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Recently, we demonstrated the capability of the ketogenic diet (KD) to influence the microRNA (miR) expression profile. Here, we report that KD is able to normalize miR expression in obese subjects when compared with lean subjects. By applying two different bioinformatics tools, we found that, amongst the miRs returning to comparable levels in lean subjects, four of them are linked to antioxidant biochemical pathways specifically, and the others are linked to both antioxidant and anti-inflammatory biochemical pathways. Of particular interest is the upregulation of hsa-miR-30a-5p, which correlates with the decrease of catalase expression protein in red blood cells.

Herein, we reported an Escherichia coli-based expression and purification method of recombinant porcine interferon alpha (rPoIFN-α). PoIFN-α coding sequence was cloned into pMD18-T vector and then subcloned into pET-32a (+) vector using standard recombinant DNA techniques and the resulting plasmid was transformed into BL21(DE3) competent cells. After induction with isopropyl-β-D-1-thiogalactopyranoside (IPTG), rPoIFN-α was purified from the supernatant of the bacteria lysate using a simple two-step chromatography process consisting of a Ni2+ affinity chromatography and a DEAE anion exchange chromatography. rPoIFN-α was purified to >95% homogeneity with a yield of 48 mg/L of culture. It has isoelectic point of 6.09 and bacterial endotoxin was less than 1 EU/mg. N-terminal amino acid sequence and the peptide map digested by trypsin provided additional evidence for the authenticity of rPoIFN-α. The biological activity of rPoIFN-α was 1.1×106 IU/ mL in HEp-2/ Vesicular Stomatitis Virus (VSV) titration system and its specific activity reached to 1.0×106 IU/mg. In conclusion, we obtained high-level expression of a soluble form of bioactive rPoIFN-α by using pET-32a (+) prokaryotic expression system.

Objective To compare the expression protein profile of seminal plasma from infertile men with oligoasthenoteratozoospermia (OAT) due to oxidative stress with that of healthy, fertile men to determine the proteins indicative of infertility. Design Experimental study. Setting University hospital and research institute. Patient(s) Semen samples from 11 healthy, fertile (according to the 1999 World Health Organization criteria) male volunteers and 11 infertile idiopathic oligoasthenoteratozoospermia (iOAT) patients. Intervention(s) None. Main Outcome Measure(s) Proteomic analysis performed by liquid chromatography mass spectrometry on a hybrid linear trap quadrupole Orbitrap Velos mass spectrometer, carbonylation assay to determine degree of oxidative stress, semiquantitative proteomic analysis, gene ontology, and pathway analysis. Result(s) A total of 2,489 proteins were identified from seminal plasma, which represents the highest number of unique proteins identified to date. Twenty-four proteins were determined as ≥1.5-fold up-regulated in the infertile iOAT males as compared with the fertile controls; and 27 proteins from iOAT patients only were identified as common across all analyses. Only five of the proteins were shared between these two groups. Conclusion(s) A panel of 46 proteins were identified in patients with iOAT that are potential candidates in understanding the etiology of OAT due to oxidative stress.

GPX is an environment for the storage and retrieval of raw and processed MIAME compliant microarray experiments. The system has been developed at the Scottish Centre for Genomic Technology and Informatics (GTI). GPX has a web accessible front end, GPX Discovery, that enables querying and retrieval of biochip data and experimental information based on various search criteria. GPX Discovery also enables the comparison of microarray platforms using the BioLink MatchMaker interface. GPX has been in use since 2003 to provide online access to raw, processed and meta microarray data analysing gene content, expression protein levels in the fields of immunity, oncology, infection and is part of the Edinburgh National Translational Cancer Research Network Centre resources. from BioSysBio: Bioinformatics and Systems Biology Conference Edinburgh, UK, 14–15 July 2005

Background The Plasmodium falciparum genome (3D7 strain) published in 2002, revealed ~5,400 genes, mostly based on in silico predictions. Experimental data is therefore required for structural and functional assessments of P. falciparum genes and expression, and polymorphic data are further necessary to exploit genomic information to further qualify therapeutic target candidates. Here, we undertook a large scale analysis of a P. falciparum FcB1-schizont-EST library previously constructed by suppression subtractive hybridization (SSH) to study genes expressed during merozoite morphogenesis, with the aim of: 1) obtaining an exhaustive collection of schizont specific ESTs, 2) experimentally validating or correcting P. falciparum gene models and 3) pinpointing genes displaying protein polymorphism between the FcB1 and 3D7 strains. Results A total of 22,125 clones randomly picked from the SSH library were sequenced, yielding 21,805 usable ESTs that were then clustered on the P. falciparum genome. This allowed identification of 243 protein coding genes, including 121 previously annotated as hypothetical. Statistical analysis of GO terms, when available, indicated significant enrichment in genes involved in "entry into host-cells" and "actin cytoskeleton". Although most ESTs do not span full-length gene reading frames, detailed sequence comparison of FcB1-ESTs versus 3D7 genomic sequences allowed the confirmation of exon/intron boundaries in 29 genes, the detection of new boundaries in 14 genes and identification of protein polymorphism for 21 genes. In addition, a large number of non-protein coding ESTs were identified, mainly matching with the two A-type rRNA units (on chromosomes 5 and 7) and to a lower extent, two atypical rRNA loci (on chromosomes 1 and 8), TARE subtelomeric regions (several chromosomes) and the recently described telomerase RNA gene (chromosome 9). Conclusion This FcB1-schizont-EST analysis confirmed the actual expression of 243 protein coding genes, allowing the correction of structural annotations for a quarter of these sequences. In addition, this analysis demonstrated the actual transcription of several remarkable non-protein coding loci: 2 atypical rRNA, TARE region and telomerase RNA gene. Together with other collections of P. falciparum ESTs, usually generated from mixed parasite stages, this collection of FcB1-schizont-ESTs provides valuable data to gain further insight into the P. falciparum gene structure, polymorphism and expression.