Use of the polymerase chain reaction to detect Mycobacterium leprae in urine

Leprosy is an infectious disease caused by Mycobacterium leprae. The polymerase chain reaction (PCR) has been applied to detect M. leprae in different clinical samples and urine seems to be attractive for this purpose. PCR was used to improve the sensitivity for diagnosing leprosy by amplifying a 151-bp PCR fragment of the M. leprae pra gene (PCR-Pra) in urine samples. Seventy-three leprosy patients (39 males and 34 females, 14 to 78 years old) were selected for leprosy diagnosis at a reference laboratory in Maringá, PR, Brazil. Of these, 36 were under anti-leprosy multidrug therapy with dapsone and rifampicin for tuberculoid (TT) and dapsone, rifampicin and clofazimine for borderline (BB) and lepromatous (LL) forms. The control group contained 50 healthy individuals without any clinical history of leprosy. DNA isolated from leprosy patients’ urine samples was successfully amplified by PCR-Pra in 46.6% (34/73) of the cases. The positivity of PCR-Pra for patients with the TT form was 75% for both patients under treatment and non-treated patients (P = 0.1306). In patients with the LL form, PCR-Pra positivity was 52 and 30% for patients under treatment and non-treated patients, respectively (P = 0.2386). PCR-Pra showed a statistically significant difference in detecting M. leprae between the TT and LL forms of leprosy in patients under treatment (P = 0.0033). Although the current study showed that the proposed PCR-Pra has some limitations in the detection of M. leprae, this method has the potential to be a useful tool for leprosy diagnosis mainly in TT leprosy where the AFB slit-skin smear is always negative.

Modeling pulmonary fibrosis by abnormal expression of telomerase/apoptosis/collagen V in experimental usual interstitial pneumonia

Limitations on tissue proliferation capacity determined by telomerase/apoptosis balance have been implicated in pathogenesis of idiopathic pulmonary fibrosis. In addition, collagen V shows promise as an inductor of apoptosis. We evaluated the quantitative relationship between the telomerase/apoptosis index, collagen V synthesis, and epithelial/fibroblast replication in mice exposed to butylated hydroxytoluene (BHT) at high oxygen concentration. Two groups of mice were analyzed: 20 mice received BHT, and 10 control mice received corn oil. Telomerase expression, apoptosis, collagen I, III, and V fibers, and hydroxyproline were evaluated by immunohistochemistry, in situ detection of apoptosis, electron microscopy, immunofluorescence, and histomorphometry. Electron microscopy confirmed the presence of increased alveolar epithelial cells type 1 (AEC1) in apoptosis. Immunostaining showed increased nuclear expression of telomerase in AEC type 2 (AEC2) between normal and chronic scarring areas of usual interstitial pneumonia (UIP). Control lungs and normal areas from UIP lungs showed weak green birefringence of type I and III collagens in the alveolar wall and type V collagen in the basement membrane of alveolar capillaries. The increase in collagen V was greater than collagens I and III in scarring areas of UIP. A significant direct association was found between collagen V and AEC2 apoptosis. We concluded that telomerase, collagen V fiber density, and apoptosis evaluation in experimental UIP offers the potential to control reepithelization of alveolar septa and fibroblast proliferation. Strategies aimed at preventing high rates of collagen V synthesis, or local responses to high rates of cell apoptosis, may have a significant impact in pulmonary fibrosis.

Hygienic-sanitary working practices and implementation of a Hazard Analysis and Critical Control Point (HACCP) plan in lobster processing industries

This study aimed to verify the hygienic-sanitary working practices and to create and implement a Hazard Analysis Critical Control Point (HACCP) in two lobster processing industries in Pernambuco State, Brazil. The industries studied process frozen whole lobsters, frozen whole cooked lobsters, and frozen lobster tails for exportation. The application of the hygienic-sanitary checklist in the industries analyzed achieved conformity rates over 96% to the aspects evaluated. The use of the Hazard Analysis Critical Control Point (HACCP) plan resulted in the detection of two critical control points (CCPs) including the receiving and classification steps in the processing of frozen lobster and frozen lobster tails, and an additional critical control point (CCP) was detected during the cooking step of processing of the whole frozen cooked lobster. The proper implementation of the Hazard Analysis Critical Control Point (HACCP) plan in the lobster processing industries studied proved to be the safest and most cost-effective method to monitor each critical control point (CCP) hazards.

Impact of pesticides on indicator and pathogenic microorganism persistence under laboratory and field conditions

On s’intéresse aux impacts des pesticides sur la microflore des plantes surtout dans le contexte des légumes contaminés par des agents pathogènes. Le but de cette étude est d'évaluer l'impact de certains pesticides sur la persistance de micro-organismes indicateurs et pathogènes. En laboratoire, la persistance d’E. coli et de Salmonella en présence de quatre pesticides (Ripcord 400EC, Copper 53W, Bioprotec CAF, Serenade MAX) a été étudiée. Les plaques de Pétrifilm et le milieu sélectif XLD sont utilisés pour énumérer les populations d’E. coli et de Salmonella. Il a été démontré que le Serenade MAX favorisait la croissance microbienne, le Bioprotec CAF et le Ripcord 400EC soutenaient la survie microbienne et le Copper 53W inhibait la croissance, à la fois d’E. coli et de Salmonella. En conditions terrain, Ripcord 400EC, Copper 53W, Bioprotec CAF ont été étudiés sur une culture de brocoli irriguée avec de l'eau expérimentalement contaminée par E. coli. Dans tous les traitements, un impact de l’irrigation a été observé sur les populations de levures et de moisissures (diminution) et les bactéries aérobies totales (augmentation). Une prévalence supérieure d’E. coli a été observée dans les parcelles traitées avec le Bioprotec CAF comparativement aux traitements au Copper 53W, ce qui est en accord avec les résultats observés lors de l'essai en laboratoire. Cependant, l'analyse statistique n'a montré aucune différence significative entre les traitements appliqués. Les effets directs des pesticides sur les micro-organismes sont confirmés dans des conditions de laboratoire mais demeurent méconnus dans les conditions expérimentales au champ.

A Cryptosystem Using the Concepts of Algebraic Geometric Code

Cryptosystem using linear codes was developed in 1978 by Mc-Eliece. Later in 1985 Niederreiter and others developed a modified version of cryptosystem using concepts of linear codes. But these systems were not used frequently because of its larger key size. In this study we were designing a cryptosystem using the concepts of algebraic geometric codes with smaller key size. Error detection and correction can be done efficiently by simple decoding methods using the cryptosystem developed. Approach: Algebraic geometric codes are codes, generated using curves. The cryptosystem use basic concepts of elliptic curves cryptography and generator matrix. Decrypted information takes the form of a repetition code. Due to this complexity of decoding procedure is reduced. Error detection and correction can be carried out efficiently by solving a simple system of linear equations, there by imposing the concepts of security along with error detection and correction. Results: Implementation of the algorithm is done on MATLAB and comparative analysis is also done on various parameters of the system. Attacks are common to all cryptosystems. But by securely choosing curve, field and representation of elements in field, we can overcome the attacks and a stable system can be generated. Conclusion: The algorithm defined here protects the information from an intruder and also from the error in communication channel by efficient error correction methods.

Chemical sensing with microbent optical fiber

We propose and demonstrate the possibility of using a permanently microbent bare optical fiber for detecting chemical species. Two detection schemes, viz., a bright-field detection scheme (for the core modes), and a dark-field detection scheme (for the cladding modes) have been employed to produce a fiber-optic sensor. The sensor described here is sensitive enough to detect concentrations as low as nanomoles per liter of a chemical species, with a dynamic range of more than 6 orders of magnitude.

A microbent fiber optic pH sensor

Optical fiber sensors developed for measuring pH values usually employ an unclad and unstrained section of the fiber. In this paper, we describe the design and fabrication of a microbent fiber optic sensor that can be used for pH sensing. In order to obtain the desired performance, a permanently microbent portion of a plastic optic fiber is coated with a thin film of dye impregnated sol–gel material. The measurements are simultaneously carried out in two independent detection schemes viz., the bright field detection configuration for detecting the core modes and dark field detection configuration, for detecting the cladding modes. The results of measurements of core mode-power and cladding mode-power variation with change in pH of a solution surrounding the coated portion of the fiber is presented. This paper thus demonstrates how a bare plastic fiber can be modified for pH sensing in a simple and cost effective manner.

Microbent optical fibers as evanescent wave sensors

Microbent optical fibers are potential candidates for evanescent wave sensing. We investigate the behavior of a permanently microbent fiber optic sensor when it is immersed in an absorbing medium. Two distinct detection schemes, namely, bright-field and dark-field detection configuration, are employed for the measurements. The optical power propagating through the sensor is found to vary in a logarithmic fashion with the concentration of the absorbing species in the surrounding medium. We observe that the sensitivity of the setup is dependent on the bending amplitude and length of the microbend region for the bright-field detection scheme, while it is relatively independent of both for the dark-field detection configuration. This feature can be exploited in compact sensor designs where reduction of the sensing region length is possible without sacrificing sensitivity.

Topological Invariants in Hydrodynamics and Hydromagnetics

In this thesis we are studying possible invariants in hydrodynamics and hydromagnetics. The concept of flux preservation and line preservation of vector fields, especially vorticity vector fields, have been studied from the very beginning of the study of fluid mechanics by Helmholtz and others. In ideal magnetohydrodynamic flows the magnetic fields satisfy the same conservation laws as that of vorticity field in ideal hydrodynamic flows. Apart from these there are many other fields also in ideal hydrodynamic and magnetohydrodynamic flows which preserves flux across a surface or whose vector lines are preserved. A general study using this analogy had not been made for a long time. Moreover there are other physical quantities which are also invariant under the flow, such as Ertel invariant. Using the calculus of differential forms Tur and Yanovsky classified the possible invariants in hydrodynamics. This mathematical abstraction of physical quantities to topological objects is needed for an elegant and complete analysis of invariants.Many authors used a four dimensional space-time manifold for analysing fluid flows. We have also used such a space-time manifold in obtaining invariants in the usual three dimensional flows.In chapter one we have discussed the invariants related to vorticity field using vorticity field two form w2 in E4. Corresponding to the invariance of four form w2 ^ w2 we have got the invariance of the quantity E. w. We have shown that in an isentropic flow this quantity is an invariant over an arbitrary volume.In chapter three we have extended this method to any divergence-free frozen-in field. In a four dimensional space-time manifold we have defined a closed differential two form and its potential one from corresponding to such a frozen-in field. Using this potential one form w1 , it is possible to define the forms dw1 , w1 ^ dw1 and dw1 ^ dw1 . Corresponding to the invariance of the four form we have got an additional invariant in the usual hydrodynamic flows, which can not be obtained by considering three dimensional space.In chapter four we have classified the possible integral invariants associated with the physical quantities which can be expressed using one form or two form in a three dimensional flow. After deriving some general results which hold for an arbitrary dimensional manifold we have illustrated them in the context of flows in three dimensional Euclidean space JR3. If the Lie derivative of a differential p-form w is not vanishing,then the surface integral of w over all p-surfaces need not be constant of flow. Even then there exist some special p-surfaces over which the integral is a constant of motion, if the Lie derivative of w satisfies certain conditions. Such surfaces can be utilised for investigating the qualitative properties of a flow in the absence of invariance over all p-surfaces. We have also discussed the conditions for line preservation and surface preservation of vector fields. We see that the surface preservation need not imply the line preservation. We have given some examples which illustrate the above results. The study given in this thesis is a continuation of that started by Vedan et.el. As mentioned earlier, they have used a four dimensional space-time manifold to obtain invariants of flow from variational formulation and application of Noether's theorem. This was from the point of view of hydrodynamic stability studies using Arnold's method. The use of a four dimensional manifold has great significance in the study of knots and links. In the context of hydrodynamics, helicity is a measure of knottedness of vortex lines. We are interested in the use of differential forms in E4 in the study of vortex knots and links. The knowledge of surface invariants given in chapter 4 may also be utilised for the analysis of vortex and magnetic reconnections.

Supramolecular Organization of Metal Nanoparticles in Solution and of Phenyleneethynylenes on Surfaces

Most of the procedures reported for the synthesis of metal nanoparticles involve the use of strong reducing agents or elevated temperatures. This limits the possibility of developing metal nanoparticle based sensors for the in situ detection of analytes. One of the objectives of the present investigations is to (i) develop newer methodologies for the synthesis of metal nanoparticles in aqueous medium at ambient conditions and (ii) their use in the detection of metal cations by taking advantage of the unique coordination ability. Ideally, biocompatible molecules which possess both the reducing and stabilizing groups are desirable for such applications. Formation of stable supramolecular assembly, by bringing metal nanoparticles close to each other, results in plasmon coupling and this strategy can be effectively utilized for the development of metal nanoparticle based sensors.Another objective of the present study is to understand the supramolecular organization of molecules on surfaces. Various noncovalent interactions between the molecules and with surface play a decisive role in their organizations. An in-depth understanding of these interactions is essential for device fabrications. Recent photophysical studies have revealed that phenyleneethynylene based molecular systems are ideal for device application. The second objective of the thesis focuses on understanding the (i) organization of phenyleneethynylenes on highly oriented pyrolytic graphite (HOPG) surface with atomic level precision and (ii) weak intermolecular interactions which drive their organization.

Detection of sandal spike phytoplasma using immunological and molecular techniques

Spike disease in sandal is generally diagnosed by the manifestation of external symptoms. Attempts have been made to detect the diseased plants by determining the length/breadth ratio of leaves (lyengar, 1961) and histochemical tests using Mann's stain (Parthasarathi et al., 1966), Dienes' stain (Ananthapadmanabha et a/., 1973) aniline blue and Hoechst 33258 (Ghosh et a/., 1985, Rangaswamy, 1995). But most of these techniques are insensitive, indirect detection methods leading to misinterpretation of results. Moreover, to identify disease resistant sandal trees, highly sensitive techniques are needed to detect the presence of the pathogen. In sandal forests, several host plants of sandal like Zizyphus oenop/ea (Fig. 1.3) also exhibit the yellows type disease symptoms. Immunological and molecular assays have to be developed to confirm the presence of sandal spike phytoplasma in such hosts. The major objectives of the present work includes:In situ detection of sandal spike phytoplasma by epifluorescence microscopy and scanning electron microscopy.,Purification of sandal spike phytoplasma and production of polyclonal antibodies.,Amino acid and total protein estimation of sandal spike phytoplasma.,Immunological detection of sandal spike phytoplasma., Molecular detection of sandal spike phytoplasma.,Screening for phytoplasma in host plants of spike disease affected sandal using immunological and molecular techniques.

Anti-lipopolysaccharide factor and crustin-III, the anti-white spot virus peptides in Penaeus monodon: Control of viral infection by up-regulation

White Spot Syndrome Virus (WSSV) is the most devastating disease affecting shrimp culture around the world. Though, considerable progress has been made in the detection and molecular characterization of WSSV in recent years, information pertaining to immune gene expression in shrimps with respect to WSSV infection remains limited. In this context, the present study was undertaken to understand the differential expression of antimicrobial peptide (AMP) genes in the haemocytes of Penaeus monodon in response to WSSV infection on a time-course basis employing semi-quantitative RT-PCR. The present work analyzes the expression profile of six AMP genes (ALF, crustin-1, crustin-2, crustin-3, penaeidin-3 and penaeidin-5), eight WSSV genes (DNA polymerase, endonuclease, immediate early gene, latency related gene, protein kinase, ribonucleotide reductase, thymidine kinase and VP28) and three control genes (18S rRNA, β-actin and ELF) in P. monodon in response to WSSV challenge. Penaeidins were found to be up-regulated during early hours of infection and crustin-3 during late period of infection. However, ALF was found to be up-regulated early to late period of WSSV infection. The present study suggests that AMPs viz. ALF and crustin-3 play an important role in antiviral defense in shrimps. WSSV gene transcripts were detected post-challenge day 1 itself and increased considerably day 5 onwards. Evaluation of the control genes confirmed ELF as the most reliable control gene followed by 18S rRNA and β-actin for gene expression studies in shrimps. This study indicated the role of AMPs in the protection of shrimps against viral infection and their possible control through the up-regulation of AMPs

Efficient phosphorus application strategies for increased crop production in sub-Saharan West Africa

Comparable data are lacking from the range of environments found in sub-Saharan West Africa to draw more general conclusions about the relative merits of locally available rockphosphate (RockP) in alleviating phosphorus (P) constraints to crop growth. To fill this gap, a multi-factorial field experiment was conducted over 4 years at eight locations in Niger, Burkina Faso and Togo. These ranged in annual rainfall from 510 to 1300 mm. Crops grown were pearl millet (Pennisetum glaucum L.), sorghum (Sorghum bicolor (L.) Moench) and maize (Zea mays L.) either continuously or in rotation with cowpea (Vigna unguiculata Walp.) and groundnut (Arachis hypogaea L.). Crops were subjected to six P fertiliser treatments comprising RockP and soluble P at different rates and combined with 0 and 60 kg N ha^-1. For legumes, time trend analyses showed P-induced total dry matter (TDM) increases between 28 and 72% only with groundnut. Similarly, rotation-induced raises in cereal TDM compared to cereal monoculture were only observed with groundnut. For cereals, at the same rate of application, RockP was comparable to single superphosphate (SSP) only at two millet sites with topsoil pH-KCl <4.2 and annual average rainfall >600 mm. Across the eight sites NPK placement at 0.4 g P per hill raised average cereal yields between 26 and 220%. This was confirmed in 119 on-farm trials revealing P placement as a promising strategy to overcome P deficiency as the regionally most growth limiting nutrient constraint to cereals.

Effects of post-harvest treatments on the carbohydrate composition of yacon roots in the Peruvian Andes

Yacon (Smallanthus sonchifolius [Poepp. & Endl.] H. Robinson) is an under-exploited native root crop of the Andes, which stores oligofructans (fructo-oligosaccharides, FOS) as its main component of dry matter (DM). FOS are of increasing economic interest because of their low caloric value in human diets and bifidogenic benefits on colon health. Two on-farm experiments were conducted to: (i) determine the effect of shaded, short-term storage at 1990 and 2930 m a.s.l. in the Andean highlands; and (ii) address the effects of a traditional sunlight exposure (‘sunning’) on the carbohydrate composition in the DM of tuberous yacon roots. After a 6-day shade storage FOS concentrations were smaller at the lower (36–48% of DM) than at the higher altitude (39–58% of DM). After 12 days FOS concentrations were nearly equal at both sites (27–39% of DM). The concentration of free sugars (fructose, glucose, sucrose) increased accordingly from 29–34 to 48–52%. During the 6-day sunning experiment FOS concentrations decreased from 50–62 to 29–44% and free sugars increased from 29–34 to 45–51%. The results indicate that partial hydrolysis of oligofructans starts shortly after harvest. Storage in highland environments should wherever possible exploit the cooler temperatures at higher altitudes. Sunning of yacon’s tuberous roots effectively reduces much of the roots’ water content, in this experiment 40%, and thus allows energy to be saved if yacon is processed into dehydrated products.

Effects of Different Feeding Regimes on the Digestibility and Faecal Excretion of Nitrogen, Soluble Carbohydrates and Fibre Fractions in Water Buffaloes kept under Subtropical Conditions

In the course of the ‘Livestock Revolution’, extension and intensification of, among others, ruminant livestock production systems are current phenomena, with all their positive and negative side effects. Manure, one of the inevitable secondary products of livestock rearing, is a valuable source of plant nutrients and its skillful recycling to the soil-plant interface is essential for soil fertility, nutrient - and especially phosphorus - uses efficiency and the preservation or re-establishment of environmentally sustainable farming systems, for which organic farming systems are exemplarily. Against this background, the PhD research project presented here, which was embedded in the DFG-funded Research Training Group 1397 ‘Regulation of soil organic matter and nutrient turnover in organic agriculture ’ investigated possibilities to manipulate the diets of water buffalo (Bubalus bubalis L.) so as to produce manure of desired quality for organic vegetable production, without affecting the productivity of the animals used. Consisting of two major parts, the first study (chapter 2) tested the effects of diets differing in their ratios of carbon (C) to nitrogen (N) and of structural to non-structural carbohydrates on the quality of buffalo manure under subtropical conditions in Sohar, Sultanate of Oman. To this end, two trials were conducted with twelve water buffalo heifers each, using a full Latin Square design. One control and four tests diets were examined during three subsequent 7 day experimental periods preceded each by 21 days adaptation. Diets consisted of varying proportions of Rhodes grass hay, soybean meal, wheat bran, maize, dates, and a commercial concentrate to achieve a (1) high C/N and high NDF (neutral detergent fibre)/SC (soluble carbohydrate) ratio (HH), (2) low C/N and low NDF/SC ratio (LL); (3) high C/N and low NDF/SC ratio (HL) and (4) low C/N and high NDF/SC (LH) ratio. Effects of these diets, which were offered at 1.45 times maintenance requirements of metabolizable energy, and of individual diet characteristics, respectively, on the amount and quality of faeces excreted were determined and statistically analysed. The faeces produced from diets HH and LL were further tested in a companion PhD study (Mr. K. Siegfried) concerning their nutrient release in field experiments with radish and cabbage. The second study (chapter 3) focused on the effects of the above-described experimental diets on the rate of passage of feed particles through the gastrointestinal tract of four randomly chosen animals per treatment. To this end, an oral pulse dose of 683 mg fibre particles per kg live weight marked with Ytterbium (Yb; 14.5 mg Yb g-1 organic matter) was dosed at the start of the 7 day experimental period which followed 21 days of adaptation. During the first two days a sample for Yb determination was kept from each faecal excretion, during days 3 – 7 faecal samples were kept from the first morning and the first evening defecation only. Particle passage was modelled using a one-compartment age-dependent Gamma-2 model. In both studies individual feed intake and faecal excretion were quantified throughout the experimental periods and representative samples of feeds and faeces were subjected to proximate analysis following standard protocols. In the first study the organic matter (OM) intake and excretion of LL and LH buffaloes were significantly lower than of HH and HL animals, respectively. Digestibility of N was highest in LH (88%) and lowest in HH (74%). While NDF digestibility was also highest in LH (85%) it was lowest in LL (78%). Faecal N concentration was positively correlated (P≤0.001) with N intake, and was significantly higher in faeces excreted by LL than by HH animals. Concentrations of fibre and starch in faecal OM were positively affected by the respective dietary concentrations, with NDF being highest in HH (77%) and lowest in LL (63%). The faecal C/N ratio was positively related (P≤0.001) to NDF intake; C/N ratios were 12 and 7 for HH and LL (P≤0.001), while values for HL and LH were 11.5 and 10.6 (P>0.05). The results from the second study showed that dietary N concentration was positively affecting faecal N concentration (P≤0.001), while there was a negative correlation with the faecal concentration of NDF (P≤0.05) and the faecal ratios of NDF/N and C/N (P≤0.001). Particle passage through the mixing compartment was lower (P≤0.05) for HL (0.033 h-1) than for LL (0.043 h-1) animals, while values of 0.034 h-1 and 0.038 h-1 were obtained for groups LH and HH. At 55.4 h, total tract mean retention time was significantly (P≤0.05) lower in group LL that in all other groups where these values varied between 71 h (HH) and 79 h (HL); this was probably due to the high dietary N concentration of diet LL which was negatively correlated with time of first marker appearance in faeces (r= 0.84, P≤0.001), while the dietary C concentration was negatively correlated with particle passage through the mixing compartment (r= 0.57, P≤0.05). The results suggest that manure quality of river buffalo heifers can be considerably influenced by diet composition. Despite the reportedly high fibre digestion capacity of buffalo, digestive processes did not suppress the expression of diet characteristics in the faeces. This is important when aiming at producing a specific manure quality for fertilization purposes in (organic) crop cultivation. Although there was a strong correlation between the ingestion and the faecal excretion of nitrogen, the correlation between diet and faecal C/N ratio was weak. To impact on manure mineralization, the dietary NDF and N concentrations seem to be the key control points, but modulating effects are achieved by the inclusion of starch into the diet. Within the boundaries defined by the animals’ metabolic and (re)productive requirements for energy and nutrients, diet formulation may thus take into account the abiotically and biotically determined manure turnover processes in the soil and the nutrient requirements of the crops to which the manure is applied, so as to increase nutrient use efficiency along the continuum of the feed, the animal, the soil and the crop in (organic) farming systems.