bluuebunny/crossref_metadata_2025_split huggingface dataset:
The importance of environmentally-acquired bacterial symbionts for the squash bug (Anasa tristis), a significant agricultural pest
Authors: Acevedo Tarik S. , Fricker Gregory P. , Garcia Justine R. , Alcaide Tiffanie , Berasategui Aileen , Stoy Kayla S. , Gerardo Nicole M. 
Published: July 2021

ABSTRACTMost insects maintain associations with microbes that shape their ecology and evolution. Such symbioses have important applied implications when the associated insects are pests or vectors of disease. The squash bug, Anasa tristis (Coreoidea: Coreidae), is a significant pest of human agriculture in its own right and also causes damage to crops due to its capacity to transmit a bacterial plant pathogen. Here, we demonstrate that complete understanding of these insects requires consideration of their association with bacterial symbionts in the family Burkholderiaceae. Isolation and sequencing of bacteria housed in midgut crypts in these insects indicates that these bacteria are consistent and dominant members of the crypt-associated bacterial communities. These symbionts are closely related to Caballeronia spp. associated other true bugs in the superfamiles Lygaeoidea and Coreoidea. Fitness assays with representative Burkholderiaceae strains indicate that the association can significantly increase survival and decrease development time, though strains do vary in the benefits that they confer to their hosts, with Caballeronia spp. providing the greatest benefit. Experiments designed to assess transmission mode indicate that unlike many other beneficial insect symbionts, the bacteria are not acquired from parents before or after hatching but are instead acquired from the environment after molting to a later development stage. The bacteria do, however, have the capacity to escape adults to be transmitted to later generations, leaving the possibility for a combination of indirect vertical and horizontal transmission.
Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data
Authors: Cho Hunyong , Qu Yixiang , Liu Chuwen , Tang Boyang , Lyu Ruiqi , Lin Bridget M. , Roach Jeffrey , Azcarate-Peril M. Andrea , de Aguiar Ribeiro Apoena , Love Michael I. , Divaris Kimon , Wu Di 
Published: July 2021

AbstractUnderstanding the function of the human microbiome is important; however, the development of statistical methods specifically for the microbial gene expression (i.e., metatranscriptomics) is in its infancy. Many currently employed differential expression analysis methods have been designed for different data types and have not been evaluated in metatranscriptomics settings. To address this gap, we undertook a comprehensive evaluation and benchmarking of ten differential analysis methods for metatranscriptomics data. We used a combination of real and simulated data to evaluate performance (i.e., model fit, type I error, false discovery rate, and sensitivity) of the methods: log-normal (LN), logistic-beta (LB), MAST, DESeq2, metagenomeSeq, ANCOM-BC, LEfSe, ALDEx2, Kruskal-Wallis, and two-part Kruskal-Wallis. The simulation was informed by supragingival biofilm microbiome data from 300 preschool-age children enrolled in a study of early childhood caries (ECC), whereas validations were sought in two additional datasets from an ECC study and an inflammatory bowel disease (IBD) study. The LB test showed the highest sensitivity in both small and large samples and reasonably controlled type I error. Contrarily, MAST was hampered by inflated type I error. Upon application of the LN and LB tests in the ECC study, we found that genes C8PHV7 and C8PEV7, harbored by the lactate-producing Campylobacter gracilis, had the strongest association with childhood dental diseases. This comprehensive model evaluation offer practical guidance for selection of appropriate methods for rigorous analyses of differential expression in metatranscriptomics. Selection of an optimal method increases the possibility of detecting true signals while minimizing the chance of claiming false ones.
Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases
Authors: Louadi Zakaria , Elkjaer Maria L. , Klug Melissa , Lio Chit T. , Fenn Amit , Illes Zsolt , Bongiovanni Dario , Baumbach Jan , Kacprowski Tim , List Markus , Tsoy Olga 
Published: July 2021

AbstractAlternative splicing (AS) is an important aspect of gene regulation. Nevertheless, its role in molecular processes and pathobiology is far from understood. A roadblock is that tools for the functional analysis of AS-set events are lacking. To mitigate this, we developed NEASE, a tool integrating pathways with protein-protein and domain-domain interactions to functionally characterize AS events. We show in four application cases how NEASE can identify pathways contributing to tissue identity and cell type development, and how it highlights splicing-related biomarkers. With a unique view on AS, NEASE generates unique and meaningful biological insights complementary to classical pathways analysis.
Automatic inference of cell neighborhood in 2D and 3D using nuclear markers
Authors: Moretti Bruno , Rodriguez Alvarez Santiago N. , Grecco Hernán E. 
Published: July 2021

AbstractSignificanceEstimating neighboring cells by using only nuclear markers is crucial in many biological applications. Although several strategies have been used for this purpose, most published methods lack a rigorous characterization of their efficiencies. Remarkably, previously described methods are not automatic and depend only on cell-cell distance, neglecting the importance of pair-neighborhood interaction.AimTo develop a robust and automatic method for assessing cell local neighborhood, while analyzing the impact of the physical variables involved in this task.ApproachWe inferred neighbors from images with nuclei labeling by approximating the cell-cell interaction graph by the Delaunay triangulation of nuclei centroids. Each edge of this graph was filtered by thresholding in cell-cell distance and the maximum angle that each pair subtends with shared neighbors (pair-neighborhood interaction). Thresholds were calculated by maximizing a new robust statistic that measures the communicability efficiency of the cell graph. Using a variety of images of diverse tissues with additional membrane labeling to find the ground truth, we characterized the assessment performance.ResultsOn average, our method detected 95% of true neighbors, with only 6% of false discoveries. Even though our method’s performance and tissue regularity are correlated, it works with performance metrics over 86% in very different organisms, including Drosophila melanogaster, Tribolium castaneum, Arabidopsis thaliana and C. elegans.ConclusionsWe automatically estimated neighboring relationships between cells in 2D and 3D using only nuclear markers. To achieve this goal, we filtered the Delaunay triangulation of nuclei centroids with a new measure of graph communicability efficiency. In addition, we found that taking pair-neighborhood interactions into account, in contrast to considering only cell-cell distances, leads to significant performance improvements. This becomes more notorious when the number of cells is low or the geometry of the cell graph is highly complex.
Improving human coronavirus OC43 (HCoV-OC43) research results comparability in studies using HCoV-OC43 as a surrogate for SARS-CoV-2
Authors: Schirtzinger Erin E. , Kim Yunjeong , Davis A. Sally 
Published: July 2021

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has renewed interest in human coronaviruses that cause the common cold, particularly as research with them at biosafety level (BSL)-2 avoids the added costs and biosafety concerns that accompany work with SARS-COV-2, BSL-3 research. One of these, human coronavirus OC43 (HCoV-OC43), is a well-matched surrogate for SARS-CoV-2 because it is also a Betacoronavirus, targets the human respiratory system, is transmitted via respiratory aerosols and droplets and is relatively resistant to disinfectants. Unfortunately, growth of HCoV-OC43 in the recommended human colon cancer (HRT-18) cells does not produce obvious cytopathic effect (CPE) and its titration in these cells requires expensive antibody-based detection. Consequently, multiple quantification approaches for HCoV-OC43 using alternative cell lines exist, which complicates comparison of research results. Hence, we investigated the basic growth parameters of HCoV-OC43 infection in three of these cell lines (HRT-18, human lung fibroblasts (MRC-5) and African green monkey kidney (Vero E6) cells) including the differential development of cytopathic effect (CPE) and explored reducing the cost, time and complexity of antibody-based detection assay. Multi-step growth curves were conducted in each cell type in triplicate at a multiplicity of infection of 0.1 with daily sampling for seven days. Samples were quantified by tissue culture infectious dose50(TCID50)/ml or plaque assay (cell line dependent) and additionally analyzed on the Sartorius Virus Counter 3100 (VC), which uses flow virometry to count the total number of intact virus particles in a sample. We improved the reproducibility of a previously described antibody-based detection based TCID50 assay by identifying commercial sources for antibodies, decreasing antibody concentrations and simplifying the detection process. The growth curves demonstrated that HCoV-O43 grown in MRC-5 cells reached a peak titer of ∼107 plaque forming units/ml at two days post infection (dpi). In contrast, HCoV-OC43 grown on HRT-18 cells required six days to reach a peak titer of ∼106.5 TCID50/ml. HCoV-OC43 produced CPE in Vero E6 cells but these growth curve samples failed to produce CPE in a plaque assay after four days. Analysis of the VC data in combination with plaque and TCID50 assays together revealed that the defective:infectious virion ratio of MRC-5 propagated HCoV-OC43 was less than 3:1 for 1-6 dpi while HCoV-OC43 propagated in HRT-18 cells varied from 41:1 at 1 dpi, to 329:4 at 4 dpi to 94:1 at 7 dpi. These results should enable better comparison of extant HCoV-OC43 study results and prompt further standardization efforts.
Evolutionary repair reveals an unexpected role of the tRNA modification m1G37 in aminoacylation
Authors: Clifton Ben E. , Fariz Muhammad Aiman , Uechi Gen-Ichiro , Laurino Paola 
Published: July 2021

AbstractThe tRNA modification m1G37, which is introduced by the tRNA methyltransferase TrmD, is thought to be essential for growth in bacteria due to its role in suppressing translational frameshift errors at proline codons. However, because bacteria can tolerate high levels of mistranslation, it is unclear why loss of m1G37 is not tolerated. Here, we addressed this question by performing experimental evolution oftrmDmutant strains ofE. coli. Surprisingly,trmDmutant strains were viable even if the m1G37 modification was completely abolished, and showed rapid recovery of growth rate, mainlyviatandem duplication or coding mutations in the proline-tRNA ligase geneproS. Growth assays andin vitroaminoacylation assays showed that G37-unmodified tRNAProis aminoacylated less efficiently than m1G37-modified tRNAPro, and that growth oftrmDmutant strains can be largely restored by single mutations inproSthat restore aminoacylation of G37-unmodified tRNAPro. These results show that inefficient aminoacylation of tRNAProis the main reason for growth defects observed intrmDmutant strains and that the ProRS enzyme may act as a gatekeeper of translational accuracy, preventing the use of error-prone unmodified tRNAProin protein translation. Our work shows the utility of experimental evolution for uncovering the hidden functions of essential genes and has implications for the development of antibiotics targeting TrmD.
Calcium signaling mediates mechanotransduction at the multicellular stage of Dictyostelium discoideum
Authors: Hashimura Hidenori , Morimoto Yusuke V. , Hirayama Yusei , Ueda Masahiro 
Published: July 2021

AbstractCalcium acts as a second messenger and regulates cellular functions, including cell motility. In Dictyostelium discoideum, the cytosolic calcium level oscillates synchronously, and calcium signal waves propagate in the cell population during the early stages of development, including aggregation. At the unicellular phase, the calcium response through Piezo channels also functions in mechanosensing. However, calcium signaling dynamics during multicellular morphogenesis is still unclear. Here, live-imaging of cytosolic calcium levels revealed that calcium wave propagation, depending on cAMP relay, temporarily disappeared at the onset of multicellular body formation. Alternatively, the occasional burst of calcium signals and their propagation were observed in both anterior and posterior regions of migrating multicellular bodies. Calcium signaling in multicellular bodies occurred in response to mechanical stimulation. Both pathways, calcium release from the endoplasmic reticulum via IP3 receptor and calcium influx from outside the cell, were involved in calcium waves induced by mechanical stimuli. These show that calcium signaling works on mechanosensing in both the unicellular and multicellular phases of Dictyostelium using different molecular mechanisms during development.Summary statementFluorescence imaging revealed that calcium signaling via both endoplasmic reticulum and extracellular pathways plays an important role in mechanosensing during the multicellular stage of Dictyostelium.
Phenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria
Authors: Pudlo Nicholas A. , Urs Karthik , Crawford Ryan , Pirani Ali , Atherly Todd , Jimenez Roberto , Terrapon Nicolas , Henrissat Bernard , Peterson Daniel , Ziemer Cherie , Snitkin Evan , Martens Eric C. 
Published: July 2021

AbstractSymbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central to defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multi-locus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens, which still harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors.
Assessing the matrix effects of pigmented and non-pigmented salmon during multi-residue antibiotic analysis with liquid chromatography coupled to tandem mass spectrometry
Authors: Emami Shiva , Taha Ameer Y. 
Published: July 2021

AbstractSeveral validated methods exist for the quantitation of antibiotics in seafood with ultra-high pressure liquid chromatography coupled with tandem spectrometry (UPLC-MS/MS). To our knowledge, none have explored the effects of co-eluting matrix components on the accuracy of quantitation. Such matrix effects could disproportionally change the ionization of analytes and their respective surrogate/internal standards during UPLC-MS/MS analysis, resulting in over-or under-estimation of antibiotic values. In this study, we measured matrix effects, alongside extraction recoveries for 30 antibiotics and their respective class-specific surrogate standards in Sockeye, King and Ivory (non-pigmented) salmon extracted using the QUEChERS method. A modified QUEChERS method involving dispersive or hydrophilic-lipophilic balance (HLB) solid phase extraction (SPE) was also tested on Sockeye salmon. Despite acceptable extraction recoveries for most antibiotics extracted using the QUEChERS method, significant matrix effects were observed for most antibiotic standards. Dispersive or HLB SPE clean-up did not improve analyte recoveries from Sockeye salmon, and in some cases, increased matrix effects. Accuracy and sensitivity were reduced when matrix effects were high. Our results demonstrate that matrix components in salmon cause matrix effects on antibiotics during UPLC-MS/MS analysis which could impact the accuracy and sensitivity of the analysis.
High-resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration
Authors: Baek Sungmin , Tran Nhung T. T. , Diaz Daniel C. , Tsai Ya-Yin , Acedo Joaquin Navajas , Lush Mark E. , Piotrowski Tatjana 
Published: July 2021

SummaryLoss of sensory hair cells in the mammalian inner ear leads to permanent hearing and vestibular defects, whereas loss of hair cells in zebrafish results in their regeneration. We used scRNA-Seq to characterize the transcriptional dynamics of hair cell regeneration in zebrafish at unprecedented spatio-temporal resolution. We uncovered three, sequentially activated modules. First, an injury/inflammatory response and downregulation of progenitor/stem cell maintenance genes within minutes after hair cell loss. Second, the transient activation of regeneration-specific genes. And third, a robust reactivation of developmental gene programs, including hair cell specification, cell cycle activation, ribosome biogenesis, and a metabolic switch to oxidative phosphorylation. The results are not only relevant for our understanding of hair cell regeneration and how we might be able to trigger it in mammals but also for regenerative processes in general. The data is searchable and publicly accessible via a web-based interface.
Plumage balances camouflage and thermoregulation in Horned Larks (Eremophila alpestris)
Authors: Mason Nicholas A. , Riddell Eric A. , Romero Felisha , Cicero Carla , Bowie Rauri C.K. 
Published: July 2021

AbstractAnimal coloration serves many biological functions and must therefore balance potentially competing selective pressures. For example, many animals have camouflage, in which coloration matches the visual background against which predators scan for prey. However, different colors reflect different amounts of solar radiation and may therefore have thermoregulatory implications as well. In this study, we examined geographic variation in dorsal patterning, color, and solar reflectance among Horned Larks (Eremophila alpestris) of the western United States. We found associations between dorsal plumage brightness, hue, and patterning relative to the soil conditions where specimens were collected. Specifically, brighter dorsal plumage corresponded to brighter soil, while redder, more saturated hues in dorsal plumage corresponded to redder soils. Furthermore, backs with more high-contrast patterning were more common among females and also associated with soil that had coarser soil fragments, suggesting that lark plumage has been selected to optimize background matching in different environments. We also found that larks exhibited higher solar reflectance in hotter and more arid environments, which lowers the water requirements for homeothermy. Taken together, these findings suggest that natural selection has balanced camouflage and thermoregulation in Horned Larks across a wide variety of soil types and abiotic conditions.
Size-dependent susceptibility of lake phytoplankton to light stress: An implication for succession of large green algae in a deep oligotrophic lake
Authors: Kazama Takehiro , Hayakawa Kazuhide , Nagata Takamaru , Shimotori Koichi , Imai Akio , Komatsu Kazuhiro 
Published: July 2021

AbstractField observations of the population dynamics and measurements of photophysiology in Lake Biwa were conducted by size class (< vs. > 30 μm) from early summer to autumn to investigate the relationships between susceptibility to light stress and cell size. Also, a nutrient bioassay was conducted to clarify whether the growth rate and photosystem II (PSII) photochemistry of small and large phytoplankton are limited by nutrient availability. Large phytoplankton, which have lower intracellular Chl-a concentrations, had higher maximum PSII photochemical efficiency (Fv/Fm) but lower non-photochemical quenching (NPQNSV) than small phytoplankton under both dark and increased light conditions. The nutrient bioassay revealed that the PSII photochemistry of small phytoplankton was restricted by N and P deficiency at the pelagic site even at the end of the stratification period, while that of large phytoplankton was not. These results suggest that large phytoplankton have lower susceptibility to PSII photodamage than small phytoplankton due to lower intracellular Chl-a concentrations. The size dependency of susceptibility to PSII photoinactivation may play a key role in large algal blooms in oligotrophic water.
Oncogenic truncations of ASXL1 enhance a motif for BRD4 ET-domain binding
Authors: Burgess Abigail E. , Kleffmann Torsten , Mace Peter D. 
Published: July 2021

AbstractProper regulation of gene-expression relies on specific protein-protein interactions between a myriad of epigenetic regulators. As such, mutation of genes encoding epigenetic regulators often drive cancer and developmental disorders. Additional sex combs-like protein 1 (ASXL1) is a key example, where mutations frequently drive haematological cancers and can cause developmental disorders. It has been reported that nonsense mutations in ASXL1 promote an interaction with BRD4, another central epigenetic regulator. Here we provide a molecular mechanism for the BRD4-ASXL1 interaction, demonstrating that a motif near to common truncation breakpoints of ASXL1 contains an epitope that binds the ET domain within BRD4. Binding-studies show that this interaction is analogous to common ET-binding modes of BRD4-interactors, and that all three ASX-like protein orthologs (ASXL1–3) contain a functional ET-domain-binding epitope. Crucially, we observe that BRD4-ASXL1 binding is markedly increased in the prevalent ASXL1Y591Xtruncation that maintains the BRD4-binding epitope, relative to full-length ASXL1 or truncated proteins that delete the epitope. Together, these results show that ASXL1 truncation enhances BRD4 recruitment to transcriptional complexes via its ET domain, which could misdirect regulatory activity of either BRD4 or ASXL1 and may inform potential therapeutic interventions.