Optimisation of an asymmetric polymerase chain reaction assay for the amplification of single-stranded DNA from Wuchereria bancrofti for electrochemical detection

Single-stranded DNA (ssDNA) is a prerequisite for electrochemical sensor-based detection of parasite DNA and other diagnostic applications. To achieve this detection, an asymmetric polymerase chain reaction method was optimised. This method facilitates amplification of ssDNA from the human lymphatic filarial parasite Wuchereria bancrofti. This procedure produced ssDNA fragments of 188 bp in a single step when primer pairs (forward and reverse) were used at a 100:1 molar ratio in the presence of double-stranded template DNA. The ssDNA thus produced was suitable for immobilisation as probe onto the surface of an Indium tin oxide electrode and hybridisation in a system for sequence-specific electrochemical detection of W. bancrofti. The hybridisation of the ssDNA probe and target ssDNA led to considerable decreases in both the anodic and the cathodic currents of the system's redox couple compared with the unhybridised DNA and could be detected via cyclic voltammetry. This method is reproducible and avoids many of the difficulties encountered by conventional methods of filarial parasite DNA detection; thus, it has potential in xenomonitoring.

The further understanding of chain topology effect on the properties of single polymer in good solvent: Special behaviors of single tadpole chain

Chain topology strongly affects the static and dynamic properties of polymer melts and polymers in dilute solution. For different chain architectures, such as ring and linear polymers, the molecular size and the diffusion behavior are different. To further understand the chain topology effect on the static and dynamic properties of polymers, we focus on the tadpole polymer which consists of a cyclic chain attached with one or more linear tails. It is found that both the number and the length of linear tails play important roles on the properties of the tadpole polymers in dilute solution. For the tadpole polymers with fixed linear tail length and number, with increasing the degree of polymerization of tadpole polymers, a transition from linear-like to ring-like behavior is observed for both the static and dynamic properties.

Influence of molecular topology on the static and dynamic properties of single polymer chain in solution

The influence of molecular topology on the structural and dynamic properties of polymer chain in solution with ring structure, three-arm branched structure, and linear structure are studied by molecular dynamics simulation. At the same degree of polymerization (N), the ring-shaped chain possesses the smallest size and largest diffusion coefficient. With increasing N, the difference of the radii of gyration between the three types of polymer chains increases, whereas the difference of the diffusion coefficients among them decreases. However, the influence of the molecular topology on the static and the dynamic scaling exponents is small. The static scaling exponents decrease slightly, and the dynamic scaling exponents increase slightly, when the topology of the polymer chain is changed from linear to ring-shaped or three-arm branched architecture. The dynamics of these three types of polymer chain in solution is Zimm-like according to the dynamic scaling exponents and the dynamic structure factors.

Extended-chain lamellar packing of poly(3-butylthiophene) in single crystals

We developed an approach, i.e. solvent-assist crystallization (SAC), for growing high quality single crystals of head-to-tail regio-regular poly(3-butylthiophene) (P3BT). By means of atomic force microscopy, electron diffraction and X-ray diffraction, we found that P3BT macromolecules formed lamella single crystals through gradient crystallization, and in the single crystals, molecules packed normal to the lamella with extended-chain conformation with alkyl side chains in the growth front during crystallization.

White electroluminescence from a single-polymer system with simultaneous two-color emission: Polyfluorene as blue host and 2,1,3-benzothiadiazole derivatives as orange dopants on the side chain

Four single polymers with two kinds of attachment of orange chromophore to blue polymer host for white electroluminescence (EL) were designed. The effect of the side-chain attachment and main-chain attachment on the EL efficiencies of the resulting polymers was compared. The side-chain-type single polymers are found to exhibit more efficient white EL than that of the main-chain-type single polymers. Based on the side-chain-type white single polymer with 4-(4-alkyloxy-phenyl)-7-(4-diphenylamino-phenyl)-2,1,3-benzothiadiazoles as the orange-dopant unit and polyfluorene as the blue polymer host, white EL with simultaneous orange (lambda(max) = 545 nm) and blue emission (lambda(max) = 432 nm/460 nm) is realised. A single-layer device (indium tin oxide/poly(3,4-ethylenedioxythiophene)/polymer/Ca/Al) made of these polymers emits white light with the Commission Internationale de l'Eclairage coordinates of (0.30,0.40), possesses a turn-on voltage of 3.5 V, luminous efficiency of 10.66 cd A(-1), power efficiency of 6.68 lm W-1, and a maximum brightness of 21240 cd m(-2).

White electrolumineseence from a single-polymer system with simultaneous two-color emission: Polyfluorene as the blue host and a 2,1,3-benzothiadiazole derivative as the orange dopant on the main chain

New single-polymer electroluminescent systems containing two individual emission species - polyfluorenes as a blue host and 2,1,3-benzothiadiazole derivative units as an orange dopant on the main chain - have been designed and synthesized. The resulting single polymers are found to have highly efficient white electroluminescence with simultaneous blue(lambda(max) = 421 nm/445 nm) and orange emission (lambda(max) = 564 nm)from the corresponding emitting species. The influence of the photoluminescence (PL) efficiencies of both the blue and orange species on the electroluminescence (EL) efficiencies of white polymer light-emitting diodes (PLEDs) based on the single-polymer systems has been investigated. The introduction of the highly efficient 4,7-bis(4-(N-phenyl-N-(4-methylphenyl)amino)phenyl)-2,1,3-benzothiadiazole unit to the main chain of polyfluorene provides significant improvement in EL efficiency. For a single-layer device fabricated in air (indium tin oxide/poly(3,4-ethylenedioxythiophene): poly(styrene sulfonic acid/polymer/Ca/Al), pure-white electroluminescence with Commission Internationale de l'Eclairage (CIE) coordinates of (0.35,0.32), maximum brightness of 12 300 cd m(-2), luminance efficiency of 7.30 cd A(-1), and power efficiency of 3.34 lm W-1 can be obtained.

Lateral habits of single crystals of metallocene-catalyzed low molecular weight short chain branched polyethylene from the melt

The lateral habits of low molecular weight short chain branched polyethylene single crystals from the melt were studied. Three crystallization temperatures (102, 104 and 106 degrees C) were selected for single crystal growth. It was found that the lateral habits of single crystals were asymmetric at all the crystallization temperatures selected. The electron diffraction patterns and tilting series experiments evidenced that there existed chain tilting in all the lamellae. It was the chain tilting that lead to the asymmetry of the growth rate and of lateral habits of the single crystals about the b-axis. The lateral habits substantially changed from the growth at 102 degrees C where the truncated lozenge single crystals formed with straight (110) faces to the growth at 104 degrees C where the lenticular single crystals appeared. This change occurred at 20 degrees C lower than that in a low molecular weight linear polyethylene with the same molecular weight. Furthermore, kinetics theory analysis evidenced that the change of lateral habits from truncated lozenge to lenticular shape resulted from the transition of growth regime. The results were the same as that of high molecular weight linear polyethylene but different to that of low molecular weight linear polyethylene. It may be attributed by the existence of short branched chains. (C) 2000 Elsevier Science Ltd. All rights reserved.

Morphologies of metallocene-catalyzed short chain branched polyethylene single crystals formed from the melt at higher temperature

Metallocene-catalyzed short chain branched polyethylene single crystals, formed from the melt at a higher crystallization temperature of 114 degreesC, were obtained. Highly elongated lamellae were formed, which are different from truncated lozenge or lenticular shaped single crystals formed at a lower crystallization temperature. It was found that there existed a definite line in the lamellae along the longitudinal growth direction and two regions were separated by the definite line. The lateral habits of both the regions were asymmetrical about the b-axis due to the chain tilting, which was the same as that at a lower crystallization temperature. Generally, the highly elongated lamellae were not straight, but curved towards the opposite direction with chain tilting direction due to a series of edge dislocation within a lamella. The inner side of a lamella was serrated and the outer side was smooth due to the lamellar curvature. The thickness of both regions of a lamella was different, the broader region was thicker than the narrower region, which was different from the uniform thickness of the lamellae formed at a lower crystallization temperature. The different thicknesses within a lamella were considered as the result of the initial thickness difference and the impact of isothermal thickening. (C) 2001 Elsevier Science Ltd. All rights reserved.

Helical single-lamellar crystals thermotropically formed in a synthetic nonracemic chiral main-chain polyester

Phase structures and transformation mechanisms of nonracemic chiral biological and synthetic polymers are fundamentally important topics in understanding their macroscopic responses in different environments. It has been known for many years that helical structures and morphologies can exist in low-ordered chiral liquid crystalline (LC) phases. However, when the chiral liquid crystals form highly ordered smectic liquid crystal phases, the helical morphology is suppressed due to the crystallization process. A double-twisted morphology has been observed in many liquid crystalline biopolymers such as dinoflaggellate chromosomes (in Prorocentrum micans) in an in vivo arrangement. Helical crystals grown from solution have been reported in the case of Bombyx mori silk fibroin crystals having the beta modification. This study describes a synthetic nonracemic chiral main-chain LC polyester that is able to thermotropically form helical single lamellar crystals. Flat single lamellar crystals can also be observed under the same crystallization condition. Moreover, flat and helical lamellae can coexist in one single lamellar crystal, within which one form can smoothly transform to the other. Both of these crystals possess the same structure, although translational symmetry is broken in the helical crystals. The polymer chain folding direction in both flat and helical lamellar crystals is determined to be identical, and it is always along the long axis of the lamellae. This finding provides an opportunity to study the chirality effect on phase structure, morphology, and transformation in condensed states of chiral materials. [S0163-1829(99)01042-5].

A Single Mutation at the Sheet Switch Region Results in Conformational Changes Favoring lambda 6 Light-Chain Fibrillogenesis

Systemic amyloid light-chain (LC) amyloidosis is a disease process characterized by the pathological deposition of monoclonal LCs in tissue. All LC subtypes are capable of fibril formation although lambda chains, particularly those belonging to the lambda 6 type, are overrepresented. Here, we report the thermodynamic and in vitro fibrillogenic properties of several mutants of the lambda 6 protein 6aJL2 in which Pro7 and/or His8 was substituted by Ser or Pro. The H8P and H8S mutants were almost as stable as the wildtype protein and were poorly fibrillogenic. In contrast, the P7S mutation decreased the thermodynamic stability of 6aJL2 and greatly enhanced its capacity to form amyloid-like fibrils in vitro. The crystal structure of the P7S mutant showed that the substitution induced both local and long-distance effects, such as the rearrangement of the V(L) (variable region of the light chain)-V(L) interface. This mutant crystallized in two orthorhombic polymorphs, P2(1)2(1)2(1) and C222(1). In the latter, a monomer that was not arranged in the typical Bence-Jones dimer was observed for the first time. Crystal-packing analysis of the C222(1) lattice showed the establishment of intermolecular beta-beta interactions that involved the N-terminus and beta-strand B and that these could be relevant in the mechanism of LC fibril formation. Our results strongly suggest that Pro7 is a key residue in the conformation of the N-terminal sheet switch motif and, through long-distance interactions, is also critically involved in the contacts that stabilized the V(L) interface in lambda 6 LCs. (C) 2009 Elsevier Ltd. All rights reserved.

New markov chain based methods for single and cross-domain sentiment classification

Nowadays communication is switching from a centralized scenario, where communication media like newspapers, radio, TV programs produce information and people are just consumers, to a completely different decentralized scenario, where everyone is potentially an information producer through the use of social networks, blogs, forums that allow a real-time worldwide information exchange. These new instruments, as a result of their widespread diffusion, have started playing an important socio-economic role. They are the most used communication media and, as a consequence, they constitute the main source of information enterprises, political parties and other organizations can rely on. Analyzing data stored in servers all over the world is feasible by means of Text Mining techniques like Sentiment Analysis, which aims to extract opinions from huge amount of unstructured texts. This could lead to determine, for instance, the user satisfaction degree about products, services, politicians and so on. In this context, this dissertation presents new Document Sentiment Classification methods based on the mathematical theory of Markov Chains. All these approaches bank on a Markov Chain based model, which is language independent and whose killing features are simplicity and generality, which make it interesting with respect to previous sophisticated techniques. Every discussed technique has been tested in both Single-Domain and Cross-Domain Sentiment Classification areas, comparing performance with those of other two previous works. The performed analysis shows that some of the examined algorithms produce results comparable with the best methods in literature, with reference to both single-domain and cross-domain tasks, in $2$-classes (i.e. positive and negative) Document Sentiment Classification. However, there is still room for improvement, because this work also shows the way to walk in order to enhance performance, that is, a good novel feature selection process would be enough to outperform the state of the art. Furthermore, since some of the proposed approaches show promising results in $2$-classes Single-Domain Sentiment Classification, another future work will regard validating these results also in tasks with more than $2$ classes.

A single-centre cohort of patients with systemic light chain AL-amyloidosis treated with conventional chemotherapy or with high-dose chemotherapy and autologous stem cell transplantation.

BACKGROUND High-dose chemotherapy (HDCT) with autologous stem cell transplantation (ASCT) has been reported to confer better prognosis in systemic light chain AL-amyloidosis as compared with conventional chemotherapy. However, only limited data are available so far on treatment and outcome of AL-amyloidosis patients in Switzerland. METHODS Within a single-centre cohort of patients with biopsy confirmed AL-amyloidosis diagnosed between January 1995 and December 2012, we aimed to investigate treatment effects in patients treated with conventional chemotherapy versus HDCT with ASCT. RESULTS We identified 50 patients with AL-amyloidosis treated with conventional chemotherapy and 13 patients who received HDCT with ASCT. Clinical characteristics differed between the groups for the age of the patients (59 years for patients with ASCT/HDCT vs 69 years; p= 0.0006) and the troponin-T value (0.015 μg/l vs 0.08 μg/l; p = 0.0279). Patients with ASCT showed a trend towards better overall survival, with median survival not yet reached compared with 53 months in patients on conventional chemotherapy (p = 0.0651). CONCLUSION Our results suggest that light chain AL-amyloidosis patients considered fit to undergo HDCT and ASCT may have a better outcome than patients treated exclusively with conventional chemotherapy regimens; however, the better performance status of patients receiving HDCT may have added to this treatment effect.

Three functional luciferase domains in a single polypeptide chain

We report a unique case of a gene containing three homologous and contiguous repeat sequences, each of which, after excision, cloning, and expression in Escherichia coli, is shown to code for a peptide catalyzing the same reaction as the native protein, Gonyaulax polyedra luciferase (Mr = 137). This enzyme, which catalyzes the light-emitting oxidation of a linear tetrapyrrole (dinoflagellate luciferin), exhibits no sequence similarities to other luciferases in databases. Sequence analysis also reveals an unusual evolutionary feature of this gene: synonymous substitutions are strongly constrained in the central regions of each of the repeated coding sequences.

Calibration of the length of a chain of single gold atoms

Using a scanning tunnelling microscope or mechanically controllable break junction it has been shown that it is possible to control the formation of a wire made of single gold atoms. In these experiments an interatomic distance between atoms in the chain of ∼3.6 Å was reported which is not consistent with recent theoretical calculations. Here, using precise calibration procedures for both techniques, we measure the length of the atomic chains. Based on the distance between the peaks observed in the chain length histogram we find the mean value of the interatomic distance before chain rupture to be 2.5±0.2 Å. This value agrees with the theoretical calculations for the bond length. The discrepancy with the previous experimental measurements was due to the presence of He gas, that was used to promote the thermal contact, and which affects the value of the work function that is commonly used to calibrate distances in scanning tunnelling microscopy and mechanically controllable break junctions at low temperatures.

Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR

With an increased emphasis on genotyping of single nucleotide polymorphisms (SNPs) in disease association studies, the genotyping platform of choice is constantly evolving. In addition, the development of more specific SNP assays and appropriate genotype validation applications is becoming increasingly critical to elucidate ambiguous genotypes. In this study, we have used SNP specific Locked Nucleic Acid (LNA) hybridization probes on a real-time PCR platform to genotype an association cohort and propose three criteria to address ambiguous genotypes. Based on the kinetic properties of PCR amplification, the three criteria address PCR amplification efficiency, the net fluorescent difference between maximal and minimal fluorescent signals and the beginning of the exponential growth phase of the reaction. Initially observed SNP allelic discrimination curves were confirmed by DNA sequencing (n = 50) and application of our three genotype criteria corroborated both sequencing and observed real-time PCR results. In addition, the tested Caucasian association cohort was in Hardy-Weinberg equilibrium and observed allele frequencies were very similar to two independently tested Caucasian association cohorts for the same tested SNP. We present here a novel approach to effectively determine ambiguous genotypes generated from a real-time PCR platform. Application of our three novel criteria provides an easy to use semi-automated genotype confirmation protocol.