Highly sensitive measurements of PNA-DNA hybridization using oxide-etched silicon nanowire biosensors

The highly sensitive and sequence-specific detection of single-stranded oligonucleotides using nonoxidized silicon nanowires (SiNWs) is demonstrated. To maximize device sensitivity, the surface of the SiNWs was functionalized with a densely packed organic monolayer via hydrosilylation, subsequently immobilized with peptide nucleic acid (PNA) capable of recognizing the label-free complementary target DNA. Because of the selective functionalization of the SiNWs, binding competition between the nanowire and the underlying oxide is avoided. Transmission electron microscopy was conducted to clearly differentiate the SiNW surface before and after removal of SiO₂. Fluorescence microscopy was used to further realize the selectivity of the oxide-etched chemistry on the SiNWs and sequence specificity of PNA-DNA hybridization. The concentration-dependent resistance change measurements upon hybridization of PNA-DNA show that detection limit down to 10 fM can be obtained. The SiNW devices also reveal the capability of an obvious discrimination against mismatched sequences. Among several efforts being made to improve detection sensitivity, this work addresses one significant issue regarding surface functionalization which enables highly sensitive biomolecular sensing with SiNWs.     

The RNA coregulator SRA, its binding proteins and nuclear receptor signaling activity

Nuclear receptor (NR) coregulators are key modulators of hormone signaling. Discovery of steroid receptor RNA activator (SRA), a coregulator that is active as a RNA, transformed thinking in the field of hormone action. The subsequent identification of SRA-binding coregulator proteins, including p68, SHARP and more recently SLIRP, has provided important insight into SRA's mechanism of action and potentially offers new opportunities to target NR signaling pathways for therapeutic gain. Here we outline advances in the field of NR coregulator biology, with a bias on recent progress in understanding SRA-protein interactions.     

Distinct diversity of KIR genes in three southern Indian populations: comparison with world populations revealed a link between KIR gene content and pre-historic human migrations

By interacting with polymorphic HLA class I molecules, the killer cell immunoglobulin-like receptors (KIR) influence the innate and adaptive immune response to infection. The KIR family varies in gene content and sequence polymorphism, thereby, distinguishing individuals and populations. To investigate KIR diversity in the earliest settlers of India, we have characterized the KIR gene content in three Dravidian-speaking populations (Mollukurumba, Kanikar, and Paravar) from the state of Tamil Nadu, southern India. The activating KIR genes and putative group-B KIR haplotypes were frequent in Paravar and Kanikar, a scenario analogous to those seen previously in other populations of Indian origin, indicating that predominance of group-B KIR haplotypes is the characteristic feature of Indian populations. In contrast, the KIR gene profile of Mollukurumba was more related to Caucasian type. It is not clear whether a local-specific selection or a recent admixture from Iran is responsible for such discrete profile in Mollukurumba. Each southern Indian population had distinct KIR genotype profile. Comparative analyses with world populations revealed that group-B KIR haplotypes were frequent in the natives of India, Australia, and America, the populations associated with those involved in extensive prehistoric human migrations. Whether or not natural selection has acted to enrich group-B KIR haplotypes in these migratory descendants is an issue that requires objective testing. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Evidence for the oligomeric state of 'elastic' titin in muscle sarcomeres

The giant protein titin has important roles in muscle sarcomere integrity, elasticity and contractile activity. The key role in elasticity was highlighted in recent years by single-molecule mechanical studies, which showed a direct relationship between the non-uniform structure of titin and the hierarchical mechanism of its force-extension behavior. Further advances in understanding mechanisms controlling sarcomere structure and elasticity require detailed knowledge of titin arrangement and interactions in situ. Here we present data on the structure and self-interactive properties of an ∼ 290 kDa (∼ 100 nm long) tryptic fragment from the I-band part of titin that is extensible in situ. The fragment includes the conserved ‘distal’ tandem Ig segment of the molecule and forms side-by-side oligomers with distinctive 4 nm cross-striations. Comparisons between these oligomers and the end filaments seen at the tips of native thick filaments indicate identical structure. This shows that end-filaments are formed by the elastic parts of six titin molecules connecting each end of the thick filament to the Z-line. Self-association of elastic titin into stiff end-filaments adds a further hierarchical level in the mechanism of titin extensibility in muscle cells. Self-association of this part of titin may be required to prevent interference of the individual flexible molecules with myosin cross-bridges interacting with actin.     

Hippocampal poly(ADP-Ribose) polymerase 1 and caspase 3 activation in neonatal bornavirus infection

Infection of neonatal rats with Borna disease virus results in a characteristic behavioral syndrome and apoptosis of subsets of neurons in the hippocampus, cerebellum, and cortex (neonatal Borna disease [NBD]). In the NBD rat hippocampus, dentate gyrus granule cells progressively degenerate. Apoptotic loss of granule cells in NBD is associated with accumulation of zinc in degenerating neurons and reduced zinc in granule cell mossy fibers. Excess zinc can trigger poly(ADP-ribose) polymerase 1 (PARP-1) activation, and PARP-1 activation can mediate neuronal death. Here, we evaluate hippocampal PARP-1 mRNA and protein expression levels, activation, and cleavage, as well as apoptosis-inducing factor (AIF) nuclear translocation and executioner caspase 3 activation, in NBD rats. PARP-1 mRNA and protein levels were increased in NBD hippocampi. PARP-1 expression and activity were increased in granule cell neurons and glia with enhanced ribosylation of proteins, including PARP-1 itself. In contrast, levels of poly(ADP-ribose) glycohydrolase mRNA were decreased in NBD hippocampi. PARP-1 cleavage and AIF expression were also increased in astrocytes in NBD hippocampi. Levels of activated caspase 3 protein were increased in NBD hippocampi and localized to nuclei, mossy fibers, and dendrites of granule cell neurons. These results implicate aberrant zinc homeostasis, PARP-1, and caspase 3 activation as contributing factors in hippocampal neurodegeneration in NBD.     

Genetic improvement of Aspergillus carbonarius for pectinase overproduction during solid state growth

Low pectinase production by Aspergillus carbonarius growing on wheat bran solid substrate was found to be due to reduced colonizational ability of the fungus. Since A. niger showed higher growth rates on wheat bran, strain improvement to obtain higher pectinase production in solid state was carried out by inter-specific fusion of protoplasts of A. carbonarius and A. niger. One of the mutants selected for higher activities of alpha-glucosidase showed improved growth rates on wheat bran solid substrate together with increased pectinase production. Size similarities of amplified polymorphic DNA of the mutant with the two parents and identification of a 66 kDa polygalacturonase specific to A. niger suggested genetic recombination in the mutant.     

Optimum growth requirements of nitrifying consortia developed from treated sewage

The optimum growth requirements of two nitrifying consortia developed from treated sewage by enrichment technique were determined by a series of experiments. There was total inhibition of nitrification at above 2.75 g l(-1) NH4(+)- N and 2.5 g l(-1) NO2(-)-N and the ammonia oxidizing consortium preferred a pH at 8.5 and the nitrite oxidizing consortium a pH of 7.5 as the optima for nitrification. Optimum temperatures were between 20 degrees and 30 degrees C for both the groups. As the rate of airflow was increased from 1 to 7 l/min, the build-up of NO2(-)-N increased 10-fold and the consumption of NO2(-)-N increased by a factor of 28.8 implying that the ammonia oxidizing consortium in a bioreactor required three times more aeration than that for nitrite oxidizers for expressing their full nitrifying potential. These data directly contribute for developing a fermentation process for the mass production of nitrifiers as well as for designing bioreactors for nitrifying sewage.     

Correlations between nucleotide frequencies and amino acid composition in 115 bacterial species

We studied the correlations between amino acid composition and mononucleotide and dinucleotide frequencies in 115 bacterial genomes of varying G+C content. Observed amino acid frequencies were compared with those expected from the actual mononucleotide and dinucleotide frequencies. Both mononucleotide and dinucleotide frequencies correlate well with the amino acid frequency, with dinucleotide frequencies doing so better. Despite the strong correlations, some of the observed amino acid frequencies, in particular for Arg, Val, Asp, Glu, Ser, and Cys, were consistently different from predicted values in all genomes. We suggest that this variation from predicted values is a consequence of selection pressure at the level of amino acids, while the close correspondence to the predictions in residues such as Thr, Phe, Lys, and Asn arises only from mutation and selection pressure at the level of the nucleic acid sequences.     

Simple and an efficient method for the synthesis of 1-[2-dimethylamino-1-(4-methoxy-phenyl)-ethyl]-cyclohexanol hydrochloride: (+/-) venlafaxine racemic mixtures

A novel synthetic method was developed for the synthesis of venlafaxine using inexpensive reagents. An improvement in the method, in the yield was achieved for the conversion of the venlafaxine. This is an improved version, simple and efficient method for the large-scale synthesis of venlafaxine.     

Accurate detection of protein:ligand binding sites using molecular dynamics simulations

Accurate prediction of location of cavities and surface grooves in proteins is important, as these are potential sites for ligand binding. Several currently available programs for cavity detection are unable to detect cavities near the surface or surface grooves. In the present study, an optimized molecular dynamics based procedure is described for detection and quantification of interior cavities as well as surface pockets. This is based on the observation that the mobility of water in such pockets is significantly lower than that of bulk water. The algorithm efficiently detects surface grooves that are sites of protein-ligand and protein-protein interaction. The algorithm was also used to substantially improve the performance of an automated docking procedure for docking monomers of nonobligate protein-protein complexes. In addition, it was applied to predict key residues involved in the binding of the E. coli toxin CcdB with its inhibitor. Predictions were subsequently validated by mutagenesis experiments.