Trimming procedures are an important part of the sequence analysis pipeline in an EST Sequencing Project. In general, trimming is done in several phases, each one detecting and removing some kind of undesirable artifact, such as low quality sequence, vectors or adapters sequence, and contamination. However, this strategy often results in a phase being unable to recognize its target because part...

Due to the potential for intentional contamination of food with crude preparations containing ricin, a real-time PCR method was developed for the detection of castor plant material in ground beef. One primer pair was identified and confirmed to be castor-specific and efficient for amplification of ricin in DNA extracts from castor or beef matrices. Of three different DNA extraction protocols co...

Surface soil samples were collected from Sarcheshmeh Copper Smelter Plant and analyzed for 16 Polycyclic Aromatic Hydrocarbons (PAHs), polychlorinated dibenzo-p-dioxin/furans (PCDD/Fs), and heavy metals to determine their concentrations, distributions, and probable sources of contamination. The mean concentrations of ΣPAHs, As, Pb, Zn, Se, Cd, and Cr in the soil samples were 878.8, 850, 2185, 2...

Aflatoxin M1 (AFM1) is a potent carcinogen, teratogen and mutagen found in the milk when lactating animals consume feed contaminated with aflatoxin B1 (AFB1). In the present study, the contamination of AFM1 was evaluated in the milk supply chain of the province of Sindh, Pakistan. For the broader profiling of targeted toxin, enzyme-linked immunosorbent assay (ELISA) was used for the determinati...

In theory, state of the art inductively coupled plasma mass spectrometry (ICP-MS) instrumentation has the prerequisite sensitivity to carry out multi-elemental trace analyses at sub-ng L-1 to sub-pg L-1 levels in solution. In practice, constraints mainly imposed by various sources of contamination in the laboratory and the instrument itself, and the need to dilute sample solutions prior to anal...

We determined the polychlorinated biphenyl (PCB) congeners in 101 marine fish obtained from tsunami-stricken areas following the Great East Japan Earthquake in 2011. In particular, to determine the degree of PCB contamination in the fish, we investigated the concentration of total PCB (∑PCB) and the proportions of 209 individual PCB congeners by high-resolution gas chromatography/high-resolutio...

The impact of heavy-metal contamination on archaean communities was studied in soils amended with sewage sludge contaminated with heavy metals to varying extents. Fluorescent in situ hybridization showed a decrease in the percentage of Archaea from 1.3% +/- 0.3% of 4', 6-diamidino-2-phenylindole-stained cells in untreated soil to below the detection limit in soils amended with heavy metals. A c...

 Out of 65 medicinal herbs and spices screened, 60 were contaminated while 5 were free from fungal contamination.  Analysis revealed that 45.31% of the samples have a fungal load above 1×10 cfu/g which is the permissible limit set by World Health Organization.  A total of 191 fungi were isolated in which Aspergillus and Penicillium were the predominant microorganism. Among the various fungal...

Scalable and efficient production of high-quality recombinant adeno-associated virus (rAAV) for gene therapy remains a challenge despite recent clinical successes. We developed a new strategy for scalable and efficient rAAV production by sequestering the AAV helper genes and the rAAV vector DNA in two different subcellular compartments, made possible by using cytoplasmic vaccinia virus as a car...

Fluorine is an element that can be either beneficial or harmful, depending on the total amount accumulated in the teeth or bones. In our laboratory, we have developed a non-invasive technique for the in vivo measurement of fluoride in bone using neutron activation analysis and performed the first pilot human study. Fluoride in humans is quantified by comparing the γ-ray signal from a person to ...