Reliable Means of Diagnosis and Serovar Determination of Blood-Borne Salmonella Strains: Quick PCR Amplification of Unique Genomic Loci by Novel Primer Sets

Typhoid fever is becoming an ever increasing threat in the developing countries. We have improved considerably upon the existing PCR-based diagnosis method by designing primers against a region that is unique to Salmonella enterica subsp. enterica serovar Typhi and Salmonella enterica subsp. enterica serovar Paratyphi A, corresponding to the STY0312 gene in S. Typhi and its homolog SPA2476 in S. Paratyphi A. An additional set of primers amplify another region in S. Typhi CT18 and S. Typhi Ty2 corresponding to the region between genes STY0313 to STY0316 but which is absent in S. Paratyphi A. The possibility of a false-negative result arising due to mutation in hypervariable genes has been reduced by targeting a gene unique to typhoidal Salmonella serovars as a diagnostic marker. The amplified region has been tested for genomic stability by amplifying the region from clinical isolates of patients from various geographical locations in India, thereby showing that this region is potentially stable. These set of primers can also differentiate between S. Typhi CT18, S. Typhi Ty2, and S. Paratyphi A, which have stable deletions in this specific locus. The PCR assay designed in this study has a sensitivity of 95% compared to the Widal test which has a sensitivity of only 63%. As observed, in certain cases, the PCR assay was more sensitive than the blood culture test was, as the PCR-based detection could also detect dead bacteria.

Highly luminescent and thermally stable lanthanide coordination polymers designed from 4-(dipyridin-2-yl)aminobenzoate: efficient energy transfer from Tb3+ to Eu3+ in a mixed lanthanide coordination compound

Herein, a new aromatic carboxylate ligand, namely, 4-(dipyridin-2-yl)aminobenzoic acid (HL), has been designed and employed for the construction of a series of lanthanide complexes (Eu3+ = 1, Tb3+ = 2, and Gd3+ = 3). Complexes of 1 and 2 were structurally authenticated by single-crystal X-ray diffraction and were found to exist as infinite 1D coordination polymers with the general formulas {Eu(L)(3)(H2O)(2)]}(n) (1) and {Tb(L)(3)(H2O)]center dot(H2O)}(n) (2). Both compounds crystallize in monoclinic space group C2/c. The photophysical properties demonstrated that the developed 4-(dipyridin-2-yl)aminobenzoate ligand is well suited for the sensitization of Tb3+ emission (Phi(overall) = 64%) thanks to the favorable position of the triplet state ((3)pi pi*) of the ligand the energy difference between the triplet state of the ligand and the excited state of Tb3+ (Delta E) = (3)pi pi* - D-5(4) = 3197 cm(-1)], as investigated in the Gd3+ complex. On the other hand, the corresponding Eu3+ complex shows weak luminescence efficiency (Phi(overall) = 7%) due to poor matching of the triplet state of the ligand with that of the emissive excited states of the metal ion (Delta E = (3)pi pi* - D-5(0) = 6447 cm(-1)). Furthermore, in the present work, a mixed lanthanide system featuring Eu3+ and Tb3+ ions with the general formula {Eu0.5Tb0.5(L)(3)(H2O)(2)]}(n) (4) was also synthesized, and the luminescent properties were evaluated and compared with those of the analogous single-lanthanide-ion systems (1 and 2). The lifetime measurements for 4 strongly support the premise that efficient energy transfer occurs between Tb3+ and Eu3+ in a mixed lanthanide system (eta = 86%).

Stable hybrid containing haploid genomes of two obligate diploid Candida species

Candida albicans and Candida dubliniensis are diploid, predominantly asexual human-pathogenic yeasts. In this study, we constructed tetraploid (4n) strains of C. albicans of the same or different lineages by spheroplast fusion. Induction of chromosome loss in the tetraploid C. albicans generated diploid or near-diploid progeny strains but did not produce any haploid progeny. We also constructed stable heterotetraploid somatic hybrid strains (2n + 2n) of C. albicans and C. dubliniensis by spheroplast fusion. Heterodiploid (n + n) progeny hybrids were obtained after inducing chromosome loss in a stable heterotetraploid hybrid. To identify a subset of hybrid heterodiploid progeny strains carrying at least one copy of all chromosomes of both species, unique centromere sequences of various chromosomes of each species were used as markers in PCR analysis. The reduction of chromosome content was confirmed by a comparative genome hybridization (CGH) assay. The hybrid strains were found to be stably propagated. Chromatin immunoprecipitation (ChIP) assays with antibodies against centromere-specific histones (C. albicans Cse4/C. dubliniensis Cse4) revealed that the centromere identity of chromosomes of each species is maintained in the hybrid genomes of the heterotetraploid and heterodiploid strains. Thus, our results suggest that the diploid genome content is not obligatory for the survival of either C. albicans or C. dubliniensis. In keeping with the recent discovery of the existence of haploid C. albicans strains, the heterodiploid strains of our study can be excellent tools for further species-specific genome elimination, yielding true haploid progeny of C. albicans or C. dubliniensis in future.

Achieving Highly Efficient, Selective, and Stable CO2 Reduction on Nitrogen-Doped Carbon Nanotubes

The challenge in the electrosynthesis of fuels from CO2 is to achieve durable and active performance with cost-effective catalysts. Here, we report that carbon nanotubes (CNTs), doped with nitrogen to form resident electron-rich defects, can act as highly efficient and, more importantly, stable catalysts for the conversion of CO2 to CO. The unprecedented overpotential (-0.18 V) and selectivity (80%) observed on nitrogen-doped CNTs (NCNTs) are attributed to their unique features to facilitate the reaction, including (i) high electrical conductivity, (ii) preferable catalytic sites (pyridinic N defects), and (iii) low free energy for CO2 activation and high barrier for hydrogen evolution. Indeed, DFT calculations show a low free energy barrier for the potential-limiting step to form key intermediate COOH as well as strong binding energy of adsorbed CON and weak binding energy for the adsorbed CO. The highest selective site toward CO production is pyridinic N, and the NCNT-based electrodes exhibit no degradation over 10 h of continuous operation, suggesting the structural stability of the electrode.

A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily

Uracil DNA glycosylases (UDGs) are an important group of DNA repair enzymes, which pioneer the base excision repair pathway by recognizing and excising uracil from DNA. Based on two short conserved sequences (motifs A and B), UDGs have been classified into six families. Here we report a novel UDG, UdgX, from Mycobacterium smegmatis and other organisms. UdgX specifically recognizes uracil in DNA, forms a tight complex stable to sodium dodecyl sulphate, 2-mercaptoethanol, urea and heat treatment, and shows no detectable uracil excision. UdgX shares highest homology to family 4 UDGs possessing Fe-S cluster. UdgX possesses a conserved sequence, KRRIH, which forms a flexible loop playing an important role in its activity. Mutations of H in the KRRIH sequence to S, G, A or Q lead to gain of uracil excision activity in MsmUdgX, establishing it as a novel member of the UDG superfamily. Our observations suggest that UdgX marks the uracil-DNA for its repair by a RecA dependent process. Finally, we observed that the tight binding activity of UdgX is useful in detecting uracils in the genomes.

Topological mimicry and epitope duplication in the guanylyl cyclase C receptor

Guanylyl cyclase C (GCC) is the receptor for the gastrointestinal hormones, guanylin, and uroguanylin, in addition to the bacterial heat-stable enterotoxins, which are one of the major causes of watery diarrhea the world over. GCC is expressed in intestinal cells, colorectal tumor tissue and tumors originating from metastasis of the colorectal carcinoma. We have earlier generated a monoclonal antibody to human GCC, GCC:B10, which was useful for the immunohistochemical localization of the receptor in the rat intestine (Nandi A et al., 1997, J Cell Biochem 66:500-511), and identified its epitope to a 63-amino acid stretch in the intracellular domain of GCC. In view of the potential that this antibody has for the identification of colorectal tumors, we have characterized the epitope for GCC:B10 in this study. Overlapping peptide synthesis indicated that the epitope was contained in the sequence HIPPENIFPLE. This sequence was unique to GCC, and despite a short stretch of homology with serum amyloid protein and pertussis toxin, no cross reactivity was detected. The core epitope was delineated using a random hexameric phage display library, and two categories of sequences were identified, containing either a single, or two adjacent proline residues. No sequence identified by phage display was identical to the epitope present in GCC, indicating that phage sequences represented mimotopes of the native epitope. Alignment of these sequences with HIPPENIFPLE suggested duplication of the recognition motif, which was confirmed by peptide synthesis. These studies allowed us not only to define the requirements of epitope recognition by GCC:B10 monoclonal antibody, but also to describe a novel means of epitope recognition involving topological mimicry and probable duplication of the cognate epitope in the native guanylyl cyclase C receptor sequence.

Expression of the extracellular domain of the human heat-stable enterotoxin receptor in Escherichia coli and generation of neutralizing antibodies

The entire extracellular domain of the human heat-stable enterotoxin (ST) receptor as well as a truncated N-terminal domain were cloned as glutathione S-transferase fusion proteins and expressed in Escherichia coli. The recombinant fusion proteins were purified from both the cytosol and the inclusion body fractions by selective detergent extraction followed by glutathione-agarose affinity chromatography. The purified protein, corresponding to the entire extracellular domain, bound the stable toxin peptide with an affinity comparable to that of the native receptor characterized from the human colonic T84 cell line. No binding was observed with the N-terminal truncated fragment of the receptor under similar conditions, Polyclonal antibodies were raised to the entire extracellular domain fusion protein as well as the truncated extracellular domain fusion protein, and the antibodies were purified by affinity chromatography. Addition of the purified antibodies to T84 cells inhibited ST binding and abolished ST-mediated cGMP production, indicating that critical epitopes involved in ligand interaction are present in the N-terminal fragment of the receptor, Purified antibodies recognized a single protein of M(r) 160,000 Da on Western blotting with T84 membranes, corresponding to a size of the native glycosylated receptor in T84 cells. These studies are the first report of the expression, purification, and characterization of any member of the guanylyl cyclase family of receptors in E. coli and show that binding of the toxin to the extracellular domain of the receptor is possible in the absence of any posttranslational modifications such as glycosylation. The recombinant fusion proteins as well as the antibodies that we have generated could serve as useful tools in the identification of critical residues of the extracellular domain involved in ligand interaction.

CCD: Connected Component Descriptor for Robust Mosaicing of Camera-Captured Document Images

We propose a robust method for mosaicing of document images using features derived from connected components. Each connected component is described using the Angular Radial Tran. form (ART). To ensure geometric consistency during feature matching, the ART coefficients of a connected component are augmented with those of its two nearest neighbors. The proposed method addresses two critical issues often encountered in correspondence matching: (i) The stability of features and (ii) Robustness against false matches due to the multiple instances of characters in a document image. The use of connected components guarantees a stable localization across images. The augmented features ensure a successful correspondence matching even in the presence of multiple similar regions within the page. We illustrate the effectiveness of the proposed method on camera captured document images exhibiting large variations in viewpoint, illumination and scale.

Comparative kinomics of human and chimpanzee reveal unique kinship and functional diversity generated by new domain combinations

Background: Phosphorylation by protein kinases is a common event in many cellular processes. Further, many kinases perform specialized roles and are regulated by non-kinase domains tethered to kinase domain. Perturbation in the regulation of kinases leads to malignancy. We have identified and analysed putative protein kinases encoded in the genome of chimpanzee which is a close evolutionary relative of human. Result: The shared core biology between chimpanzee and human is characterized by many orthologous protein kinases which are involved in conserved pathways. Domain architectures specific to chimp/human kinases have been observed. Chimp kinases with unique domain architectures are characterized by deletion of one or more non-kinase domains in the human kinases. Interestingly, counterparts of some of the multi-domain human kinases in chimp are characterized by identical domain architectures but with kinase-like non-kinase domain. Remarkably, out of 587 chimpanzee kinases no human orthologue with greater than 95% sequence identity could be identified for 160 kinases. Variations in chimpanzee kinases compared to human kinases are brought about also by differences in functions of domains tethered to the catalytic kinase domain. For example, the heterodimer forming PB1 domain related to the fold of ubiquitin/Ras-binding domain is seen uniquely tethered to PKC-like chimpanzee kinase. Conclusion: Though the chimpanzee and human are evolutionary very close, there are chimpanzee kinases with no close counterpart in the human suggesting differences in their functions. This analysis provides a direction for experimental analysis of human and chimpanzee protein kinases in order to enhance our understanding on their specific biological roles.

Side Chain Structure Determines Unique Physiologic and Therapeutic Properties of norUrsodeoxycholic Acid in Mdr2(-/-) Mice

24-norursodeoxycholic acid (norUDCA), a side chain-modified ursodeoxycholic acid derivative, has dramatic therapeutic effects in experimental cholestasis and may be a promising agent for the treatment of cholestatic liver diseases. We aimed to better understand the physiologic and therapeutic properties of norUDCA and to test if they are related to its side chain length and/or relative resistance to amidation. For this purpose, Mdr2-/- mice, a model for sclerosing cholangitis, received either a standard diet or a norUDCA-, tauro norursodeoxycholic acid (tauro- norUDCA)-, or di norursodeoxycholic acid (di norUDCA)-enriched diet. Bile composition, serum biochemistry, liver histology, fibrosis, and expression of key detoxification and transport systems were investigated. Direct choleretic effects were addressed in isolated bile duct units. The role of Cftr for norUDCA-induced choleresis was explored in Cftr-/- mice. norUDCA had pharmacologic features that were not shared by its derivatives, including the increase in hepatic and serum bile acid levels and a strong stimulation of biliary HCO3- -output. norUDCA directly stimulated fluid secretion in isolated bile duct units in a HCO3- -dependent fashion to a higher extent than the other bile acids. Notably, the norUDCA significantly stimulated HCO 3- -output also in Cftr-/- mice. In Mdr2-/- mice, cholangitis and fibrosis strongly improved with norUDCA, remained unchanged with tauro- norUDCA, and worsened with di norUDCA. Expression of Mrp4, Cyp2b10, and Sult2a1 was increased by norUDCA and di norUDCA, but was unaffected by tauro- norUDCA. Conclusion:The relative resistance of norUDCA to amidation may explain its unique physiologic and pharmacologic properties. These include the ability to undergo cholehepatic shunting and to directly stimulate cholangiocyte secretion, both resulting in a HCO3- -rich hypercholeresis that protects the liver from cholestatic injury.

A Unique Filter-Preserver Device for Digital Photonic Circuits

We discuss micro ring resonator based optical logic gates using Kerr-type nonlinearity. Resonant wavelength selectivity is one key factor in achieving the desired gate. Based on basic gates like AND gate, OR gate etc. We proceed to propose a 3-bit binary adder circuit.Due to the presence of more than a single wavelength, the system gets complicated as we increase the number of components in the circuit. Hence it has been observed that for efficient designing and functioning of digital circuits in optical domain, we need a device which can give single wavelength output, filtering out all other wavelengths and at the same time preserve the digital characteristics of the output. We propose such filter-preserver device based on micro ring resonator.

On evolutionarily stable compositions of populations of interacting genotypes.

Consider an organism in which the genetic fitness of an individual depends to a large extent on its social interactions. Assuming the genotypes to differ only in the choice of strategies they adopt in social interactions, and equating the variation in genetic fitness to the mean payoff to an individual averaged over all possible encounters, we develop a dynamical model for the evolution of genotypic frequencies in such a population. Such a system is characterised by frequency dependent selection, and depending on the initial composition, the population evolves towards one of several possible compositions. We term as evolutionarily stable compositions (ESC) any such composition towards which a population can evolve and which is stable against small fluctuations in the frequencies of existing genotypes as well as to invasions by any other postulated genotype. We state the necessary and sufficient conditions for the identification of all possible ESC's for any number of interacting genotypes. Our results conform to those derived earlier in connection with the concept of evolutionarily stable strategies only in the case of two interacting genotypes; when more than two genotypes interact the conditions under which various ESC's exist become far richer. We consider interactions with mixed strategists and show that in a conflict with pure strategists the optimal mixed strategist will be the only one to ultimately survive. We illustrate our approach by considering the specific case of a primitively social wasp.

Reversal of handedness in DNA: A stable link between RU and LZ helices

Two types of left-handed zig-zag (LZ) helices were obtained following stereochemical guideline. They are referred to as LZ1 and LZ2 helices. LZ1 helices have conformations similar to those found in the single crystals of d(C-G)3 and d(C-G)25,6. Z-character is more prominent in LZ2 than in LZ1 helix. The conformations of a stable link between RU and LZ helical fragments are given. The link involves inverted stacking arrangement of the bases: a characteristic feature of all RL models proposed by us

Amide catalysed facile isomerization of 5,6-dihydroisoquinolines: synthesis of stable 1,2-dihydroisoquinolines

Stable 1,2-dihydroisoquinolines have been synthesized by an amide catalysed novel isomerization reaction of 5,6-dihydroisoquinolines.