Ontology Categories Research Articles

Genomic insights into evolution and control of Wohlfahrtia magnifica, a widely distributed myiasis-causing fly of warm-blooded vertebrates.

Wohlfahrtia magnifica is a pest fly species, invading livestock in many European, African and Asian countries, and causing heavy agroeconomic losses. In the life cycle of this obligatory parasite, adult flies infect the host by depositing the first‐stage larvae into body cavities or open wounds. The feeding larvae cause severe (skin) tissue damage and potentially fatal infections if untreated. Despite serious health detriments and agroeconomic concerns, genomic resources for understanding the biology of W. magnifica have so far been lacking. Here, we present a complete genome assembly from a single adult female W. magnifica using a Low‐DNA Input workflow for PacBio HiFi library preparation. The de novo assembled genome is 753.99 Mb in length, with a scaffold N50 of 5.00 Mb, consisting of 16,718 predicted protein‐encoding genes. Comparative genomic analysis revealed that W. magnifica has the closest phylogenetic relationship to Sarcophaga bullata followed by Lucilia cuprina. Evolutionary analysis of gene families showed expansions of 173 gene families in W. magnifica that were enriched for gene ontology (GO) categories related to immunity, insecticide‐resistance mechanisms, heat stress response and cuticle development. In addition, 45 positively selected genes displaying various functions were identified. This new genomic resource contributes to the evolutionary and comparative analysis of dipterous flies and an in‐depth understanding of many aspects of W. magnifica biology. Furthermore, it will facilitate the development of novel tools for controlling W. magnifica infection in livestock.

Architecture in the mind

Pinpointing the precise nature of the relation that a viewer has to an artwork s/he is appreciating is not an easy question. Understanding exactly what is the nature of our relationship to a specific art, such as architecture, is even less obvious. To tackle this intricate issue, there will be a common thread, which is the work of Constantine Cavafy, a Greek poet whose life and poetry were closely tied to his beloved city: Alexandria. Through his work, we will aim to grasp better the nature of this particular relationship one can have to one's own city: what such a relation consists of and what its properties are. A main hypothesis put forth is that the relationship between the viewer–citizen and their own city is imposed and inescapable and, as such, the architecture of one’s city, is not only outside us—“in the city”—but also within us— “in our mind.” To make this claim more precise, we will examine some metaphysical properties of the city, as an ontological category, and in particular, its relation to time.

A Decade's Experience in Pediatric Chromosomal Microarray Reveals Distinct Characteristics Across Ordering Specialties

Chromosomal microarray (CMA) is a testing modality frequently used in pediatric patients; however, published data on its utilization are limited to the genetic setting. We performed a database search for all CMA testing performed from 2010 to 2020, and delineated the diagnostic yield based on patient characteristics, including sex, age, clinical specialty of providers, indication of testing, and pathogenic finding. The indications for testing were further categorized into Human Phenotype Ontology categories for analysis. This study included a cohort of 14,541 patients from 29 different medical specialties, of whom 30% were from the genetics clinic. The clinical indications for testing suggested that neonatology patients demonstrated the greatest involvement of multiorgan systems, involving the most Human Phenotype Ontology categories, compared with developmental behavioral pediatrics and neurology patients being the least. The top pathogenic findings for each specialty differed, likely due to the varying clinical features and indications for testing. Deletions involving the 22q11.21 locus were the top pathogenic findings for patients presenting to genetics, neonatology, cardiology, and surgery. Our data represent the largest pediatric cohort published to date. This study is the first to demonstrate the diagnostic utility of this assay for patients seen in the setting of different specialties, and it provides normative data of CMA results among a general pediatric population referred for testing because of variable clinical presentations.

A method to produce metadata describing and assessing the quality of spatial landmark datasets in mountain area

Abstract. The increase of recreational activities in the mountains and a growing amount of websites proposing geographic data, offer new opportunities for societal needs such as mountain rescue, biodiversity monitoring, outdoor activities. However, the main issue with the websites data is the lack of metadata that minimizes its reuse outside the community that produced the data. The goal of this paper is to study and generate quality and descriptive metadata using ISO standards. To this end, we propose a method based on a common vocabulary such as an ontology and a data matching process. The first one allows to associate to each type of feature from an available geographic dataset an ontology class that will facilitate data matching, reproducibility of results and minimize semantic heterogeneity. The second one allows to define matching links between features representing the same entity in the real world and compute quality indicators based on the validated links. Finally, at the end of this process, we are able to generate descriptive and quality metadata. By following ISO standards and using the QualityML dictionary for measures, the metadata is serialized to XML and can finally be published as open source. Our approach was applied to five different landmark datasets in the French Alps region. New insights were acquired regarding positional accuracy and semantic granularity.

Multi-Omics Approaches Unravel Specific Features of Embryo and Endosperm in Rice Seed Germination.

Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive “multi-omics” analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination.

Advanced content-based retrieval for digital correspondence documents with ontology classification

The growth of digital correspondence documents with various types, different naming rules, and no sufficient search system complicates the search process with certain content, especially if there are unclassified documents, the search becomes inaccurate and takes a long time. This research proposed archiving method with automatic hierarchical classification and the content-based search method which displays ontology classification information as the solution to the content-based search problems. The method consists of preprocessing (creation of automatic hierarchical classification model using a combination of convolutional neural network (CNN) and regular expression method), archiving (document archiving with automatic classification), and retrieval (content-based search by displaying ontology relationships from the document classification). The archiving of 100 documents using the automatic hierarchical classification was found to be 79% accurate as indicated by the 99% accuracy for CNN and 80% for Regex. Moreover, the search results for classified content-based documents through the display of ontology relationships were discovered to be 100% accurate. This research succeeded in improving the quality of search results for digital correspondence documents as indicated by its higher specificity, accuracy, and speed compared to conventional methods based on file names, annotations, and unclassified content.

Novelty Knows No Boundaries: Why a Proper Investigation of Novelty Effects Within SHRI Should Begin by Addressing the Scientific Plurality of the Field.

Research on psychological novelty effects within the fields of Social Robotics and Human-Robot Interaction (together: SHRI) so far has failed to gather the momentum it deserves. With the aid of exemplary descriptions of how psychological novelty is currently approached and researched across (certain main regions of) the larger scientific landscape, I argue that the treatment of novelty effects within the multidisciplinary SHRI reflects larger circumstances of fragmentation and heterogeneity in novelty research in general. I further propose that while the concept of novelty may currently function as a Boundary Object between the contributing domains of SHRI, a properly integrated, interdisciplinary concept of novelty is needed in order to capture and investigate the scope and scale of novelty effects within research on social human-robot interaction. Building on research on the New Ontological Category Hypothesis and related studies, I argue that the novelty of social robots can be understood as radical to the extent that their comprehension requires revisions of traditional core categories of being. In order to investigate the sui generis effects of such novelty, which should not be narrowly understood as mere “noise” in the data, it is paramount that the field of SHRI begin by working out a shared, integrative framework of psychological novelty and novelty effects.

Genome-Wide Identification, Classification, Expression and Duplication Analysis of bZIP Family Genes in Juglans regia L.

Basic leucine zipper (bZIP), a conserved transcription factor widely found in eukaryotes, has important regulatory roles in plant growth. To understand the information related to the bZIP gene family in walnut, 88 JrbZIP genes were identified at the genome-wide level and classified into 13 subfamilies (A, B, C, D, E, F, G, H, I, J, K, M, and S) using a bioinformatic approach. The number of exons in JrbZIPs ranged from 1 to 12, the number of amino acids in JrbZIP proteins ranged from 145 to 783, and the isoelectric point ranged from 4.85 to 10.05. The majority of JrbZIP genes were localized in the nucleus. The promoter prediction results indicated that the walnut bZIP gene contains a large number of light-responsive and jasmonate-responsive action elements. The 88 JrbZIP genes were involved in DNA binding and nucleus and RNA biosynthetic processes of three ontological categories, molecular functions, cellular components and biological processes. The codon preference analysis showed that the bZIP gene family has a stronger bias for AGA, AGG, UUG, GCU, GUU, and UCU than other codons. Moreover, the transcriptomic data showed that JrbZIP genes might play an important role in floral bud differentiation. The results of a protein interaction network map and kegg enrichment analysis indicated that bZIP genes were mainly involved in phytohormone signaling, anthocyanin synthesis and flowering regulation. qRT-PCR demonstrated the role of the bZIP gene family in floral bud differentiation. Co-expression network maps were constructed for 29 walnut bZIP genes and 6 flowering genes, and JrCO (a homolog of AtCO) was significantly correlated (p < 0.05) with 13 JrbZIP genes in the level of floral bud differentiation expression, including JrbZIP31 (homolog of AtFD), and JrLFY was significantly and positively correlated with JrbZIP10,11,51,59,67 (p < 0.05), and the above results suggest that bZIP family genes may act together with flowering genes to regulate flower bud differentiation in walnut. This study was the first genome-wide report of the walnut bZIP gene family, which could improve our understanding of walnut bZIP proteins and provide a solid foundation for future cloning and functional analyses of this gene family.

Forty years of metonymy

Abstract This study contributes to the existing body of research that aims at showing the impact of metonymy in grammar. In this case, new evidence will be provided by exploring the English pseudo-partitive construction of time measurement, illustrated by ten years of marriage. By using corpus data, it will be shown that metonymy is at work in many instantiations of this construction. The second noun in these expressions should prima facie be semantically eligible for time measurement, that is, a temporal entity or a second-order entity. However, this is not the only type of noun that appears in the second noun slot, which can also be occupied by first and third-order entities as well as places. The presence of an expression of time-measurement in the first part of the construction coerces different ontological categories into a second-order reading and can be regarded as a guide for the correct interpretation when the second noun includes several facets, illustrating the cognitive process of cueing.

RNA-Seq of amniotic fluid cell-free RNA: a discovery phase study of the pathophysiology of congenital cytomegalovirus infection

Congenital cytomegalovirus infection is the most common perinatal infection and a significant cause of sensorineural hearing loss, cerebral palsy, and neurodevelopmental disability. There is a paucity of human gene expression studies examining the pathophysiology of cytomegalovirus infection. This study aimed to perform a whole transcriptomic assessment of amniotic fluid from pregnancies with live fetuses to identify differentially expressed genes and enriched Gene Ontology categories associated with congenital cytomegalovirus infection. Amniotic fluid supernatant was prospectively collected from pregnant women undergoing amniocentesis for suspected congenital cytomegalovirus infection because of first-trimester maternal primary infection or ultrasound features suggestive of fetal infection. Women who had received therapy to prevent fetal infection were excluded. Congenital cytomegalovirus infection was diagnosed via viral polymerase chain reaction of amniotic fluid; cytomegalovirus-infected fetuses were paired with noninfected controls, matched for gestational age and fetal sex. Paired-end RNA sequencing was performed on amniotic fluid cell-free RNA with the Novaseq 6000 at a depth of 30 million reads per sample. Following quality control and filtering, reads were mapped to the human genome and counts summarized across genes. Differentially expressed genes were identified using 2 approaches: voomWithQualityWeights in conjunction with limma and RUVSeq with edgeR. Genes with a false discovery rate <0.05 were considered statistically significant. Differential exon use was analyzed using DEXSeq. Functional analysis was performed using gene set enrichment analysis and Ingenuity Pathway Analysis. Manual curation of differentially regulated genes was also performed. Amniotic fluid samples were collected from 50 women; 16 (32%) had congenital cytomegalovirus infection confirmed by polymerase chain reaction. After excluding 3 samples without matched controls, 13 cytomegalovirus-infected samples collected at 18 to 23 weeks and 13 cytomegalovirus-negative gestation-matched controls were submitted for RNA sequencing and analysis (N=26). Ten of the 13 pregnancies with cytomegalovirus-infected fetuses had amniocentesis because of serologic evidence of maternal primary infection with normal fetal ultrasound, and 3 had amniocentesis because of ultrasound abnormality suggestive of cytomegalovirus infection. Four cytomegalovirus-infected pregnancies ended in termination (n=3) or fetal death (n=1), and 9 resulted in live births. Pregnancy outcomes were available for 11 of the 13 cytomegalovirus-negative controls; all resulted in live births of clinically-well infants. Differential gene expression analysis revealed 309 up-regulated and 32 down-regulated genes in the cytomegalovirus-infected group compared with the cytomegalovirus-negative group. Gene set enrichment analysis showed significant enrichment of multiple Gene Ontology categories involving the innate immune response to viral infection and interferon signaling. Of the 32 significantly down-regulated genes, 8 were known to be involved in neurodevelopment and preferentially expressed by the brain. Six specific cellular restriction factors involved in host defense to cytomegalovirus infection were up-regulated in the cytomegalovirus-infected group. Ingenuity Pathway Analysis predicted the activation of pathways involved in progressive neurologic disease and inflammatory neurologic disease. In this next-generation sequencing study, we revealed new insights into the pathophysiology of congenital cytomegalovirus infection. These data on the up-regulation of the intraamniotic innate immune response to cytomegalovirus infection and the dysregulation of neurodevelopmental genes may inform future approaches to developing prognostic markers and assessing fetal responses to in utero therapy.

Blurring ontological boundaries: The transactional nature of material engagement

The target article provides valuable reflections regarding the study of cognition-in-the-world and proposes a methodology that could help researchers unravel the structure and temporal unfolding of lived experience. In this commentary, we discuss the authors' commitment to the enactive notion of sense-making as the activity of an autonomous system that brings forth a meaningful world to maintain its self-constituted identity. From Material Engagement Theory, we hold that defending such a notion leads to unnecessary ontological asymmetries that obscure the fundamental role of materiality for cognition. On the one hand, we argue that the relationship of close intertwinement and co-constitution that unites organism and environment makes it untenable to characterise cognition as being driven by individuals. In our view, cognition arises from the dynamic encounter between brains, bodies and culture. On the other hand, we suggest that organism and environment should not be seen as separate ontological categories that come to interact with each other but as two terms of a transactional process of continuous becoming. Consistently, we propose to consider meaning as emerging from the in-between space that material engagement creates rather than from the activity of an organism.

Metaphysics as a First Science, Again: How a Textbook on Metaphysics Is Possible. Book Review: Lowe E. J. The Possibility of Metaphysics: Substance, Identity, and Time. Clarendon Press, 1998

Jonathan Lowe believes that metaphysics should regain its central place in philosophy. It is an autonomous philosophical discipline, which task is to outline the realm of what is really possible by defining a system of fundamental ontological categories under which everything that exists falls, and relations of ontological dependence in which objects of various ontological categories are related to each other. Metaphysical categories are what gives meaning to our experience, however, unlike I. Kant, they are not the result of a priori constraints – on the contrary, they are subject to revision in the face of experience. The question of why there is something in the world rather than nothing, is solved with a non-Wittgensteinian understanding of what the world is (world is the sum of all existing objects because world as “the totality of facts” lacks determinate identity-conditions), as well as an understanding that universals must be actually instantiated in particulars. Far from being an easy textbook in the proper sense, this book is a brilliant example of the return of Aristotle to modern metaphysics.Reflections on the book: Lowe E. J. The Possibility of Metaphysics: Substance, Identity, and Time. Clarendon Press, 1998.

RNA-Seq analysis of duck embryo fibroblast cells gene expression during duck Tembusu virus infection

Duck Tembusu virus (DTMUV), a member of the family Flaviviridae and an economically important pathogen with a broad host range, leads to markedly decreased egg production. However, the molecular mechanism underlying the host-DTMUV interaction remains unclear. Here, we performed high-throughput RNA sequencing (RNA-Seq) to study the dynamic changes in host gene expression at 12, 24, 36, 48 and 60 h post-infection (hpi) in duck embryo fibroblasts (DEF) infected with DTMUV. A total of 3129 differentially expressed genes (DEG) were identified after DTMUV infection. Gene Ontology (GO) category and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these DEG were associated with multiple biological functions, including signal transduction, host immunity, virus infection, cell apoptosis, cell proliferation, and pathogenicity-related and metabolic process signaling pathways. This study analyzed viral infection and host immunity induced by DTMUV infection from a novel perspective, and the results provide valuable information regarding the mechanisms underlying host-DTMUV interactions, which will prove useful for the future development of antiviral drugs or vaccines for poultry, thus benefiting the entire poultry industry.

RESEARCH TRENDS IN ENGLISH LANGUAGE EDUCATION FROM ONTOLOGICAL PERSPECTIVE: A SYSTEMATIC REVIEW

&lt;div class="page" title="Page 1"&gt;&lt;div class="section" style="background-color: rgb(100.000000%, 100.000000%, 100.000000%);"&gt;&lt;div class="layoutArea"&gt;&lt;div class="column"&gt;&lt;p&gt; &lt;/p&gt;&lt;p&gt;This study aims to produce a systematic literature review on trends in English language education research in Indonesia over the last three years (2019-2021) from an ontological perspective. The Systematic Literature Review (SLR) writing process was conducted in accordance with the PRISMA (Preferred Reporting Items for Systematic Review and Meta-Analysis) framework. The analysis of data resulted in identifying the categories of ontology, namely the categories of teaching, learning, assessing, development of teaching documents like syllabus, learning materials, learning media and instructional model. From these categories of ontology, these studies have been identified and discussed. From the result, it is shown that from the 152 included studies, some areas of English language education tend to have great interest in researching trends of teaching, learning and learning media development. The study also identifies the number of study topics categorized as teaching has increased significantly in the last three years, while the number of research topics categorized as evaluation has decreased. Furthermore, there are two key sources which influence these trends. Firstly, it is due to the COVID-19 pandemic. Second, it is because of the dependency on convenience sampling. Based on the results and interpretations, the authors suggest future research to inform the current situation of research development in English language education.&lt;/p&gt;&lt;p&gt;&lt;span style="font-size: 10.000000pt; font-family: 'TimesNewRomanPSMT';"&gt;&lt;br /&gt; &lt;/span&gt;&lt;/p&gt;&lt;/div&gt;&lt;/div&gt;&lt;/div&gt;&lt;/div&gt;

Profiling Yeast Deletion Strains Using Sample Multiplexing and Network-Based Analyses.

The yeast, Saccharomyces cerevisiae, is a widely used model system for investigating conserved biological functions and pathways. Advancements in sample multiplexing have facilitated the study of the yeast proteome, yet many yeast proteins remain uncharacterized or only partially characterized. Yeast deletion strain collections are powerful resources for yeast proteome studies, uncovering the effects of gene function, genetic interactions, and cellular stresses. As complex biological systems cannot be understood by simply analyzing the individual components, a systems approach is often required in which a protein is represented as a component of large, interacting networks. Here, we evaluate the current state of yeast proteome analysis using isobaric tag-based sample multiplexing (TMTpro16) to profile the proteomes of 75 yeast deletion strains for which we measured the abundance of nearly 5000 proteins. Using statistical approaches, we highlighted covariance and regulation subnetworks and the enrichment of gene ontology classifications for covarying and coregulated proteins. This dataset presents a resource that is amenable to further data mining to study individual deletion strains, pathways, proteins, and/or interactions thereof while serving as a template for future network-based investigations using yeast deletion strain collections.

Material Stories, Old and New

Material Stories, Old and New

Comparative high-throughput analysis of sperm membrane proteins from crossbred bulls with contrasting fertility.

The aim of the present study was to identify fertility associated sperm membrane proteins in crossbred bulls. Sperm membrane proteins from high- and low-fertile Holstein Friesian crossbred bulls (n=3 each) were subjected to high-throughput liquid chromatography-mass spectrometry (LC-MS/MS) for comparative proteomic analysis. Proteomic profiling identified a total of 456 proteins in crossbred bull spermatozoa; it was found that 108 proteins were up regulated while 26 proteins were down regulated (>1.5-folds) in spermatozoa from low- compared to high-fertile bulls. Gene ontology classification revealed that upregulated proteins in low-fertile bulls were involved in biological process such as oxidation-reduction process (p=3.14E-06), fusion of sperm to egg plasma membrane (p=7.51E-04), sperm motility (p=0.03), and capacitation (p=0.09), while down regulated proteins were associated with transport (p=6.94E-04), superoxide metabolic process (p=0.02), and tricarboxylic acid cycle (p=0.04). KEGG pathway analysis revealed that oxidative phosphorylation and tricarboxylic acid cycle pathways are the most significantly affected pathway in low-fertile bulls. It was concluded that expression of proteins associated with oxidative phosphorylation and tricarboxylic acid cycle pathways were altered in low-fertile crossbred bulls, and expression levels of SPATA19, ELSPBP1, ACRBP, CLU, SUCLA2, and SPATC1 could aid in assessing potential fertility of crossbred bulls.

Transcriptome Analysis of the Cf-13-Mediated Hypersensitive Response of Tomato to Cladosporium fulvum Infection.

Tomato leaf mold disease caused by Cladosporium fulvum (C. fulvum) is one of the most common diseases affecting greenhouse tomato production. Cf proteins can recognize corresponding AVR proteins produced by C. fulvum, and Cf genes are associated with leaf mold resistance. Given that there are many physiological races of C. fulvum and that these races rapidly mutate, resistance to common Cf genes (such as Cf-2, Cf-4, Cf-5, and Cf-9) has decreased. In the field, Ont7813 plants (carrying the Cf-13 gene) show effective resistance to C. fulvum; thus, these plants could be used as new, disease-resistant materials. To explore the mechanism of the Cf-13-mediated resistance response, transcriptome sequencing was performed on three replicates each of Ont7813 (Cf-13) and Moneymaker (MM; carrying the Cf-0 gene) at 0, 9, and 15 days after inoculation (dai) for a total of 18 samples. In total, 943 genes were differentially expressed, specifically in the Ont7813 response process as compared to the Moneymaker response process. Gene ontology (GO) classification of these 943 differentially expressed genes (DEGs) showed that GO terms, including “hydrogen peroxide metabolic process (GO_Process)”, “secondary active transmembrane transporter activity (GO_Function)”, and “mismatch repair complex (GO_Component)”, which were the same as 11 other GO terms, were significantly enriched. An analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that many key regulatory genes of the Cf-13-mediated resistance response processes were involved in the “plant hormone signal transduction” pathway, the “plant–pathogen interaction” pathway, and the “MAPK signaling pathway–plant” pathway. Moreover, during C. fulvum infection, jasmonic acid (JA) and salicylic acid (SA) contents significantly increased in Ont7813 at the early stage. These results lay a vital foundation for further understanding the molecular mechanism of the Cf-13 gene in response to C. fulvum infection.

Brominated Carbazole with Antibiotic Adjuvant Activity Displays Pleiotropic Effects in MRSA's Transcriptome.

Methicillin-resistant Staphylococcus aureus (MRSA) is a major threat to human health, as the US mortality rate outweighs those from HIV, tuberculosis, and viral hepatitis combined. In the wake of the COVID-19 pandemic, antibiotic-resistant bacterial infections acquired during hospital stays have increased. Antibiotic adjuvants are a key strategy to combat these bacteria. We have evaluated several small molecule antibiotic adjuvants that have strong potentiation with β-lactam antibiotics and are likely inhibiting a master regulatory kinase, Stk1. Here, we investigated how the lead adjuvant (compound 8) exerts its effects in a more comprehensive manner. We hypothesized that the expression levels of key resistance genes would decrease once cotreated with oxacillin and the adjuvant. Furthermore, bioinformatic analyses would reveal biochemical pathways enriched in differentially expressed genes. RNA-seq analysis showed 176 and 233 genes significantly up- and downregulated, respectively, in response to cotreatment. Gene ontology categories and biochemical pathways that were significantly enriched with downregulated genes involved carbohydrate utilization, such as the citrate cycle and the phosphotransferase system. One of the most populated pathways was S. aureus infection. Results from an interaction network constructed with affected gene products supported the hypothesis that Stk1 is a target of compound 8. This study revealed a dramatic impact of our lead adjuvant on the transcriptome that is consistent with a pleiotropic effect due to Stk1 inhibition. These results point to this antibiotic adjuvant having potential broad therapeutic use in combatting MRSA.

Newly developed sugarbeet lines with altered postharvest respiration rates differ in transcription factor and glycolytic enzyme expression

AbstractRespiration is the principal cause for postharvest sucrose loss in sugarbeet (Beta vulgaris L.) roots. Although reductions in respiration rate could mitigate these losses, developing sugarbeet cultivars and storage procedures that reduce respiration are hindered by a lack of knowledge of the genetic and metabolic factors that control storage respiration rate. Research was conducted to identify genes and gene products that affect storage respiration rate by creating two sugarbeet lines that differ in respiration rate and characterizing gene expression differences between these lines. Sugarbeet lines F1056 and F1057, which differ by up to 42% in respiration rate, were created by divergent selection of a sugarbeet population using root respiration rate after 30 d in storage as the principal selection criterion. RNA sequencing identified 287 differentially expressed genes (DEGs) between these lines on the day of harvest and after 28‐d storage. Of these DEGs, nine encoded transcription factors and five encoded enzymes involved in the respiratory pathway. Other DEGs contributed to a variety of biological and molecular functions based on gene ontology classifications. Of respiratory pathway DEGS, genes for NAD+‐ and NADP+‐dependent forms of glyceraldehyde‐3‐phosphate dehydrogenase were of note due to their high upregulation in the high respiring line and for their established role in glycolysis, a pathway identified as a likely bottleneck in respiratory substrate production. Overall, lines F1056 and F1057 provide new tools for investigating genetic and physiological differences in storage respiration rate, and their DEGs identify candidates for genes affecting sugarbeet root respiration rate.