bluuebunny/crossref_metadata_2025 huggingface dataset:
STAYGREEN-mediated chlorophyll a catabolism is critical for photosystem stability upon heat stress in ryegrass
Authors: Zhang Jing , Li Hui , Huang Xinru , Xing Jing , Yao Jiaming , Jiang Jiafu , Wang Puchang , Xu Bin
Published: September 2021

Chlorophyll (Chl) loss is one of the most visible symptoms of heat-induced leaf senescence, especially for cool-season grass species. Suppression of the Chl a Me-dechelatase gene,SGR(also named asnye1), blocked the degradation of Chl a and resulted in the ‘stay-green’ trait during leaf senescence. However, effect of Chl a catabolism on plant tolerance to long-term moderate heat stress (35-40°C) remains unclear. In this study, we suppressed the expression of Chl a catabolic gene,LpSGR, in both constitutive and inducible manners in perennial ryegrass. Constitutive suppression ofLpSGRaggravated heat stress-induced chloroplast structure and photosystem damages, disrupted energy utilization/dissipation during photosynthesis, activated ROS generation with weakened ROS-scavenging enzyme activities. Transcriptome comparison among wildtype (WT) and transgenic RNAi plants under either the optimum or high temperature conditions also emphasized the effect of Chl a catabolism on expression of genes encoding photosynthesis system, ROS-generation and scavenging system, and heat shock transcription factors. Furthermore, making use of a modified ethanol-inducible system, we generated stable transgenic perennial ryegrass to suppressLpSGRin an inducible manner. Without ethanol induction, these transgenic lines exhibited the same growth and heat tolerance traits to WT, while under the induction of ethanol spray, the transgenic lines also showed compromised heat tolerance. Taken together, our data suggest that Chl a catabolism is critical for energy dissipation and electron transfer in photosynthesis, ROS-balancing and chloroplast membrane system stability upon long-term moderate heat stress.
Quercetin prevents insulin dysfunction in hypertensive animals
Authors: Serra Cristiane Alves , dos Reis Alexandre Freire , Calsa Bruno , Bueno Cintia Sena , Helaehil Júlia Venturini , de Souza Suelen Aparecida Ribeiro , de Oliveira Camila Andrea , Vanzella Emerielle Cristine , do Amaral Maria Esméria Corezola
Published: September 2021

Angiotensin II induced increase in hypertension enhances oxidative stress and compromises insulin action and pancreatic function. Quercetin-rich foods are beneficial for hypertensive and diabetic animals owing to their antioxidant function. The aim of this study was to evaluate the antioxidant effects of quercetin in hypertensive rats on insulin action, signaling, and secretion. Wistar rats were randomly divided into three groups: sham, hypertensive rats (H), and hypertensive rats supplemented with quercetin (HQ). After three months of initial hypertension, quercetin was administered at 50 mg/kg/day for 30 days. Our results indicate that hypertension and serum lipid peroxidation levels were reduced by quercetin supplementation. We observed increased insulin sensitivity in adipose tissue, corroborating the insulin tolerance test, HOMA index, and improvements in lipid profile. Despite normal insulin secretion at 2.8 and 20 mM of glucose, animals treated with quercetin exhibited increased number of islets per section; increased protein expression of muscarinic receptor type 3, VEGF, and catalase in islets; and hepatic mRNA levels of Ide were normalized. In conclusion, supplementation with quercetin improved insulin action and prevented pancreatic and metabolic dysfunction.
Orientations of Mistaken Point fronds indicate morphology impacted ability to survive turbulence
Authors: Vixseboxse Philip B. , Kenchington Charlotte G. , Dunn Frances S. , Mitchell Emily G.
Published: September 2021

The Ediacaran organisms of the Mistaken Point E surface have provided crucial insight into early animal communities, including how they reproduced, the importance of Ediacaran height and what the most important factors were to their community dynamics. Here, we use this iconic community to investigate how morphological variation between eight taxa affected their ability to withstand different flow conditions. For each of Beothukis, Bradgatia, Charniodiscus procerus, Charniodiscus spinosus, Plumeropriscum, Primocandelabrum and Fractofusus we measured the orientation and length of their stems (if present) and their fronds. We statistically tested each taxon’s stem and frond orientation distributions to see whether they displayed a uniform or multimodal distribution. Where multimodal distributions were identified, the stem/frond length of each cohort was tested to identify if there were differences in size between different orientation groups. We find that Bradgatia and Thectardis show a bimodal felling direction, and infer that they were felled by the turbulent head of the felling flow. In contrast, the frondose rangeomorphs including Beothukis, Plumeropriscum, Primocandelabrum, and the arboreomorphs were felled in a single direction, indicating that they were upright in the water column, and were likely felled by the laminar tail of the felling flow. These differences in directionality suggests that an elongate habit, and particularly possession of a stem, lent greater resilience to frondose taxa against turbulent flows, suggesting that such taxa would have had improved survivability in conditions with higher background turbulence than taxa like Bradgatia and Thectardis, which lacked a stem and which had a higher centre of mass, which may have fared better in quieter water conditions.
Modeling the underlying environmental factors of milky sea case and luminous bacteria presence in Java Southern Sea in 2019
Authors: Wibowo Andri
Published: September 2021

The milky sea is one of the unique natural phenomena caused by the presence of luminousVibriobacteria in marine ecosystems. Recently a milky sea has been reported frequently included in the Java Southern Sea. Simultaneously, numerous remote sensing based approaches have been developed to detect the presence of luminous bacteria and the milky sea. Despite this state of the art, the information of detrimental factors of the marine bioluminescence was still limited. Then this research aims to model the underlying environmental factors causing the milky sea and luminous bacteria presence in the Java Southern Sea in 2019. The remote sensing assessment for the period of July 29-August 6, 2019 shows that the magnitude of bioluminescence measured in radiance was having a maximum value of 255 nanoW/cm2/sr and an average of 107 nanoW/cm2/sr/day (95%CI: 71.9 to 142 nanoW/cm2/sr/day). The milky sea size increased and reached its peak with a size of 44,124 km2and then declined. The average milky sea size was 37,942 km2(95% CI: 33,400 to 42,500 km2) and increased with average rate of 16.01% (95%CI: 5.41% to 26.66%). While Akaike Information Criterion (AIC) indicates that the best model to infer the relationship of bacterial bioluminescence with its environmental factors contained Chlorophyll a followed by sea surface temperature factors with AICcvalues of 101.16 (AICweight: 0.50) and 101.95 (AICweight: 0.34). This indicates that low temperature and high plankton cells is the limiting factors of the bacterial bioluminescence.
Vasoactive Intestinal Peptide Amphiphile Micelle Chemical Structure and Hydrophobic Domain Influence Immunomodulatory Potentiation
Authors: Wang Xiaofei , Zhang Rui , Lindaman Bryce D. , Leeper Caitlin N. , Schrum Adam G. , Ulery Bret D.
Published: September 2021

Vasoactive intestinal peptide (VIP) is a neuropeptide capable of downregulating innate immune responses in antigen presenting cells (APCs) by suppressing their pro-inflammatory cytokine secretion and cell surface marker expression. Though VIP’s bioactivity could possibly be leveraged as a treatment for autoimmune disorders and transplant tolerance, drug delivery innovation is required to overcome its intrinsically limited cellular delivery capacity due to its shortin vivolifetime. One option is to employ peptide amphiphiles (PAs) which are lipidated peptides capable of self-assembling into micelles in water that can enhance cellular association. With this approach in mind, a series of triblock VIP amphiphiles (VIPAs) has been synthesized to explore the influence of block arrangement and hydrophobicity on micelle biocompatibility and bioactivity. VIPA formulation has been found to influence the shape, size, and surface charge of VIPA micelles (VIPAMs) as well as their cytotoxicity and immunomodulatory effects. Specifically, the enclosed work provides strong evidence that cylindrical VIPAMs with aspect ratios of 1.5 - 150 and moderate positive surface charge are able to potentiate the bioactivity of VIP limiting TNF-α secretion and MHC II and CD86 surface expression on APCs. With this criteria, we have identified PalmK-(EK)4-VIP as our lead formulation, which showed comparable or enhanced anti-inflammatory effects relative to the unmodified VIP at all dosages evaluated. Additionally, the relationships between peptide block location and lipid block size provide further information on the chemistry-structure-function relationships of peptide amphiphile micelles for the delivery of VIP as well as potentially for other peptides more broadly.
Effectors from a Bacterial Vector-Borne Pathogen Exhibit Diverse Subcellular Localization, Expression Profiles and Manipulation of Plant Defense
Authors: Reyes-Caldas PA , Zhu Jie , Breakspear A , Thapa SP , Toruño TY , Perilla-Henao L , Casteel C , Faulkner C , Coaker G
Published: September 2021

Climate change is predicted to increase the prevalence of vector borne disease due to expansion of insect populations. Candidatus Liberibacter solanacearum (CLso) is a phloem-limited pathogen associated with multiple economically important diseases in Solanaceous crops. Little is known about the strategies and pathogenicity factors CLso uses to colonize vector and host. We determined the CLso effector repertoire by predicting SEC secreted proteins across four different CLso haplotypes, investigated effector localization in planta, and profiled effector expression in vector and host. The localization of CLso effectors in Nicotiana revealed diverse eukaryotic subcellular targets. The majority of tested effectors were unable to suppress plant immune responses, indicating they possess unique activities. Expression profiling in tomato and the psyllid Bactericera cockerelli indicated CLso differentially interacts with its host and vector and can switch effector expression in response to the environment. This study reveals CLso effectors possess complex expression patterns, target diverse host organelles and the majority are unable to suppress host immune responses. A mechanistic understanding of Lso effector function will reveal novel targets and provide insight into phloem biology.
A-Prot: Protein structure modeling using MSA transformer
Authors: Hong Yiyu , Lee Juyong , Ko Junsu
Published: September 2021

In this study, we propose a new protein 3D structure modeling method, A-Prot, using MSA Transformer, one of the state-of-the-art protein language models. For a given MSA, an MSA feature tensor and row attention maps are extracted and converted into 2D residue-residue distance and dihedral angle predictions. We demonstrated that A-Prot predicts long-range contacts better than the existing methods. Additionally, we modeled the 3D structures of the free modeling and hard template-based modeling targets of CASP14. The assessment shows that the A-Prot models are more accurate than most top server groups of CASP14. These results imply that A-Prot captures evolutionary and structural information of proteins accurately with relatively low computational cost. Thus, A-Prot can provide a clue for the development of other protein property prediction methods.
iCn3D: From Web-based 3D Viewer to Structural Analysis Tool in Batch Mode
Authors: Wang Jiyao , Youkharibache Philippe , Marchler-Bauer Aron , Lanczycki Christopher , Zhang Dachuan , Lu Shennan , Madej Thomas , Marchler Gabriele H. , Cheng Tiejun , Chong Li Chuin , Zhao Sarah , Yang Kevin , Lin Jack , Cheng Zhiyu , Dunn Rachel , Malkaram Sridhar Acharya , Tai Chin-Hsien , Enoma David , Busby Ben , Johnson Nicholas L. , Tabaro Francesco , Song Guangfeng , Ge Yuchen
Published: September 2021

iCn3D was initially developed as a web-based 3D molecular viewer. It then evolved from visualization into a full-featured interactive structural analysis software. It became a collaborative research instrument through the sharing of permanent, shortened URLs that encapsulate not only annotated visual molecular scenes, but also all underlying data and analysis scripts in a FAIR manner. More recently, with the growth of structural databases, the need to analyze large structural datasets systematically led us to use Python scripts and convert the code to be used in Node.js scripts. We showed a few examples of Python scripts at https://github.com/ncbi/icn3d/tree/master/icn3dpython to export secondary structures or PNG images from iCn3D. Users just need to replace the URL in the Python scripts to export other annotations from iCn3D. Furthermore, any interactive iCn3D feature can be converted into a Node.js script to be run in batch mode, enabling an interactive analysis performed on one or a handful of protein complexes to be scaled up to analysis features of large ensembles of structures. Currently available Node.js analysis scripts examples are available at https://github.com/ncbi/icn3d/tree/master/icn3dnode. This development will enable ensemble analyses on growing structural databases such as AlphaFold or RoseTTAFold on one hand and Electron Microscopy on the other. In this paper, we also review new features such as DelPhi electrostatic potential, 3D view of mutations, alignment of multiple chains, assembly of multiple structures by realignment, dynamic symmetry calculation, 2D cartoons at different levels, interactive contact maps, and use of iCn3D in Jupyter Notebook as described at https://pypi.org/project/icn3dpy.
Metagenomic identification of viral sequences in laboratory reagents
Authors: Porter Ashleigh F. , Cobbin Joanna , Li Cixiu , Eden John-Sebastian , Holmes Edward C.
Published: September 2021

2.

Metagenomic next-generation sequencing has transformed the discovery and diagnosis of infectious disease, with the power to characterize the complete ‘infectome’ (bacteria, viruses, fungi, parasites) of an individual host organism. However, the identification of novel pathogens has been complicated by widespread microbial contamination in commonly used laboratory reagents. Using total RNA sequencing (“metatranscriptomics”) we documented the presence of contaminant viral sequences in multiple libraries of ‘blank’ negative control sequencing libraries that comprise a sterile water and reagent mix. Accordingly, we identified 14 viral sequences in 7 negative control sequencing libraries. As in previous studies, several circular replication-associated protein encoding (CRESS) DNA virus-like sequences were recovered in the blank libraries, as well as contaminating sequences from the RNA virus families Totiviridae, Tombusviridae and Lentiviridae. These data suggest that the contamination of common laboratory reagents is likely widespread and can comprise a wide variety of viruses.

3.

Data summary

The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

1.5

Repositories

The viral genome sequence data generated in this study has been deposited in the NCBI database under accession numbers MZ824225-MZ824237. Sequence reads are available at the public Sequence Read Archive (SRA) database with accession SRX6803604 and under the BioProject accession PRJNA735051 reference numbers SRR14737466-71 and BioSample numbers SAMN20355437-40.
Novel prokaryotic sensing and regulatory system employing previously unknown nucleic acids-based receptors
Authors: Tetz Victor , Tetz George
Published: September 2021

The present study describes a previously unknown universal signaling and regulatory system, which we named TRB receptor system. This system is responsible for sensing, remembering, and regulating cell responses to various chemical, physical or biological stimuli. It controls cell survival, variability, reproduction, adaptation, genome changes, and gene transfer. Importantly, the TRB-receptor system is responsible for the formation and maintenance of cell memory, as well the ability to “forget” preceding events. The system is composed of DNA- and RNA-based receptors located outside the membrane named “TezRs”, as well as reverse transcriptases and integrases. The sensory and regulatory functions of TezRs enable the TRB-receptor system to control all major aspects of bacterial behavior, such as growth, biofilm formation and dispersal, utilization of nutrients including xenobiotics, virulence, chemo- and magnetoreception, response to external factors (e.g., temperature, UV, light and gas content), mutation events, phage-host interaction and recombination activity. Additionally, it supervises the function of other receptor-mediated signaling pathways. Transcriptome analysis revealed that the loss of different TezRs instigates significant alterations in gene expression.

HIGHLIGHTS

The TRB-receptor system regulates bacterial sensing and response to various stimuli.

The TRB-receptor system is responsible for maintenance and loss of cell memory.

The TRB-receptor system comprises DNA- and RNA-based “TezRs” receptors.

The TRB-receptor system relies on reverse transcriptases and recombinases.

The TRB-receptor system oversees other receptor-mediated signaling pathways.

TezRs are implicated in cell mutation and recombination events.
Engineering of human mini-bones for the standardized modeling of healthy hematopoiesis, leukemia and solid tumor metastasis
Authors: Grigoryan Ani , Zacharaki Dimitra , Balhuizen Alexander , Côme Christophe RM , Frank Anne-Katrine , Garcia Garcia Alejandro , Aaltonen Kristina , Mañas Adriana , Esfandyari Javanshir , Kalantari Nasim , Kjellman Pontus , Prithiviraj Sujeethkumar , Englund Emelie , Madsen Chris D , Porse Bo , Bexell Daniel , Bourgine Paul E
Published: September 2021

The bone marrow microenvironment provides indispensable factors to sustain blood production throughout life. It is also a hotspot for the progression of hematologic disorders and the most frequent site of solid tumor metastasis. Pre-clinical research relies on xenograft mouse models, precluding the human-specific functional interactions of stem cells with their bone marrow microenvironment. Human mesenchymal cells can be exploited for the in vivo engineering of humanized ossicles (hOss). Those mini-bones provide a human niche conferring engraftment of human healthy and malignant blood samples, yet suffering from major reproducibility issue. Here, we report the standardized generation of hOss by developmental priming of a custom-designed human mesenchymal cell line. We demonstrate superior engraftment of cord blood hematopoietic cells and primary acute myeloid leukemia samples, but also validate our hOss as metastatic site for breast cancer cells. Finally, we report the first engraftment of neuroblastoma patient-derived xenograft cells in a humanized model, recapitulating clinically reported osteolytic lesions. Collectively, our hOss constitute a powerful standardized and malleable platform to model normal hematopoiesis, leukemia and solid tumor metastasis.
Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2
Authors: Kistler Kathryn E. , Huddleston John , Bedford Trevor
Published: September 2021

Given the importance of variant SARS-CoV-2 viruses with altered receptor-binding or antigenic phenotypes, we sought to quantify the degree to which adaptive evolution is driving accumulation of mutations in the SARS-CoV-2 genome. Here we assessed adaptive evolution across genes in the SARS-CoV-2 genome by correlating clade growth with mutation accumulation as well as by comparing rates of nonsynonymous to synonymous divergence, clustering of mutations across the SARS-CoV-2 phylogeny and degree of convergent evolution of individual mutations. We find that spike S1 is the focus of adaptive evolution, but also identify positively-selected mutations in other genes that are sculpting the evolutionary trajectory of SARS-CoV-2. Adaptive changes in S1 accumulated rapidly, resulting in a remarkably high ratio of nonsynonymous to synonymous divergence that is 2.5X greater than that observed in HA1 at the beginning of the 2009 H1N1 pandemic.
Cold shock induces a terminal investment reproductive response in C. elegans
Authors: Gulyas Leah , Powell Jennifer R.
Published: September 2021

Challenges from environmental stressors have a profound impact on many life-history traits of an organism, including reproductive strategy. Examples across multiple taxa have demonstrated that maternal reproductive investment resulting from stress can improve offspring survival; a form of matricidal provisioning when death appears imminent is known as terminal investment. Here we report a reproductive response in the nematode Caenorhabditis elegans upon exposure to acute cold shock at 2°C, whereby vitellogenic lipid movement from the soma to the germline appears to be massively upregulated at the expense of parental survival. This response is dependent on functional TAX-2;TAX-4 cGMP-gated channels that are part of canonical thermosensory mechanisms in worms and can be prevented in the presence of activated SKN-1/Nrf2, the master stress regulator. Increased maternal provisioning promotes improved embryonic cold shock survival, which is notably suppressed in animals with impaired vitellogenesis. These findings suggest that cold shock in C. elegans triggers terminal investment to promote progeny fitness at the expense of parental survival and may serve as a tractable model for future studies of stress-induced progeny plasticity.
Mitochondrial ATP production is required for endothelial cell control of vascular tone
Authors: Wilson Calum , Lee Matthew D. , Buckley Charlotte , Zhang Xun , McCarron John G.
Published: September 2021

Arteries and veins are lined by non-proliferating endothelial cells that play a critical role in regulating blood flow. Endothelial cells also regulate tissue perfusion, metabolite exchange, and thrombosis. It is thought that endothelial cells rely on ATP generated via glycolysis to fuel each of these energy-demanding processes. However, endothelial metabolism has mainly been studied in the context of proliferative cells in angiogenesis, and little is known about energy production in endothelial cells within the fully-formed vascular wall. Using intact arteries isolated from rats and mice, we show that inhibiting mitochondrial oxidative phosphorylation disrupts endothelial control of vascular tone. The role for endothelial cell energy production is independent of species, sex, or vascular bed. Basal, mechanically-activated, and agonist-evoked calcium activity in intact artery endothelial cells are each prevented by inhibiting mitochondrial ATP synthesis. This effect is mimicked by blocking the transport of pyruvate, the master fuel for mitochondrial energy production, through the mitochondrial pyruvate carrier. These data show that mitochondrial ATP is necessary for calcium-dependent, nitric oxide mediated endothelial control of vascular tone, and identifies the critical role of endothelial mitochondrial energy production in fueling perfused blood vessel function.
Co-variation of viral recombination with single nucleotide variants during virus evolution revealed by CoVaMa
Authors: Wang Shiyi , Sotcheff Stephanea L. , Gallardo Christian M. , Jaworski Elizabeth , Torbett Bruce E. , Routh Andrew L.
Published: September 2021

Adaptation of viruses to their environments occurs through the acquisition of both novel Single-Nucleotide Variants (SNV) and recombination events including insertions, deletions, and duplications. The co-occurrence of SNVs in individual viral genomes during their evolution has been well-described. However, unlike covariation of SNVs, studying the correlation between recombination events with each other or with SNVs has been hampered by their inherent genetic complexity and a lack of bioinformatic tools. Here, we expanded our previously reported CoVaMa pipeline (v0.1) to measure linkage disequilibrium between recombination events and SNVs within both short-read and long-read sequencing datasets. We demonstrate this approach using long-read nanopore sequencing data acquired from Flock House virus (FHV) serially passaged in vitro. We found SNVs that were either correlated or anti-correlated with large genomic deletions generated by nonhomologous recombination that give rise to Defective-RNAs. We also analyzed NGS data from longitudinal HIV samples derived from a patient undergoing antiretroviral therapy who proceeded to virological failure. We found correlations between insertions in the p6Gag and mutations in Gag cleavage sites. This report confirms previous findings and provides insights on novel associations between SNVs and specific recombination events within the viral genome and their role in viral evolution.
COVID-19 vaccine effectiveness against hospitalizations and ICU admissions in the Netherlands, April- August 2021
Authors: de Gier Brechje , Kooijman Marjolein , Kemmeren Jeanet , de Keizer Nicolette , Dongelmans Dave , van Iersel Senna C.J.L. , van de Kassteele Jan , Andeweg Stijn P. ,   the RIVM COVID-19 epidemiology and surveillance team, de Melker Hester E. , Hahné Susan J. M. , Knol Mirjam J. , van den Hof Susan
Published: September 2021

The objective of this study was to estimate vaccine effectiveness (VE) against COVID-19 hospitalization and ICU admission, per period according to dominating SARS-CoV-2 variant (Alpha and Delta), per vaccine and per time since vaccination. To this end, data from the national COVID-19 vaccination register was added to the national register of COVID-19 hospitalizations. For the study period 4 April – 29 August 2021, 15,571 hospitalized people with COVID-19 were included in the analysis, of whom 887 (5.7%) were fully vaccinated. Incidence rates of hospitalizations and ICU admissions per age group and vaccination status were calculated, and VE was estimated as 1-incidence rate ratio, adjusted for calendar date and age group in a negative binomial regression model. VE against hospitalization for full vaccination was 94% (95%CI 93-95%) in the Alpha period and 95% (95%CI 94-95%) in the Delta period. The VE for full vaccination against ICU admission was 93% (95%CI 87-96%) in the Alpha period and 97% (95%CI 97-98%) in the Delta period. VE was high in all age groups and did not show waning with time since vaccination up to 20 weeks after full vaccination.
Uterus-specific transcriptional regulation underlies eggshell pigment production in Japanese quail
Authors: Ishishita Satoshi , Kitahara Shumpei , Takahashi Mayuko , Iwasaki Sakura , Tatsumoto Shoji , Hara Izumi , Kaneko Yoshiki , Kinoshita Keiji , Yamaguchi Katsushi , Harada Akihito , Ohmori Yasushige , Ohkawa Yasuyuki , Go Yasuhiro , Shigenobu Shuji , Matsuda Yoichi , Suzuki Takayuki
Published: September 2021

The precursor of heme, protoporphyrin IX (PPIX), accumulates abundantly in the uterus of birds, such as Japanese quail, Coturnix japonica, resulting in brown-speckled eggshells. The molecular basis of PPIX production in the uterus remains largely unknown. Here, we investigated the cause of low PPIX production in a classical Japanese quail mutant exhibiting white eggshells by comparing its gene expression in the uterus with that of the wild type using transcriptome analysis and performed genetic linkage mapping to identify the causative genomic region of the white eggshell phenotype. We showed that 11 genes, including the 5-aminolevulinic acid synthase 1 (ALAS1) and ferroxidase hephaestin-like 1 (HEPHL1) genes, were specifically upregulated in the wild-type uterus and downregulated in the mutant. We mapped the 172 kb candidate genomic region on chromosome 6, which contains several genes, including a part of the paired-like homeodomain 3 (PITX3), which encodes a transcription factor. ALAS1, HEPHL1, and PITX3 were expressed in the apical cells of the luminal epithelium and lamina propria cells of the uterine mucosa of the wild-type quail, and their expression was downregulated in these cells of the mutant quail. Biochemical analysis using uterine homogenates indicated that the restricted availability of 5-aminolevulinic acid is the main cause of low PPIX production. These results suggest that uterus-specific transcriptional regulation of heme-biosynthesis-related genes is an evolutionarily acquired mechanism of eggshell pigment production in Japanese quail.
Genome-wide identification of genes important for growth of Dickeya dadantii and D. dianthicola in potato (Solanum tuberosum) tubers
Authors: Helmann Tyler C. , Filiatrault Melanie J. , Stodghill Paul V.
Published: September 2021

Dickeya species are causal agents of soft rot diseases in many economically important crops, including soft rot disease of potato (Solanum tuberosum). Using random barcode transposon-site sequencing (RB-TnSeq), we generated genome-wide mutant fitness profiles of Dickeya dadantii 3937, Dickeya dianthicola ME23, and Dickeya dianthicola 67-19 isolates collected after passage through several in vitro and in vivo conditions. Tubers from the potato cultivars “Atlantic”, “Dark Red Norland”, and “Upstate Abundance” provided highly similar conditions for bacterial growth. Using the homolog detection software PyParanoid, we matched fitness values for orthologous genes in the three bacterial strains. Direct comparison of fitness among the strains highlighted shared and variable traits important for growth. Bacterial growth in minimal medium required many metabolic traits that were also essential for competitive growth in planta, such as amino acid, carbohydrate, and nucleotide biosynthesis. Growth in tubers specifically required the pectin degradation gene kduD. Disruption in three putative DNA-binding proteins had strain-specific effects on competitive fitness in tubers. Though the Soft Rot Pectobacteriaceae can cause disease with little host specificity, it remains to be seen the extent to which strain-level variation impacts virulence.
Regulating expression of mistranslating tRNAs by readthrough RNA polymerase II transcription
Authors: Berg Matthew D. , Isaacson Joshua R. , Cozma Ecaterina , Genereaux Julie , Lajoie Patrick , Villén Judit , Brandl Christopher J.
Published: September 2021

Transfer RNA (tRNA) variants that alter the genetic code increase protein diversity and have many applications in synthetic biology. Since the tRNA variants can cause a loss of proteostasis, regulating their expression is necessary to achieve high levels of novel protein. Mechanisms to positively regulate transcription with exogenous activator proteins like those often used to regulate RNA polymerase II (RNAP II) transcribed genes are not applicable to tRNAs as their expression by RNA polymerase III requires elements internal to the tRNA. Here, we show that tRNA expression is repressed by overlapping transcription from an adjacent RNAP II promoter. Regulating the expression of the RNAP II promoter allows inverse regulation of the tRNA. Placing either Gal4 or TetR-VP16 activated promoters downstream of a mistranslating tRNASer variant that mis-incorporates serine at proline codons in Saccharomyces cerevisiae allows mistranslation at a level not otherwise possible because of the toxicity of the unregulated tRNA. Using this inducible tRNA system, we explore the proteotoxic effects of mistranslation on yeast cells. High levels of mistranslation cause cells to arrest in G1 phase. These cells are impermeable to propidium iodide, yet growth is not restored upon repressing tRNA expression. High levels of mistranslation increase cell size and alter cell morphology. This regulatable tRNA expression system can be applied to study how native tRNAs and tRNA variants affect the proteome and other biological processes. Variations of this inducible tRNA system should be applicable to other eukaryotic cell types.
FGF21-FGFR4 signaling in cardiac myocytes promotes concentric cardiac hypertrophy in mouse models of diabetes
Authors: Yanucil Christopher , Kentrup Dominik , Li Xueyi , Grabner Alexander , Schramm Karla , Martinez Eliana C. , Li Jinliang , Campos Isaac , Czaya Brian , Heitman Kylie , Westbrook David , Wende Adam , Sloan Alexis , Roche Johanna M. , Fornoni Alessia , Kapiloff Michael S. , Faul Christian
Published: September 2021

Fibroblast growth factor (FGF) 21, a hormone that increases insulin sensitivity, has shown promise as a therapeutic agent to improve metabolic dysregulation. Here we report that FGF21 directly targets cardiac myocytes by binding β-klotho and FGF receptor (FGFR) 4. In combination with high glucose, FGF21 induces cardiac myocyte growth in width mediated by extracellular signal-regulated kinase 1/2 (ERK1/2) signaling. While short-term FGF21 elevation can be cardio-protective, we find that in type 2 diabetes (T2D) in mice, where serum FGF21 levels are elevated, FGFR4 activation induces concentric cardiac hypertrophy. As T2D patients are at risk for heart failure with preserved ejection fraction (HFpEF), we propose that induction of concentric hypertrophy by elevated FGF21-FGFR4 signaling constitutes a novel mechanism promoting T2D-associated HFpEF and that FGFR4 blockade might serve as a cardio-protective therapy in T2D. In addition, potential adverse cardiac effects of FGF21 mimetics currently in clinical trials should be investigated.
Unlabeled salivary gland organoids have distinct Raman signatures following FGF2-induced proacinar cell differentiation
Authors: Tubbesing Kate , Moskwa Nicholas , Khoo Ting Chean , Nelson Deirdre A. , Sharikova Anna , Larsen Melinda , Khmaladze Alexander
Published: September 2021

Organoids are self-organized three-dimensional (3D) tissue cultures that model the structure and function of organs to provide insights into signaling during organ formation and have translational applications in disease modeling and assessing drug responses. Due to their heterogeneity, there is a need for non-destructive methods to identify the differentiation state, or the phenotype, of organoids. As organoids often contain complex mixtures of basement membrane and/or extracellular matrix proteins, which are often highly auto-fluorescent, it typically makes low-resolution Raman measurements a challenge. We developed Raman confocal micro-spectroscopy methods to avoid and minimize the matrix signal and define specific Raman signatures for growth factor-differentiated and non-differentiated organoids. In complex, branched salivary gland organoids derived from mouse embryonic epithelial and stromal cells embedded within the laminin-rich basement membrane matrix, Matrigel, we identified specific Raman spectral signatures for organoids in different differentiation states. We report that either comparison of spectral signatures or multivariate SVD analysis can be used to distinguish between organoids treated with FGF2, organoids treated with EGF, and non-treated controls. Raman spectral signatures can be used to non-invasively distinguish between different phenotypes in the 3D context of unlabeled organoids.

Highlights

FGF2-dependent proacinar cell differentiation in salivary organoids have unique Raman signatures detected with a novel confocal-based Raman imaging approach.

These signatures can be used in unlabeled salivary organoids to monitor proacinar cell differentiation.

Confocal-based Raman imaging may be applicable to monitoring differentiation state of other types of organoids.
Structural transitions permitting ligand entry and exit in bacterial fatty acid binding proteins
Authors: Gullett Jessica M. , Cuypers Maxime G. , Grace Christy R. , Pant Shashank , Subramanian Chitra , Tajkhorshid Emad , Rock Charles O. , White Stephen W.
Published: September 2021

Fatty acid (FA) transfer proteins extract FA from membranes and sequester their ligand to facilitate its movement through the cytosol. While detailed views of soluble protein-FA complexes are available, how FA exchange occurs at the membrane has remained unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we determine the conformational change from this closed state to an open state that engages the phospholipid bilayer. Upon membrane binding, a dynamic loop in FakB1 that covers the FA binding site disengages and folds into an amphipathic helix. This helix inserts below the phosphate plane of the bilayer to create a diffusion channel for the FA to exchange between the protein and the membrane. The structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a general conceptual framework for how these proteins interact with the membrane to promote lipid transfer.
X-ray crystal structure of [L
2Ag3]+[OTf]−·5C6D6: a monoanionic bisphosphinimine ligand supported trisilver complex
Authors: Drescher Sam L. , Forfar Christopher P. , Boeré René T. , Hayes Paul G.
Published: September 2021

The compound bis{μ3-2,5-bis[N-(4-isopropylphenyl)-P,P-diphenylphosphorimidoyl]pyrrol-1-ido-κ3
N:N′:N′′}trisilver(I) trifluoromethanesulfonate deuterated benzene pentasolvate, [Ag3(C46H44N3P2)2](CF3O3S)·5C6D6, (I), was synthesized from two equivalents of NaL [L = 2,5-(4-
i
PrC6H4N=PPh2)C4H2N] and three equivalents of AgOTf (OTf = OSO2CF3). High-quality crystals of (I) formed with five deuterated benzene solvent molecules in the asymmetric unit. Notably, the bond lengths and angles between the three silver atoms are markedly different, unlike in most other reported trisilver complexes that tend to form three equivalent metal centers. Additionally, to the best of our knowledge, this is the first report of a trisilver complex with six nitrogen donors from two bisphosphinimine ligands.
“I thought I was prepared to do this”: an exploration of the learning and development of leadership coaches
Authors: Huggins Kristin Shawn , Klar Hans W. , Andreoli Parker M.
Published: September 2021

Purpose

The purpose of this paper was to determine what experienced school leaders learned through participating in a three-year leadership initiative, called the Leadership Learning Community (LLC), that helped them coach less experienced leaders to lead school improvement efforts.

Design/methodology/approach

Data were collected and analyzed using a qualitative design throughout the three-year initiative.

Findings

The findings indicate the LLC leadership coaches learned to accept and navigate the leaders' developmental and contextual needs, practiced and honed their coaching skills and recognized their own developmental needs.

Originality/value

These findings address the paucity of research on leadership coach learning and development.
Brand positioning and business performance of alcoholic beverage firms in an emerging market context: the mediation effect of brand equity
Authors: Ameyibor Leeford Edem Kojo , Anabila Peter , Saini Yvonne Kabeya
Published: September 2021

Purpose

This study aims to investigate the relationship between brand positioning and business performance, as well as the mediation effect of brand equity between them within the context of Ghana’s alcoholic beverages industry.

Design/methodology/approach

A sample of 196 staff across four alcoholic beverage firms in Accra, Ghana was selected using a judgemental sampling technique. A structural equation modelling approach using partial least squares was used to conduct the analyses to answer the research hypotheses.

Findings

All the hypotheses were confirmed in line with extant literature. Specifically, the study found a positive relationship between brand positioning and business performance. The study also found that brand equity partially mediates the relationship between brand positioning and business performance.

Practical implications

The study serves as a useful guide to strategy and policy formulation in branding in general and specifically on how brand positioning can be effectively deployed as a key strategy to enhance business performance.

Originality/value

The study has practical implications not only for the marketing and sale of alcoholic beverages in Ghana to achieve financial performance but also for lasting competitive advantage.
A novel tracking system for human following robots with fusion of MMW radar and monocular vision
Authors: Zhu Yipeng , Wang Tao , Zhu Shiqiang
Published: September 2021

Purpose

This paper aims to develop a robust person tracking method for human following robots. The tracking system adopts the multimodal fusion results of millimeter wave (MMW) radars and monocular cameras for perception. A prototype of human following robot is developed and evaluated by using the proposed tracking system.

Design/methodology/approach

Limited by angular resolution, point clouds from MMW radars are too sparse to form features for human detection. Monocular cameras can provide semantic information for objects in view, but cannot provide spatial locations. Considering the complementarity of the two sensors, a sensor fusion algorithm based on multimodal data combination is proposed to identify and localize the target person under challenging conditions. In addition, a closed-loop controller is designed for the robot to follow the target person with expected distance.

Findings

A series of experiments under different circumstances are carried out to validate the fusion-based tracking method. Experimental results show that the average tracking errors are around 0.1 m. It is also found that the robot can handle different situations and overcome short-term interference, continually track and follow the target person.

Originality/value

This paper proposed a robust tracking system with the fusion of MMW radars and cameras. Interference such as occlusion and overlapping are well handled with the help of the velocity information from the radars. Compared to other state-of-the-art plans, the sensor fusion method is cost-effective and requires no additional tags with people. Its stable performance shows good application prospects in human following robots.
Considering visual cueing and practice type for software training’s optimisation: a study of domain experts
Authors: Ragazou Vasiliki , Karasavvidis Ilias
Published: September 2021

Purpose

Software training is a new trend in software applications. A key problem with software training is that video tutorials are developed without considering the target audience. Although video tutorials are popular, little attention is given to their design features. This study aims to investigate how two multimedia research principles, visual cueing (VC) and practice type, influence task performance, mental effort and motivation.

Design/methodology/approach

Three video tutorials on non-linear editing were viewed by 118 Computer Science undergraduate students with high information communication technology experience. To analyse the relationships between the research variables, a 2 (non-VC versus VC) × 2 (post-video viewing practice versus stepwise viewing-based practice (SVBP) mixed factorial design was used.

Findings

The results indicated that neither VC nor SVBP influenced task performance; however, both practice type conditions led to higher levels of motivation.

Research limitations/implications

The incorporation of VC and practice type in complex software training is less likely to be beneficial for domain experts. Future studies should record eye tracking data to capture learners’ behaviours whilst learning a software application. Moreover, practice targeted with immediate feedback should be incorporated as it enhances scaffolding.

Practical implications

Neither practice type was considered effective by experts. A practice strategy with user-controlled pausing (i.e. markers) could enhance retention by allowing users to practice tasks after locating the most relevant parts of the video tutorial.

Originality/value

This study contributes to the literature by investigating two guidelines: VC and practice type in the context of complex software training targeting domain experts.
Determinants of project management success: view from an emerging economy
Authors: Fauzi Muhammad Ashraf , Anuar Khairul Firdaus , Rahman Rahimi A. , Jupir Jamaludin , Sapuan Noraina Mazuin
Published: September 2021

Purpose

Achieving project success is the goal of every project. Due to various project requirements, some of the key determinants of project success cannot be met. The purpose of this paper is to understand relying factors that can lead to a successful project that includes project management maturity, decision-making, coordination and knowledge management.

Design/methodology/approach

A self-administered survey was distributed to 231 project managers in the Malaysian project management community. Analysis using partial least square structural equation modelling was applied in testing the proposed relationship between these latent variables.

Findings

Finding shows that all the hypotheses were supported and significant. The most impactful factor is project management maturity, followed by knowledge management.

Practical implications

Implication to the project management industry includes providing autonomy to individuals involved in their expertise and management of efficient cross-functional teams between teams in the project. A systematic knowledge management system through a central repository would contribute to the efficient and flexible distribution of knowledge throughout the project process.

Originality/value

This study is one of the few studies focussing on determinants of project success in Malaysia.
A systematic review on the internationalization of Chinese SMEs: thematic expansion, new impulses and potential avenues for future research
Authors: Hänle Fabian , Cambré Bart , Weil Stefanie
Published: September 2021

Purpose

Supplementing an earlier review paper on the internationalization of Chinese small- and medium-sized enterprises (SMEs) (ICS) that covers the period 1991–2012, the purpose of this paper is to examine how research on this topic has thematically expanded in recent years. Specifically, the authors aim to examine the literature between 2013 and 2020, highlight advancements and synthesize potential avenues for future research.

Design/methodology/approach

Based on the systematic literature review method (Denyer and Tranfield, 2009; Kraus et al., 2020), the authors considered more than 5,700 peer-reviewed journal articles, of which 107 were included in the narrative synthesis.

Findings

Research on the ICS has become more widespread and mature in the period since 2013. First, there are more papers investigating firm-level characteristics and sources of internal capabilities. Second, the state of knowledge regarding social networks and institutional contexts in the internationalization process has increased. Consequently, new knowledge exists regarding push and pull patterns and the role China’s institutional environment is playing. Third, growing interest can be noted in studying entrepreneurship in the context of Chinese SMEs’ global expansion. Additionally, the paper exposes promising areas for future research and suggests more than 20 potential research questions.

Originality/value

This review in the growing debate on the ICS is the first of its kind that consciously drives the work of a previous review study forward. This enables tracking the progress of research (“mapping of the field”) and identifying important avenues for future research that can further advance the debate. The comprehensive review also discovered one relatively new variable – the role of Chinese returnee entrepreneurs – which shows the significant influence on SME internationalization and attracts growing scholarly attention.