Chromatin regulatory genes differentially interact in networks to facilitate distinct GAL1 activity and noise profiles.

Controlling chromatin state constitutes a major regulatory step in gene expression regulation across eukaryotes. While global cellular features or processes are naturally impacted by chromatin state alterations, little is known about how chromatin regulatory genes interact in networks to dictate downstream phenotypes. Using the activity of the canonical galactose network in yeast as a model, here, we measured the impact of the disruption of key chromatin regulatory genes on downstream gene expression, genetic noise and fitness. Using Trichostatin A and nicotinamide, we characterized how drug-based modulation of global histone deacetylase activity affected these phenotypes. Performing epistasis analysis, we discovered phenotype-specific genetic interaction networks of chromatin regulators. Our work provides comprehensive insights into how the galactose network activity is affected by protein interaction networks formed by chromatin regulators.

Characterization of the impact of GMP/GDP synthesis inhibition on replicative lifespan extension in yeast.

Slowing down aging-associated accumulation of molecular damage or its prevention represents a promising therapeutic paradigm to combat aging-related disease and death. While several chemical compounds extend lifespan in model organisms, their mechanism of action is often unknown, reducing their therapeutic potential. Using a systematic approach, here we characterize the impact of the GMP pathway on yeast lifespan and elucidate GMP synthesis inhibition as a lifespan extension mechanism. We further discover that proteasome activation extends lifespan in part through the GMP pathway. GMP synthesis inhibition exerts its lifespan extension effect independently of the canonical nutrient-sensing pathway regulating lifespan. Exposing longitudinally aging yeast cells to GMP pathway inhibition in an age-dependent manner, we demonstrate that the lifespan extension is facilitated by slowing, rather than reversing, the aging process in cells. Using a GUK1 mutant with lower GMP-to-GDP conversion activity, we observe lifespan extension, suggesting that reduced GDP level by itself can also extend yeast lifespan. These findings elucidate the involvement of nucleotide metabolism in the aging process. The existence of clinically-approved GMP pathway inhibitors elicits the potential of a new class of therapeutics for aging-related disorders.

Photophysical Properties of Some Fluorescent Dyes in SDS Micellar Solutions.

Photophysical properties of fluorescent dyes such as Safranin T, Acridine Orange, Pyronin B and Pyronin Y in SDS micelles were examined by using spectroscopic techniques. Firstly, spherical micelles in deionized water were prepared with Sodium Dodecyl Sulfate (SDS) surfactants and they were transformed into their layered structures (lamellar micelles) by the aid of NaCl (sodium chloride). SEM studies confirmed the transformation of SDS micelles from the spherical structures to the lamellar structures. Secondly, absorption and fluorescence characteristics of the dyes in deionized water and the SDS micelles aqueous solutions were characterized in the presence of various NaCl concentrations at above the critical micelle concentration (CMC). Moreover, the photophysical properties of the dyes in various media were discussed by fluorescence quantum yield and fluorescence lifetime data. The micellar structures called a mimetic membrane system changed the photophysical properties of the dyes compared to those in deionized water.

Stochastic modeling of aging cells reveals how damage accumulation, repair, and cell-division asymmetry affect clonal senescence and population fitness.

BACKGROUND: Asymmetry during cellular division, both in the uneven partitioning of damaged cellular components and of cell volume, is a cell biological phenomenon experienced by many unicellular organisms. Previous work based on a deterministic model claimed that such asymmetry in the partitioning of cell volume and of aging-associated damage confers a fitness benefit in avoiding clonal senescence, primarily by diversifying the cellular population. However, clonal populations of unicellular organisms are already naturally diversified due to the inherent stochasticity of biological processes. RESULTS: Applying a model of aging cells that accounts for natural cell-to-cell variations across a broad range of parameter values, here we show that the parameters directly controlling the accumulation and repair of damage are the most important factors affecting fitness and clonal senescence, while the effects of both segregation of damaged components and division asymmetry are frequently minimal and generally context-dependent. CONCLUSIONS: We conclude that damage segregation and division asymmetry, perhaps counterintuitively, are not necessarily beneficial from an evolutionary perspective.

Scarless genome editing: progress towards understanding genotype-phenotype relationships.

The ability to predict phenotype from genotype has been an elusive goal for the biological sciences for several decades. Progress decoding genotype-phenotype relationships has been hampered by the challenge of introducing precise genetic changes to specific genomic locations. Here we provide a comparative review of the major techniques that have been historically used to make genetic changes in cells as well as the development of the CRISPR technology which enabled the ability to make marker-free disruptions in endogenous genomic locations. We also discuss how the achievement of truly scarless genome editing has required further adjustments of the original CRISPR method. We conclude by examining recently developed genome editing methods which are not reliant on the induction of a DNA double strand break and discuss the future of both genome engineering and the study of genotype-phenotype relationships.

Mechanisms for the epigenetic inheritance of stress response in single cells.

Cells have evolved to dynamically respond to different types of environmental and physiological stress conditions. The information about a previous stress stimulus experience by a mother cell can be passed to its descendants, allowing them to better adapt to and survive in new environments. In recent years, live-cell imaging combined with cell-lineage tracking approaches has elucidated many important principles that guide stress inheritance at the single-cell and population level. In this review, we summarize different strategies that cells can employ to pass the 'memory' of previous stress responses to their descendants. Among these strategies, we focus on a recent discovery of how specific features of Msn2 nucleo-cytoplasmic shuttling dynamics could be inherited across cell lineages. We also discuss how stress response can be transmitted to progenies through changes in chromatin and through partitioning of anti-stress factors and/or damaged macromolecules between mother and daughter cells during cell division. Finally, we highlight how emergent technologies will help address open questions in the field.

Acute aortic dissection mimicking acute abdomen in a 14-year-old boy.

Aortic dissection is extremely rare in children. Although it usually presents with severe chest pain, atypical clinical presentations mimicking various illnesses may cause misdiagnosis. In this report, the case of a 14-year-old boy with symptoms suggestive of acute abdomen, which was finally diagnosed as aortic dissection, is discussed.

Rhodamine 101-graphene oxide composites in aqueous solution: the fluorescence quenching process of rhodamine 101.

The interaction of rhodamine 101 (Rh101) with graphene oxide (GO) in aqueous dispersion was examined using advanced spectroscopic techniques. Rh101-GO composites in water were easily prepared by mixing an aqueous solution of both components since GO sheets interacted with the cationic dyes via π-π and electrostatic cooperative interactions. In the composites, the fluorescence of Rh101, which was a well-known laser dye with a high fluorescence quantum yield, could be efficiently quenched by GO. The quenching mechanism of Rh101 by GO sheets was evaluated by the Stern-Volmer (SV) equation and the time-resolved fluorescence studies. The results revealed that the fluorescence quenching of Rh101 by GO in the aqueous dispersion is due to the static quenching mechanism. The formation of the Rh101-GO composites at various pH values was spectroscopically monitored, and the spectroscopic results revealed that the composites were formed at the pH values studied except in the strong acidic media (pH ≈ 2). The interaction of Rh101 with GO in aqueous solution was spectroscopically followed in the presence of SDS (sodium dodecyl sulphate) at the surfactant concentrations above and below the CMC (critical micelle concentration). The fluorescence studies revealed that the fluorescence of Rh101 in the aqueous solution remarkably increased at the surfactant concentration forming the micelle of SDS.

Integration of ultrasound findings with Alvarado score in children with suspected appendicitis.

BACKGROUND: The aim of this study was to investigate the integration of ultrasound (US) findings with Alvarado score in diagnosing or excluding acute appendicitis. METHODS: Data were analyzed in 122 pediatric patients with suspected appendicitis who had undergone US. The US findings were classified into four groups, and the patients were classified into three groups according to Alvarado score. US results and Alvarado score were compared. RESULTS: Alvarado score was a good predictor of appendicitis for scores ≥7. CONCLUSION: In the case of non-visualization of the appendix without a high Alvarado score, appendicitis can be safely ruled out.

Comparison between flexible collagen and vein conduits used for size-discrepant nerve repair: an experimental study in rats.

Primary nerve repair is the gold standard in nerve reconstruction. When primary repair is not possible for injured nerves, conduit-assisted repair methods are frequently used. As conduits, autologous vein segments or allogenic biodegradable products can be used. However, their effectiveness when used in a nerve defect where a size discrepancy exists has not been compared. In this study, either a vein graft or a synthetic collagen conduit was used to bridge 10-mm defects between size-discrepant tibial and peroneal nerves in a rat model. After 90 days, nerve regeneration was evaluated using electrophysiological and histological methods. It can be concluded based on the results of this study that bridging a 10-mm nerve gap with synthetic collagen conduits and autologous vein grafts yielded similar results in small-to-large nerve coaptations, with the vein graft being slightly more effective.

Fluorometric and colorimetric sensor for selective detection of cyanide anion by dibenzosuberenone-based dihydropyridazine in aqueous solution.

A new chemosensory based on deprotonation and intramolecular charge transfer (ICT) was developed to detect cyanide in food samples. Deprotonation was facilitated by increasing the acidity of the NH proton in the dibenzosuberenone-based dihydropyridazine chemosensor Pz3 with -CN substituents. Addition of cyanide to acetonitrile and aqueous acetonitrile solution (1/9) of Pz3 resulted in their significant color change from colorless to purple in visible light, accompanied by a strong red shift in the absorption spectrum. Meanwhile, the near-infrared (NIR) emission (ex. 525 nm, em. 670 nm) of Pz3- resulting from deprotonation showed fluorescence switching behavior to detect the cyanide anion. While the acidic NH protons interact with basic anions as F-, CN-, OAc- and H2PO4- in organic solution (MeCN), just CN ions interact with in aqueous organic solutions (H2O-MeCN 1/9 HEPES pH 7.4). The limit of detection of cyanide from the fluorescence spectrum is 80 nM, which is well below the value determined for drinking water by World Health Organization (WHO). The interference effect of cations and anions showed that Pz3 could play an important role in the determination of waste NaCN. In addition, Pz3 successfully carried out the selective detection of cyanide in food samples such as bitter almonds and sprouting potatoes.

Rationally reprogramming single-cell aging trajectories and lifespan through dynamic modulation of environmental inputs.

How do variations in nutrient levels influence cellular lifespan? A dynamical systems model of a core circuit involved in yeast aging suggests principles underlying lifespan extension observed at static and alternating glucose levels that are reminiscent of intermittent fasting regimens.

Astaxanthin and meclizine extend lifespan in UM-HET3 male mice; fisetin, SG1002 (hydrogen sulfide donor), dimethyl fumarate, mycophenolic acid, and 4-phenylbutyrate do not significantly affect lifespan in either sex at the doses and schedules used.

In genetically heterogeneous (UM-HET3) mice produced by the CByB6F1 × C3D2F1 cross, the Nrf2 activator astaxanthin (Asta) extended the median male lifespan by 12% (p = 0.003, log-rank test), while meclizine (Mec), an mTORC1 inhibitor, extended the male lifespan by 8% (p = 0.03). Asta was fed at 1840 ± 520 (9) ppm and Mec at 544 ± 48 (9) ppm, stated as mean ± SE (n) of independent diet preparations. Both were started at 12 months of age. The 90th percentile lifespan for both treatments was extended in absolute value by 6% in males, but neither was significant by the Wang-Allison test. Five other new agents were also tested as follows: fisetin, SG1002 (hydrogen sulfide donor), dimethyl fumarate, mycophenolic acid, and 4-phenylbutyrate. None of these increased lifespan significantly at the dose and method of administration tested in either sex. Amounts of dimethyl fumarate in the diet averaged 35% of the target dose, which may explain the absence of lifespan effects. Body weight was not significantly affected in males by any of the test agents. Late life weights were lower in females fed Asta and Mec, but lifespan was not significantly affected in these females. The male-specific lifespan benefits from Asta and Mec may provide insights into sex-specific aspects of aging.

MRI assessment of percutaneous ablation of liver tumors: value of subtraction images.

PURPOSE: To evaluate the value of subtraction images when using MRI to assess liver tumors treated with percutaneous ablation. MATERIALS AND METHODS: Following percutaneous ablation of 35 liver tumors, two abdominal radiologists, blinded to outcomes, independently reviewed follow-up MRI examinations for tumoral enhancement suggestive of residual/recurrent tumor and rated their confidence level. After one year, the readers reviewed the same examinations with added subtraction images. Accuracy of the detection of residual/recurrent tumor and contrast-to-noise ratios (CNR; for tumoral enhancement-to-liver, tumoral enhancement-to-ablation zone, and ablation zone-to-liver) were calculated with and without subtraction images and compared using Wilcoxon signed rank test. Interobserver variability was computed using Kappa (κ) statistics. RESULTS: Residual/recurrent tumor was present in 8 (23.5%) of 34 tumors. Accuracy of detecting residual/recurrent tumor with subtraction images and interobserver agreement (κ = 0.72, good) were better than accuracy of detecting residual/recurrent tumor and interobserver agreement (κ = 0.57, moderate) of enhanced MR images without subtraction. Mean CNR of subtraction images was significantly higher than that of enhanced MR images for tumoral enhancement-to-liver (0.2 ± 5 versus 11.6 ± 14.4, P = 0.03), tumoral enhancement-to-ablation zone (10.1 ± 12.5 versus 34.4 ± 29.4, P = 0.02), and ablation zone-to-liver (11.8 ± 13.3 versus 102.5 ± 238.4, P = 0.03). CONCLUSION: When using MRI, subtraction images help both detect and exclude residual/recurrent tumor following percutaneous liver ablations.

Sis2 regulates yeast replicative lifespan in a dose-dependent manner.

Application of microfluidic platforms facilitated high-precision measurements of yeast replicative lifespan (RLS); however, comparative quantification of lifespan across strain libraries has been missing. Here we microfluidically measure the RLS of 307 yeast strains, each deleted for a single gene. Despite previous reports of extended lifespan in these strains, we found that 56% of them did not actually live longer than the wild-type; while the remaining 44% showed extended lifespans, the degree of extension was often different from what was previously reported. Deletion of SIS2 gene led to the largest RLS increase observed. Sis2 regulated yeast lifespan in a dose-dependent manner, implying a role for the coenzyme A biosynthesis pathway in lifespan regulation. Introduction of the human PPCDC gene in the sis2Δ background neutralized the lifespan extension. RNA-seq experiments revealed transcriptional increases in cell-cycle machinery components in sis2Δ background. High-precision lifespan measurement will be essential to elucidate the gene network governing lifespan.

Age-related volumetric changes in pancreas: a stereological study on computed tomography.

PURPOSE: (1) To explore age-related changes in the volume of the pancreas on computed tomography (CT) images calculated by the method of Cavalieri. (2) To investigate the relationship between these changes and body mass index (BMI), gender, abdominal diameter, abdominal skinfold thickness. METHODS: We retrospectively reviewed abdominal CT examinations of 272 adults between the ages of 20-88 years. There were seven groups of patients, with 40 patients (only ninth decade has 32 patients) for each decade. RESULTS: Pancreatic volume (PV) was found to be 63.68 ± 15.08 cm(3) in females, 71.75 ± 15.99 cm(3) in males (mean value of both groups, 67.71 ± 16.03 cm(3)). Maximum value of PV was found in the fourth decade in females, males and also for mean of both groups (73.50, 84.21 and 78.85 cm(3), respectively). PV remained constant until ~60 years of age. Thereafter, it gradually decreased in both genders. There was a negative correlation between PV and age (p < 0.001, r: -0.473). We found positive correlation between PV and BMI, sagittal abdominal diameter (SAD), transverse abdominal diameter (TAD), anterior subcutaneous adipose tissue thicknesses (ASAT), posterior subcutaneous adipose tissue thicknesses (PSAT), bilateral subcutaneous adipose tissue thicknesses (BSAT). CONCLUSIONS: Quantitative data may allow clinicians to better estimate age-related PV changes and help them in decision making.

Phenotypic selection during laboratory evolution of yeast populations leads to a genome-wide sustainable chromatin compaction shift.

In a previous study, we have shown how microbial evolution has resulted in a persistent reduction in expression after repeatedly selecting for the lowest PGAL1-YFP-expressing cells. Applying the ATAC-seq assay on samples collected from this 28-day evolution experiment, here we show how genome-wide chromatin compaction changes during evolution under selection pressure. We found that the chromatin compaction was altered not only on GAL network genes directly impacted by the selection pressure, showing an example of selection-induced non-genetic memory, but also at the whole-genome level. The GAL network genes experienced chromatin compaction accompanying the reduction in PGAL1-YFP reporter expression. Strikingly, the fraction of global genes with differentially compacted chromatin states accounted for about a quarter of the total genome. Moreover, some of the ATAC-seq peaks followed well-defined temporal dynamics. Comparing peak intensity changes on consecutive days, we found most of the differential compaction to occur between days 0 and 3 when the selection pressure was first applied, and between days 7 and 10 when the pressure was lifted. Among the gene sets enriched for the differential compaction events, some had increased chromatin availability once selection pressure was applied and decreased availability after the pressure was lifted (or vice versa). These results intriguingly show that, despite the lack of targeted selection, transcriptional availability of a large fraction of the genome changes in a very diverse manner during evolution, and these changes can occur in a relatively short number of generations.

Phenotypic plasticity as a facilitator of microbial evolution.

Tossed about by the tides of history, the inheritance of acquired characteristics has found a safe harbor at last in the rapidly expanding field of epigenetics. The slow pace of genetic variation and high opportunity cost associated with maintaining a diverse genetic pool are well-matched by the flexibility of epigenetic traits, which can enable low-cost exploration of phenotypic space and reactive tuning to environmental pressures. Aiding in the generation of a phenotypically plastic population, epigenetic mechanisms often provide a hotbed of innovation for countering environmental pressures, while the potential for genetic fixation can lead to strong epigenetic-genetic evolutionary synergy. At the level of cells and cellular populations, we begin this review by exploring the breadth of mechanisms for the storage and intergenerational transmission of epigenetic information, followed by a brief review of common and exotic epigenetically regulated phenotypes. We conclude by offering an in-depth coverage of recent papers centered around two critical issues: the evolvability of epigenetic traits through Baldwinian adaptive phenotypic plasticity and the potential for synergy between epigenetic and genetic evolution.

Enhancement of cellular memory by reducing stochastic transitions.

On induction of cell differentiation, distinct cell phenotypes are encoded by complex genetic networks. These networks can prevent the reversion of established phenotypes even in the presence of significant fluctuations. Here we explore the key parameters that determine the stability of cellular memory by using the yeast galactose-signalling network as a model system. This network contains multiple nested feedback loops. Of the two positive feedback loops, only the loop mediated by the cytoplasmic signal transducer Gal3p is able to generate two stable expression states with a persistent memory of previous galactose consumption states. The parallel loop mediated by the galactose transporter Gal2p only increases the expression difference between the two states. A negative feedback through the inhibitor Gal80p reduces the strength of the core positive feedback. Despite this, a constitutive increase in the Gal80p concentration tunes the system from having destabilized memory to having persistent memory. A model reveals that fluctuations are trapped more efficiently at higher Gal80p concentrations. Indeed, the rate at which single cells randomly switch back and forth between expression states was reduced. These observations provide a quantitative understanding of the stability and reversibility of cellular differentiation states.