Molecular Genetic Analysis of Multi-drug Resistance in Indian Isolates of Mycobacterium tuberculosis

A total of 116 isolates from patients attending the out-patient department at the All India Institute of Medical Sciences, New Delhi and the New Delhi Tuberculosis Centre, New Delhi, India were collected. They were analyzed for resistance to drugs prescribed in the treatment for tuberculosis. The drug resistance was initially determined by microbiological techniques. The Bactec 460TB system was employed to determine the type and level of resistance in each isolate. The isolates were further characterized at molecular level. The multi-drug loci corresponding to rpo b, gyr A, kat G were studied for mutation(s) by the polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) technique. The SSCP positive samples were sequenced to characterize the mutations in rpo b, and gyr A loci. While previously reported mutations in the gyr A and rpo b loci were found to be present, several novel mutations were also scored in the rpo b locus. Interestingly, analysis of the gyr A locus showed the presence of point mutation(s) that could not be detected by PCR-SSCP. Furthermore, rifampicin resistance was found to be an important marker for checking multi-drug resistance (MDR) in clinical isolates of Mycobacterium tuberculosis. This is the first report on molecular genetic analysis of MDR tuberculosis one from India, highlights the increasing incidence of MDR in the Indian isolates of M. tuberculosis.

Detection of Mycobacterium tuberculosis in sputum from Suruí Indian subjects, Brazilian Amazon

This investigation aimed at the detection of Mycobacterium tuberculosis (MTB) in the sputum of Suruí Indian subjects from Amazonia, Brazil. Polymerase chain reaction analyses were positive for12 samples, five of which were also culture-positive (N = 147). Four MTB genotypes were identified, one of which showed resistance to rifampicin and isoniazid. The study also highlighted one village complex as of particular importance, considering the relatively high number of tuberculosis cases reported and of MTB isolates obtained.

RFLP clusters of Mycobacterium tuberculosis strains from the Indian Ocean Region: local and South Asian characteristics

This is the first study describing the genetic polymorphism of Mycobacterium tuberculosis strains in the Indian Ocean Region. Using IS6110 RFLP analysis, 475 M. tuberculosis isolates from Madagascar, Comoros, Mauritius, Mozambique and La Reunion were compared. Of the 332 IS6110 profiles found, 43 were shared by clusters containing 2-65 strains. Six clusters were common to at least two countries. Of 52 families of strains with similar IS6110 profiles, 10 were common to at least two countries. Interestingly, another characteristic was the frequency (16.8%) of IS6110 single-copy strains. These strains could be distinguished using the DR marker. This preliminary evaluation suggests genetic similarity between the strains of the Indian Ocean Region. However, additional markers would be useful for epidemiological studies and to assess the ancient transmission of strains between countries of this region.

Failure to demonstrate experimental vertical transmission of the epidemic strain of Chikungunya virus in Aedes albopictus from La Réunion Island, Indian Ocean

Aedes albopictus was responsible for transmission in the first outbreak of chikungunya (CHIK) on La Réunion Island, Indian Ocean, in 2005-2006. The magnitude of the outbreak on this island, which had been free of arboviral diseases for over 30 years, as well as the efficiency of Ae. albopictus as the main vector, raises questions about the maintenance of the CHIK virus (CHIKV) through vertical transmission mechanisms. Few specimens collected from the field as larvae were found to be infected. In this study, Ae. albopictus originating from La Réunion were orally infected with a blood-meal containing 10(8) pfu/mL of the CHIKV epidemic strain (CHIKV 06.21). Eggs from the first and second gonotrophic cycles were collected and raised to the adult stage. The infectious status of the progeny was checked (i) by immunofluorescence on head squashes of individual mosquitoes to detect the presence of viral particles or (ii) by quantitative RT-PCR on mosquito pools to detect viral RNA. We analysed a total of 1,675 specimens from the first gonotrophic cycle and 1,709 from the second gonotrophic cycle without detecting any viral particles or viral RNA. These laboratory results are compared to field records.

Eimeria pavoaegyptica sp. nov. (Apicomplexa: Eimeriidae) in faeces of Indian peacocks, Pavo cristatus Linnaeus, 1758 (Galliformes: Phasianidae) from Egypt

Coprological examination of 15 Indian peacocks, Pavo cristatus, revealed the presence of a coccidium species of the genus Eimeria, which apparently represents a previously undescribed species. Sporulation is exogenous and fully developed oocysts of Eimeria pavoaegyptica sp. nov. are ellipsoidal, with a dimension of 15 (13-16) × 12 (10-12.9) μm and with a shape index of 1.25 (1-1.3). The sporulated oocysts have no micropyle but enclose one large rectangular-shaped polar granule and an oocyst residuum. The oocysts have a distinct two-layered wall, which is ~1.7 μm thick. The outer layer has a smooth texture; it fills ~¾ of the total thickness and appears bicolored. The sporocysts are boat-shaped, of about 10 (9-11) × 4 (4-4.7) μm; their average shape-index is 2.5 μm with a small pointed Stieda body and a smooth, thin single-layered wall. No substieda body is detected. The sporocysts contain numerous, nearly uniform granular residua. The sporozoites are banana-shaped, 6 × 3 μm and each has two different-sized refractile bodies.

Mitochondrial genome sequence diversity of Indian Plasmodium falciparum isolates

We have analysed the whole mitochondrial (mt) genome sequences (each ~6 kilo nucleotide base pairs in length) of four field isolates of the malaria parasite Plasmodium falciparum collected from different locations in India. Comparative genomic analyses of mt genome sequences revealed three novel India-specific single nucleotide polymorphisms. In general, high mt genome diversity was found in Indian P. falciparum, at a level comparable to African isolates. A population phylogenetic tree placed the presently sequenced Indian P. falciparum with the global isolates, while a previously sequenced Indian isolate was an outlier. Although this preliminary study is limited to a few numbers of isolates, the data have provided fundamental evidence of the mt genome diversity and evolutionary relationships of Indian P. falciparum with that of global isolates.

An experimental test of rainfall as a control agent of Glycaspis brimblecombei Moore (Hemiptera, Psyllidae) on seedlings of Eucalyptus camaldulensis Dehn (Myrtaceae)

An experimental test of rainfall as a control agent of Glycaspis brimblecombei Moore (Hemiptera, Psyllidae) on seedlings of Eucalyptus camaldulensis Dehn (Myrtaceae). Glycaspis brimblecombei is one the greatest threats to eucalyptus plantations in Brazil. The effects of rainfall to reduce the abundance of lerp of Glycaspis brimblecombei on experimentally infested seedlings of Eucalyptus camaldulensis were assessed. The number of lerps on the adaxial and abaxial surfaces of every leaf of 60 seedlings was recorded, before and after submission to the following treatments: "artificial rain", "leaf wetting" and control. A drastic reduction in lerp abundance per plant was observed after the treatments "leaf wetting" and artificial rain (F = 53.630; p < 0.001), whereas lerp abundance remained roughly constant in the control treatment along the experiment (F = 1.450; p = 0.232). At the end of the experiment, lerp abundance was significantly lower in both the "artificial rain" and "leaf wetting" than in the control treatment. Two days of rainfall simulation were sufficient to decrease more than 50% of the lerp population, with almost 100% of effectiveness after 5 days of experiment. Our results indicate that lerp solubilization and mechanical removal by water are potential tools to the population regulation of G. brimblecombei on E. camaldulensis seedlings.

Phosphorous forms in cultivated indian black earth (anthrosols) of varying texture in the brazilian Amazon

Despite the agricultural importance of Indian Black Earth (IBE) in the Amazon region, there are few studies that report on the relation between soil texture and chemical fertility of IBE. These soils of pre-Colombian origin, with high contents of P, Ca and other nutrients are found across the Amazon valley. IBE profiles were studied to evaluate the total contents of P, its primary chemical forms and the P transformation phases in areas with IBE soils of variable texture and in adjacent reference soils. The soil texture strongly influenced soil fertility, changing in terms of transformation of the primary P forms and, consequently, predominant P forms in IBE. Soils with texture varying between clay and heavy clay had higher total P contents and primary Ca-P forms. Highest P-Al and lowest total P amounts were observed at the site Rio Preto da Eva, where texture varies from sandy loam to sandy clay loam. In the IBE with clay texture the amounts of soluble P, extracted with NH4Cl were highest, although different from Mehlich 1-extractable amounts.

Rainfall erosivity and rainfall return period in the experimental watershed of Aracruz, in the coastal plain of Espirito Santo, Brazil

Knowledge on the factors influencing water erosion is fundamental for the choice of the best land use practices. Rainfall, expressed by rainfall erosivity, is one of the most important factors of water erosion. The objective of this study was to determine rainfall erosivity and the return period of rainfall in the Coastal Plains region, near Aracruz, a town in the state of Espírito Santo, Brazil, based on available data. Rainfall erosivity was calculated based on historic rainfall data, collected from January 1998 to July 2004 at 5 min intervals, by automatic weather stations of the Aracruz Cellulose S.A company. A linear regression with individual rainfall and erosivity data was fit to obtain an equation that allowed data extrapolation to calculate individual erosivity for a 30-year period. Based on this data the annual average rainfall erosivity in Aracruz was 8,536 MJ mm ha-1 h-1 yr-1. Of the total annual rainfall erosivity 85 % was observed in the most critical period October to March. Annual erosive rains accounted for 38 % of the events causing erosion, although the runoff volume represented 88 % of the total. The annual average rainfall erosivity return period was estimated to be 3.4 years.

Heavy rainfall equations for Santa Catarina, Brazil

Knowledge of intensity-duration-frequency (IDF) relationships of rainfall events is extremely important to determine the dimensions of surface drainage structures and soil erosion control. The purpose of this study was to obtain IDF equations of 13 rain gauge stations in the state of Santa Catarina in Brazil: Chapecó, Urussanga, Campos Novos, Florianópolis, Lages, Caçador, Itajaí, Itá, Ponte Serrada, Porto União, Videira, Laguna and São Joaquim. The daily rainfall data charts of each station were digitized and then the annual maximum rainfall series were determined for durations ranging from 5 to 1440 min. Based on these, with the Gumbel-Chow distribution, the maximum rainfall was estimated for durations ranging from 5 min to 24 h, considering return periods of 2, 5, 10, 20, 25, 50, and 100 years,. Data agreement with the Gumbel-Chow model was verified by the Kolmogorov-Smirnov test, at 5 % significance level. For each rain gauge station, two IDF equations of rainfall events were adjusted, one for durations from 5 to 120 min and the other from 120 to 1440 min. The results show a high variability in maximum intensity of rainfall events among the studied stations. Highest values of coefficients of variation in the annual maximum series of rainfall were observed for durations of over 600 min at the stations of the coastal region of Santa Catarina.

Duration-frequency relationships of heavy rainfall in Santa Catarina, Brazil

The purpose of this study was to adjust equations that establish relationships between rainfall events with different duration and data from weather stations in the state of Santa Catarina, Brazil. In this study, the relationships between different duration heavy rainfalls from 13 weather stations of Santa Catarina were analyzed. From series of maximum annual rainfalls, and using the Gumbel-Chow distribution, the maximum rainfall for durations between 5 min and 24 h were estimated considering return periods from 2 to 100 years. The data fit to the Gumbel-Chow model was verified by the Kolmogorov-Smirnov test at 5 % significance. The coefficients of Bell's equation were adjusted to estimate the relationship between rainfall duration t (min) and the return period T (y) in relation to the maximum rainfall with a duration of 1 hour and a 10 year return period. Likewise, the coefficients of Bell's equation were adjusted based on the maximum rainfall with a duration of 1 day and a 10 year return period. The results showed that these relationships are viable to estimate short-duration rainfall events at locations where there are no rainfall records.

Relations between soil surface roughness, tortuosity, tillage treatments, rainfall intensity and soil and water losses from a red yellow latosol

The soil surface roughness increases water retention and infiltration, reduces the runoff volume and speed and influences soil losses by water erosion. Similarly to other parameters, soil roughness is affected by the tillage system and rainfall volume. Based on these assumptions, the main purpose of this study was to evaluate the effect of tillage treatments on soil surface roughness (RR) and tortuosity (T) and to investigate the relationship with soil and water losses in a series of simulated rainfall events. The field study was carried out at the experimental station of EMBRAPA Southeastern Cattle Research Center in São Carlos (Fazenda Canchim), in São Paulo State, Brazil. Experimental plots of 33 m² were treated with two tillage practices in three replications, consisting of: untilled (no-tillage) soil (NTS) and conventionally tilled (plowing plus double disking) soil (CTS). Three successive simulated rain tests were applied in 24 h intervals. The three tests consisted of a first rain of 30 mm/h, a second of 30 mm/h and a third rain of 70 mm/h. Immediately after tilling and each rain simulation test, the surface roughness was measured, using a laser profile meter. The tillage treatments induced significant changes in soil surface roughness and tortuosity, demonstrating the importance of the tillage system for the physical surface conditions, favoring water retention and infiltration in the soil. The increase in surface roughness by the tillage treatments was considerably greater than its reduction by rain action. The surface roughness and tortuosity had more influence on the soil volume lost by surface runoff than in the conventional treatment. Possibly, other variables influenced soil and water losses from the no-tillage treatments, e.g., soil type, declivity, slope length, among others not analyzed in this study.

Soil losses from typic cambisols and red latosol as related to three erosive rainfall patterns

Rainfall erosivity is one of the main factors related to water erosion in the tropics. This work focused on relating soil loss from a typic dystrophic Tb Haplic Cambisol (CXbd) and a typic dystrophic Red Latosol (LVdf) to different patterns of natural erosive rainfall. The experimental plots of approximately 26 m² (3 x 8.67 m) consisted of a CXbd area with a 0.15 m m-1 slope and a LVdf area with 0.12 m m-1 slope, both delimited by galvanized plates. Drainpipes were installed at the lower part of these plots to collect runoff, interconnected with a Geib or multislot divisor. To calculate erosivity (EI30), rainfall data, recorded continuously at a weather station in Lavras, were used. The data of erosive rainfall events were measured (10 mm precipitation intervals, accuracy 0.2 mm, 24 h period, 20 min intervals), characterized as rainfall events with more than 10 mm precipitation, maximum intensity > 24 mm h-1 within 15 min, or kinetic energy > 3.6 MJ, which were used in this study to calculate the rainfall erosivity parameter, were classified according to the moment of peak precipitation intensity in advanced, intermediate and delayed patterns. Among the 139 erosive rainfall events with CXbd soil loss, 60 % were attributed to the advanced pattern, with a loss of 415.9 Mg ha-1, and total losses of 776.0 Mg ha-1. As for the LVdf, of the 93 erosive rainfall events with soil loss, 58 % were listed in the advanced pattern, with 37.8 Mg ha-1 soil loss and 50.9 Mg ha-1 of total soil loss. The greatest soil losses were observed in the advanced rain pattern, especially for the CXbd. From the Cambisol, the soil loss per rainfall event was greatest for the advanced pattern, being influenced by the low soil permeability.

Hydrological processes obtained on the plot scale under four simulated rainfall tests during the cycle of different crop systems

The cropping system influences the interception of water by plants, water storage in depressions on the soil surface, water infiltration into the soil and runoff. The aim of this study was to quantify some hydrological processes under no tillage cropping systems at the edge of a slope, in 2009 and 2010, in a Humic Dystrudept soil, with the following treatments: corn, soybeans, and common beans alone; and intercropped corn and common bean. Treatments consisted of four simulated rainfall tests at different times, with a planned intensity of 64 mm h-1 and 90 min duration. The first test was applied 18 days after sowing, and the others at 39, 75 and 120 days after the first test. Different times of the simulated rainfall and stages of the crop cycle affected soil water content prior to the rain, and the time runoff began and its peak flow and, thus, the surface hydrological processes. The depth of the runoff and the depth of the water intercepted by the crop + soil infiltration + soil surface storage were affected by the crop systems and the rainfall applied at different times. The corn crop was the most effective treatment for controlling runoff, with a water loss ratio of 0.38, equivalent to 75 % of the water loss ratio exhibited by common bean (0.51), the least effective treatment in relation to the others. Total water loss by runoff decreased linearly with an increase in the time that runoff began, regardless of the treatment; however, soil water content on the gravimetric basis increased linearly from the beginning to the end of the rainfall.

Erosivity of rainfall in Lages, Santa Catarina, Brazil

The erosive capacity of rainfall can be expressed by an index and knowing it allows recommendation of soil management and conservation practices to reduce water erosion. The objective of this study was to calculate various indices of rainfall erosivity in Lages, Santa Catarina, Brazil, identify the best one, and discover its temporal distribution. The study was conducted at the Center of Agricultural and Veterinary Sciences, Lages, Santa Catarina, using daily rainfall charts from 1989 to 2012. Using the computer program Chuveros , 107 erosivity indices were obtained, which were based on maximum intensity in 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90, 100, 110, 120, 135, 150, 165, 180, 210, and 240 min of duration and on the combination of these intensities with the kinetic energy obtained by the equations of Brown & Foster, Wagner & Massambani, and Wischmeier & Smith. The indices of the time period from 1993 to 2012 were correlated with the respective soil losses from the standard plot of the Universal Soil Loss Equation (USLE) in order to select the erosivity index for the region. Erosive rainfall accounted for 83 % of the mean annual total volume of 1,533 mm. The erosivity index (R factor) of rainfall recommended for Lages is the EI30, whose mean annual value is 5,033 MJ mm ha-1 h-1, and of this value, 66 % occurs from September to February. Mean annual erosivity has a return period estimated at two years with a 50 % probability of occurrence.