Microfabricated free standing, tuneable, porous microfilters from an epoxy based photoresist for effective bioseparation.

SU-8 is an epoxy-based, biocompatible thermosetting polymer, which has been utilized mainly to fabricate biomedical devices and scaffolds. In this study, thin, single-layered, freestanding tuneable porous SU-8 membranes were microfabricated and surface hydrophilized for efficient bioseparation. Unlike the previous thicker membranes of 200-300 µm, these thin SU-8 membranes of 50-60 µm thickness and pores with 6-10 µm diameter were fabricated and tested for blood-plasma separation, without any additional support structure. The method is based on making a patterned SU-8 layer by electrospin coating and UV lithography on a sacrificial polyethylene terephthalate (PET) sheet attached to a silicon wafer. Poor adhesion between PET and SU-8 aid in the convenient release of the thin porous membranes with uniform pore formation. The single-layered self-supporting membranes were strong, safe, sterilizable, reusable, and suitable for plasma separation and postfermentation broth enrichment.

DNA-Aptamer-Based qPCR Using Light-Up Dyes for the Detection of Nucleic Acids.

Quantitative polymerase chain reaction (qPCR) is widely used in detection of nucleic acids, but existing methods either lack sequence-specific detection or are costly because they use chemically modified DNA probes. In this work, we apply a DNA aptamer and light-up dye-based chemistry for qPCR for nucleic acid quantification. In contrast to the conventional qPCR, in our method, we observe an exponential decrease in fluorescence upon DNA amplification. The qPCR method we developed produced consistent Ct vs log10 (DNA amount) standard curves, which have a linearfit with R2 value > 0.99. This qPCR technique was validated by quantifying gene targets from Streptococcus zooepidemicus (SzhasB) and Mycobacterium tuberculosis (MtrpoB). We show that our strategy is able to successfully detect DNA at as low as 800 copies/µL. To the best of our knowledge, this is the first study demonstrating the application of light-up dyes and DNA aptamers in qPCR.

Effective clearance of uremic toxins using functionalised silicon Nanoporous membranes.

In-house fabricated silicon nanoporous membranes (SNMs), functionalized for efficient clearance of uremic toxins, can lead to compact and portable dialysis systems. Efficacy of 15 nm thick SNMs, with average pore diameter of 8 nm, was tested for dialysis of two uremic toxins - urea and creatinine using custom made teflon apparatus of 2, 10 and 30 ml. The apparatus consisted of two reservoirs, with the cis containing the uremic fluid, and the trans containing the dialysate. Peristalsis was found to enhance the clearance rate by a factor of four as compared to unstirred condition. Functionalisation of the SNMs reduced protein binding, and surface binding of urea from 23% to negligible values. A lateral array of nine SNMs and a new design for the dialysis apparatus, increased the clearance rate by a factor of twelve from that of the single SNM. The arrays cleared about 42% of urea and 48% of creatinine from 30 ml of diluted serum samples, in 15 min. Periodic replacement of the trans fluid cleared about 81% of high concentration uremic toxins from the cis reservoir in 45 mins. The SNM arrays are stable, reproducible, and with the superior clearance rates for urea and creatinine, they have the potential to be used as membranes for portable hemodialysers.

Metabolic engineering of a novel muconic acid biosynthesis pathway via 4-hydroxybenzoic acid in Escherichia coli.

cis,cis-Muconic acid (MA) is a commercially important raw material used in pharmaceuticals, functional resins, and agrochemicals. MA is also a potential platform chemical for the production of adipic acid (AA), terephthalic acid, caprolactam, and 1,6-hexanediol. A strain of Escherichia coli K-12, BW25113, was genetically modified, and a novel nonnative metabolic pathway was introduced for the synthesis of MA from glucose. The proposed pathway converted chorismate from the aromatic amino acid pathway to MA via 4-hydroxybenzoic acid (PHB). Three nonnative genes, pobA, aroY, and catA, coding for 4-hydroxybenzoate hydrolyase, protocatechuate decarboxylase, and catechol 1,2-dioxygenase, respectively, were functionally expressed in E. coli to establish the MA biosynthetic pathway. E. coli native genes ubiC, aroF(FBR), aroE, and aroL were overexpressed and the genes ptsH, ptsI, crr, and pykF were deleted from the E. coli genome in order to increase the precursors of the proposed MA pathway. The final engineered E. coli strain produced nearly 170 mg/liter of MA from simple carbon sources in shake flask experiments. The proposed pathway was proved to be functionally active, and the strategy can be used for future metabolic engineering efforts for production of MA from renewable sugars.

Live cell fluorescence imaging for early expression and localization of RIB1 and RIB3 genes in Ashbya gossypii.

Ashbya gossypii is a riboflavin overproducing filamentous fungus. RIB1 and RIB3 genes encode GTP-cyclohydrolase II (GCH II) and DHBP synthase, respectively, the two rate limiting enzymes of the riboflavin biosynthetic pathway. The genes encoding yeast enhanced green fluorescent protein (yEGFP) and mCherry were fused with RIB1 and RIB3 genes, under their native promoters by PCR-based gene tagging method for their early in vivo expression and cellular localization in A. gossypii. In the integrative transformants, the fusion proteins were expressed as cytoplasmic proteins from the germ bubble stage, in all the cells throughout the hypha. This was evident from the observation that mCherry fusion proteins were seen outside the vacuoles in the cytoplasm. The older matured cells of 14 h hyphae developed large vacuoles which showed green autofluorescence due to riboflavin. It is concluded that RIB1 and RIB3 genes are constitutively expressed in all the cells of this multicellular multinucleate fungus.

Development of fluorescent reporter tagged RIB gene cassettes for replicative transformation, early expression, and enhanced riboflavin production in Eremothecium ashbyi.

Eremothecium ashbyi is a riboflavin overproducing filamentous fungus in which the metabolic pathways have not been genetically characterized. Two genes of the riboflavin biosynthetic (RIB) pathway, RIB1 and RIB3, which encode GTP-cyclohydrolase II (GCH II) and 3,4-dihydroxy-2-butanone 4-phosphate (DHBP) synthase respectively, were selected for the present study. The two RIB genes under their native promoters were obtained from Ashbya gossypii genomic library. Yeast enhanced green fluorescent protein (yEGFP) and mCherry genes were tagged to the C-terminal ends of RIB1 and RIB3 genes to analyse the functionality of the RIB transgenes in E. ashbyi. Shuttle vectors with the reporter tagged RIB genes contained the Escherichia coli kan(R) gene and Saccharomyces cerevisiae ARS element. On transformation with these plasmids, the ARS element was found to be functional in E. ashbyi. The E. ashbyi transcription factors could recognize the Ashbya RIB gene promoters and express the reporter tagged RIB genes as cytoplasmic proteins, in early cell development. Replicative transformants carrying RIB1-mCherry plasmids showed 2.95 times more GCH II activity and 2.44 times more riboflavin production when compared to untransformed. This is the first report of genetic transformation of E. ashbyi and is of significance as the first step towards genetic engineering of this genus.

Sequence analysis and structural characterization of a glyceraldehyde-3-phosphate dehydrogenase gene from the phytopathogenic fungus Eremothecium ashbyi.

Eremothecium ashbyi is a phytopathogenic fungus infesting cotton, soybeans and several other plants. This highly flavinogenic fungus has been phylogenetically characterized, but the genetic aspects of its central metabolic and riboflavin biosynthetic pathways are unknown. An ORF of 996 bp was obtained from E. ashbyi by using degenerate primers for glyceraldehyde-3-phosphate dehydrogenase (GPD) through reverse transcriptase polymerase chain reaction (RT-PCR) and 5'-3' rapid amplification of cDNA ends (RACE-PCR). This nucleotide sequence had a high similarity of 88% with GPD sequence of Ashbya gossypii. The putative GPD peptide of 331-aa had a high similarity of 85% with the GPD sequence from other ascomycetes. The ORF had an unusually strong codon bias with 5 amino acids showing strict preference of a single codon. The theoretical molecular weight for the putative peptide was 35.58 kDa with an estimated pI of 5.7. A neighbor-joining tree showed that the putative peptide from E. ashbyi displayed the highest similarity to GPD of A. gossypii. The gene sequence is available at the GenBank, accession number EU717696. Homology modeling done with Kluyveromyces marxianus GPD (PDB: 2I5P) as template indicated high structural similarity.

Molecular and structural characterization of GTP-cyclohydrolase II in Eremothecium ashbyi NRRL Y-1363: cDNA cloning, comparative sequence analysis and molecular modeling.

GTP-cyclohydrolase II (GCH II) encoded by RIB1 gene catalyzes the first committed step in the riboflavin biosynthetic pathway. We report here the cloning and characterization of the entire RIB1 ORF (EaRIB1) of 942bp by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE-PCR) in Eremothecium ashbyi where it was found to be present as a single-copy gene. EaRIB1 sequence is available at the GenBank Accession Number EF565374. The putative peptide of 313-aa has a high similarity of 60-70% with GCH II sequences from other ascomycete fungi. Gene expression and alignment studies confirmed the functional annotation of this gene. Homology model was developed with Escherichia coli (PDB 2BZ1) as template to identify the catalytic domains and to explore its functional architecture. We report here the first three-dimensional model of any fungal GCH II which due to its absence in humans assumes significance for anti-fungal drug targeting.