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Pantoea ananatis is a member of a Pantoea species complex that causes center rot of bulb onions ( A. cepa ) and also infects other Allium crops like leeks ( Allium porrum ), chives ( Allium schoenoprasum ), bunching onion or Welsh onion ( Allium fistulosum ), and garlic ( Allium sativum ). This pathogen relies on a chromosomal phosphonate biosynthetic gene cluster (HiVir) and a plasmid-borne thiosulfinate tolerance cluster ( alt ) for onion pathogenicity and virulence, respectively. However, pathogenicity and virulence factors associated with other Allium species remain unknown. We used phenotype-dependent genome-wide association (GWAS) and phenotype-independent gene-pair coincidence (GPC) analyses on a panel of diverse 92 P. ananatis strains, which were inoculated on A. porrum and A. fistulosum  ×  A. cepa under greenhouse conditions. Phenotypic assays showed that, in general, these strains were more aggressive on A. fistulosum  ×  A. cepa as opposed to A. porrum . Of the 92 strains, only six showed highly aggressive foliar lesions on A. porrum compared to A. fistulosum  ×  A. cepa . Conversely, nine strains showed highly aggressive foliar lesions on A. fistulosum  ×  A. cepa compared to A. porrum . These results indicate that there are underlying genetic components in P. ananatis that may drive pathogenicity in these two Allium spp. Based on GWAS for foliar pathogenicity, 835 genes were associated with P. ananatis ' pathogenicity on A. fistulosum  ×  A. cepa whereas 243 genes were associated with bacterial pathogenicity on A. porrum . The Hivir as well as the alt gene clusters were identified among these genes. Besides the 'HiVir' and the alt gene clusters that are known to contribute to pathogenicity and virulence from previous studies, genes annotated with functions related to stress responses, a potential toxin-antitoxin system, flagellar-motility, quorum sensing, and a previously described phosphonoglycan biosynthesis (pgb) cluster were identified. The GPC analysis resulted in the identification of 165 individual genes sorted into 39 significant gene-pair association components and 255 genes sorted into 50 significant gene-pair dissociation components. Within the coincident gene clusters, several genes that occurred on the GWAS outputs were associated with each other but dissociated with genes that did not appear in their respective GWAS output. To focus on candidate genes that could explain the difference in virulence between hosts, a comparative genomics analysis was performed on five P. ananatis strains that were differentially pathogenic on A. porrum or A. fistulosum  ×  A. cepa . Here, we found a putative type III secretion system, and several other genes that occurred on both GWAS outputs of both Allium hosts. Further, we also demonstrated utilizing mutational analysis that the pepM gene in the HiVir cluster is important than the pepM gene in the pgb cluster for P. ananatis pathogenicity in A. fistulosum  ×  A. cepa and A. porrum . Overall, our results support that P. ananatis may utilize a common set of genes or gene clusters to induce symptoms on A. fistulosum × A. cepa foliar tissue as well as A. cepa but implicates additional genes for infection on A. porrum ., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Myers, Shin, Agarwal, Stice, Gitaitis, Kvitko and Dutta.)

This review provides a synopsis of transcriptional responses pertaining to interactions between plant viruses and the insect vectors that transmit them in diverse modes. In the process, it attempts to catalog differential gene expression pertinent to virus-vector interactions in vectors such as virus reception, virus cell entry, virus tissue tropism, virus multiplication, and vector immune responses. Whiteflies, leafhoppers, planthoppers, and thrips are the main insect groups reviewed, along with aphids and leaf beetles. Much of the focus on gene expression pertinent to vector-virus interactions has centered around whole-body RNA extraction, whereas data on virus-induced tissue-specific gene expression in vectors is limited. This review compares transcriptional responses in different insect groups following the acquisition of non-persistent, semi-persistent, and persistent (non-propagative and propagative) plant viruses and identifies parallels and divergences in gene expression patterns. Understanding virus-induced changes in vectors at a transcriptional level can aid in the identification of candidate genes for targeting with RNAi and/or CRISPR editing in insect vectors for management approaches.

Pantoea ananatis, a gram negative and facultative anaerobic bacterium is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally comprised of 14 genes), for a phosphonate secondary metabolite, and the ' alt ' gene cluster (located in plasmid and comprised of 11 genes) that aids in bacterial colonization in onion bulbs by imparting tolerance to thiosulfinates. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains ( n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic ( n = 51)- vs. non-pathogenic ( n = 30)-strains phenotypically. Pan-genome analysis revealed a large core genome of 3,153 genes and a flexible accessory genome. Pan-GWAS using the presence and absence variants (PAVs) predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, conjugal transfer, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. Further, a core-genome SNPs-based phylogeny and horizontal gene transfer (HGT) studies were also conducted to assess the extent of lateral gene transfer among diverse P. ananatis strains. Phylogenetic analysis based on PAVs and whole genome multi locus sequence typing (wgMLST) rather than core-genome SNPs distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis . A total of 1182 HGT events including the HiVir/PASVIL and alt cluster genes were identified. These events could be regarded as a major contributing factor to the diversification, niche-adaptation and potential acquisition of pathogenicity/virulence genes in P. ananatis ., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Agarwal, Choudhary, Stice, Myers, Gitaitis, Venter, Kvitko and Dutta.)

Zinc (Zn) accumulation and deficiency affect plant response to pests and diseases differently in varying pathosystems. The concentrations of Zn in plants aid in priming defense signaling pathways and help in enhanced structural defenses against plant pathogens. Studies are lacking on how concentrations of Zn in watermelon plants influence defense against two important soil-borne pathogens: Fusarium oxysporum f. sp. niveum (FON) and southern root-knot nematode (RKN, Meloidogyne incognita ). In this study a comparative transcriptomics evaluation of watermelon plants in response to high (1.2 ppm) and low (0.2 ppm) levels of Zn were determined. Differential transcript-level responses differed in watermelon plants when infected with FON or RKN or both under high- and low-Zn treatment regimes in a controlled hydroponics system. Higher numbers of differentially expressed genes (DEGs) were observed in high-Zn-treated than in low-Zn-treated non-inoculated plants, in plants inoculated with FON alone and in plants inoculated with RKN alone. However, in the co-inoculated system, low-Zn treatment had higher DEGs as compared to high-Zn treatment. In addition, most DEGs were significantly enriched in hormone signal transduction and MAPK signaling pathway, suggesting an induction of systemic resistance with high-Zn concentrations. Taken together, this study substantially expands transcriptome data resources and suggests a molecular potential framework for watermelon-Zn interaction in FON and RKN.

End groups play a critical role in macromolecular coupling reactions for building complex polymer architectures, yet their identity and purity can be difficult to ascertain using traditional analytical technique. Recent advances in mass spectrometry techniques have made matrix-assisted laser desorption/ionization time-of-fight (MALDI-TOF) mass spectrometry a rapid and powerful tool for providing detailed information about the identity and purity of homopolymer end groups. In this work, MALDI-TOF mass spectrometry was used to study end groups of linear polyethylene glycols. In particular, the identifications of alcohol, amine and thiol end groups are investigated because these nucleophilic moieties are among the most common within biological and synthetic macromolecules. Through comparative characterization of alcohol, amine, and thiol end groups, the exact identification of these end groups could be confirmed by selective and quantitative modification. The precision of this technique enables the unambiguous differentiation of primary amino groups relative to hydroxyl groups, which differ by only 1 mass unit. In addition, the quantitative conversion of various polyethylene glycol end groups using highly efficient coupling reactions such as the thiol-ene and azide-alkyne click reactions can be confirmed using MALDI-TOF mass spectrometry., (Copyright © 2014 Elsevier B.V. All rights reserved.)

The utilization of dendrimer calibrants as an alternative to peptides and proteins for high mass calibration is explored. These synthetic macromolecules exhibited a number of attractive advantages, including exceptional shelf-lives, broad compatibility with a wide range of matrices and solvents, and evenly spaced calibration masses across the mass range examined, 700-30,000 u. The exceptional purity of these dendrimers and the technical simplicity of this calibration platform validate their broad relevance for high molecular weight mass spectrometry.

The synthesis of branched poly(ethylene glycol) (PEG) derivatives, namely star PEG and dendronized PEG, can be challenging and their purity can be difficult to ascertain using traditional techniques, such as NMR and GPC. Herein, the detailed characterization of these branched PEGs using MALDI-ToF MS was investigated in order to confirm their structural purity. In this light, mass spectrometry offers a number of advantages for polymer characterization, including the ability to get detailed structural data, such as end group masses, from microgram-scale samples. In addition, the ability to rapidly acquire data from crude reaction aliquots makes MALDI-ToF MS ideal for monitoring end group transformations., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Intrapulmonary chemoreceptors (IPC) and extrapulmonary afferents (EPA) have been shown to interact in ventilatory control in the chicken. It is not clear, however, if all or only some of the EPA are involved in this interaction with IPC. We therefore designed this study to determine if afferents carried in the middle cardiac nerve (MCN) interact centrally with IPC. We anesthetized six cockerels with sodium pentobarbital (ca. 30 mg/kg), cannulated the cutaneous ulnar vein and carotid artery, opened the thorax, and unidirectionally ventilated each lung separately. The right, denervated lung was used to fix PaCO2 at the following levels: 89.5 +/- 1.1, 41.9 +/- 0.6, 35.9 +/- 0.8, and 23.6 +/- 0.5 Torr. At each PaCO2, we measured ventilatory and blood pressure responses while the left, non-perfused lung was ventilated with gases ranging from 70.2 to 15.7 Torr PCO2. We then cut the MCN and repeated the protocol. We found that MCN section increased the amplitude of sternal deflections (SD/SDmax) at all levels of intrapulmonary PCO2 and reduced the respiratory period (T/Tmax) at all but the highest level of intrapulmonary PCO2. Mean arterial pressure increased following MCN section, and this increase was independent of intrapulmonary PCO2. Multiple regression analyses of SD/SDmax revealed that MCN section reduced both arterial CO2 sensitivity and the interaction between EPA and IPC. These findings suggest that afferents carried in the MCN interact with IPC to reduce ventilatory amplitude during hypocapnia.

This study examined the saving and spending behaviors of 1,619 employed high school seniors from over 1,000 private and public schools across the United States. Students were categorized as savers, necessity spenders, and discretionary spenders based on their responses to the question, "How do you spend the money that you earn?" Associations of student spending and saving patterns with individual and family factors were analyzed. Student savers were from families who saved and planned money use. Students who spent more for necessities were from families with fewer resources and greater financial difficulties. Discretionary spenders felt that money was important and were from families with higher income and socioeconomic status. Findings are discussed in light of the importance of families as socializing agents of their children.