An infantile case of Zellweger syndrome presented with Kabuki-like phenotype

Zellweger syndrome is a peroxisomal disorder resulting from the mutations in PEX genes generally presenting in the neonatal period with profound hypotonia seizures, inability to feed, liver cysts with hepatic dysfunction, chondrodysplasia punctata. Kabuki make-up syndrome is a multiple congenital anomalies and mental retardation syndrome with characteristic facial appearance, skeletal abnormalities, dermatoglyphic abnormalities, mental retardation and short stature. Abnormal liver functions and some atypical findings were also reported in some patients with Kabuki syndrome. In this report a case with late onset Zellweger syndrome who had some phenotypical findings which are also seen in Kabuki Syndrome will be presented. The inclusion of Zellweger syndrome into the differential diagnosis of the patients with Kabuki-like phenotype in addition to abnormal liver functions is emphasized.     

The impact of the marine sewage outfalls on the sediment quality: The Black Sea and the Marmara case

Marine sewage outfalls are the cheapest method of disposal for municipalities with restricted funds, despite their negative effects on marine ecosystems. This study was conducted on the marine sewage outfalls of the Turkish cities Rize (Black Sea) and Yalova (Sea of Marmara). Heavy metals, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and organochlorine pesticides (OCPs) were investigated in the sediments for determine pollution degree. Two of Yalova stations were classified as having high contamination levels (1034.436 and 1476.483 ng/g, respectively) and all the other stations suffered moderate pollution in terms of ∑₁₆PAHs. ∑DTTs in sediments above probable effect levels (PELs), were observed both stations Yalova and Rize. The highest metal concentrations in the sediments from the eight stations ranged from 4.97 to 29.65 mg/kg for Ni; 7.57–44.14 mg/kg for Cr; 9.84–42.76 mg/kg for Cu; and 48.08–103.77 mg/kg for Zn. In sum, examination of pollutant sources provides clear evidence of an anthropogenic effect on the discharge environments.     

GUItars: A GUI Tool for Analysis of High-Throughput RNA Interference Screening Data

Background

High-throughput RNA interference (RNAi) screening has become a widely used approach to elucidating gene functions. However, analysis and annotation of large data sets generated from these screens has been a challenge for researchers without a programming background. Over the years, numerous data analysis methods were produced for plate quality control and hit selection and implemented by a few open-access software packages. Recently, strictly standardized mean difference (SSMD) has become a widely used method for RNAi screening analysis mainly due to its better control of false negative and false positive rates and its ability to quantify RNAi effects with a statistical basis. We have developed GUItars to enable researchers without a programming background to use SSMD as both a plate quality and a hit selection metric to analyze large data sets.

Results

The software is accompanied by an intuitive graphical user interface for easy and rapid analysis workflow. SSMD analysis methods have been provided to the users along with traditionally-used z-score, normalized percent activity, and t-test methods for hit selection. GUItars is capable of analyzing large-scale data sets from screens with or without replicates. The software is designed to automatically generate and save numerous graphical outputs known to be among the most informative high-throughput data visualization tools capturing plate-wise and screen-wise performances. Graphical outputs are also written in HTML format for easy access, and a comprehensive summary of screening results is written into tab-delimited output files.

Conclusion

With GUItars, we demonstrated robust SSMD-based analysis workflow on a 3840-gene small interfering RNA (siRNA) library and identified 200 siRNAs that increased and 150 siRNAs that decreased the assay activities with moderate to stronger effects. GUItars enables rapid analysis and illustration of data from large- or small-scale RNAi screens using SSMD and other traditional analysis methods. The software is freely available at http://sourceforge.net/projects/guitars/.