The footprint of metabolism in the organization of mammalian genomes

<p>Abstract</p> <p>Background</p> <p>At present five evolutionary hypotheses have been proposed to explain the great variability of the genomic GC content among and within genomes: the mutational bias, the biased gene conversion, the DNA breakpoints distribution, the thermal stability and the metabolic rate. Several studies carried out on bacteria and teleostean fish pointed towards the critical role played by the environment on the metabolic rate in shaping the base composition of genomes. In mammals the debate is still open, and evidences have been produced in favor of each evolutionary hypothesis. Human genes were assigned to three large functional categories (as well as to the corresponding functional classes) according to the KOG database: (i) information storage and processing, (ii) cellular processes and signaling, and (iii) metabolism. The classification was extended to the organisms so far analyzed performing a reciprocal Blastp and selecting the best reciprocal hit. The base composition was calculated for each sequence of the whole CDS dataset.</p> <p>Results</p> <p>The GC3 level of the above functional categories was increasing from (i) to (iii). This specific compositional pattern was found, as footprint, in all mammalian genomes, but not in frog and lizard ones. Comparative analysis of human versus both frog and lizard functional categories showed that genes involved in the metabolic processes underwent the highest GC3 increment. Analyzing the KOG functional classes of genes, again a well defined intra-genomic pattern was found in all mammals. Not only genes of metabolic pathways, but also genes involved in chromatin structure and dynamics, transcription, signal transduction mechanisms and cytoskeleton, showed an average GC3 level higher than that of the whole genome. In the case of the human genome, the genes of the aforementioned functional categories showed a high probability to be associated with the chromosomal bands.</p> <p>Conclusions</p> <p>In the light of different evolutionary hypotheses proposed so far, and contributing with different potential to the genome compositional heterogeneity of mammalian genomes, the one based on the metabolic rate seems to play not a minor role. Keeping in mind similar results reported in bacteria and in teleosts, the specific compositional patterns observed in mammals highlight metabolic rate as unifying factor that fits over a wide range of living organisms.</p

Clinical Use of a 180-Day Implantable Glucose Monitoring System in Dogs with Diabetes Mellitus: A Case Series

Simple Summary A novel continuous glucose monitoring system (CGMS) equipped with a long-term sensor has recently been developed for humans with diabetes mellitus. The sensor is inserted under the skin and continuously measures the glucose in the interstitial fluid over a period of up to 180 days. The aim of this study was to describe, for the first time, the clinical use of this novel CGMS in three diabetic dogs (DD). The insertion and use of the device were straightforward and well tolerated by the dogs. Some device-related issues, such as sensor dislocation and trouble with daily calibrations, were reported. A good correlation between the glucose values measured by this CGMS and those obtained with a flash glucose monitoring system and a portable-blood glucose meter, previously validated for use in DD, was found (rs = 0.85 and rs = 0.81, respectively). The functional life of the sensor was 180 days in two of the three dogs, and the use of the device provided high satisfaction to the owners. This innovative device might be considered a future alternative for continuous glucose monitoring in dogs with diabetes mellitus. The novel Eversense XL continuous glucose monitoring system (Senseonics, Inc., Germantown, Maryland) has recently been developed for monitoring diabetes in humans. The sensor is fully implanted and has a functional life of up to 180 days. The present study describes the use of Eversense XL in three diabetic dogs (DD) with good glycemic control managed by motivated owners. The insertion and use of the device were straightforward and well tolerated by the dogs. During the wearing period, some device-related drawbacks, such as sensor dislocation and daily calibrations, were reported. A good correlation between the glucose values measured by the Eversense XL and those obtained with two commercially available devices, previously validated for use in DD, was found (r(s) = 0.85 and r(s) = 0.81, respectively). The life of the sensor was 180 days in two of the DD and provided high satisfaction. This innovative device might be considered a future alternative for home glucose monitoring in DD

Just Drink a Glass of Water? Effects of Bicarbonate-Sulfate-Calcium-Magnesium Water on the Gut-Liver Axis

Background and Aim: Fonte Essenziale (R) water is a bicarbonate-sulfate-calcium-magnesium water, low in sodium, recognized by the Italian health care system in hydropinotherapy and hepatobiliary dyspepsia therapy. We wanted to explore its effects on the gut-liver axis and microbiota in non-alcoholic fatty liver disease patients.Patients and Methods: We considered enrollment for 70 patients, of which four were excluded. We finally enrolled 55 patients with ultrasound-documented steatosis (SPs+) and 11 patients without it (SPs-). They then drank 400 ml of water for 6 months in the morning on an empty stomach. Routine hematochemical and metabolic parameters, oxidative stress parameters, gastrointestinal hormone levels, and fecal parameters of the gut microbiota were evaluated at three different assessment times, at baseline (T0), after 6 months (T6), and after a further 6 months of water washout (T12). We lost, in follow-up, 4 (T6) and 22 (T12) patients.Results: Between T0-T6, we observed a significant Futuin A and Selenoprotein A decrease and a GLP-1 and PYY increase in SPs+ and the same for Futuin A and GLP-1 in SPs-. Effects were lost at T12. In SPs+, between T0-T12 and T6-12, a significant reduction in Blautia was observed; between T0-T12, a reduction of Collinsella unc. was observed; and between T0-T12 and T6-12, an increase in Subdoligranulum and Dorea was observed. None of the bacterial strains we analyzed varied significantly in the SPs- population.Conclusion: These results indicate beneficial effects of water on gastrointestinal hormones and hence on the gut-liver axis in the period in which subjects drank water both in SPs- and in SPs+

New silibinin glyco-conjugates: Synthesis and evaluation of antioxidant properties

New silibinin glyco-conjugates have been synthesized by efficient method and in short time. Exploiting our solution phase strategy, several structurally diverse silibinin glyco-conjugates (gluco, manno, galacto, and lacto-) were successfully realized in very good yields and in short time. In preliminary study to evaluate their antioxidant and neuroprotective activities new derivatives were subjected to DPPH free radical scavenging assay and the Xanthine oxidase (XO) inhibition models assay. Irrespective of the sugar moiety examined, new glyco-conjugates are more than 50 times water-soluble of silibinin. In the other hand they exhibit a radical scavenging activities slightly higher than to silibinin and XO inhibition at least as silibinin. (C) 2014 Elsevier Ltd. All rights reserved

Knowledge of HIV infection and ways of its transmission: a knowledge, attitudes, beliefs and practices (KABP) survey among a sample of students at the “Magna Graecia”, University of Catanzaro

Background. Continuous spreading of HIV infection may be due to a lack of knowledge, especially among young people. Methods. We decided to assess  knowledge of HIV infection and risk factors in a sample of students at the “Magna Graecia” University of Catanzaro, using an anonymous multiple-choice questionnaire. Results. An anonymous multiple-choice questionnaire was administered in December 2015. Two hundred and sixty-six students responded (216 attending the medical school and 50 attending School of Law). Knowledge of HIV infection was scarce in a significant percentage of students who practice behaviours at risk for acquisition of HIV infection and STDs (sexually transmitted diseases) in general. Conclusion. This study shows that preventative and informative campaigns are urgently needed in earlier stage of adolescence to avoid acquisition of HIV infection and other STD

Ameliorative effect of VIP family members on blood retinal barrier breakdown in diabetic macular edema

Diabetic macular edema (DME) is one of the main complications of diabetic retinopathy [1]. This pathology is owed to impairment of the blood-retinal barrier (BRB) [2]. Many factors, such as hypoxia, contribute to barrier dysfunction and progression of the disease. Low oxygen tension is one of the main events involved in the formation of new blood vessels that characterize the typical uncontrolled angiogenesis in proliferative stage of diabetic retinopathy. In the last decades, various studies have focused their attention on the role of pituitary adenylate cyclase-activating polypeptide (PACAP) and vasoactive intestinal peptide (VIP) in the pathophysiology of DME. However, the effects of these peptides in maintaining the integrity of the BRB exposed to hypoxia remains to be elucidated. In the present work we have studied, for the first time, the effect of these peptides on outer BRB integrity following hypoxic insult in an experimental model of DME. To this end, we have used the human retinal pigment epithelial cells (ARPE-19) to test the effect of both peptides on cellular permeability, transepithelial electrical resistance, tight junctions expression and hypoxia-induced apoptosis. Results have demonstrated that both PACAP and VIP are able to rescue the integrity of cell monolayer during the hypoxic event, minimizing apoptotic damages induced by low tissue oxygen tension through the activation of phosphoinositide 3 kinase /Akt and mammalian mitogen activated protein kinase/Erk kinase signaling pathways. Furthermore, these peptides modulate the expression of vascular endothelial growth factor which is one of the downstream transcription factor activated during the hypoxic process. In conclusion, we have demonstrated that PACAP and VIP are able to counteract the damage induced by hypoxia on BRB through the modulation of hypoxia inducible factors expression

Silybin-Phosphatidylcholine Complex Protects Human Gastric and Liver Cells from Oxidative Stress

Silybin is the main component of silymarin with antioxidant, anti-inflammatory and cytoprotective actions. Our aim was to compare the effect of silybin used as single substance, silybin-phosphatidylcholine complex (SilPho), and derivatives of silybin (MannpSil, GalpSil, GlcpSil, LactpSil) on MKN28 and HepG2 cell viability and cell death, in vitro, after induction of oxidative stress

The radial arrangement of the human chromosome 7 in the lymphocyte cell nucleus is associated with chromosomal band gene density

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ Springer-Verlag 2008.In the nuclei of human lymphocytes, chromosome territories are distributed according to the average gene density of each chromosome. However, chromosomes are very heterogeneous in size and base composition, and can contain both very gene-dense and very gene-poor regions. Thus, a precise analysis of chromosome organisation in the nuclei should consider also the distribution of DNA belonging to the chromosomal bands in each chromosome. To improve our understanding of the chromatin organisation, we localised chromosome 7 DNA regions, endowed with different gene densities, in the nuclei of human lymphocytes. Our results showed that this chromosome in cell nuclei is arranged radially with the gene-dense/GC-richest regions exposed towards the nuclear interior and the gene-poorest/GC-poorest ones located at the nuclear periphery. Moreover, we found that chromatin fibres from the 7p22.3 and the 7q22.1 bands are not confined to the territory of the bulk of this chromosome, protruding towards the inner part of the nucleus. Overall, our work demonstrates the radial arrangement of the territory of chromosome 7 in the lymphocyte nucleus and confirms that human genes occupy specific radial positions, presumably to enhance intra- and inter-chromosomal interaction among loci displaying a similar expression pattern, and/or similar replication timing

Focus on the Use of Resveratrol in Bladder Cancer

Bladder cancer is the most common tumor of the urinary system, with a high incidence in the male population. Surgery and intravesical instillations can eradicate it, although recurrences are very common, with possible progression. For this reason, adjuvant therapy should be considered in all patients. Resveratrol displays a biphasic dose response both in vitro and in vivo (intravesical application) with an antiproliferative effect at high concentrations and antiangiogenic action in vivo (intraperitoneal application) at a low concentration, suggesting a potential role for it in clinical management as an adjuvant to conventional therapy. In this review, we examine the standard therapeutical approach to bladder cancer and the preclinical studies that have investigated resveratrol in xenotransplantation models of bladder cancer. Molecular signals are also discussed, with a particular focus on the STAT3 pathway and angiogenic growth factor modulation