Information on Transcriptional Regulation and Signal Transduction of _Escherichia coli_ K-12 Integrated in the Database RegulonDB.

Since its inception, RegulonDB ("http://regulondb.ccg.unam.mx/":http://regulondb.ccg.unam.mx/) has been a database that compiles information about the regulation of transcription initiation of _Escherichia coli_ K-12. However, we are aware that transcriptional regulation is not an isolated process; instead, it is the response to the different environmental conditions that trigger a series of concatenated reactions that end in transcriptional regulation, and it implies an adequate response in terms of induced and repressed gene products. We are working now to include all these new data in RegulonDB. As a consequence, transcriptional regulation in RegulonDB will be part of a unit that initiates with the signal, continues with the signal transduction to the core of regulation to modify expression of the affected set of target genes, and ends with an adequate response. We refer to these units as genetic sensory response units, or Gensor Units.

The inclusion of Gensor Units will bring a dramatic change and expansion of RegulonDB, due to the fact that we will be adding several new types of reactions and interactions. We started to collect data about signal transduction of the sigma factors, the two-component systems, of some transcription factors involved in carbon source utilization, and of genes involved in the synthesis of amino acids. We plan a high-level curation with super-pathways summarizing concatenated sets of reactions linked to those other databases that curate such information, while enabling with RegulonDB a compilation of complete Gensor Units.

In addition, the number of DNA binding sites for some transcription factors has grown considerably, and therefore we decided to review systematically those sites whose lengths ranging from 40 to 60 bp with orientation and consensus sequences that are not easy to identify. The current version of RegulonDB is the beginning of a higher-level curation of gene regulation information, and eventually our database will include all regulatory mechanisms and their regulated genes. 
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Information on Transcriptional Regulation and Signal Transduction of _Escherichia coli_ K-12 Integrated in the Database RegulonDB.

Since its inception, RegulonDB ("http://regulondb.ccg.unam.mx/":http://regulondb.ccg.unam.mx/) has been a database that compiles information about the regulation of transcription initiation of _Escherichia coli_ K-12. However, we are aware that transcriptional regulation is not an isolated process; instead, it is the response to the different environmental conditions that trigger a series of concatenated reactions that end in transcriptional regulation, and it implies an adequate response in terms of induced and repressed gene products. We are working now to include all these new data in RegulonDB. As a consequence, transcriptional regulation in RegulonDB will be part of a unit that initiates with the signal, continues with the signal transduction to the core of regulation to modify expression of the affected set of target genes, and ends with an adequate response. We refer to these units as genetic sensory response units, or geSorgans.

The inclusion of geSorgans will bring a dramatic change and expansion of RegulonDB, due to the fact that we will be adding several new types of reactions and interactions. We started to collect data about signal transduction of the sigma factors, the two-component systems, of some transcription factors involved in carbon source utilization, and of genes involved in the synthesis of amino acids. We plan a high-level curation with super-pathways summarizing concatenated sets of reactions linked to those other databases that curate such information, while enabling with RegulonDB a compilation of complete geSorgans.

In addition, the number of DNA binding sites for some transcription factors has grown considerably, and therefore we decided to review systematically those sites whose lengths ranging from 40 to 60 bp with orientation and consensus sequences that are not easy to identify. The current version of RegulonDB is the beginning of a higher-level curation of gene regulation information, and eventually our database will include all regulatory mechanisms and their regulated genes. 
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Influence of Protein Type on the Antimicrobial Activity of LAE Alone or in Combination with Methylparaben

The cationic surfactant Lauric arginate (LAE) has gained approval for utilization in meat products (limit: 200 mg/kg). However, as for other antimicrobials, its activity is reduced when applied to complex food matrices. The current study therefore aims to better understand protein-antimicrobial agent-interactions and their influence on the antimicrobial activity of (i) LAE and (ii) methylparaben against Listeria innocua and Pseudomonas fluorescens in defined model systems (pH 6). Antimicrobials were utilized alone or in combination with nutrient broth containing either no protein or 2% bovine serum albumin, whey protein isolate, or soy protein hydrolysate. LAE was found to form complexes with all proteins due to electrostatic attraction, determined using microelectrophoretic and turbidity measurements. Minimal lethal concentrations of LAE were remarkably increased (4–13 fold) in the presence of proteins, with globular proteins having the strongest impact. Combinations of LAE (0–200 µg/mL) with the less structure-sensitive component methylparaben (approved concentration 0.1%) remarkably decreased the concentrations of LAE needed to strongly inhibit or even kill both, L. innocua and P. fluorescens in the presence of proteins. The study highlights the importance of ingredient interactions impacting microbial activity that are often not taken into account when examining antimicrobial components having different structure sensitivitie

Iron in the Tumor Microenvironment—Connecting the Dots

Iron metabolism and tumor biology are intimately linked. Iron facilitates the production of oxygen radicals, which may either result in iron-induced cell death, ferroptosis, or contribute to mutagenicity and malignant transformation. Once transformed, malignant cells require high amounts of iron for proliferation. In addition, iron has multiple regulatory effects on the immune system, thus affecting tumor surveillance by immune cells. For these reasons, inconsiderate iron supplementation in cancer patients has the potential of worsening disease course and outcome. On the other hand, chronic immune activation in the setting of malignancy alters systemic iron homeostasis and directs iron fluxes into myeloid cells. While this response aims at withdrawing iron from tumor cells, it may impair the effector functions of tumor-associated macrophages and will result in iron-restricted erythropoiesis and the development of anemia, subsequently. This review summarizes our current knowledge of the interconnections of iron homeostasis with cancer biology, discusses current clinical controversies in the treatment of anemia of cancer and focuses on the potential roles of iron in the solid tumor microenvironment, also speculating on yet unknown molecular mechanisms

EcoCyc: fusing model organism databases with systems biology.

EcoCyc (http://EcoCyc.org) is a model organism database built on the genome sequence of Escherichia coli K-12 MG1655. Expert manual curation of the functions of individual E. coli gene products in EcoCyc has been based on information found in the experimental literature for E. coli K-12-derived strains. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc

Ferritin H deficiency deteriorates cellular iron handling and worsens Salmonella typhimurium infection by triggering hyperinflammation

Iron is an essential nutrient for mammals as well as for pathogens. Inflammation-driven changes in systemic and cellular iron homeostasis are central for host-mediated antimicrobial strategies. Here, we studied the role of the iron storage protein ferritin H (FTH) for the control of infections with the intracellular pathogen Salmonella enterica serovar Typhimurium by macrophages. Mice lacking FTH in the myeloid lineage (LysM-Cre+/+Fthfl/fl mice) displayed impaired iron storage capacities in the tissue leukocyte compartment, increased levels of labile iron in macrophages, and an accelerated macrophage-mediated iron turnover. While under steady-state conditions, LysM-Cre+/+Fth+/+ and LysM-Cre+/+Fthfl/fl animals showed comparable susceptibility to Salmonella infection, i.v. iron supplementation drastically shortened survival of LysM-Cre+/+Fthfl/fl mice. Mechanistically, these animals displayed increased bacterial burden, which contributed to uncontrolled triggering of NF-κB and inflammasome signaling and development of cytokine storm and death. Importantly, pharmacologic inhibition of the inflammasome and IL-1β pathways reduced cytokine levels and mortality and partly restored infection control in iron-treated ferritin-deficient mice. These findings uncover incompletely characterized roles of ferritin and cellular iron turnover in myeloid cells in controlling bacterial spread and for modulating NF-κB and inflammasome-mediated cytokine activation, which may be of vital importance in iron-overloaded individuals suffering from severe infections and sepsis

Mitotic activity patterns and cytoskeletal changes throughout the progression of diapause developmental program in Daphnia

Abstract Background Diapause is a form of dormancy that is genetically predetermined to allow animals to overcome harsh environmental conditions. It is induced by predictive environmental cues bringing cellular activity levels into a state of suspended animation. Entering diapause requires organismal, molecular and cellular adaptation to severely reduced energy flows. Cells must therefore have evolved strategies that prepare them for periods with limited metabolic resources. However, changes that occur on the (sub-)cellular level have not been thoroughly described. Results We investigated mitotic activity and we monitored cytoskeletal network changes in successive stages of diapausing and non-diapausing Daphnia magna embryos using (immuno-)fluorescent labeling. We find that embryos destined to diapause show a delayed and 2.5x slower mitotic activity in comparison to continuously developing embryos. Development is halted when D. magna embryos reach ~ 3500 cells, whereupon mitotic activity is absent and cytoskeletal components are severely reduced, rendering diapause cells compact and condensed. Conclusion In the initiation phase of diapause, the slower cell division rate points to prolonged interphase duration, preparing the cells for diapause maintenance. During diapause, cytoskeletal depletion and cellular condensation may be a means to save energy resources. Our data provide insights into the sub-cellular change of diapause in Daphnia

Genomic CDKN2A/2B deletions in adult Ph+ ALL are adverse despite allogeneic stem cell transplantation

We investigated the role of copy number alterations to refine risk stratification in adult Philadelphia chromosome positive (Ph)+ ALL treated with tyrosine kinase inhibitors (TKI) and allogeneic stem cell transplantation (aSCT). 97 Ph+ ALL patients (median age 41 years, range 18-64 years) within the prospective multicenter GMALL studies 06/99 (n=8) and 07/2003 (n=89) were analysed. All patients received TKI and aSCT in first complete remission (CR1). Copy number analysis was performed with SNP arrays and validated by multiplex ligation-dependent probe amplification (MLPA). The frequencies of recurrently deleted genes were: IKZF1, 76%, CDKN2A/2B, 45%, PAX5, 43%, BTG1, 18%, EBF1, 13%, ETV6, 5%, RB, 14%. In univariate analyses, the presence of CDKN2A/2B deletions had a negative impact on all endpoints: overall survival (p=0.023), disease free survival (p=0.012) and remission duration (p=0.036). The negative predictive value of CDKN2A/2B deletions was retained in multivariable analysis along with other factors such as timing of TKI therapy, intensity of conditioning, achieving remission after induction phase I and BTG1 deletions. We therefore conclude that acquired genomic CDKN2A/2B deletions identify a subgroup of Ph+ ALL patients, who have an inferior prognosis despite aSCT in CR1. Their poor outcome was attributable primarily to a high relapse rate after aSCT

Investigating the zoonotic origin of the West African Ebola epidemic

The severe Ebola virus disease epidemic occurring in West Africa stems from a single zoonotic transmission event to a 2‐year‐old boy in Meliandou, Guinea. We investigated the zoonotic origins of the epidemic using wildlife surveys, interviews, and molecular analyses of bat and environmental samples. We found no evidence for a concurrent outbreak in larger wildlife. Exposure to fruit bats is common in the region, but the index case may have been infected by playing in a hollow tree housing a colony of insectivorous free‐tailed bats (Mops condylurus). Bats in this family have previously been discussed as potential sources for Ebola virus outbreaks, and experimental data have shown that this species can survive experimental infection. These analyses expand the range of possible Ebola virus sources to include insectivorous bats and reiterate the importance of broader sampling efforts for understanding Ebola virus ecology

MOSAiC Extended Acknowledgement

For years, the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), together with the international MOSAiC partners, had been planning and developing the scientific, logistical and financial concept for the implementation of the MOSAiC expedition. The planning and organization of this endeavor was an enormous e˙ort, involving more than 80 institutions from 20 countries. The number of groups and individuals that significantly contributed to the success of the drift observatory goes far beyond the scope of usual polar expeditions