Turning off Bacillus cereus quorum sensing system with peptidic analogs
. Chemical Communications 2018
, 9777 - 9780. Publisher's VersionAbstract
We explored quenching of the PlcR–PapR quorum-sensing system in Bacillus cereus. We generated PapR7-peptidic derivatives that inhibit this system and thus the production of virulence factors, reflected by a loss in hemolytic activity, without affecting bacterial growth. To our knowledge, these peptides represent the first potent synthetic inhibitors of quorum-sensing in B. cereus.
A concise guide to active agents for active food packaging
. Trends in Food Science & Technology 2018
, 212 - 222. Publisher's VersionAbstract
BackgroundThe ever-growing world population results in the ineluctable increase of food demand which translates in the augment of the global market of packaging materials. Hence, the concept of active packaging materializes as a technology to enhance the safety, quality and shelf-life of the packaged foods. Active packaging systems can contribute to the reduction of food waste by providing, apart from an inert barrier to external conditions, several functions associated with food preservation, namely absorbing/scavenging, releasing/emitting and removing properties, temperature, microbial and quality control. Scope and approach The purpose of this review is to present a concise (but wide-ranging) appraisal on the latest advances in active agents for active food packaging. Emphasis is placed on active functions such as antimicrobial and antioxidant activity, oxygen and ethylene scavenging, and carbon dioxide emitting. An effort was made to highlight representative articles that prompted research on active agents towards viable market solutions. Key findings and conclusions Active packaging is a thriving field given its duality as barrier to external detrimental factors and active role in food preservation and quality. The use of natural active agents is a flourishing field due to the general concern towards natural-based additives. Nevertheless, research is still in its early stages with a long way to go in the design of innovative and economical active packaging materials containing appropriate active agents. The interaction between packaging, environment and food is the key challenge for achieving commercial translation.
Dynamic enhancer function in the chromatin context
. Wiley Interdiscip Rev Syst Biol Med 2018
Enhancers serve as critical regulatory elements in higher eukaryotic cells. The characterization of enhancer function has evolved primarily from genome-wide methodologies, including chromatin immunoprecipitation (ChIP-seq), DNase-I hypersensitivity (DNase-seq), digital genomic footprinting (DGF), and the chromosome conformation capture techniques (3C, 4C, and Hi-C). These population-based assays average signals across millions of cells and lead to enhancer models characterized by static and sequential binding. More recently, fluorescent microscopy techniques, including fluorescence recovery after photobleaching, fluorescence correlation spectroscopy, and single molecule tracking (SMT), reveal a highly dynamic binding behavior for these factors in live cells. Furthermore, a refined analysis of genomic footprinting suggests that many transcription factors leave minimal or no footprints in chromatin, even when present and active in a given cell type. In this study, we review the implications of these new approaches for an accurate understanding of enhancer function in real time. In vivo SMT, in particular, has recently evolved as a promising methodology to probe enhancer function in live cells. Integration of findings from the many approaches now employed in the study of enhancer function suggest a highly dynamic view for the action of enhancer activating factors, viewed on a time scale of milliseconds to seconds, rather than minutes to hours. WIREs Syst Biol Med 2018, 10:e1390. doi: 10.1002/wsbm.1390 This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Laboratory Methods and Technologies > Imaging.
The Three Ds of Transcription Activation by Glucagon: Direct, Delayed, and Dynamic
. Endocrinology 2018
Upon lowered blood glucose occurring during fasting, glucagon is secreted from pancreatic islets, exerting various metabolic effects to normalize glucose levels. A considerable portion of these effects is mediated by glucagon-activated transcription factors (TFs) in liver. Glucagon directly activates several TFs via immediate cyclic adenosine monophosphate (cAMP)- and calcium-dependent signaling events. Among these TFs, cAMP response element-binding protein (CREB) is a major factor. CREB recruits histone-modifying enzymes and cooperates with other TFs on the chromatin template to increase the rate of gene transcription. In addition to direct signal transduction, the transcriptional effects of glucagon are also influenced by dynamic TF cross talk. Specifically, assisted loading of one TF by a companion TF leads to increased binding and activity. Lastly, transcriptional regulation by glucagon is also exerted by TF cascades by which a primary TF induces the gene expression of secondary TFs that bring about their activity a few hours after the initial glucagon signal. This mechanism of a delayed response may be instrumental in establishing the temporal organization of the fasting response by which distinct metabolic events separate early from prolonged fasting. In this mini-review, we summarize recent advances and critical discoveries in glucagon-dependent gene regulation with a focus on direct TF activation, dynamic TF cross talk, and TF cascades.
The Circadian Clock in White and Brown Adipose Tissue: Mechanistic, Endocrine, and Clinical Aspects
. Endocrine reviews 2018
, 261 - 273. Publisher's VersionAbstract
Obesity is a major risk factor for the development of illnesses, such as insulin resistance and hypertension, and has become a serious public health problem. Mammals have developed a circadian clock located in the hypothalamic suprachiasmatic nuclei (SCN) that responds to the environmental light-dark cycle. Clocks similar to the one located in the SCN are found in peripheral tissues, such as the kidney, liver, and adipose tissue. The circadian clock regulates metabolism and energy homeostasis in peripheral tissues by mediating activity and/or expression of key metabolic enzymes and transport systems. Knockouts or mutations in clock genes that lead to disruption of cellular rhythmicity have provided evidence to the tight link between the circadian clock and metabolism. In addition, key proteins play a dual role in regulating the core clock mechanism, as well as adipose tissue metabolism, and link circadian rhythms with lipogenesis and lipolysis. Adipose tissues are distinguished as white, brown, and beige (or brite), each with unique metabolic characteristics. Recently, the role of the circadian clock in regulating the differentiation into the different adipose tissues has been investigated. In this review, the role of clock proteins and the downstream signaling pathways in white, brown, and brite adipose tissue function and differentiation will be reviewed. In addition, chronodisruption and metabolic disorders and clinical aspects of circadian adiposity will be addressed.
The Circadian Clock Drives Mast Cell Functions in Allergic Reactions
. Frontiers in immunology 2018
1526 - 1526. Publisher's VersionAbstract
Allergic diseases are known to vary in the severity of their symptoms throughout the day/night cycle. This rhythmicity is also observed in mast cell function and responsiveness. Mast cells are key effector cells of allergic reactions and release cytokines, chemokines, and important inflammatory mediators such as histamine, which have been shown to display diurnal variation. Recent research clarified that mast cells are controlled by their internal clock-which is regulated by a specific set of clock genes-as well as external factors such as light sensed by the suprachiasmatic nuclei, hormonal status, or diet. Here, we give an overview of the connections between circadian clock, mast cells, and allergic disease. Further work aimed at studying the role of chronotherapy/chronomedicine should take into account this rhythmic nature of not only mast cells but also the immune responses generated by mast cell signaling.
P334 Does the circadian clock have a role in the pathogenesis of inflammatory bowel disease (IBD)?
. Journal of Crohn's and Colitisecco-jcc 2018
, S270 - S271. Publisher's VersionAbstract
Sleep dysfunction modifies the immune system and has been implicated as a potential trigger of IBD flares. Sleep dysfunction also alters the synchrony among clock genes leading to disruption of overall circadian regulation. Specifically, in the intestine, it is manifested by increased gut cellular permeability. We hypothesised that changes in mucosal immune balance may be reflected by alterations in the circadian clock and constitute an unattended pathogenic mechanism of IBD. Our aim was to investigate intestinal and systemic clock gene expression (in patients with newly diagnosed IBD and in healthy controls).Patients and controls were recruited upon diagnostic endoscopic evaluation. Demographics, familial medical history, sleep questionnaires, disease activity indices, and endoscopic scores were recorded. Anthropometric parameters, C-reactive protein (CRP), albumin, haemoglobin (Hb), and fecal calprotectin (Fcal) were measured as well. Peripheral blood and tissue samples were analysed for clock gene (Clock, Bmal1, Cry1, Cry2, Per1, and Per2) expression.Of the 32 participants recruited (age 8–25 years, median: 16.1), 14 had newly diagnosed IBD and 18 were healthy controls. Age, gender, sleep questionnaire scores, and time of endoscopy were not statistically different between the groups. Hb, CRP, and Fcal levels were significantly higher in the IBD compared with the healthy controls group (p < 0.05), while albumin was significantly lower (p < 0.05). Clock gene expression (Clock, Cry1, Cry2, Per1, and Per2) in WBC was decreased in newly diagnosed IBD patients compared with health controls (p < 0.05). Similarly, the expression level of the aforementioned genes was lower in inflamed intestinal tissues (p < 0.05). Interestingly, similar reduction in clock gene expression was seen even in healthy (non-inflamed) intestinal tissue from IBD patients (p < 0.05).Clock gene expression is reduced in both inflamed and non-inflamed intestinal tissue in patients with newly diagnosed IBD. Moreover, IBD patients show a systemic reduction in clock gene expression. Our findings may lead to new therapeutic approaches and strategies as well as serve as diagnostic tools in IBD.
Circadian rhythms, nutrition and implications for longevity in urban environments
. Proceedings of the Nutrition Society 2018
, 216-222. Publisher's VersionAbstract
Presently, about 12% of the population is 65 years or older and by the year 2030 that figure is expected to reach 21%. In order to promote the well-being of the elderly and to reduce the costs associated with health care demands, increased longevity should be accompanied by ageing attenuation. Energy restriction, which limits the amount of energy consumed to 60–70% of the daily intake, and intermittent fasting, which allows the food to be available ad libitum every other day, extend the life span of mammals and prevent or delay the onset of major age-related diseases, such as cancer, diabetes and cataracts. Recently, we have shown that well-being can be achieved by resetting of the circadian clock and induction of robust catabolic circadian rhythms via timed feeding. In addition, the clock mechanism regulates metabolism and major metabolic proteins are key factors in the core clock mechanism. Therefore, it is necessary to increase our understanding of circadian regulation over metabolism and longevity and to design new therapies based on this regulation. This review will explore the present data in the field of circadian rhythms, ageing and metabolism.
Falling water ice affinity purification of ice-binding proteins
. Scientific Reports 2018
11046. Publisher's VersionAbstract
Ice-binding proteins (IBPs) permit their hosts to thrive in the presence of ice. The ability of IBPs to control ice growth makes them potential additives in industries ranging from food storage and cryopreservation to anti-icing systems. For IBPs to be used in commercial applications, however, methods are needed to produce sufficient quantities of high-quality proteins. Here, we describe a new method for IBP purification, termed falling water ice affinity purification (FWIP). The method is based on the affinity of IBPs for ice and does not require molecular tags. A crude IBP solution is allowed to flow over a chilled vertical surface of a commercial ice machine. The temperature of the surface is lowered gradually until ice crystals are produced, to which the IBPs bind but other solutes do not. We found that a maximum of 35 mg of IBP was incorporated in 1 kg of ice. Two rounds of FWIP resulted in >95% purity. An ice machine that produces 60 kg of ice per day can be used to purify one gram of IBP per day. In combination with efficient concentration of the protein solution by tangential flow filtration the FWIP method is suitable for the purification of grams of IBPs for research purposes and applications.
Application of Algebraic Topology to Homologous Recombination of DNA
. iScience 2018
64 - 67. Publisher's VersionAbstract
SummaryBrouwer's fixed point theorem, a fundamental theorem in algebraic topology proved more than a hundred years ago, states that given any continuous map from a closed, simply connected set into itself, there is a point that is mapped unto itself. Here we point out the connection between a one-dimensional application of Brouwer's fixed point theorem and a mechanism proposed to explain how extension of single-stranded DNA substrates by recombinases of the RecA superfamily facilitates significantly the search for homologous sequences on long chromosomes.
Directional freezing for the cryopreservation of adherent mammalian cells on a substrate
. PLOS ONE 2018
, e0192265 -. Publisher's VersionAbstract
Successfully cryopreserving cells adhered to a substrate would facilitate the growth of a vital confluent cell culture after thawing while dramatically shortening the post-thaw culturing time. Herein we propose a controlled slow cooling method combining initial directional freezing followed by gradual cooling down to -80°C for robust preservation of cell monolayers adherent to a substrate. Using computer controlled cryostages we examined the effect of cooling rates and dimethylsulfoxide (DMSO) concentration on cell survival and established an optimal cryopreservation protocol. Experimental results show the highest post-thawing viability for directional ice growth at a speed of 30 μm/sec (equivalent to freezing rate of 3.8°C/min), followed by gradual cooling of the sample with decreasing rate of 0.5°C/min. Efficient cryopreservation of three widely used epithelial cell lines: IEC-18, HeLa, and Caco-2, provides proof-of-concept support for this new freezing protocol applied to adherent cells. This method is highly reproducible, significantly increases the post-thaw cell viability and can be readily applied for cryopreservation of cellular cultures in microfluidic devices.
Structure of a bacterial ice binding protein with two faces of interaction with ice
. The FEBS Journal 2018
, 1653 - 1666. Publisher's VersionAbstract
Ice-binding proteins (IBPs) contribute to the survival of many living beings at subzero temperature by controlling the formation and growth of ice crystals. This work investigates the structural basis of the ice-binding properties of EfcIBP, obtained from Antarctic bacteria. EfcIBP is endowed with a unique combination of thermal hysteresis and ice recrystallization inhibition activity. The three-dimensional structure, solved at 0.84 Å resolution, shows that EfcIBP belongs to the IBP-1 fold family, and is organized in a right-handed ?-solenoid with a triangular cross-section that forms three protein surfaces, named A, B, and C faces. However, EfcIBP diverges from other IBP-1 fold proteins in relevant structural features including the lack of a ?capping? region on top of the ?-solenoid, and in the sequence and organization of the regions exposed to ice that, in EfcIBP, reveal the presence of threonine-rich ice-binding motifs. Docking experiments and site-directed mutagenesis pinpoint that EfcIBP binds ice crystals not only via its B face, as common to other IBPs, but also via ice-binding sites on the C face. Database Coordinates and structure factors have been deposited in the Protein Data Bank under accession number 6EIO.