity in that they are reemployed into mesodermal lineages through transdifferentiation after they complete their initial role in KV.
Does heat tolerance actually predict animals’ geographic thermal limits?
Authors: Camacho Agustín , Rodrigues Miguel Trefaut , Jayyusi Refat , Harun Mohamed , Geraci Marco , Vinagre Catarina , Carretero Miguel , Tejedo Miguel
Published: December 2021

To understand species′ climatic vulnerability, our measures of species’ thermal tolerance should predict their geographic thermal limits. Yet, this assumption is ungranted. We tested if animals′ heat tolerance restrict the warmest temperatures they can live at (Tmax), distinguishing among species differently challenged by their thermal environment. For that, we compiled 2350 measurements of species’ heat tolerance indexes and corresponding Tmax, measured at different microhabitats. We show that reptiles, a flagship for climatic vulnerability studies, are particularly unbounded by their heat tolerance. Contrarily, tolerance restricted marine fish’ geography in a non-linear fashion which contrasts with terrestrial taxa. Behavioral tolerance indexes, widely used to predict vulnerability, predicted Tmax inconsistently across Tmax indexes, or were inversely related to it. Animals’ heat tolerance restricts geographic limits more strongly for more thermally challenged species. In turn, factors uncoupling heat tolerance and Tmax (plasticity, thermoregulation, adaptation) should be more important for less thermally challenged species.

Significance Statement

To identify climatic vulnerability, heat tolerance indices need to predict species′ thermal limits to geographic distribution. Yet, we show that heat tolerance predicts geographic limits quite heterogeneously, depending on taxa, the type of measure of heat tolerance and how challenged are species at their hottest known location. Particularly, reptiles, a flagship of vulnerability studies, were less bounded by tolerance than taxa regarded as more capable to evade high temperatures, due to their capacity to evaporate water, find refuge, or migrate (Ex. amphibians, arthropods, birds and mammals). Measures of species’ behavioral heat tolerance may still need to improve. Factors thought to uncouple thermal tolerance and geographic limits should be stronger for less thermally challenged species.
In vitro evolution of uracil glycosylase towards DnaKJ and GroEL binding evolves different misfolded states
Authors: Melanker Oran , Goloubinoff Pierre , Schreiber Gideon
Published: December 2021

Natural evolution is driven by random mutations that improve fitness. In vitro evolution mimics this process, however, on a short time-scale and is driven by the given bait. Here, we used directed in vitro evolution of a random library of Uracil glycosylase (eUNG) displayed on yeast surface to select for binding to chaperones GroEL, DnaK+DnaJ+ATP (DnaKJ) or E.coli cell extract (CE). Using binding to the eUNG inhibitor Ugi as probe for native foldedess, the CE selected population was further divided to Ugi binders (+U) (native) or non-binders (-U). We found that GroEL, DnaKJ and CE-U select and enrich for mutations causing eUNG to misfold, with the three being enriched in mutations in buried and conserved positions, with a tendency to increase positive charge. Still, each selection, as well as CE+U and natural evolution of eUNG has its own trajectory. While GroEL and CE-U selected for mutants highly sensitive to protease cleavage, DnaKJ selected for partially structured misfolded species with a tendency to refold, making them less sensitive to proteases. CE+U selected for more neutral mutations than natural evolution. In a more general context, our results show that GroEL has a higher tendency to purge promiscuous misfolded protein mutants from the system, while DnaKJ binds mutants misfolding-prone species that are, upon chaperone release, more likely to natively refold. CE-U shares some of the properties of GroEL and DnaKJ selected populations, while harboring also unique properties, explained by the existence of additional chaperones in CE, such as Tig, HtpG and ClpB.
Community-wide epigenetics provides novel perspectives on the ecology and evolution of marine microbiome
Authors: Seong Hoon Je , Roux Simon , Hwang Chung Yeon , Sul Woo Jun
Published: December 2021

DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life. We show that overall, DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark.

One-Sentence Summary

DNA methylation patterns are associated with ecological changes and virus-host dynamics in the marine microbiome.
The Long Noncoding RNA FEDORA is a Cell-Type- and Sex-Specific Regulator of Depression
Authors: Issler Orna , van der Zee Yentl Y , Ramakrishnan Aarthi , Xia Sunhui , Zinsmaier Alexander K , Tan Chunfeng , Li Wei , Browne Caleb J , Walker Deena M , Salery Marine , Torres-Berrío Angélica , Futamura Rita , Duffy Julia E , Labonte Benoit , Tamminga Carol A , Dupree Jeffrey L , Dong Yan , Murrough James W , Shen Li , Nestler Eric J
Published: December 2021

Women suffer from depression at twice the rate of men, but the underlying molecular mechanisms are poorly understood. Here, we identify dramatic baseline sex differences in expression of long noncoding RNAs (lncRNAs) in human postmortem brain tissue that are profoundly lost in depression. One such lncRNA, RP11-298D21.1 (which we termed FEDORA), is enriched in oligodendrocytes and neurons and upregulated in several cortical regions of depressed females but not males. We found that virally-expressing FEDORA selectively either in neurons or in oligodendrocytes of prefrontal cortex promoted depression-like behavioral abnormalities in female mice only, changes associated with cell-type-specific regulation of synaptic properties, myelin thickness, and gene expression. We also found that blood FEDORA levels have diagnostic significance for depressed women. These findings demonstrate the important role played by lncRNAs, and FEDORA in particular, in shaping the sex-specific landscape of the brain and contributing to sex differences in depression.
Remote sensing reveals multi-decadal losses of tree cover in California driven by increasing fire disturbance and climate stress
Authors: Wang Jonathan A. , Randerson James T. , Goulden Michael L. , Knight Clarke , Battles John B.
Published: December 2021

Forests provide natural climate solutions for sequestering carbon and mitigating climate change yet are threatened by increasing temperatures and disturbance. Accurate information on vegetation dynamics is lacking in some regions with forest carbon offset programs and dense forests like California. To address this, we combined remote sensing observations with geospatial databases to develop annual maps of vegetation cover (tree, shrub, herbaceous) and disturbance type (fires, harvest, and forest die-off) in California at 30 m resolution from 1985 to 2021. California lost 3783 km2 of its tree cover area (5.5% relative to initial cover). Early gains in tree cover area were more than offset by fire-driven declines, resulting in greater shrub and herbaceous cover area. Fires and tree cover area loss occurred where temperatures were high or increasing, whereas tree cover gain occurred in cooler areas. Disturbance and warming are threatening the integrity of California’s forests and its carbon offsets program.

Teaser

Climate and disturbance-driven tree cover loss challenges the viability of forests as natural climate solutions in California
sciCAN: Single-cell chromatin accessibility and gene expression data integration via Cycle-consistent Adversarial Network
Authors: Xu Yang , Begoli Edmon , McCord Rachel Patton
Published: December 2021

The booming single-cell technologies bring a surge of high dimensional data that come from different sources and represent cellular systems from different views. With advances in single-cell technologies, integrating single-cell data across modalities arises as a new computational challenge and gains more and more attention within the community. Here, we present a novel adversarial approach, sciCAN, to integrate single-cell chromatin accessibility and gene expression data in an unsupervised manner. We benchmarked sciCAN with 3 state-of-the-art (SOTA) methods in 5 scATAC-seq/scRNA-seq datasets, and we demonstrated that our method dealt with data integration with better balance of mutual transferring between modalities than the other 3 SOTA methods. We further applied sciCAN to 10X Multiome data and confirmed the integrated representation preserves information of the hematopoietic hierarchy. Finally, we investigated CRSIPR-perturbed single-cell K562 ATAC-seq and RNA-seq data to identify cells with related responses to different perturbations in these different modalities.
Label-free characterisation of amyloids and alpha-Synuclein polymorphs by exploiting their intrinsic fluorescence property
Authors: Chung Chyi Wei , Stephens Amberley D. , Ward Edward , Feng Yuqing , Davis Molly Jo , Kaminski Clemens F. , Kaminski Schierle Gabriele S.
Published: December 2021

Conventional in vitro aggregation assays often involve tagging with extrinsic fluorophores which can interfere with aggregation. We propose the use of intrinsic amyloid fluorescence lifetime probed using two-photon excitation and represented by model-free phasor plots, as a label-free assay to characterise amyloid structure. Intrinsic amyloid fluorescence arises from structured packing of β-sheets in amyloids and is independent of aromatic-based fluorescence. We show that different amyloids (i.e., α-Synuclein (αS), β-Lactoglobulin and TasA) and different polymorphic populations of αS (induced by aggregation in salt-free and salt buffers mimicking the intra-/extracellular environments) can be differentiated by their unique fluorescence lifetimes. Moreover, we observe that disaggregation of pre-formed fibrils of αS and βLG leads to increased fluorescence lifetimes, distinct to those of their fibrillar counterpart. Our assay presents a medium-throughput method for rapid classification of amyloids and their polymorphs (the latter of which recent studies have shown lead to different disease pathology), and for testing small molecule inhibitory compounds.
Staining Sodium Dodecyl Sulfate–Polyacrylamide Gels with Silver Salts
Authors: Kielkopf Clara L. , Bauer William , Urbatsch Ina L.
Published: December 2021

This protocol describes silver staining procedures to detect low-abundance proteins in sodium dodecyl sulfate-polyacrylamide gels.
Selecting the Antigen
Authors: Greenfield Edward A. , DeCaprio James , Brahmandam Mohan
Published: December 2021

The classical method for generating polyclonal or monoclonal antibodies relies on the in vivo humoral response of animals. Here we describe the factors that antigens can have that might influence the strength and quality of an antibody response. This introduction is divided into three sections: (1) an overview of immunogenicity, (2) choosing the best form for the immunogen, and (3) methods for modifying antigens to make them more immunogenic.
A Brief History of Xenopus in Biology
Authors: De Robertis Edward M. , Gurdon John B.
Published: December 2021

Xenopus is one of the premier model systems to study cell and developmental biology in vivo in vertebrates. Here we briefly review how this South African frog came to be favored by a large community of scientists after the explosive growth of molecular biology and examine some of the original discoveries arising from this sturdy frog. Experimental embryology started in Rana but developed in newt embryos for historical reasons. A long lineage of mentorship, starting with Theodor Boveri, Hans Spemann, Fritz Baltzer, Ernst Hadorn, and Michail Fischberg, used newt embryos. In Oxford, Fischberg made the transition to Xenopus laevis because it was widely available for human pregnancy tests and laid eggs year-round, and he fortuitously isolated a one-nucleolus mutant. This mutant allowed nuclear transfer experiments showing that genetic information is not lost during cell differentiation and the demonstration that the nucleolus is the locus of transcription of the large ribosomal RNAs. With the advent of DNA cloning, the great equalizer among all fields of biology, microinjected Xenopus oocytes became an indispensable tool, providing the first living-cell mRNA translation, polymerase II and III transcription, and coupled transcription–translation systems in eukaryotes. Xenopus embryos provide abundant material to study the earliest signaling events during vertebrate development and have been subjected to saturating molecular screens in the genomic era. Many novel principles of development and cell biology owe their origins to this remarkably resilient frog.
Pro-poor and inclusive growth in West Africa
Authors: Adeosun Opeoluwa Adeniyi , Tabash Mosab I.
Published: December 2021

Purpose

This paper focuses on three key metrics of poverty, income distribution and employment to ascertain the pro-poor and inclusive-growth position of the western African region. The roles of governance structures and their interactive effects are also accommodated to capture the peculiarity of the region.

Design/methodology/approach

The paper employs fixed and dynamic models.

Findings

Evidence suggests that growth is pro-poor, although virtually all governance indicators are sterile in stimulating poverty reduction. The authors observe that health and education spending coupled with trade-openness stimulate pro-poor growth potentials, whereas conflicts culminate the pervasiveness of poverty in the region. By empirically answering the question of how inclusive is economic growth through the lens of income-distribution and employment, the authors show that growth has been exclusive as per-capita-GDP growth rather dampens income shared by the poorest 20%. Also, it is observed that growth has not been inclusive as the jobless-growth argument remains valid while high inequality further exacerbates unemployment in the region. It is further shown that governance has been generally weak in propelling inclusive growth except where the institutional-component of governance stimulates inclusive growth through improvement in equality and labor employability.

Originality/value

The study jointly examines the metrics of poverty, income distribution and employment to ascertain growth pro-poorness and inclusivity which are key for the achievement of African-union (AU) agenda 2063. The study captures cross-sectional dependence among selected countries which previous studies ignored.
Believing and acting on fake news related to natural food: the influential role of brand trust and system trust
Authors: Bezbaruah Subhalakshmi , Dhir Amandeep , Talwar Shalini , Tan Teck Ming , Kaur Puneet
Published: December 2021

Purpose

Fake news represents a real risk for brands, particularly for firms selling essential products, such as food items. Despite this anecdotal acknowledgement, the dynamics of the relationship between fake news and brand reputation remain under-explored. The present study addresses this gap by examining the association of consumer values (universalism and openness to change), brand trust, fake news risk and system trust in the context of natural food products.

Design/methodology/approach

The study utilised a cross-sectional survey design and the mall-intercept method to collect data from 498 consumers of natural food residing in India. To test the hypotheses, which were grounded in the stimulus-organism-response (SOR) framework, the collected data were analysed using covariance-based structural equation modelling in SPSS AMOS. The conceptual model proposed universalism and openness to change as stimuli, brand trust as an internal state or organism and fake news risk – captured through the tendency of consumers to believe and act on fake news – as a response.

Findings

The findings support a positive association of universalism with brand trust and a negative association with fake news risk. In comparison, openness to change has no association with either brand trust or fake news risk. Brand trust, meanwhile, is negatively related to fake news, and this association is moderated by system trust. Furthermore, brand trust partially mediates the relationship between universalism value and fake news risk.

Originality/value

Notably, the present study is one of the first attempts to understand the fake news risk associated with natural food brands by utilising the SOR framework in an emerging market setting. The study provides interesting insights for policymakers, brands and consumers.
Forecasting the schedule performance resulting from the adoption of social distancing in construction projects
Authors: Onubi Hilary Omatule , Yusof Nor'Aini , Hassan Ahmad Sanusi , Bahdad Ali Ahmed Salem
Published: December 2021

Purpose

The coronavirus disease 2019 (COVID-19) pandemic has had major impacts on the performance of construction projects that have adopted social distancing measures. This study examines the effect of social distancing measures on project schedule performance through job reorganization on construction project sites.

Design/methodology/approach

Responses were obtained through a survey of 154 construction projects and analysed using the partial least square structural equation modeling (PLS-SEM) technique.

Findings

The findings established that social distancing has a negative effect on schedule performance, social distancing has a positive effect on job re-organization and job re-organization has a positive effect on schedule performance. Additionally, the results indicate that job re-organization partially mediates the relationship between social distancing and schedule performance, while social distancing moderates the relationship between job re-organization and schedule performance with low social distancing having the stronger positive effect.

Originality/value

This study contributes theoretically to a greater understanding of the impact of adopting COVID-19 safety measures such as social distancing on the schedule performance of construction projects. The study also shows how social distancing could lead to schedule performance through job reorganization.
Identifying institutional barriers when implementing new technologies in the healthcare industry
Authors: Kulkov Ignat , Tsvetkova Anastasia , Ivanova-Gongne Maria
Published: December 2021

Purpose

Virtual and augmented reality solutions in medicine are generally applied in communication, training, simulation and therapy. However, like most new digital developments, these technologies face a large number of institutional barriers that are inherent to the medical sector.

Design/methodology/approach

Following Richard Scott's view on institutions and organizations, a multiple case study is used to analyze regulatory, normative and cultural-cognitive institutional pillars in the medical industry.

Findings

The results of the study demonstrate that (1) the regulatory pillar inhibits the advancement of new technologies in the approach to treatment, regulation of patient data, educational processes for medical staff, and information and financial flows; (2) the number of barriers increases based on the solution's level of disruption and the number of variable conventional procedures; (3) trust between participants in the medical industry plays an important role in introducing new technologies; (4) new participants need to address certain pillars depending on the area of application.

Originality/value

The authors discuss top-down and bottom-up approaches for overcoming institutional barriers when implementing augmented and virtual reality solutions for companies focusing on the medical market.
Work and health-related factors of presenteeism: a mediation analysis on the role of menopausal symptoms between job demands and presenteeism among a sample of social service women employees
Authors: Guidetti Gloria , Viotti Sara , Converso Daniela , Sottimano Ilaria
Published: December 2021

Purpose

Building on prior studies on the role of health-related and job-related issues in affecting presenteeism, the present study tested a mediation model of the relationship between job demands and presenteeism by exploring the mediation effect of menopausal symptoms.

Design/methodology/approach

Data were collected through a self-report questionnaire involving social service menopausal employees (N = 204) from a public municipal organization. The survey was cross-sectional and non-randomized.

Findings

Results revealed that job demands, namely emotional, cognitive and physical demands, were significantly and positively associated with presenteeism. Furthermore, mediation analysis evidenced that physical job demands were also associated with higher levels of menopausal physical symptom bothersomeness, which in turn serves as a condition to increase the act of presenteeism.

Originality/value

The findings of this study widen the perspective on presenteeism research by evidencing the role of an overlooked health-related factor in relation to the act of presenteeism, that is the menopausal transition. Insights for the development of targeted preventive measures of the act of presenteeism and menopausal symptom management in the workplace may also be derived from these results.
Intellectual capital and institutional governance as capital structure determinants in the tourism sector
Authors: Dalwai Tamanna , Sewpersadh Navitha Singh
Published: December 2021

Purpose

This study investigates the capital structure determinants of the Middle East tourism sector by examining intellectual capital (IC) efficiency and institutional governance along with firm-specific and macroeconomic variables. This research also identifies the determinants of capital structure for tourism companies in the Gulf Cooperation Council (GCC) and non-GCC countries.

Design/methodology/approach

Data were collected from 45 listed tourism companies of nine Middle Eastern countries over five years from 2014 to 2018. The data were analysed using ordinary least squares (OLS) regression and checked for robustness using the generalised methods of moment (GMM) estimation.

Findings

Overall, the results indicate that tourism companies rely more on short-term debt (STD) than long-term debt (LTD), thus decreasing liquidity and increasing financial risk. Furthermore, tourism companies in non-GCC countries have higher IC efficiency compared to those in GCC countries. The aggregate institutional index is much higher for GCC countries compared to non-GCC countries. The OLS estimations suggest IC efficiency and institutional governance index provide inconclusive evidence as a determinant of capital structure proxy. High capital employed efficiency (CEE) is associated with more leverage for tourism firms. Theoretically, the results support pecking order and trade-off theories due to the relationships between firm-specific indicators and debt.

Originality/value

This study closes the gap in the capital structure debate by providing valuable insights into IC efficiency and institutional governance. These two factors serve as capital structure determinants in the Middle East and the GCC and non-GCC regions.