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27 mar 2015 02:00

Germline epigenome reprogramming

Background: Exposure to environmental endocrine-disrupting chemicals during pregnancy reportedly causes transgenerationally inherited reproductive defects. We hypothesized that to affect the grandchild, endocrine-disrupting chemicals must alter the epigenome of the germ cells of the in utero-exposed G1 male fetus. Additionally, to affect the great-grandchild, the aberration must persist in the germ cells of the unexposed G2 grandchild. Results: Here, we treat gestating female mice with vinclozolin, bisphenol A, or di-(2-ethylhexyl)phthalate during the time when global de novo DNA methylation and imprint establishment occurs in the germ cells of the G1 male fetus. We map genome-wide features in purified G1 and G2 prospermatogonia, in order to detect immediate and persistent epigenetic aberrations, respectively. We detect changes in transcription and methylation in the G1 germline immediately after endocrine-disrupting chemicals exposure, but changes do not persist into the G2 germline. Additional analysis of genomic imprints shows no persistent aberrations in DNA methylation at the differentially methylated regions of imprinted genes between the G1 and G2 prospermatogonia, or in the allele-specific transcription of imprinted genes between the G2 and G3 soma. Conclusions: Our results suggest that endocrine-disrupting chemicals exert direct epigenetic effects in exposed fetal germ cells, which are corrected by reprogramming events in the next generation. Avoiding transgenerational inheritance of environmentally-caused epigenetic aberrations may have played an evolutionary role in the development of dual waves of global epigenome reprogramming in mammals.

biologia | biomed central - latest articles

27 mar 2015 02:00

Background: Symptom burden in chronic kidney disease (CKD) is poorly understood. To date, the majority of research focuses on single symptoms and there is a lack of suitable multidimensional symptom measures. The purpose of this study was to modify, translate, cross-culturally adapt and psychometrically analyse the Dialysis Symptom Index (DSI). Methods: The study methods involved four phases: modification, translation, pilot-testing with a bilingual non-CKD sample and then psychometric testing with the target population. Content validity was assessed using an expert panel. Inter-rater agreement, test-retest reliability and Cronbach’s alpha coefficient were calculated to demonstrate reliability of the modified DSI. Discriminative and convergent validity were assessed to demonstrate construct validity. Results: Content validity index during translation was 0.98. In the pilot study with 25 bilingual students a moderate to perfect agreement (Kappa statistic = 0.60-1.00) was found between English and Arabic versions of the modified DSI. The main study recruited 433 patients CKD with stages 4 and 5. The modified DSI was able to discriminate between non-dialysis and dialysis groups (p < 0.001) and demonstrated convergent validity with domains of the Kidney Disease Quality of Life short form. Excellent test-retest and internal consistency (Cronbach’s α = 0.91) reliability were also demonstrated. Conclusion: The Arabic version of the modified DSI demonstrated good psychometric properties, measures the multidimensional nature of symptoms and can be used to assess symptom burden at different stages of CKD. The modified instrument, renamed the CKD Symptom Burden Index (CKD-SBI), should encourage greater clinical and research attention to symptom burden in CKD.

biologia | biomed central - latest articles

27 mar 2015 02:00

Disputing Lamarckian epigenetic inheritance in mammals

A recent study finds that changes to transcription and DNA methylation resulting from in utero exposure to environmental endocrine-disrupting chemicals are not inherited across generations.

biologia | biomed central - latest articles

27 mar 2015 02:00

Tracheal extubation and reintubation of the critically ill - challenges coming and going

Tracheal reintubation is a common event in critical care. Elmer and colleagues provide the first comparison of complication rates of initial and subsequent reintubation(s) during the same hospitalization. Their work shows an increased risk of complications associated with reintubation, in particular hypoxemia and hypotension, reminding us to be cautious with patients having minimal reserve and potentially altered airway anatomy.See related research by Elmer et al., http://ccforum.com/content/19/1/12

biologia | biomed central - latest articles

27 mar 2015 02:00

FlowClus: efficiently filtering and denoising pyrosequenced amplicons

Background: Reducing the effects of sequencing errors and PCR artifacts has emerged as an essential component in amplicon-based metagenomic studies. Denoising algorithms have been designed that can reduce error rates in mock community data, but they change the sequence data in a manner that can be inconsistent with the process of removing errors in studies of real communities. In addition, they are limited by the size of the dataset and the sequencing technology used. Results: FlowClus uses a systematic approach to filter and denoise reads efficiently. When denoising real datasets, FlowClus provides feedback about the process that can be used as the basis to adjust the parameters of the algorithm to suit the particular dataset. When used to analyze a mock community dataset, FlowClus produced a lower error rate compared to other denoising algorithms, while retaining significantly more sequence information. Among its other attributes, FlowClus can analyze longer reads being generated from all stages of 454 sequencing technology, as well as from Ion Torrent. It has processed a large dataset of 2.2 million GS-FLX Titanium reads in twelve hours; using its more efficient (but less precise) trie analysis option, this time was further reduced, to seven minutes. Conclusions: Many of the amplicon-based metagenomics datasets generated over the last several years have been processed through a denoising pipeline that likely caused deleterious effects on the raw data. By using FlowClus, one can avoid such negative outcomes while maintaining control over the filtering and denoising processes. Because of its efficiency, FlowClus can be used to re-analyze multiple large datasets together, thereby leading to more standardized conclusions. FlowClus is freely available on GitHub (jsh58/FlowClus); it is written in C and supported on Linux.

biologia | biomed central - latest articles

27 mar 2015 02:00

Background: Plasmodium falciparum has become resistant to some of the available drugs. Several plant species are used for the treatment of malaria, such as Himatanthus articulatus in parts of Brazil. The present paper reports the phyto-chemistry, the anti-plasmodial and anti-malarial activity, as well as the toxicity of H. articulatus. Methods: Ethanol and dichloromethane extracts were obtained from the powder of stem barks of H. articulatus and later fractionated and analysed. The anti-plasmodial activity was assessed against a chloroquine resistant strain P. falciparum (W2) in vitro, whilst in vivo anti-malarial activity against Plasmodium berghei (ANKA strain) was tested in mice, evaluating the role of oxidative stress (total antioxidant capacity - TEAC; lipid peroxidation – TBARS, and nitrites and nitrates - NN). In addition, cytotoxicity was evaluated using the HepG2 A16 cell-line. The acute oral and sub-chronic toxicity of the ethanol extract were evaluated in both male and female mice. Results: Plumieride was isolated from the ethyl acetate fraction of ethanol extract, Only the dichloromethane extract was active against clone W2. Nevertheless, both extracts reduced parasitaemia in P. berghei-infected mice. Besides, a significant reduction in pulmonary and cerebral levels of NN (nitrites and nitrates) was found, as well as in pulmonary TBARS, indicating a reduced oxidative damage to these organs. The ethanol extract showed low cytotoxicity to HepG2 A16 cells in the concentrations used. No significant changes were observed in the in vivo toxicity studies. Conclusions: The ethanol extract of H. articulatus proved to be promising as anti-malarial medicine and showed low toxicity.

biologia | biomed central - latest articles

27 mar 2015 02:00

Genome sequencing of Clostridium butyricum DKU-01, isolated from infant feces

Background: Clostridium butyricum is a butyric acid-producing anaerobic bacteriuma, and commonly present as gut microbiota in humans. This species has been used as a probiotic for the prevention of diarrhea in humans. In this study, we report the draft genome of C. butyricum DKU-01, which was isolated from infant feces, to better understand the characteristics of this strain so that it can later be used in the development of probiotic products. Results: A total of 79 contigs generated by hybrid assembly of sequences obtained from Roche 454 and Illumina Miseq sequencing systems were investigated. The assembled genome of strain DKU-01 consisted of 4,519,722 bp (28.62% G + C content) with a N50 contig length of 108,221 bp and 4,037 predicted CDSs. The extracted 16S rRNA gene from genome sequences of DKU-01 was similar to Clostridium butyricum with 99.63% pairwise similarity. The sequence of strain DKU-01 was compared with previously reported genome sequences of C. butyricum. The value of average nucleotide identity between strains DKU-01 and C. butyricum 60E3 was 98.74%, making it the most similar strain to DKU-01. Conclusions: We sequenced the DKU-01 strain isolated from infant feces, and compared it with the available genomes of C. butyricum on a public database. Genes related to Fructooligosaccharide utilization were detected in the genome of strain DKU-01 and compared with other genera, such as Bifidobacterium and Streptococcus. We found that strain DKU-01 can metabolize a wide range of carbohydrates in comparative genome result. Further analyses of the comparative genome and fermentation study can provide the information necessary for the development of strain DKU-01 for probiotics.

biologia | biomed central - latest articles

27 mar 2015 02:00

Diagnosing and managing PCOS

In this podcast, we talk to Professor Richard Legro about the recommendations for the diagnosis and treatment of polycystic ovary syndrome (PCOS) based on clinical practice guidelines and discuss the challenges of diagnosis PCOS at specific age groups. The controversies associated with treatment of PCOS, including therapies for infertility as this is a problem commonly observed in PCOS subjects, are highlighted together with future directions on the topic.The podcast for this interview is available at. http://www.biomedcentral.com/content/supplementary/s12916-015-0299-2-s1.mp3

biologia | biomed central - latest articles