Music of metagenomics—a review of its applications,analysis pipeline,and associated tools

Functional & Integrative Genomics - This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the...     

Phosphorylation of p40AUF1 regulates binding to A + U-rich mRNA-destabilizing elements and protein-induced changes in ribonucleoprotein structure

Messenger RNA turnover directed by A + U-rich elements (AREs) involves selected ARE-binding proteins. Whereas several signaling systems may modulate ARE-directed mRNA decay and/or post-translationally modify specific trans-acting factors, it is unclear how these mechanisms are linked. In THP-1 monocytic leukemia cells, phorbol ester-induced stabilization of some mRNAs containing AREs was accompanied by dephosphorylation of Ser83 and Ser87 of polysome-associated p40AUF1. Here, we report that phosphorylation of p40AUF1 influences its ARE-binding affinity as well as the RNA conformational dynamics and global structure of the p40AUF1-ARE ribonucleoprotein complex. Most notably, association of unphosphorylated p40AUF1 induces a condensed RNA conformation upon ARE substrates. By contrast, phosphorylation of p40AUF1 at Ser83 and Ser87 inhibits this RNA structural transition. These data indicate that selective AUF1 phosphorylation may regulate ARE-directed mRNA turnover by remodeling local RNA structures, thus potentially altering the presentation of RNA and/or protein determinants involved in subsequent trans-factor recruitment.     

Concentations of copper, Zinc, and magnesium in sera from patients with idiopathic dilated cardiomyopathy

Trace elements are known to have a key role in myocardial metabolism. The accumulation (cobalt, arsenic, copper) or deficiency (selenium, zinc) of trace elements may be responsible for idiopathic dilated cardiomyopathy. We investigated the trace element concentrations (Cu, Zn, Mg) in sera from patients with dilated cardiomyopathy by atomic absorption spectrophotometry. We observed that patients with dilated cardiomyopathies have higher copper and lower zinc concentrations in serum than healthy controls. The magnesium concentrations of patients did not differ significantly from that of control subjects.     

Serum free prostate-specific antigen and zinc levels in experimental acute pancreatitis

Serum free prostate-specific antigen (fPSA) is the most useful tumor marker for prostatic cancer screening. However, recently, fPSA has also been detected in sera from patients with pancreatic diseases. In addition, it has been shown that zinc (Zn) concentration might change in both serum and tissues in pancreatic disease. In the present study, we measured serum concentrations of fPSA and Zn as possible markers and prognostic factors in an experimental acute-pancreatitis model. Twenty-five female Wistar albino rats were divided into two groups: the control group (n=10) and the experimental group (n=15). Acute pancreatitis was induced by injection of ethyl alcohol into the common biliary duct. The animals were sacrificed 24 h later to detect the concentrations of serum fPSA and Zn. fPSA values were detected to be significantly higher in the experimental group p<0.001). There was also a significant decrease in the serum Zn level of the acute-pancreatitis group (p<0.001). In conclusion, these findings suggested that a combination of these parameters might represent a significant improvement on the diagnostic value of each of them separately and provide a powerful tool for differential diagnosis and prognosis in pancreatic diseases.     

Prevalence of enterotoxigenic Bacteroides fragilis in patients with diarrhea: a controlled study

In this age matched controlled study performed in Malatya, a city in east region of Turkey, enterotoxigenic Bacteroides fragilis (ETBF) was investigated in stool specimens obtained from children and adults with and without diarrhea. A nested polymerase chain reaction (PCR) method was used to detect the enterotoxin gene of B. fragilis in a total of 418 stool samples, including 221 samples from 117 children (aged 0-16 years) and 104 adults (aged >16 years) with diarrhea, and 197 samples from 102 children and 95 adults as control group that was the same age group with those having diarrhea. ETBF was detected in 13 of 117 diarrheal children (11.1%) and 8 of 102 control children (7.8%) (P>0.05). In children aged 1-5 years, the rate of ETBF was significantly higher in patients than in controls (25% versus 9.5%, respectively; P<0.05). On the other hand ETBF was detected similar rates (2.2% and 2.4%, respectively) in children younger than 1 year in both patients and controls. ETBF positivity was not significantly difference between patient and control groups who were older than 5 years of age and adults. The frequency of ETBF in the controls was slightly higher in older persons than in younger ones; however, it was not significant. The rate of ETBF as the only enteropathogen in the patients with ETBF was significantly higher than in controls with ETBF (88% versus 39%, respectively; P<0.02). We found that in east region of Turkey, the prevalence of ETBF was higher in the childhood diarrhea, particularly in aged 1-5. As the only enteropathogen, ETBF may play an important role in diarrheal diseases. Persons after 6 years old can be carrier for ETBF regardless diarrhea.     

Impact of Cu and Fe concentrations on oxidative damage in male infertility

Oxidative stress in the reproductive system is thought to have an effect on the fertilizing ability of sperm. The purpose of this study was to assess the interaction of iron (Fe) and copper (Cu) ions in suspected subfertile and fertile male groups and to find out the relationships of the semen parameters (sperm count, motility, and abnormal morphology), glutathione, malondialdehyde, and reactive oxygen species with these variables. Semen and blood obtained from 60 subfertile men and from 40 fertile volunteers were examined. The sperm count and motility in the subfertile male group were found lower than those in fertile male group (p<0.001). Cu levels in serum and seminal plasma in the subfertile male group were significantly higher than those in the fertile male group (p<0.001 and p<0.05, respectively). There was also a significant increase in the Fe level of seminal plasma in the subfertile male group (p<0.001). However, there was no significant difference in the Fe level of serum in the subfertile male group. In conclusion, these findings suggest that Cu and Fe might be mediators of the effects of oxidative damage and play an essential role in spermatogenesis and male infertility; the determination of Fe and Cu levels in serum and seminal plasma during infertility investigation is recommended.     

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454

We present an automated, high throughput library construction process for 454 technology. Sample handling errors and cross-contamination are minimized via end-to-end barcoding of plasticware, along with molecular DNA barcoding of constructs. Automation-friendly magnetic bead-based size selection and cleanup steps have been devised, eliminating major bottlenecks and significant sources of error. Using this methodology, one technician can create 96 sequence-ready 454 libraries in 2 days, a dramatic improvement over the standard method.