bluuebunny/crossref_metadata_2025 huggingface dataset:
Locomotor performance and CNS responses to hypoxia in a cyclic nucleotide-gated channel mutant of adultDrosophila
Authors: Qiu Shuang , Xiao Chengfeng , Robertson R Meldrum
Published: February 2021

Drosophilaprovides an excellent opportunity to explore the genetic basis for behavioral and CNS responses to hypoxia. Cyclic guanosine monophosphate (cGMP) modulates the speed of recovery from anoxia in adults and mediates hypoxia-related behaviors in larvae. Cyclic nucleotide-gated channels (CNG) and cGMP-activated protein kinase (PKG) are two cGMP downstream targets. PKG is involved in behavioral tolerance to hypoxia and anoxia in adults, however little is known about CNG channels. We used a CNGL mutant with reducedCNGLtranscripts to investigate the contribution of CNGL to the hypoxia response. In control flies (w1118), hypoxia immediately reduced path length per minute in a locomotor assay. Flies took 30-40 mins in air to recover from 15 mins hypoxia. CNGL mutants had reduced locomotion under normoxia and impaired recovery from hypoxia, similar to the effects of pan-neuralCNGLknockdown. In the CNGL mutants hypoxia caused an acute increase in path length per minute followed by a gradual increase during hypoxia. Basal levels of CNS extracellular K+concentrations were reduced in the mutants. In response to hypoxia, the mutants had an increased extracellular K+concentration change, reduced time to reach the K+concentration peak, and delayed recovery time. Genetic manipulation to increase cGMP in the CNGL mutants eliminated the impairment of recovery from hypoxia and partially compensated for the effects of hypoxia on CNS K+. Although the neural mechanisms have yet to be determined, CNGL channels and cGMP signaling are involved in the hypoxia response of adultDrosophila.
Musicianship and melodic predictability enhance neural gain in auditory cortex during pitch deviance detection
Authors: Quiroga-Martinez D.R. , Hansen N. C. , Højlund A. , Pearce M. , Brattico E. , Holmes E. , Friston K. , Vuust P
Published: February 2021

When listening to music, pitch deviations are more salient and elicit stronger prediction error responses when the melodic context is predictable and when the listener is a musician. Yet, the neuronal dynamics and changes in synaptic efficacy underlying such effects remain unclear. Here, we employed dynamic causal modeling (DCM) to investigate whether the magnetic mismatch negativity response (MMNm)—and its modulation by context predictability and musical expertise—are associated with enhanced neural gain of auditory areas, as a plausible mechanism for encoding precision-weighted prediction errors. Using Bayesian model comparison, we asked whether models with intrinsic connections within primary auditory cortex (A1) and superior temporal gyrus (STG)—typically related to gain control—or extrinsic connections between A1 and STG—typically related to propagation of prediction and error signals—better explained magnetoencephalography (MEG) responses. We found that, compared to regular sounds, out-of-tune pitch deviations were associated with lower intrinsic (inhibitory) connectivity in A1 and STG, and lower backward (inhibitory) connectivity from STG to A1, consistent with disinhibition and enhanced neural gain in these auditory areas. More predictable melodies were associated with disinhibition in right A1, while musicianship was associated with disinhibition in left A1 and reduced connectivity from STG to left A1. These results indicate that musicianship and melodic predictability, as well as pitch deviations themselves, enhance neural gain in auditory cortex during deviance detection. Our findings are consistent with predictive processing theories suggesting that precise and informative error signals are selected by the brain for subsequent hierarchical processing.

Significance statement

In complex auditory contexts, being able to identify informative signals is of paramount importance. Such is the case of music listening, where surprising sounds play a fundamental role in its perceptual, aesthetical, and emotional experience. Crucially, surprising sounds in the pitch dimension are more easily detected and generate stronger cortical responses when melodies are predictable and when the listener is a musician. Using Dynamic Causal Modelling, here we show that such effects arise from a local increase in neural gain within auditory areas, rather than from passing of prediction and error signals between brain regions. Consistent with predictive processing theories, this suggests that the enhanced precision of auditory predictive models—through melodic predictability and musical training—up-regulates the processing of informative error signals in the brain.
Using a Human Circulation Mathematical Model to Simulate the Effects of Hemodialysis and Therapeutic Hypothermia
Authors: Joseph Jermiah J. , Hunter Timothy J. , Sun Clara , Goldman Daniel , Kharche Sanjay R. , McIntyre Christopher W.
Published: February 2021

Background

The human blood circulation is an intricate process regulated by multiple biophysical factors. Our patients often suffer from renal disease and atrial fibrillation, and are given treatments such as therapeutic hypothermia, exercise, and hemodialysis. In this work, a hemodynamic mathematical model of human circulation coupled to a representative dialysis machine is developed and used to explore causal mechanisms of our recent clinical observations.

Methods

An ordinary differential equation model consisting of human whole body circulation, baroreflex control, and a hemodialysis machine was implemented. Experimentally informed parameter alterations were used to implement hemodialysis and therapeutic hypothermia. By means of parameter perturbation, four model populations encompassing baseline, dialysed, hypothermia treated, and simultaneous dialysed with hypothermia were generated. In model populations, multiple conditions including atrial fibrillation, exercise, and renal failure were simulated. The effects of all conditions on clinically relevant non-invasive measurables such as heart rate and blood pressure were quantified. A parameter sensitivity analysis was implemented to rank model output influencing parameters in the presented model.

Results

Results were interpreted as alterations of the respective populations mean values and standard deviations of the clinical measurables, both in relation to the baseline population. A clinical measurable’s smaller standard deviation (in comparison to baseline population) was interpreted as a stronger association between a given clinical measure and the corresponding underlying process, which may permit the use of deducing one by observation of the other.

The modelled dialysis was observed to increase systolic blood pressure, vessel shear, and heart rate. Therapeutic hypothermia was observed to reduce blood pressure as well as the intra-population standard deviation (heterogeneity) of blood flow in the large (aorta) and small (kidney) vasculature. Therapeutic hypothermia reduced shear in vessels, suggesting a potential benefit with respect to endothelial dysfunction and maintenance of microcirculatory blood flow. The action of therapeutic hypothermia under conditions such as atrial fibrillation, exercise, and renal failure was to reduce total blood flow, which was applicable in all simulated populations. Therapeutic hypothermia did not affect the dialysis function, but exercise improved the efficacy of dialysis by facilitating water removal.

Conclusions

This study illuminates some mechanisms of action for therapeutic hypothermia. It also suggests clinical measurables that may be used as surrogates to diagnose underlying diseases such as atrial fibrillation.
Phenotypic analysis of catastrophic childhood epilepsy genes: The Epilepsy Zebrafish Project
Authors: Griffin Aliesha , Carpenter Colleen , Liu Jing , Paterno Rosalia , Grone Brian , Hamling Kyla , Moog Maia , Dinday Matthew T. , Figueroa Francisco , Anvar Mana , Ononuju Chinwendu , Qu Tony , Baraban Scott C.
Published: February 2021

Genetic engineering techniques have contributed to the now widespread use of zebrafish to investigate gene function, but zebrafish-based human disease studies, and particularly for neurological disorders, are limited. Here we used CRISPR-Cas9 to generate 40 single-gene mutant zebrafish lines representing catastrophic childhood epilepsies. We evaluated larval phenotypes using electrophysiological, behavioral, neuro-anatomical, survival and pharmacological assays. Phenotypes with unprovoked electrographic seizure activity (i.e., epilepsy) were identified in zebrafish lines for 8 genes;ARX, EEF1A, GABRB3, GRIN1, PNPO, SCN1A, STRADAandSTXBP1. A unifying epilepsy classification scheme was developed based on local field potential recordings and blinded scoring from ~3300 larvae. We also created an open-source database containing sequencing information, survival curves, behavioral profiles and representative electrophysiology data. We offer all zebrafish lines as a resource to the neuroscience community and envision them as a starting point for further functional analysis and/or identification of new therapies.
Unbiased profiling of CRISPR RNA-guided transposition products by long-read sequencing
Authors: Vo Phuc Leo H. , Acree Christopher , Smith Melissa L. , Sternberg Samuel H.
Published: February 2021

Bacterial transposons propagate through either non-replicative (cut-and-paste) or replicative (copy-and-paste) pathways, depending on how the mobile element is excised from its donor source. In the well-characterizedE. colitransposon Tn7, a heteromeric TnsA-TnsB transposase directs cut-and-paste transposition by cleaving both strands at each transposon end during the excision step. Whether a similar pathway is involved for RNA-guided transposons, in which CRISPR-Cas systems confer DNA target specificity, has not been determined. Here, we apply long-read, population-based whole-genome sequencing (WGS) to unambiguously resolve transposition products for two evolutionarily distinct transposon types that employ either Cascade or Cas12k for RNA-guided DNA integration. Our results show that RNA-guided transposon systems lacking functional TnsA primarily undergo copy-and-paste transposition, generating cointegrate products that comprise duplicated transposon copies and insertion of the vector backbone. Finally, we report natural and engineered transposon variants encoding a TnsAB fusion protein, revealing a novel strategy for achieving RNA-guided transposition with fewer molecular components.
Reaction of ependymal cells to spinal cord injury: a potential role for oncostatin pathway and microglial cells
Authors: Chevreau R. , Ghazale H , Ripoll C , Chalfouh C , Delarue Q , Hemonnot-Girard A.L. , Hirbec H , Wahane S , Perrin F , Noristani H , Guerout N , Hugnot JP
Published: February 2021

Ependymal cells with stem cell properties reside in the adult spinal cord around the central canal. They rapidly activate and proliferate after spinal cord injury, constituting a source of new cells. They produce neurons and glial cells in lower vertebrates but they mainly generate glial cells in mammals. The mechanisms underlying their activation and their glial-biased differentiation in mammals remain ill-defined. This represents an obstacle to control these cells. We addressed this issue using RNA profiling of ependymal cells before and after injury. We found that these cells activate STAT3 and ERK/MAPK signaling during injury and downregulate cilia-associated genes and FOXJ1, a central transcription factor in ciliogenesis. Conversely, they upregulate 510 genes, six of them more than 20 fold, namelyCrym, Ecm1, Ifi202b, Nupr1, Rbp1, Thbs2 and Osmr. OSMR is the receptor for the inflammatory cytokine oncostatin (OSM) and we studied its regulation and role using neurospheres derived from ependymal cells. We found that OSM induces strong OSMR and p-STAT3 expression together with proliferation reduction and astrocytic differentiation. Conversely, production of oligodendrocyte-lineage OLIG1+cells was reduced. OSM is specifically expressed by microglial cells and was strongly upregulated after injury. We observed microglial cells apposed to ependymal cells in vivo and co-cultures experiments showed that these cells upregulate OSMR in neurosphere cells. Collectively, these results support the notion that microglial cells and OSMR/OSM pathway regulate ependymal cells in injury. In addition, the generated high throughput data provides a unique molecular resource to study how ependymal cell react to spinal cord lesion.
Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies
Authors: Planas Delphine , Bruel Timothée , Grzelak Ludivine , Guivel-Benhassine Florence , Staropoli Isabelle , Porrot Françoise , Planchais Cyril , Buchrieser Julian , Rajah Maaran Michael , Bishop Elodie , Albert Mélanie , Donati Flora , Behillil Sylvie , Enouf Vincent , Maquart Marianne , Gonzalez Maria , De Sèze Jérôme , Péré Hélène , Veyer David , Sève Aymeric , Simon-Lorière Etienne , Fafi-Kremer Samira , Stefic Karl , Mouquet Hugo , Hocqueloux Laurent , van der Werf Sylvie , Prazuck Thierry , Schwartz Olivier
Published: February 2021

SARS-CoV-2 B.1.1.7 and B.1.351 variants emerged respectively in United Kingdom and South Africa and spread in many countries. Here, we isolated infectious B.1.1.7 and B.1.351 strains and examined their sensitivity to anti-SARS-CoV-2 antibodies present in sera and nasal swabs, in comparison with a D614G reference virus. We established a novel rapid neutralization assay, based on reporter cells that become GFP+ after overnight infection. B.1.1.7 was neutralized by 79/83 sera from convalescent patients collected up to 9 months post symptoms, almost similar to D614G. There was a mean 6-fold reduction in titers and even loss of activity against B.1.351 in 40% of convalescent sera after 9 months. Early sera from 19 vaccinated individuals were almost as potent against B.1.1.7 but less efficacious against B.1.351, when compared to D614G. Nasal swabs from vaccine recipients were not neutralizing, except in individuals who were diagnosed COVID-19+ before vaccination. Thus, faster-spreading variants acquired a partial resistance to humoral immunity generated by natural infection or vaccination, mostly visible in individuals with low antibody levels.
Joint changes in RNA, RNA polymerase II, and promoter activity through the cell cycle identify non-coding RNAs involved in proliferation
Authors: Hegre Siv Anita , Samdal Helle , Klima Antonin , Stovner Endre B. , Nørsett Kristin G. , Liabakk Nina Beate , Olsen Lene Christin , Chawla Konika , Aas Per Arne , Sætrom Pål
Published: February 2021

Proper regulation of the cell cycle is necessary for normal growth and development of all organisms. Conversely, altered cell cycle regulation often underlies proliferative diseases such as cancer. Long non-coding RNAs (lncRNAs) are recognized as important regulators of gene expression and are often found dysregulated in diseases, including cancers. However, identifying lncRNAs with cell cycle functions is challenging due to their often low and cell-type specific expression. We present a highly effective method that analyses changes in promoter activity, transcription, and RNA levels for identifying genes enriched for cell cycle functions. Specifically, by combining RNA sequencing with ChIP sequencing through the cell cycle of synchronized human keratinocytes, we identified 1009 genes with cell cycle-dependent expression and correlated changes in RNA polymerase II occupancy or promoter activity as measured by histone 3 lysine 4 trimethylation (H3K4me3). These genes were highly enriched for genes with known cell cycle functions and included 59 lncRNAs. We selected four of these lncRNAs –AC005682.5, RP11-132A1.4, ZFAS1, andEPB41L4A-AS1– for further experimental validation and found that knockdown of each of the four lncRNAs affected cell cycle phase distributions and reduced proliferation in multiple cell lines. These results show that many genes with cell cycle functions have concomitant cell-cycle dependent changes in promoter activity, transcription, and RNA levels and support that our multi-omics method is well suited for identifying lncRNAs involved in the cell cycle.
Recurrent Vulvovaginal Candidiasis; a dynamic interkingdom biofilm disease ofCandidaandLactobacillus
Authors: McKloud Emily , Sherry Leighann , Kean Ryan , Delaney Christopher , Williams Shanice , Metcalfe Rebecca , Thomas Rachael , Williams Craig , Ramage Gordon
Published: February 2021

Vulvovaginal Candidiasis (VVC) is the most prevalentCandidainfection in humans affecting 75% of women at least once throughout their lifetime. In its debilitating recurrent form, RVVC is estimated to affect 140 million women annually. Despite this strikingly high prevalence, treatment options for RVVC remain limited with many women experiencing failed clinical treatment with frontline azoles. Further, the cause of onset and recurrence of disease is largely unknown with few studies identifying potential mechanisms of failed treatment. This study aimed to assess a panel of clinical samples from healthy women and those with RVVC to investigate the influence ofCandida, vaginal microbiome and antagonism betweenCandidaandLactobacilluson disease pathology. 16S rRNA sequencing characterised disease by a reduction in specific health-associatedLactobacillussuch asL. crispatus, coupled with an increase inL. iners.In vitroanalysis showedCandida albicansclinical isolates are capable of heterogeneous biofilm formation and show the presence of hyphae andC. albicansaggregates in vaginal lavage. Additionally, the ability ofLactobacillusto inhibitC. albicansbiofilm formation and biofilm-related gene expression was demonstrated. Using RNA sequencing technology, we were able to exploit a possible mechanism by whichL. crispatusmay aim to re-establish a healthy vaginal environment through amino-acid acquisition fromC. albicans. This study suggests RVVC is not entirely due to an arbitrary switch inC. albicansfrom commensal to pathogen and understanding interactions between the yeast and vaginalLactobacillusspecies may be more crucial to elucidating the cause of RVVC and developing appropriate therapies.
Direct-from-specimen microbial growth inhibition spectrums under antibiotic exposure and comparison to conventional antimicrobial susceptibility testing
Authors: Chen Jade , San Su Su Soe , Kung Amelia , Tomasek Michael , Liu Dakai , Rodgers William , Gau Vincent
Published: February 2021

Increasing global travel and changes in the environment may increase the frequency of contact with a natural host carrying an infection, and therefore increase our chances of encountering microorganisms previously unknown to humans. During an emergency (man-made, natural disaster, or pandemic), the etiology of infection might be unknown at the time of patient treatment. The existing local or global Antimicrobial Stewardship Programs might not be fully prepared for emerging/re-emerging infectious disease outbreaks, especially if they are caused by an unknown organism, engineered bioterrorist attack, or rapidly evolving superbug. We demonstrate an antimicrobial efficacy profiling method that can be performed in hours directly from clinical urine specimens. The antimicrobial potency is determined by the microbial growth inhibition and compared to conventional antimicrobial susceptibility testing (AST) results. The oligonucleotide probe pairs on the sensor were designed to target gram-negative bacteria, specificallyEnterobacteralesandPseudomonas aeruginosa. A total of 10 remnant clinical specimens from the CLIA labs of New York-Presbyterian Queens were tested, resulting in 100% categorical agreement with reference AST methods (Vitek and broth microdilution method). The combined categorical susceptibility reporting of 12 contrived urine specimens was 100% for ciprofloxacin, gentamicin, and meropenem over a range of microbial loads from 105to 108CFU/mL.
Promiscuous specialists: Host specificity patterns among generalist louse flies
Authors: Lehikoinen Aleksi , Pohjola Pekka , Valkama Jari , Mutanen Marko , Pohjoismäki Jaakko L.O.
Published: February 2021

Ectoparasites such as louse flies (Diptera: Hippoboscidae) have tendency for host specialization, which is driven by adaptation to host biology as well as competition avoidance between parasites of the same host. However, some louse fly species, especially in genera attacking birds, show wide range of suitable hosts. In the presented study, we have surveyed the current status of bird attacking louse flies in Finland to provide comprehensive host association data to analyse the ecological requirements of the generalist species. A thorough sampling of 9342 birds, representing 134 species, recovered 576 specimens of louse flies, belonging to six species:Crataerina hirundinis, C. pallida, Ornithomya avicularia, O. chloropus, O. fringillinaandOrnithophila metallica. Despite some overlapping hosts, the threeOrnithomyaspecies showed a notable pattern in their host preference, which was influenced not only by the host size but also by the habitat and host breeding strategy. We also provide DNA barcodes for most Finnish species of Hippoboscidae, which can be used as a resource for species identification as well as metabarcoding studies in the future.
Genome sequencing of the bacteriophage CL31 and interaction with the host strainCorynebacterium glutamicumATCC 13032
Authors: Hünnefeld Max , Viets Ulrike , Sharma Vikas , Wirtz Astrid , Hardy Aël , Frunzke Julia
Published: February 2021

In this study, we provide a comprehensive analysis of the genomic features of the phage CL31 and the infection dynamics with the biotechnologically relevant host strainCorynebacterium glutamicumATCC 13032. Genome sequencing and annotation of CL31 revealed a 45-kbp genome composed of 72 open reading frames, mimicking the GC content of its host strain (54.4 %). An ANI-based distance matrix showed the highest similarity of CL31 to the temperate corynephage Φ16. While theC. glutamicumATCC 13032 wild type strain showed only mild propagation of CL31, a strain lacking thecglIR-cglIIR-cglIMrestriction-modification system was efficiently infected by this phage. Interestingly, the prophage-free strainC. glutamicumMB001 featured an even accelerated amplification of CL31 compared to the Δresmodstrain suggesting a role of cryptic prophage elements in phage defense. Proteome analysis of purified phage particles and transcriptome analysis provide important insights into structural components of the phage and the response ofC. glutamicumto CL31 infection. Isolation and sequencing of CL31-resistant strains revealed SNPs in genes involved in mycolic acid biosynthesis suggesting a role of this cell envelope component in phage adsorption. Altogether, these results provide an important basis for further investigation of phage-host interactions in this important biotechnological model organism.
Role of endopeptidases in peptidoglycan synthesis mediated by alternative cross-linking enzymes inEscherichia coli
Authors: Voedts Henri , Dorchêne Delphine , Lodge Adam , Vollmer Waldemar , Arthur Michel , Hugonnet Jean-Emmanuel
Published: February 2021

Bacteria resist to the turgor pressure of the cytoplasm through a net-like macromolecule, the peptidoglycan, made of glycan strands connected via peptides cross-linked by penicillin-binding proteins (PBPs). We recently reported the emergence of β-lactam resistance resulting from a bypass of PBPs by the YcbB L,D-transpeptidase (LdtD), which form chemically distinct 3→3 cross-links compared to 4→3 formed by PBPs. Here we show that peptidoglycan expansion requires controlled hydrolysis of cross-links and identify amongst eight endopeptidase paralogues the minimum enzyme complements essential for bacterial growth with 4→3 (MepM) and 3→3 (MepM and MepK) cross-links. Purified Mep endopeptidases unexpectedly displayed a 4→3 and 3→3 dual specificity implying recognition of a common motif in the two cross-link types. Uncoupling of the polymerization of glycan chains from the 4→3 cross-linking reaction was found to facilitate the bypass of PBPs by YcbB. These results illustrate the plasticity of the peptidoglycan polymerization machinery in response to the selective pressure of β-lactams.
Chlorine inactivation ofEscherichia coli O157:H7in fresh produce wash process: effectiveness and modeling
Authors: Abnavi Mohammadreza Dehghan , Kothapalli Chandrasekhar R. , Munther Daniel , Srinivasan Parthasarathy
Published: February 2021

This study presents a modified disinfection kinetics model to evaluate the potential effect of organic content on the chlorine inactivation coefficient ofEscherichia coli O157:H7in fresh produce wash processes. Results show a significant decrease in the bactericidal efficacy of free chlorine (FC) in the presence of organic load compared to its absence. While the chlorine inactivation coefficient ofEscherichia coli O157:H7is 70.39 ± 3.19 L.mg−1.min−1in the absence of organic content, it drops by 73% in chemical oxygen demand (COD) level of 600 - 800 mg.L−1. Results also indicate that the initial chlorine concentration and bacterial load have no effect on the chlorine inactivation coefficient. A second-order chemical reaction model for FC decay, which utilizes a percentage of COD as an indicator of organic content in fresh produce wash was employed, yielding an apparent reaction rate of (9.45 ± 0.22) × 10−4μM−1.min−1. This model was validated by predicting FC concentration (R2= 0.96) in multi-run continuous wash cycles with periodic replenishment of chlorine.
TargetingGys1with AAV‐SaCas9 decreases pathogenic polyglucosan bodies and neuroinflammation in Adult Polyglucosan Body and Lafora disease mouse models
Authors: Gumusgoz Emrah , Guisso Dikran R , Kasiri Sahba , Wu Jun , Dear Matthew , Verhalen Brandy , Nitschke Silvia , Mitra Sharmistha , Nitschke Felix , Minassian Berge A.
Published: February 2021

Many adult and most childhood neurological diseases have a genetic basis. CRISPR/Cas9 biotechnology holds great promise in neurological therapy, pending the clearance of major delivery, efficiency and specificity hurdles. We apply CRISPR/Cas9 genome editing in its simplest modality, namely inducing gene sequence disruption, to one adult and one pediatric disease. Adult polyglucosan body disease is a neurodegenerative disease resembling amyotrophic lateral sclerosis. Lafora disease is a severe late childhood onset progressive myoclonus epilepsy. The pathogenic insult in both is formation in the brain of glycogen with overlong branches, which precipitates and accumulates into polyglucosan bodies that drive neuroinflammation and neurodegeneration. We packagedStaphylococcus aureusCas9 and a guide RNA targeting the glycogen synthase geneGys1responsible for brain glycogen branch elongation in AAV9 virus, which we delivered by neonatal intracerebroventricular injection to one mouse model of adult polyglucosan body disease and two mouse models of Lafora disease. This resulted, in all three models, in editing of approximately 17% ofGys1alleles and a similar extent of reduction ofGys1mRNA across the brain. The latter led to approximately 50% reductions of GYS1 protein, of abnormal glycogen accumulation and of polyglucosan bodies, as well as corrections of neuroinflammatory markers in all three models. Our work represents proof of principle for virally-delivered CRISPR/Cas9 neurotherapeutics in an adult-onset (adult polyglucosan body) and a childhood-onset (Lafora) neurological diseases.
slim shadyis a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201
Authors: Dash Linkan , McEwan Robert E. , Montes Christian , Mejia Ludvin , Walley Justin W. , Dilkes Brian P. , Kelley Dior R.
Published: February 2021

Auxin is a hormone that is required for hypocotyl elongation during seedling development. In response to auxin rapid changes in transcript and protein abundance occur in hypocotyls and some auxin responsive gene expression is linked to hypocotyl growth. To functionally validate proteomic studies, a reverse genetics screen was performed on mutants in auxin-regulated proteins to identify novel regulators of plant growth. This uncovered a long hypocotyl mutant, which we calledslim shady, in an annotated insertion line inIMMUNOREGULATORY RNA-BINDING PROTEIN (IRR). Overexpression of theIRRgene failed to rescue theslim shadyphenotype and characterization of a second T-DNA allele ofIRRfound that it had a wild-type hypocotyl length. Theslim shadymutant has an elevated expression of numerous genes associated with the brassinosteroid-auxin-phytochrome (BAP) regulatory module compared to wild-type, including transcription factors that regulate brassinosteroid, auxin and phytochrome pathways. Additionally,slim shadyseedlings fail to exhibit a strong transcriptional response to auxin. Using whole genome sequence and transcriptomics data for SALK_015201C we determined that a novel single nucleotide polymorphism inPHYTOCHROME Bwas responsible for theslim shadyphenotype. This is predicted to convert induce a frameshift and premature stop codon at leucine 1125, within the histidine kinase-related domain of the carboxy terminus of PHYB, which is required for phytochrome signaling and function. Genetic complementation analyses withphyb-9confirmed that slim shady is a mutant allele ofPHYB. This study advances our understanding of the molecular mechanisms in seedling development, by furthering our understanding of how light signaling is linked to auxin dependent cell elongation. Furthermore, this study highlights the importance of confirming the genetic identity of research material before attributing phenotypes to known mutations sourced from T-DNA stocks.
SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization
Authors: Hoffmann Markus , Zhang Lu , Krüger Nadine , Graichen Luise , Kleine-Weber Hannah , Hofmann-Winkler Heike , Kempf Amy , Nessler Stefan , Riggert Joachim , Winkler Martin Sebastian , Schulz Sebastian , Jäck Hans-Martin , Pöhlmann Stefan
Published: February 2021

Transmission of SARS-CoV-2 from humans to farmed mink was observed in Europe and the US. In the infected animals viral variants arose that harbored mutations in the spike (S) protein, the target of neutralizing antibodies, and these variants were transmitted back to humans. This raised concerns that mink might become a constant source of human infection with SARS-CoV-2 variants associated with an increased threat to human health and resulted in mass culling of mink. Here, we report that mutations frequently found in the S proteins of SARS-CoV-2 from mink were mostly compatible with efficient entry into human cells and its inhibition by soluble ACE2. In contrast, mutation Y453F reduced neutralization by an antibody with emergency use authorization for COVID-19 therapy and by sera/plasma from COVID-19 patients. These results suggest that antibody responses induced upon infection or certain antibodies used for treatment might offer insufficient protection against SARS-CoV-2 variants from mink.
Strong trait correlation and phylogenetic signal in North American ground beetle (Carabidae) morphology
Authors: Stachewicz Jacob D. , Fountain-Jones Nicholas M. , Koontz Austin , Woolf Hillary , Pearse William D. , Gallinat Amanda S.
Published: February 2021

Functional traits mediate species’ responses to and roles within their environment, and are constrained by evolutionary history. While we have a strong understanding of trait evolution for macro-taxa such as birds and mammals, our understanding of invertebrates is comparatively limited. Here we address this gap in North American beetles with a sample of ground beetles (Carabidae), leveraging a large-scale collection and digitization effort by the National Ecological Observatory Network (NEON). For 154 ground beetle species, we measured seven morphological traits, which we placed into a recently-developed effect-response framework that characterizes traits by how they predict species’ effects on their ecosystems or responses to environmental stressors. We then used cytochrome oxidase one sequences from the same specimens to generate a phylogeny and tested evolutionary tempo and mode of the traits. We found strong phylogenetic signal in, and correlations among, morphological ground beetle traits. These results indicate that, for these species, beetle body shape trait evolution is constrained, and phylogenetic inertia is a stronger driver of beetle traits than (recent) environmental responses. Strong correlations among effect and response traits suggest that future environmental drivers are likely to affect both ecological composition and functioning in these beetles.
Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere
Authors: Liu Yangminghao , Patko Daniel , Engelhardt Ilonka , George Timothy S , Stanley-Wall Nicola , Ladmiral Vincent , Ameduri Bruno , Daniell Tim J , Holden Nicola , MacDonald Michael P , Dupuy Lionel X
Published: February 2021

Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants’ large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 μm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point “first contact”, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.
Unravelling cotton RNAseq repositories to the fiber development specific modules and their alliance with the fiber-related traits
Authors: Prasad Priti , Khatoon Uzma , Verma Rishi Kumar , Kumar Ajay , Mohapatra Debashish , Bhattacharya Parthasarthi , Bag Sumit K , Sawant Samir V
Published: February 2021

Cotton fiber development is still an intriguing question to understand the fiber commitment and development. Here, we remapped >350 publicly available cotton RNA sequencing data on recently published cotton genome with ∼400 fold coverage. The differentially expressed genes were clustered in six modules whose functions are specific to commitment, initiation, elongation and Secondary Cell Wall (SCW) fiber development stages. Gene Ontology analysis of commitment and initiation specific modules suggests enrichment of genes involved in organ development. The modules specific for elongation and SCW showed significant enrichment of hydroxyproline-rich proteins and hydrolases. Transcription factors (TFs) binding frequency of defined modules suggested that homeodomain, MYB and NAC expresses at commitment stages but their expression was governed by other TFs. We also mined the stage-specific transcriptional biomarker and Exclusively Expressed Transcripts (EETs) for fiber. These EETs were positively selected during fiber evolution and cotton domestication. The extensive expression profiling of six EETs in 100 cotton genotypes at different fiber developmental stages using nCounter assay and their correlation with eight fiber-related suggests that several EETs are correlated with different fiber quality-related traits. Thus, our study reveals several important genes and pathways that may be important for cotton fiber development and future improvement of cotton.
NGO responses to financial evaluation: auditability, purification and performance
Authors: Cazenave Bruno , Morales Jeremy
Published: February 2021

Purpose

Literature has widely studied the financial accountability pressures on NGOs but rarely analysed how NGOs respond to them. This paper studies one large humanitarian NGO to address this question. It investigates the NGO's responses to understand the extent to which NGOs are able to regain control over their own work and turn the frames of evaluation and accountability to their own advantage.

Design/methodology/approach

This article draws on a case study of one of the largest French humanitarian NGOs. Interviews and observation (both participant and non-participant) were conducted in the financial department of the NGO. These data are supplemented with field-level contextual interviews.

Findings

In the NGO studied, institutional pressure is largely mediated by compliance audits. The paper thus traces the consequences of compliance audits for the NGO's central finance teams and describes how they respond. The findings detail three responses to evaluation. First, to respond to the burden of evaluation, the organisation makes itself auditable and develops preparedness. Second, to respond to the anxiety of evaluation, the organisation engages in a process of purification and succumbs to the allure of the single figure. Third, building on its newly acquired auditability and purity, the organisation performs itself as a “corporatised NGO”. Together, these three responses constitute the NGO as an “entrepreneur” competing for eligibility, and financial literacy and managerialism become crucial to respond to pressure from institutional funders.

Originality/value

This paper extends the understanding of organisational responses to evaluation. The authors show the influence of evaluation systems on NGOs, but also how NGOs can react to regain control over their work and turn the frames of evaluation and accountability to their own advantage. However, despite several decades of calls for broader conceptions of NGO accountability, the case NGO prefers to promote a very narrow view of its performance, based solely on accounting compliance. It takes some pride in its ability to comply with funders' and auditors' demands. Turning a simple matter of compliance into a display of good performance, it builds a strategy and competitive advantage on its ability to respond competently to evaluation.
Thought favorability: mediating role in fit and brand advocacy
Authors: Vashisht Devika , Mohan HFO Surindar , Chauhan Abhishek , Vashisht Raveesh
Published: February 2021

Purpose

The purpose of this study is to investigate the effect of game-product fit on brand advocacy and mediating role of thought favorability in fit and brand advocacy relationship in the context of in-game advertising (IGA) using congruity theory and heuristic systematic model. This expounds the conditions under which in-game brand placements form favorable or unfavorable thoughts about the game and the advertised brand, and following brand advocacy.

Design/methodology/approach

A total of 144 student-gamers participated in the study. One-way ANOVA and a path analysis were used for hypotheses testing.

Findings

Results showed that the high-fit game resulted in higher thought favorability and greater levels of brand advocacy than the low-fit game. Furthermore, results also revealed that thought favorability mediated the relationship of game-product fit and brand advocacy among players.

Research limitations/implications

Research on IGA is still in its relative infancy, and how gamers respond to brand placements in games has yet to be fully established. This paper’s theoretical implications are primarily in the context of in-game advertising and explain the role played by game-product fit as an originator to thought favorability that further adds value to thought favorability and brand advocacy relationship.

Practical implications

The study offers important implications for marketers, advertisers, policy-makers in terms of effective game-designing and IGA execution.

Originality

Since very little research has been done focusing on mediating role of thought favorability in game-product fit and brand advocacy relationship in the context of IGA from attention and elaboration perspectives, this paper scores as a pioneering study of its kind in India.
A probabilistic-based analysis for wind distribution determination of a runway
Authors: Suzer Ahmet Esat , Kaba Aziz
Published: February 2021

Purpose

The purpose of this study is to describe precisely the wind speed regime and characteristics of a runway of an International Airport, the north-western part of Turkey.

Design methodology approach

Three different probability distributions, namely, Inverse Gaussian (IG), widely used two-parameter Weibull and Rayleigh distributions in the literature, are used to represent wind regime and characteristics of the runway. The parameters of each distribution are estimated by the pattern search (PS)-based heuristic algorithm. The results are compared with the other three methods-based numerical computation, including maximum-likelihood method, moment method (MoM) and power density method, respectively. To evaluate the fitting performance of the proposed method, several statistical goodness tests including the mostly used root mean square error (RMSE) and chi-squared (X2) are conducted.

Findings

In the light of the statistical goodness tests, the results of the IG-based PS attain better performance than the classical Weibull and Rayleigh functions. Both the RMSE and X2 values achieved by the IG-based PS method lower than that of Weibull and Rayleigh distributions. It exhibits a better fitting performance with 0.0074 for RMSE and 0.58 × 10−4 for X2 for probability density function (PDF) in 2012 and with RMSE of 0.0084 and X2 of 0.74 × 10−4 for PDF in 2013. As regard the cumulative density function of the measured wind data, the best results are found to be Weibull-based PS with RMSE of 0.0175 and X2 of 3.25 × 10−4 in 2012. However, Weibull-based MoM shows more excellent ability in 2013, with RMSE of 0.0166 and X2 of 2.94 × 10−4. Consequently, it is considered that the results of this study confirm that IG-based PS with the lowest error value can a good choice to model more accurately and characterize the wind speed profile of the airport.

Practical implications

This paper presents a realistic point of view regarding the wind regime and characteristics of an airport. This study may cast the light on researchers, policymakers, policy analysts and airport designers intending to investigate the wind profile of a runway at the airport in the world and also provide a significant pathway on how to determine the wind distribution of the runway.

Originality value

Instead of the well-known Weibull distribution for the representing of wind distribution in the literature, in this paper, IG distribution is used. Furthermore, the suitability of IG to represent the wind distribution is validated when compared with two-parameter Weibull and Rayleigh distributions. Besides, the performance and efficiency of PS have been evaluated by comparing it with other methods.
Budgeting as practice and knowing in action: experimenting with Bourdieu's theory of practice: an empirical evidence from a public university
Authors: Seneviratne Chaturika Priyadarshani , Martino Ashan Lester
Published: February 2021

Purpose

The present study aims to explore how various doings, strategic actions and power relations stemming from internal agents are instrumental in (re)constituting the different forms and meanings of budgeting in a specific field.

Design/methodology/approach

The paper uses a single-case study method based on a Sri Lankan public university. Data are collected using interviews, documentary evidence and observations.

Findings

The empirical evidence suggested that internal agents are crucial, and they are the producers of budgetary practice as they possess practical knowledge and power relations in the field where they operate. The case data demonstrate that organisational agents do have real essence as active and acting to produce effects in budgeting practices, and the significance of exploring the singularity of multiple agents in terms of their viewpoints, trajectories, dispositions and power relations, who may form, sustain or interrupt budgetary practices in a given setting.

Research limitations/implications

As the research is directed towards the selection of in-depth enquiry of specific setting infused with culture, values, perception and ideology, it might cause to diminish the researcher's analytical objectivity and independence of the research.

Practical implications

As budgetary practices are product of human interaction, it is important to note that practitioners should be concerned with what agents do in actual practice and their inactions, influences and power relations in budgeting practices, which might not align with the structural forces enlisted in the budgeting. It would be of interest for future empirical research to explore the interplay between the diverse interests of organisational agents and agents beyond the individual organisations.

Originality/value

This study contributes to the literature on management control practices by documenting the importance of understanding the “practice” through relational thinking of all three concepts is emphasised, such interrelated theoretical insights are seldom used to understand accounting practices. This research emphasises the importance of bringing out the microprocessual facets of management control to open up its non-conscious, non-strategic and non-rationalist forms.
Fixed point theorems for Geraghty-type mappings applied to solving nonlinear Volterra-Fredholm integral equations in modularG-metric spaces
Authors: Okeke Godwin Amechi , Francis Daniel
Published: February 2021

Purpose

The authors prove the existence and uniqueness of fixed point of mappings satisfying Geraghty-type contractions in the setting of preordered modularG-metric spaces. The authors apply the results in solving nonlinear Volterra-Fredholm-type integral equations. The results extend generalize compliment and include several known results as special cases.

Design/methodology/approach

The results of this paper are theoretical and analytical in nature.

Findings

The authors prove the existence and uniqueness of fixed point of mappings satisfying Geraghty-type contractions in the setting of preordered modularG-metric spaces. apply the results in solving nonlinear Volterra-Fredholm-type integral equations. The results extend, generalize, compliment and include several known results as special cases.

Research limitations/implications

The results are theoretical and analytical.

Practical implications

The results were applied to solving nonlinear integral equations.

Social implications

The results has several social applications.

Originality/value

The results of this paper are new.