The RHNumtS compilation: Features and bioinformatics approaches to locate and quantify Human NumtS

<p>Abstract</p> <p>Background</p> <p>To a greater or lesser extent, eukaryotic nuclear genomes contain fragments of their mitochondrial genome counterpart, deriving from the random insertion of damaged mtDNA fragments. NumtS (Nuclear mt Sequences) are not equally abundant in all species, and are redundant and polymorphic in terms of copy number. In population and clinical genetics, it is important to have a complete overview of NumtS quantity and location. Searching PubMed for NumtS or Mitochondrial pseudo-genes yields hundreds of papers reporting Human NumtS compilations produced by <it>in silico </it>or wet-lab approaches. A comparison of published compilations clearly shows significant discrepancies among data, due both to unwise application of Bioinformatics methods and to a not yet correctly assembled nuclear genome. To optimize quantification and location of NumtS, we produced a consensus compilation of Human NumtS by applying various bioinformatics approaches.</p> <p>Results</p> <p>Location and quantification of NumtS may be achieved by applying database similarity searching methods: we have applied various methods such as Blastn, MegaBlast and BLAT, changing both parameters and database; the results were compared, further analysed and checked against the already published compilations, thus producing the Reference Human Numt Sequences (RHNumtS) compilation. The resulting NumtS total 190.</p> <p>Conclusion</p> <p>The RHNumtS compilation represents a highly reliable reference basis, which may allow designing a lab protocol to test the actual existence of each NumtS. Here we report preliminary results based on PCR amplification and sequencing on 41 NumtS selected from RHNumtS among those with lower score. In parallel, we are currently designing the RHNumtS database structure for implementation in the HmtDB resource. In the future, the same database will host NumtS compilations from other organisms, but these will be generated only when the nuclear genome of a specific organism has reached a high-quality level of assembly.</p

Phenolic Compounds Recovery from Grape Fruit and By- Products: An Overview of Extraction Methods

Phenolic compounds are considered as bioactive compounds having beneficial effects on human health. Because of their biological properties, they have wide applications on pharmaceutical and food industries, and for this reason, it is important to identify most appropriate procedures, which permits the standardization for recovery of these compounds from several plant materials including grapes. Grape fruit and by-products are excellent sources of bioactive compounds such as pigments, organic acids, and phenolic compounds. Several convectional and emerging technologies have been evaluated in order to recover phenolic compounds from grape fruits and wastes such as chemical, physical, and biotechnological techniques, which offer different advantages related to economic, environmental, time-saving, and yield aspects. Nowadays, there is no updated information, which provides an overview about the techniques applied of these bioactive compound recovery in order to obtain high-quality and high-activity extracts rich in phenolic compounds from grape fruit and by-products. This chapter offers relevant aspects related to the techniques employed during the last five years by researches for phenolic compound recovery from grapes

Evaluation of the Environmental Fate of a Semivolatile Transformation Product of Ibuprofen Based on a Simple Two-Media Fate Model

Partitioning between surface waters and the atmosphere is an important process, influencing the fate and transport of semi-volatile contaminants. In this work, a simple methodology that combines experimental data and modeling was used to investigate the degradation of a semi-volatile pollutant in a two-phase system (surface water + atmosphere). 4-Isobutylacetophenone (IBAP) was chosen as a model contaminant; IBAP is a toxic transformation product of the non-steroidal, anti-inflammatory drug ibuprofen. Here, we show that the atmospheric behavior of IBAP would mainly be characterized by reaction with center dot OH radicals, while degradation initiated by center dot NO3 or direct photolysis would be negligible. The present study underlines that the gas phase reactivity of IBAP with center dot OH is faster, compared to the likely kinetics of volatilization from aqueous systems. Therefore, it might prove very difficult to detect gas-phase IBAP. Nevertheless, up to 60% of IBAP occurring in a deep and dissolved organic carbon-rich water body might be eliminated via volatilization and subsequent reaction with gas-phase center dot OH. The present study suggests that the gas-phase chemistry of semi-volatile organic compounds which, like IBAP, initially occur in natural water bodies in contact with the atmosphere is potentially very important in some environmental conditions.Peer reviewe

Fluctuations in phenolic content, ascorbic acid and total carotenoids and antioxidant activity of fruit beverages during storage

Stability of the total phenolic content, ascorbic acid, total carotenoids and antioxidant activity in eight fruit beverages was analyzed. The influence of storage temperature (4, 8 and 11 °C) during the product shelf-life (20 days) was evaluated. Pomegranate Juice presented the highest values for antioxidant activity by DPPH• assay (552.93 ± 6.00 GAE μg mL−1), total carotenoids (3.18 ± 0.11 βCE μgmL−1), and total phenolic content (3967.07 ± 2.47 GAE μg mL−1); while Splash Blend recorded the highest levels of ascorbic acid (607.39 ± 2.13 AAE μg mL−1). The antioxidant capacity was stable at 4 and 8 °C for the first 8 days of storage; while carotenoids and ascorbic acid were slightly degraded through the storage time, possibly due to oxidation and/or reactions with other compounds. The results suggest that the observed variation during testing could be related to storage conditions of the final product

Mutant MYO1F alters the mitochondrial network and induces tumor proliferation in thyroid cancer

Familial aggregation is a significant risk factor for the development of thyroid cancer and Familial Non-Medullary Thyroid Cancer (FNMTC) accounts for 5-7% of all NMTC. Whole Exome Sequencing analysis in the family affected by FNMTC with oncocytic features where our group previously identified a predisposing locus on chromosome 19p13.2, revealed a novel heterozygous mutation (c.400G>A, NM_012335; p.Gly134Ser) in exon 5 of MYO1F, mapping to the linkage locus. In the thyroid FRTL-5 cell model stably expressing the mutant MYO1F p.Gly134Ser protein we observed an altered mitochondrial network, with increased mitochondrial mass and a significant increase of both intracellular and extracellular Reactive Oxygen Species, compared to cells expressing the wild-type protein or carrying the empty vector. The mutation conferred a significant advantage in colony formation, invasion and anchorage independent growth. These data were corroborated by in vivo studies in zebrafish, since we demonstrated that the mutant MYO1F p.Gly134Ser, when overexpressed, can induce proliferation in whole vertebrate embryos, compared to the wild-type one. MYO1F screening in additional 192 FNMTC families identified another variant in exon 7, which leads to exon skipping, and is predicted to alter the ATP-binding domain in MYO1F. Our study identified for the first time a role for MYO1F in NMTC. This article is protected by copyright. All rights reserved

Chronic pain and spinal cord stimulation.

Chronic pain can have a devastating impact and lead to patient isolation. Many people with chronic pain are predisposed to anxiety-depressant symptoms, due to a lower quality life. The aim of the study is to demonstrate how neuromodulation methods, can encourage the reduction of chronic pain and an improvement in the quality of life, therefore advancing the restoration of psychological well-being.We involved 50 patients with a diagnosis of pain that not respond to traditional pharmacological therapies. Interventions: All subject had depression and anxiety symptoms and a low-quality life. We used the spinal cord stimulation treatment and a psychological evaluation for assessment of depression-anxiety symptomatology and the level of quality life.We observed a significant difference in physical functioning, role limitations due to physical health, general health perceptions, vitality, social functioning, role limitations due to emotional problems and mental health.Our study affirms that the perception of chronic pain has a great impact on the perception of psychological well-being, quality of life, and the performance of normal daily social and professional activities

Polyphenolic Profile and Antioxidant Activity of Leaf Purified Hydroalcoholic Extracts from Seven Mexican Persea americana Cultivars

Persea americana (avocado) is a fruit consumed worldwide; however, since avocado leaves are apparently a natural ingredient that can be used as a traditional medicine, they can be a potential source of bioactive compounds. This study aimed to analyze the antioxidant activity of seven Mexican avocado leaf extracts by DPPH•, ABTS•+, and lipid peroxidation (LPO), and to identify the compoundprofilebyliquidchromatographycoupledtomassspectrometry/electronsprayionization. The highest free radical-scavenging activity was observed for Platano Delgado and Criollo 6 avocado cultivars havin IC50 values of 271.86 ± 13.69 and 269.56 ± 6.53 for DPPH• and ABTS•+ radicals, respectively, while the best result for lipid oxidation inhibition was registered in Criollo 6 cultivar extract. Inthisstudyfortyonecompoundsweredetectedinavocadoleavesofthethesevencultivars analyzed, and of these compounds, eighteen phenolics were identified for first time in such plant material. The present study demonstrated that Mexican cultivars of Persea americana possess diverse polyphenolic compounds with strong antioxidant activity, which might be useful in the food and pharmaceutical industries

Atmospheric breakdown chemistry of the new "green" solvent 2,2,5,5-tetramethyloxolane via gas-phase reactions with OH and Cl radicals

The atmospheric chemistry of 2,2,5,5-tetramethyloxolane (TMO), a promising "green"solvent replacement for toluene, was investigated in laboratory-based experiments and computational calculations. Results from both absolute and relative rate studies demonstrated that the reaction OH + TMO (Reaction R1) proceeds with a rate coefficient k1(296 K) = (3.1±0.4) ×10-12 cm3 molecule-1 s-1, a factor of 3 smaller than predicted by recent structure-activity relationships. Quantum chemical calculations (CBS-QB3 and G4) demonstrated that the reaction pathway via the lowest-energy transition state was characterised by a hydrogen-bonded pre-reaction complex, leading to thermodynamically less favoured products. Steric hindrance from the four methyl substituents in TMO prevents formation of such H-bonded complexes on the pathways to thermodynamically favoured products, a likely explanation for the anomalous slow rate of Reaction (R1). Further evidence for a complex mechanism was provided by k1(294-502 K), characterised by a local minimum at around T=340 K. An estimated atmospheric lifetime of τ1 ≈3 d was calculated for TMO, approximately 50 % longer than toluene, indicating that any air pollution impacts from TMO emission would be less localised. An estimated photochemical ozone creation potential (POCPE) of 18 was calculated for TMO in north-western Europe conditions, less than half the equivalent value for toluene. Relative rate experiments were used to determine a rate coefficient of k2(296 K) = (1.2±0.1) ×10-10 cm3 molecule-1 s-1 for Cl + TMO (Reaction R2); together with Reaction (R1), which is slow, this may indicate an additional contribution to TMO removal in regions impacted by high levels of atmospheric chlorine. All results from this work indicate that TMO is a less problematic volatile organic compound (VOC) than toluene