Quinol Oxidase Encoded by \u3cem\u3ecyoABCD\u3c/em\u3e in \u3cem\u3eRhizobium etli\u3c/em\u3e CFN42 is Regulated by ActSR and is Crucial for Growth at Low pH or Low Iron Conditions

Rhizobium etli aerobically respires with several terminal oxidases. The quinol oxidase (Cyo) encoded by cyoABCD is needed for efficient adaptation to low oxygen conditions and cyo transcription is upregulated at low oxygen. This study sought to determine how transcription of the cyo operon is regulated. The 5′ sequence upstream of cyo was analysed in silico and revealed putative binding sites for ActR of the ActSR two-component regulatory system. The expression of cyo was decreased in an actSR mutant regardless of the oxygen condition. As ActSR is known to be important for growth under low pH in another rhizobial species, the effect of growth medium pH on cyo expression was tested. As the pH of the media was incrementally decreased, cyo expression gradually increased in the WT, eventually reaching ∼10-fold higher levels at low pH (4.8) compared with neutral pH (7.0) conditions. This upregulation of cyo under decreasing pH conditions was eliminated in the actSR mutant. Both the actSR and cyo mutants had severe growth defects at low pH (4.8). Lastly, the actSR and cyo mutants had severe growth defects when grown in media treated with an iron chelator. Under these conditions, cyo was upregulated in the WT, whereas cyo was not induced in the actSR mutant. Altogether, the results indicated cyo expression is largely dependent on the ActSR two-component system. This study also demonstrated additional physiological roles for Cyo in R. etli CFN42, in which it is the preferred oxidase for growth under acidic and low iron conditions

A Quinol Oxidase, Encoded by \u3cem\u3ecyoABCD\u3c/em\u3e, Is Utilized to Adapt to Lower O\u3csub\u3e2\u3c/sub\u3e Concentrations in \u3cem\u3eRhizobium etli\u3c/em\u3e CFN42

Bacteria have branched aerobic respiratory chains that terminate at different terminal oxidases. These terminal oxidases have varying properties such as their affinity for oxygen, transcriptional regulation and proton pumping ability. The focus of this study was a quinol oxidase encoded by cyoABCD. Although this oxidase (Cyo) is widespread among bacteria, not much is known about its role in the cell, particularly in bacteria that contain both cytochrome c oxidases and quinol oxidases. Using Rhizobium etli CFN42 as a model organism, a cyo mutant was analysed for its ability to grow in batch cultures at high (21 % O2) and low (1 and 0.1 % O2) ambient oxygen concentrations. In comparison with other oxidase mutants, the cyo mutant had a significantly longer lag phase under low-oxygen conditions. Using a cyo :: lacZ transcriptional fusion, it was shown that cyo expression in the wild type peaks between 1 and 2.5 % O2. In addition, it was shown with quantitative reverse transcriptase PCR that cyoB is upregulated approximately fivefold in 1 % O2 compared with fully aerobic (21 % O2) conditions. Analysis of the cyo mutant during symbiosis with Phaseolous vulgaris indicated that Cyo is utilized during early development of the symbiosis. Although it is commonly thought that Cyo is utilized only at higher oxygen concentrations, the results from this study indicate that Cyo is important for adaptation to and sustained growth under low oxygen

Transcriptome Profiling and Long Non-Coding Rna Identification in Grapevine

Next-generation sequencing technologies have provided access to vast quantities of nucleic acid sequence data. The resulting wealth of information enables biologists to address complex biological questions in species for which a high-quality well-annotated reference genome sequence has yet to be generated. The cultivated grapevine, Vitis vinifera, has a relatively poorly annotated reference genome. In addition, it is a highly heterozygous species which further hinders the annotation of its genome and the characterization of its transcriptome. Here, I annotated Version 2 of the 12X V. vinifera genome using RNA-seq data derived from the variety ‘Riesling\u27 by employing the most up-to-date computational methods. The results provide the first annotation of ‘Riesling\u27 and the first profile of its transcriptome in relation to the reference transcriptome of the model grape variety ‘Pinot Noir\u27. In addition, I develop a computational pipeline for the identification of long non-coding RNAs (lncRNAs) in non-model plant species that lack well-sequenced reference genomes. This pipeline was then applied to ‘Riesling\u27 RNA- seq data for the first analysis of lncRNAs in that variety

hagis, an R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean

Phytophthora sojae is a significant pathogen of soybean worldwide. Pathotype surveys for Phytophthora sojae are conducted to monitor resistance gene efficacy and determine if new resistance genes are needed. Valuable measurements for pathotype analysis include the distribution of susceptible reactions, pathotype complexity, pathotype frequency, and diversity indices for pathotype distributions. Previously the Habgood-Gilmour Spreadsheet (HaGiS), written in Microsoft Excel, was used for data analysis. However, the growing popularity of the R programming language in plant pathology and desire for reproducible research made HaGiS a prime candidate for conversion into an R package. Here we report on the development and use of an R package, hagis, that can be used to produce all outputs from the HaGiS Excel sheet for P. sojae or other gene-for-gene pathosystem studies

Discussion Group Report: Prevention & Enforcement

New Mexico has a mix of ethical canons and statutes, including the Government Conduct Act, the Procurement Code, Financial Disclosure Act, and others. The Judicial branch has its own code of conduct, as does the Legislative branch. The Government Conduct Act encourages Executive branch agencies to develop and maintain agency specific codes of conduct. It is important to note the distinction between ethical canons, which could result in administrative discipline or sanctions, and criminal/civil statutory provisions, violations of which can result in criminal fines, penalties, etc. This report provides a brief summary of the existing ethics laws, mechanisms for enforcement, and responsibility for ethics education, by branch of government. Next, problem areas are addressed before presenting recommendations

Omitted Variable Bias in the Link Between Planning and Performance

This article argues that existing research poorly specifies the link between planning and performance because of omitted variable bias. Researchers agree planning is a critical part of creating any new venture. Many researchers assess planning by whether a small firm has a written business plan. Unfortunately, efforts empirically to validate this relationship have been inconclusive. This article proposes that researchers should assess business plans both on the quality of the plan (and the planning process that produced it), and on the quality of the underlying business opportunity. Failure to account for both aspects of a business plan amounts to omitted variable bias, frustrating attempts to accurately estimate the true relationship

Sink or swim: Virtual life challenges among African American families during COVID-19 lockdown

This study explores African American parents’ experiences with using technology toengage their children in meaningful activities (e.g., e-learning) during COVID-19 and its impact on family health. Eleven African American families were recruited through a local health department program from a rural Midwestern community to participate in semi-structured interviews. The majority of participants reported stresses from feelings of “sink or swim” in a digital world, without supports from schools to effectively provide for their children’s technology needs. The COVID-19 pandemic underscored the importance of family-school collaborative engagement and empowerment. Digital technology needs to become part of our school education system so that technology use among African Americans is elevated and families protected against future outbreaks. Further research with a more diverse African American sample is needed

SoK: Contemporary Issues and Challenges to Enable Cyber Situational Awareness for Network Security

Cyber situational awareness is an essential part of cyber defense that allows the cybersecurity operators to cope with the complexity of today's networks and threat landscape. Perceiving and comprehending the situation allow the operator to project upcoming events and make strategic decisions. In this paper, we recapitulate the fundamentals of cyber situational awareness and highlight its unique characteristics in comparison to generic situational awareness known from other fields. Subsequently, we provide an overview of existing research and trends in publishing on the topic, introduce front research groups, and highlight the impact of cyber situational awareness research. Further, we propose an updated taxonomy and enumeration of the components used for achieving cyber situational awareness. The updated taxonomy conforms to the widely-accepted three-level definition of cyber situational awareness and newly includes the projection level. Finally, we identify and discuss contemporary research and operational challenges, such as the need to cope with rising volume, velocity, and variety of cybersecurity data and the need to provide cybersecurity operators with the right data at the right time and increase their value through visualization

Pharmacokinetic evaluation of the PNC disassembler metarrestin in wild-type and Pdx1-Cre;LSL-KrasG12D/+;Tp53R172H/+ (KPC) mice, a genetically engineered model of pancreatic cancer

This work is licensed under a Creative Commons Attribution 4.0 International License.Purpose Metarrestin is a first-in-class small molecule clinical candidate capable of disrupting the perinucleolar compartment, a subnuclear structure unique to metastatic cancer cells. This study aims to define the pharmacokinetic (PK) profile of metarrestin and the pharmacokinetic/pharmacodynamic relationship of metarrestin-regulated markers. Methods PK studies included the administration of single or multiple dose of metarrestin at 3, 10, or 25 mg/kg via intravenous (IV) injection, gavage (PO) or with chow to wild-type C57BL/6 mice and KPC mice bearing autochthonous pancreatic tumors. Metarrestin concentrations were analyzed by UPLC–MS/MS. Pharmacodynamic assays included mRNA expression profiling by RNA-seq and qRT-PCR for KPC mice. Results Metarrestin had a moderate plasma clearance of 48 mL/min/kg and a large volume of distribution of 17 L/kg at 3 mg/kg IV in C57BL/6 mice. The oral bioavailability after single-dose (SD) treatment was > 80%. In KPC mice treated with SD 25 mg/kg PO, plasma AUC0–∞ of 14400 ng h/mL, Cmax of 810 ng/mL and half-life (t1/2) of 8.5 h were observed. At 24 h after SD of 25 mg/kg PO, the intratumor concentration of metarrestin was high with a mean value of 6.2 µg/g tissue (or 13 µM), well above the cell-based IC50 of 0.4 µM. At multiple dose (MD) 25 mg/kg/day PO in KPC mice, mean tissue/plasma AUC0–24h ratio for tumor, spleen and liver was 37, 30 and 31, respectively. There was a good linear relationship of dosage to AUC0–24h and C24h. AUC0–24h MD to AUC0–24h SD ratios ranged from two for liver to five for tumor indicating additional accumulation in tumors. Dose-dependent normalization of FOXA1 and FOXO6 mRNA expression was observed in KPC tumors. Conclusions Metarrestin is an effective therapeutic candidate with a favorable PK profile achieving excellent intratumor tissue levels in a disease with known poor drug delivery.Intramural Research Program (IRP) of the NIHNational Cancer InstituteCenter for Cancer Research (ZIA BC 011267