bluuebunny/crossref_metadata_2025 huggingface dataset:
Ing4-deficiency enhances HSC quiescence and confers resistance to inflammatory stress
Authors: Thompson Zanshé , Anderson Georgina A. , Rodriguez Melanie , Gabriel Seth , Binder Vera , Taylor Alison M. , Kathrein Katie L.
Published: July 2021

Hematopoiesis is tightly regulated by a network of transcription factors and complexes that are required for the development and maintenance of hematopoietic stem cells (HSCs). We recently identified the tumor suppressor, Ing4, as a critical regulator of HSC homeostasis. Though the Ing4 mechanism of action remains poorly characterized, it has been shown to promote stem-like cell characteristics in malignant cells. This activity is, in part, due to Ing4 mediated regulation of several major signaling pathways, including NF-κB and c-Myc. In murine hematopoiesis, Ing4 deficiency induces G0 arrest in HSCs, while simultaneously promoting gene expression signatures associated with differentiation. This results in a poised state for Ing4-deficient HSCs. Long term HSCs are unable to overcome this block, but short-term HSCs convert the poised state into regenerative capacity during hematopoietic challenges, including irradiation and transplantation. Overall, our findings suggest that Ing4 plays a crucial role in the regulation of hematopoiesis. Our model provides key tools for further identification and characterization of pathways that control quiescence and differentiation in HSCs.
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

Most 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

Understanding 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

Alternative 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

Significance

Estimating 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.

Aim

To develop a robust and automatic method for assessing cell local neighborhood, while analyzing the impact of the physical variables involved in this task.

Approach

We 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.

Results

On 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.

Conclusions

We 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.
Task-related hemodynamic responses in human early visual cortex are modulated by task difficulty and behavioral performance
Authors: Burlingham Charlie S. , Ryoo Minyoung , Roth Zvi N. , Mirbagheri Saghar , Heeger David J. , Merriam Elisha P.
Published: July 2021

Early visual cortex exhibits widespread hemodynamic responses in the absence of visual stimulation, which are entrained to the timing of a task and not predicted by local spiking or local field potential (LFP). Such task-related responses (“TRRs”) covary with reward magnitude and physiological signatures of arousal. It is unknown, however, if TRRs change on a trial-to-trial basis according to behavioral performance and task difficulty. If so, this would suggest that TRRs reflect arousal on a trial-to-trial timescale and covary with critical task and behavioral variables. We measured fMRI-BOLD responses in the early visual cortex of human observers performing an orientation discrimination task consisting of separate easy and hard runs of trials. Stimuli were presented in a small portion of one hemifield, but the fMRI response was measured in the ipsilateral hemisphere, far from the stimulus representation and focus of spatial attention. TRRs scaled in amplitude with task difficulty, behavioral accuracy, reaction time, and lapses across trials. These modulations were not explained by the influence of respiration, cardiac activity, or head movement on the fMRI signal. Similar modulations with task difficulty and behavior were observed in pupil size. These results suggest that TRRs reflect arousal and behavior on the timescale of individual trials.
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

The 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

The 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

Calcium 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 statement

Fluorescence 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

Symbiotic 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

Several 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

Loss 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

Animal 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

Field 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

Proper 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.
Large-scale all-optical dissection of motor cortex connectivity reveals a segregated functional organization of mouse forelimb representations
Authors: Resta Francesco , Montagni Elena , de Vito Giuseppe , Scaglione Alessandro , Mascaro Anna Letizia Allegra , Pavone Francesco Saverio
Published: July 2021

In rodent motor cortex, the rostral forelimb area (RFA) and the caudal forelimb area (CFA) are major actors in orchestrating the control of forelimb complex movements. However, their intrinsic connections and reciprocal functional organization are still unclear, limiting our understanding of how the brain coordinates and executes voluntary movements. Here we causally probed cortical connectivity and activation patterns triggered by transcranial optogenetic stimulation of ethologically relevant complex movements exploiting a novel large-scale all-optical method in awake mice. Results show specific activation features for each movement class, providing evidence for a segregated functional organization of CFA and RFA. Importantly, we identified a second discrete lateral grasping representation area, namely lateral forelimb area (LFA), with unique connectivity and activation patterns. Therefore, we propose the LFA as a distinct motor representation in the forelimb somatotopic motor map.
ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamic
Authors: Serre Nelson BC , Fendrych Matyas
Published: July 2021

Plants respond to the surrounding environment in countless ways. One of these responses is their ability to sense and orient their root growth toward the gravity vector. Root gravitropism is studied in many laboratories as a hallmark of auxin-related phenotypes. However, manual analysis of images and microscopy data is known to be subjected to human bias. This is particularly the case for manual measurements of root bending as the selection lines to calculate the angle are set subjectively. Therefore, it is essential to develop and use automated or semi-automated image analysis to produce reproducible and unbiased data. Moreover, the increasing usage of vertical-stage microscopy in plant root biology yields gravitropic experiments with an unprecedented spatiotemporal resolution. To this day, there is no available solution to measure root bending angle over time for vertical-stage microscopy. To address these problems, we developed ACORBA (Automatic Calculation Of Root Bending Angles), a fully automated software to measure root bending angle over time from vertical-stage microscope and flatbed scanner images. Moreover, the software can be used semi-automated for camera, mobile phone or stereomicroscope images. ACORBA represents a flexible approach based on both traditional image processing and deep machine learning segmentation to measure root angle progression over time. By its automated nature, the workflow is limiting human interactions and has high reproducibility. ACORBA will support the plant biologist community by reducing time and labor and by producing quality results from various kinds of inputs.

Significance statement

ACORBA is implementing an automated and semi-automated workflow to quantify root bending and waving angles from images acquired with a microscope, a scanner, a stereomicroscope or a camera. It will support the plant biology community by reducing time and labor and by producing trustworthy and reproducible quantitative data.
DNA double strand break position leads to distinct gene expression changes and regulates VSG switching pathway choice
Authors: Thivole Alix , Mehnert Ann-Kathrin , Tihon Eliane , McLaughlin Emilia , Dujeancourt-Henry Annick , Glover Lucy
Published: July 2021

Antigenic variation is an immune evasion strategy used by Trypanosoma brucei that results in the periodic exchange of the surface protein coat. Underlying this process is the movement of variant surface glycoprotein genes in or out of a specialized locus known as bloodstream form expression site by homologous recombination, facilitated by blocks of repetitive sequence known as the 70-bp repeats, that provide homology for gene conversion events. DNA double strand breaks are potent drivers of antigenic variation, however where these breaks must fall to elicit a switch is not well understood. To understand how the position of a break influences antigenic variation we established a series of cell lines to study the effect of an I-SceI meganuclease break in the active expression site. We found that a DNA break within repetitive regions is not productive for VSG switching, and show that the break position leads to a distinct gene expression profile and DNA repair response which dictates how antigenic variation proceeds in African trypanosomes.
Differential requirements for mitochondrial electron transport chain components in the adult murine liver
Authors: Lesner Nicholas P. , Wang Xun , Chen Zhenkang , Frank Anderson , Menezes Cameron , House Sara , Shelton Spencer D. , McFadden David G. , Wansapura Janaka , DeBerardinis Ralph J. , Mishra Prashant
Published: July 2021

Mitochondrial electron transport chain (ETC) dysfunction due to mutations in the nuclear or mitochondrial genome is a common cause of metabolic disease in humans, and displays striking tissue specificity depending on the affected gene. The mechanisms underlying tissue specific phenotypes are not understood. Complex I (cI) is classically considered the entry point for electrons into the ETC, and in vitro experiments indicate that cI is required for basal respiration and maintenance of the NAD+/NADH ratio, an indicator of cellular redox status. This finding has largely not been tested in vivo. Here, we report that mitochondrial complex I (cI) is dispensable for homeostasis of the adult mouse liver; animals with hepatocyte-specific loss of cI function display no overt phenotypes or signs of liver damage, and maintain liver function, redox and oxygen status. Further analysis of cI-deficient livers did not reveal significant proteomic or metabolic changes, indicating little to no compensation is required in the setting of complex I loss. In contrast, complex IV (cIV) dysfunction in adult hepatocytes results in decreased liver function, impaired oxygen handling, steatosis, and liver damage, accompanied by significant metabolomic and proteomic perturbations. Metabolomic analysis suggests that the electron transfer flavoprotein complex constitutes a major route for electron entry into the hepatic ETC. Our results support a model whereby complex I loss is tolerated in the mouse liver because hepatocytes use alternative electron donors to fuel the mitochondrial ETC.
RAD51AP1 and RAD54 underpin two distinct RAD51-dependent routes of DNA damage repair via homologous recombination
Authors: Selemenakis Platon , Sharma Neelam , Kwon Youngho , Uhrig Mollie , Sung Patrick , Wiese Claudia
Published: July 2021

Homologous recombination (HR) is a complex DNA damage repair pathway and an attractive target of inhibition in anti-cancer therapy. To help guide the development of efficient HR inhibitors, it is critical to identify compensatory sub-pathways.

In this study, we describe a novel synthetic interaction between RAD51AP1 and RAD54, two structurally unrelated proteins that function downstream of the RAD51 recombinase in HR. We show that deletion of both RAD51AP1 and RAD54 synergistically sensitizes human cancer cell lines to treatment with a Poly(adenosine 5’ s-diphosphate-ribose) polymerase inhibitor, to the DNA inter-strand crosslinking agent mitomycin C, and to hydroxyurea, which stalls the progression of DNA replication forks. We infer that HR-directed anti-cancer treatment modalities shall consider this intra-pathway functional overlap, and we hypothesize that in cancerous cells the simultaneous inactivation of both RAD54 and RAD51AP1 will accentuate tumor kill.
The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection
Authors: Liu Jialin , Viales Rebecca R. , Khoueiry Pierre , Reddington James P. , Girardot Charles , Furlong Eileen E.M. , Robinson-Rechavi Marc
Published: July 2021

Inter-species comparisons of both morphology and gene expression within a phylum have revealed a period in the middle of embryogenesis with more similarity between species compared with earlier and later time points. This “developmental hourglass” pattern has been observed in many phyla, yet the evolutionary constraints on gene expression, as well as the underlying mechanisms of how this is regulated, remain elusive. Moreover, the role of positive selection on gene regulation in the more diverged earlier and later stages of embryogenesis remains unknown. Here, using DNase-seq to identify regulatory regions in two distant Drosophila species (D. melanogaster and D. virilis), we assessed the evolutionary conservation and adaptive evolution of enhancers throughout multiple stages of embryogenesis. This revealed a higher proportion of conserved enhancers at the phylotypic period, providing a regulatory basis for the hourglass expression pattern. Using an in silico mutagenesis approach, we detect signatures of positive selection on developmental enhancers at early and late stages of embryogenesis, with a depletion at the phylotypic period, suggesting positive selection as one evolutionary mechanism underlying the hourglass pattern of animal evolution.
Anticipation of novel environments enhances memory for incidental information
Authors: Cen Danlu , Gkoumas Christos , Gruber Matthias J.
Published: July 2021

Novelty is a potent driver of learning, but little is known about whether anticipation of novelty can enhance memory for incidental information. Here, participants incidentally encountered objects while they actively navigated toward novel or previously familiarized virtual rooms. Across immediate and delayed surprise memory tests, participants showed superior recollection for incidental objects encountered while anticipating novel as compared with familiarized rooms. Furthermore, memory for incidental objects correlated positively with between-participants average curiosity about novel rooms but negatively with within-participants trial-specific curiosity. Our findings contribute to the growing literature on how salient processes impact memory for incidental material.
Greater dependence on working memory and restricted familiarity in orangutans compared with rhesus monkeys
Authors: Brady Ryan J. , Mickelberg Jennifer M. , Hampton Robert R.
Published: July 2021

The prefrontal cortex is larger than would be predicted by body size or visual cortex volume in great apes compared with monkeys. Because prefrontal cortex is critical for working memory, we hypothesized that recognition memory tests would engage working memory in orangutans more robustly than in rhesus monkeys. In contrast to working memory, the familiarity response that results from repetition of an image is less cognitively taxing and has been associated with nonfrontal brain regions. Across three experiments, we observed a striking species difference in the control of behavior by these two types of memory. First, we found that recognition memory performance in orangutans was controlled by working memory under conditions in which this memory system plays little role in rhesus monkeys. Second, we found that unlike the case in monkeys, familiarity was not involved in recognition memory performance in orangutans, shown by differences with monkeys across three different measures. Memory in orangutans was not improved by use of novel images, was always impaired by a concurrent cognitive load, and orangutans did not accurately identify images seen minutes ago. These results are surprising and puzzling, but do support the view that prefrontal expansion in great apes favored working memory. At least in orangutans, increased dependence on working memory may come at a cost in terms of the availability of familiarity.
Detailed analysis of deformation potentials with application in orbital-free density functional theory
Authors: Finzel Kati
Published: July 2021

A detailed analysis of the recently published deformation potentials for application in orbital-free density functional theory is given. Since orbital-free density functional theory is a purely density-based description of quantum mechanics, it may in the future provide itself useful in quantum crystallography as it establishes a direct link between experiment and theory via a single meaningful quantity: the electron density. In order to establish this goal, sufficiently accurate approximations for the kinetic energy have to be found. The present work is a further step in this direction. The so-called deformation potentials allow the interaction between the atoms to be taken into account through the help of their electron density only. It is shown that the present ansatz provides a systematic pathway beyond the recently introduced atomic fragment approach.
A deep auto-encoder satellite anomaly advance warning framework
Authors: Chen Junfu , Zhao Xiaodong , Pi Dechang
Published: July 2021

Purpose

The purpose of this paper is to ensure the stable operation of satellites in orbit and to assist ground personnel in continuously monitoring the satellite telemetry data and finding anomalies in advance, which can improve the reliability of satellite operation and prevent catastrophic losses.

Design/methodology/approach

This paper proposes a deep auto-encoder (DAE) satellite anomaly advance warning framework for satellite telemetry data. Firstly, this study performs grey correlation analysis, extracts important feature attributes to construct feature vectors and builds the variational auto-encoder with bidirectional long short-term memory generative adversarial network discriminator (VAE/BLGAN). Then, the Mahalanobis distance is used to measure the reconstruction score of input and output. According to the periodic characteristic of satellite operation, a dynamic threshold method based on periodic time window is proposed. Satellite health monitoring and advance warning are achieved using reconstruction scores and dynamic thresholds.

Findings

Experiment results indicate DAE methods can probe that satellite telemetry data appear abnormal, trigger a warning before the anomaly occurring and thus allow enough time for troubleshooting. This paper further verifies that the proposed VAE/BLGAN model has stronger data learning ability than other two auto-encoder models and is sensitive to satellite monitoring data.

Originality/value

This paper provides a DAE framework to apply in the field of satellite health monitoring and anomaly advance warning. To the best of the authors’ knowledge, this is the first paper to combine DAE methods with satellite anomaly detection, which can promote the application of artificial intelligence in spacecraft health monitoring.
The use of information management towards strategic decision effectiveness in higher education institutions in the context of Bahrain
Authors: Al Dhaen Esra Saleh
Published: July 2021

Purpose

Strategic decision importance has rarely been investigated as a decision-specific characteristic in the strategic decision-making process (SDMP) literature taking into consideration information management while taking important strategic decisions. Here, the ability of decision importance to predict decision effectiveness as an outcome of SDMPs in higher education institutions (HEIs) is examined in the context of Bahrain.

Design/methodology/approach

A conceptual model is developed relating decision importance to decision effectiveness indirectly via the SDMP characteristics intuition, rationality and decentralization. Data from a cross-sectional questionnaire completed by leaders of HEIs and academics involved in strategic decision-making in Bahrain are used to test the model and hypotheses via correlation analysis. The paper also considers a literature review of the use of information management while taking a strategic decision.

Findings

Decision importance is shown to positively influence decision effectiveness in Bahraini HEIs mediated by rationality and by decentralization in decision-making, although negative effects of decentralization are also demonstrated. However, decision importance does not influence decision effectiveness mediated by intuition.

Research limitations/implications

Due to the small sample size, the results cannot be generalized to contexts beyond HEIs in Bahrain. Additional SDMP characteristics of significance in the context of HEIs could be future investigated, for instance, political behaviour and lateral communication, are not included in the model. Future research exploring the latter two aspects could provide deeper insight into the findings.

Practical implications

The findings of this paper could be considered by HEIs senior management and members of the governing body while strategic decision-making, which could be at different levels, including strategic planning or assessing a strategic decision in terms of effectiveness. This paper will also provide insight one the use of information while considering strategic decision-making.

Social implications

A model leading for effective strategic decision-making could be used by leaders of HEIs and regulators including licensing bodies and QA agencies to set standards for HEIs for sustainable performance and quality education in line with United Nations Sustainable Development Goals and Initiative. Strategic decision-making will have an impact on the overall performance of HEIs and serve all relevant stakeholder’s including parents, students, employers and industry.

Originality/value

Little research conducted in relation to strategic decision-making in the Gulf Cooperation Council therefore, this research will add original findings and the outcome of this study will lead to future research related to SDMP and the use of information management in the overall strategic decision-making.
A social practice theory perspective on green marketing initiatives and green purchase behavior
Authors: Ali Muhammad
Published: July 2021

Purpose

The purpose of this study is to ascertain the effects of environmental knowledge and green consumption as mediators on the relationship between green marketing and green buying behavior. This study utilized the definition that needs to customers that are based on environmental concerns and influence the buying behavior for green products. This not only focuses on the ecological concern in organizational operations but also focuses on the customers' knowledge about the environment and how it influences their decisions. Three dimensions have been identified in this research to describe green marketing. These are ecolabeling, green branding and green advertising.

Design/methodology/approach

A survey research method has been utilized to collect data on a questionnaire adapted from previous research. The data collected have been analyzed with SmartPLS to assess the measurement model for reliability and validity and structural model for hypothesis testing and confirmation.

Findings

Focusing on the level of environmental knowledge of customers, it comes to surface that customers in developing countries have lesser knowledge in comparison to the customers in developed countries. This causes concern for the marketing departments in organizations since different customer niches demand different marketing solutions to influence their buying decision. Environmental knowledge does not mediate the relationship between green marketing and green buying behavior whereas green consumption mediates the relationship between green marketing and green buying behavior.

Originality/value

This study incorporates the social practice theory in green marketing research on the organizational level. This study brings together marketing practices under the influence of environmental knowledge for buying behavior formation in a novel manner. The influencing of customer decisions through green marketing strategies determines the success of the marketing initiative. Also, the theoretical foundations on social practice theory and the empirical design of the study to observe the relationships with the survey are new steps.
Effect of eWom on purchase intention: meta-analysis
Authors: Albayrak Merve , Ceylan Cemil
Published: July 2021

Purpose

The aim of this research is to combine and synthesize the findings of previous studies search for the effects of eWom on purchase intention by meta-analysis.

Design/methodology/approach

The paper shows a meta-analysis process step by step. Within the scope of certain criteria, the studies in the Google Scholar and ITÜ library databases were eliminated and the results of the remaining 19 studies were analyzed in CMA (Comprehensive Meta-Analysis) program.

Findings

By conducting a meta-analysis of the research question, a common effect size was obtained from 19 studies. In addition, the effect size of 21 eWom (electronic word of mouth communication) factor on purchasing intention related to the 21 hypotheses defined in the study was obtained by means of meta-analysis separately.

Originality/value

With the increasing number of Internet users, the desire to share their comments and ideas on the Internet, and the increasing importance of electronic word of mouth communication in our lives, people's decisions have started to be affected by this situation. One of the decision-making movements is the purchase intention. Therefore, it is expected to see more researches on meta-analysis for the effect of eWom on purchase intention in the following years.