Manganese substitution induced magnetic transformation and magnetoelectricity in SrFe12O19.

In this study, manganese substituted strontium hexaferrite (SrFe12-xMnxO19; x = 0, 3, 5, and 7) prepared by the sol-gel auto-combustion method are studied. We observed that the substituted Mn preferentially goes to the 2a and 12k sites of Fe. Raman modes related to the 12k site suggest the stiffening of the lattice. The transformation of the grain's shape from hexagonal (x = 0 and 3) to rhombohedral (x = 7) was observed, as shown in the micrographs obtained from FESEM. The thermomagnetic curves show the shift of TC to lower temperatures with the increase in the Mn content. From x = 5 onwards, the growth of another magnetic phase (FiM2) of lower coercivity apart from the parent phase (FiM1) of higher coercivity is seen. The FiM2 phase was found to increase with the Mn content in the sample (16.4(3)% for x = 5 but 66.2(5)% for x = 7). Although the magnetization for both FiM1 and FiM2 decreases with the increase in temperature, both magnetic phases behave in contrast to each other for x = 5 and x = 7. The study suggests a transformation of the compound from high magnetic anisotropy (x = 0) to low magnetic anisotropy (x = 7). The x = 5 composition sample displays the highest value of the first-order ME coefficient (0.83(2) mV × cm-1 × Oe-1). The observed value for x = 5 composition is ∼2.5 times higher than that of the parent x = 0 composition sample (0.33(2) mV × cm-1 × Oe-1). The studies thus suggest that the x = 5 composition is one of the viable candidates for magnetoelectric applications.

De-colourization of textile effluent using immobilized Geotrichum candidum: an insight into mycoremediation.

Textile effluent is generally complicated to manage because of its extremely noxious and recalcitrant coloured compositions. Mycoremediation is an extensively used strategy for the competent degradation of hazardous pollutants present in textile effluent. Fungus could be immobilized in synthetic or natural matrices. The current study shows the decolourization of the textile effluent by 85·5 and 98·5% within 6 h using suspended and immobilized fungus, Geotrichum candidum with optimized parameters like inoculum size (5%), pH (4·5), and temperature (30°C). To maintain a high biomass of fungal population and enhance the retention of fungal strain in the contaminated sites, the fungi need to be immobilized. Hence, the fungus was immobilized naturally onto the selected inert support that is, coconut fibres by the means of adsorption, where they grew as active films on the fibres after being grown in the culture broth. The optimized process parameters of inoculum size, fibre quantity and agitation speed for immobilized G. candidum were 5%, 2·2 g l-1 of effluent and 100 rev min-1 respectively. High level of laccase (22 and 25 U l-1 in suspended and immobilized fungal cells treatment respectively) was observed during the process of decolourization and it was found that decolourization was directly proportional to the laccase activity. The UV-vis, FTIR, 1 H NMR and GC-MS analyses of treated textile industrial wastewater revealed the degradation of toxic pollutants in the textile effluent and formation of lower molecular weight intermediates. The study revealed a higher efficacy of immobilized G. candidum in comparison to suspended fungal culture, employing ligninolytic enzyme laccase, which catalyzes the degradation/transformation of aromatic dyes in the textile effluent thus decolourizing it.

Elucidation of fungal dye-decolourizing peroxidase (DyP) and ligninolytic enzyme activities in decolourization and mineralization of azo dyes.

AIM: The aim of the study is to investigate the efficiency of Geotrichum candidum in the decolourization and mineralization of synthetic azo dyes. METHODS AND RESULTS: It includes screening of enzymes from G. candidum and its optimization, followed by decolourization and mineralization studies. Decolourization was observed to be maximum in methyl orange (94·6%) followed by Congo red (85%), trypan blue (70·4%) and Eriochrome Black T (55·6%) in 48 h, suggesting the plausible degradation of the azo dyes by G. candidum. The enzyme activity study showed that DyP-type peroxidase has highest activity of 900 mU ml-1 compared to that of laccase (405 mU ml-1 ) and lignin peroxidase (LiP) (324 mU ml-1 ) at optimized pH (6) and temperature (35°C). Moreover, the rate of decolourization was found to be directly proportional to the production of laccase and LiP, unlike DyP-type peroxidase. Furthermore, mineralization study demonstrated reduction in aromatic amines, showing 20% mineralization of methyl orange. CONCLUSION: Geotrichum candidum with its enzyme system is able to efficiently decolourize and mineralize the experimental azo dyes. SIGNIFICANCE AND IMPACT OF THE STUDY: The efficient decolourization and mineralization of azo dyes makes G. candidum a promising alternative in the treatment of textile effluent contaminated with azo dyes.

Cloning, expression and characterization of recombinant CagA protein of Helicobacter pylori using monoclonal antibodies: Its potential in diagnostics.

Helicobacter pylori CagA protein plays an important role in the severity of the gastric diseases. Our aims were to clone the cagA 5'- conserved region of the gene, characterize the recombinant CagA (rCagA) protein by monoclonal antibodies (mAbs) and to use this protein for the detection of anti-CagA antibodies by an ELISA test. Our developed rCagA protein (67 kDa) showed an amino acid sequence homology of 83% and 80% with Western and East Asian type strains respectively. Two anti-rCagA (BS-53, CK-02) mAbs and 2 additional rCagA proteins of smaller sizes (60 kDa, 28 kDa) were developed for epitope determination. The BS-53 mAb recognized all 3 rCagA proteins while CK-02 mAb recognized only 2 of them indicating recognition of different epitopes. An in-house indirect ELISA using rCagA was developed to detect anti-CagA antibodies in sera of 59 patients. The ELISA results obtained when compared to those of the PCR gave a sensitivity, specificity and accuracy of 81%, 100% and 88% respectively. We have developed for the first time: a rCagA protein that showed high sequence homology with both Western and East Asian type strains and an indirect ELISA of high performance which can be used to detect anti-CagA antibodies in sera of infected patients worldwide.

Two-sex life table and feeding dynamics of Spilosoma obliqua Walker (Lepidoptera: Arctiidae) on three green gram cultivars.

The effect of three green gram cultivars (PDM 54, PUSA BAISAKHI and SAMRAT) on the biology of Spilosoma obliqua Walker (Lepidoptera: Arctiidae) was studied using age-stage, two-sex life table. We also studied food utilization efficiency measures of larvae on green gram cultivars. The nutritional and antinutritional factors of leaves of green gram cultivars were determined. The preadult development time of S. obliqua was shortest on PDM 54 (35.54 days) and longest on SAMRAT (39.29 days). The fecundity was highest on PDM 54 (318.32) and lowest on SAMRAT (250.20). The net reproductive rate (R0) ranged from 37.53 on SAMRAT to 79.58 on PDM 54. The intrinsic rate of increase (r) was higher on PDM 54 (0.1148 day-1) and PUSA BAISAKHI (0.1018 day-1) than SAMRAT (0.0875 day-1). The finite rate of increase (λ) was lowest on SAMRAT (1.0915 day-1). Mean generation time (T) was shortest on PDM 54 (38.12 days) and longest on SAMRAT (41.42 days). Population projection revealed that the population growth was slowest on SAMRAT. The growth rate of sixth instar larvae was highest on PDM 54 and lowest on SAMRAT. The lower level of nutritional factors such as total carbohydrates, proteins, lipids, amino acids and nitrogen content, and a higher level of antinutritional factors such as total phenols, flavonols and tannins influenced higher development time and lower fecundity of S. obliqua on SAMRAT than other cultivars. These findings suggested that SAMRAT is a less suitable cultivar to S. obliqua than other cultivars, and this cultivar can be promoted for cultivation.

Biology and life history of Lema praeusta (Fab.) (Coleoptera: Chrysomelidae), a biocontrol agent of two Commelinaceae weeds, Commelina benghalensis and Murdannia nudiflora.

We examined previous reports of Lema praeusta (Fab.) (Coleoptera: Chrysomelidae) as a minor pest of turmeric, eggplant, bottle gourd and pumpkin leaves, but no feeding damage by larvae and adults of L. praeusta were recorded by us on these leaves. We observed feeding by the larvae and adults of L. praeusta on ten species of Commelinaceae plants in no-choice tests. The biology, fecundity and life table parameters of L. praeusta on two Commelinaceae weeds, Commelina benghalensis L. and Murdannia nudiflora (L.) Brenan were determined under laboratory conditions (27 ± 1°C, 65 ± 5% RH and 12L:12D). Total larval development times of L. praeusta were 6.36 ± 0.07 and 7.28 ± 0.11 days (mean ± SE) on C. benghalensis and M. nudiflora, respectively. Adult females lived 106.25 ± 1.17 and 77.65 ± 0.91 days (mean ± SE) on C. benghalensis and M. nudiflora, respectively. Each female laid 272.95 ± 2.39 and 224 ± 1.74 eggs (mean ± SE) during a lifetime on C. benghalensis and M. nudiflora, respectively. The net reproductive rate (Ro), intrinsic rate of increase (rm), generation time (Tc), doubling time (DT) and finite rate of increase (λ) were 136.48, 0.14, 36.17, 5.10 and 1.41 on C. benghalensis, respectively, whereas Ro, rm, Tc, DT and λ were 112, 0.20, 23.64, 3.47 and 1.51 on M. nudiflora, respectively, suggesting that L. praeusta could be a potential biocontrol agent against C. benghalensis and M. nudiflora in the fields of rice, maize, sorghum, soybean, mung bean, peanut and cotton.

Ultrafast photoinduced anisotropy in GeSe2thin film.

In this Letter, we demonstrate for the first time that anisotropy can be induced at ultrafast time scales in an otherwise isotropic a-GeSe2 thin film using polarized femtosecond light. This photoinduced anisotropy (PA) spans the bandgap to the sub-bandgap region and self-annihilates over picosecond time scales. The ultrafast decay rate of PA is a clear indication that the observed effect is due to photoinduced transient defects in the sub-bandgap region and associated structural rearrangement in the near-bandgap region.

Long-chain alkanes and fatty acids from Ludwigia octovalvis weed leaf surface waxes as short-range attractant and ovipositional stimulant to Altica cyanea (Weber) (Coleoptera: Chrysomelidae).

The importance of leaf surface wax compounds from the rice-field weed Ludwigia octovalvis (Jacq.) Raven (Onagraceae) was determined in the flea beetle Altica cyanea (Weber) (Coleoptera: Chrysomelidae). Extraction, thin layer chromatography and GC-MS and GC-FID analyses of surface waxes of young, mature and senescent leaves revealed 20, 19 and 19 n-alkanes between n-C15 and n-C35, respectively; whereas 14, 14 and 12 free fatty acids between C12:0 and C22:0 fatty acids were identified in young, mature and senescent leaves, respectively. Tricosane was predominant n-alkane in young and mature leaves, whilst eicosane predominated in senescent leaves. Heneicosanoic acid, palmitic acid and docosanoic acid were the most abundant free fatty acids in young, mature and senescent leaves, respectively. A. cyanea females showed attraction to 0.25 mature leaf equivalent surface waxes compared with young or senescent leaves in a short glass Y-tube olfactometer bioassay. The insects were attracted to a synthetic blend of 0.90, 1.86, 1.83, 1.95, 0.50 and 0.18 µg ml-1 petroleum ether of hexadecane, octadecane, eicosane, tricosane, palmitic acid and alpha-linolenic acid, respectively, comparable with the proportions as present in 0.25 mature leaf equivalent surface waxes. A. cyanea also laid eggs on a filter paper moistened with 0.25 mature leaf equivalent surface waxes or a synthetic blend of 0.90, 1.86, 1.83, 1.95, 0.50 and 0.18 µg ml-1 petroleum ether of hexadecane, octadecane, eicosane, tricosane, palmitic acid and alpha-linolenic acid, respectively. This finding could provide a basis for monitoring of the potential biocontrol agent in the field.

Attraction of Callosobruchus maculatus (F.) (Coleoptera: Bruchidae) to four varieties of Lathyrus sativus L. seed volatiles.

Callosobruchus maculatus (F.) (Coleoptera: Bruchidae) is an important stored grain pest of Lathyrus sativus L. (Leguminosae), commonly known as khesari, in India, Bangladesh and Ethiopia. Volatiles were collected from four varieties, i.e., Bio L 212 Ratan, Nirmal B-1, WBK-14-7 and WBK-13-1 of uninfested khesari seeds, and subsequently identified and quantified by gas chromatography mass spectrometry and gas chromatography flame ionization detector analyses, respectively. A total of 23 volatiles were identified in the four varieties of khesari seeds. In Bio L 212 Ratan and WBK-13-1 seeds, nonanal was the most abundant followed by farnesyl acetone; whereas farnesyl acetone was predominant followed by nonanal in Nirmal B-1 and WBK-14-7 khesari seeds. The olfactory responses of female C. maculatus toward volatile blends from four varieties of khesari seeds, and individual synthetic compounds and their combinations were examined through Y-shaped glass tube olfactometer bioassays. Callosobruchus maculatus showed significant preference for the whole volatile blends from Bio L 212 Ratan seeds compared to whole volatile blends from other three varieties. The insect exhibited attraction to five individual synthetic compounds, 3-octanone, 3-octanol, linalool oxide, 1-octanol and nonanal. A synthetic blend of 448, 390, 1182, 659 and 8114 ng/20 µl methylene chloride of 3-octanone, 3-octanol, linalool oxide, 1-octanol and nonanal, respectively, was most attractive to C. maculatus, and this combination might be used for insect pest management program such as baited traps.

Evaluation of the effect of cagPAI genes of Helicobacter pylori on AGS epithelial cell morphology and IL-8 secretion.

Helicobacter pylori cagPAI genes play an important role in pathogenesis, however little is known about their functions in isolates from Turkish patients. We aimed to evaluate the intactness and the effect of the cagPAI genes (cagT, cagM, cagE, cagA) and cagA EPIYA motifs on the AGS morphological changes and IL-8 induction. Of 53 patients 38 were found infected with H. pylori. PCR amplification of the cagPAI genes showed 42.1 % intact, 39.5 % partially deleted and 18.4 % with complete deletions. Isolates from gastritis, duodenal and gastric ulcer patients with intact and partially deleted cagPAI genes induced higher IL-8 secretion than those with complete deletions. Isolates from gastritis patients had higher deletion frequencies of the cagT and cagM genes than the other two genes. Infection of AGS cells with isolates that possess intact cagPAI and EPIYA-ABC resulted in the formation of the hummingbird phenotype. The cagA positive isolates induced higher IL-8 secretion than cagA negative isolates. Isolates from DU patients with more than one EPIYA-C motif induced higher concentrations of IL-8 than those with EPIYA-ABC. In conclusion, the intactness of the cagPAI in our isolates from different patients was not conserved. An intact cagPAI was found to play an important role in the pathogenesis of DU but not GU or gastritis. The cagA gene, but not other cagPAI genes, was associated with the induction of IL-8 and the morphological changes of the AGS cells. An increase in the number of EPIYA-C motifs had noticeable effect on the formation of the hummingbird phenotype.

Crossover from photodarkening to photobleaching in a-Ge(x)Se(100-x) thin films.

In this Letter, we present the interesting results of photodarkening (PD), transition toward photostability, and a slow crossover from PD to photobleaching when composition of the chalcogenide glassy thin film changes from Ge-deficient to rich. A subsequent Raman analysis on these as-prepared and irradiated samples provide the direct evidence of photoinduced structural rearrangement, i.e., photocrystallization of Se and the removal of edge-sharing GeSe4 tetrahedra. Further, our experimental results clearly demonstrate that light-induced effects can be effectively controlled by choosing the right composition and provide valuable information on synthesizing photostable/sensitive glasses.

In silico investigation on sensing of tyramine by boron and silicon doped C60 fullerenes.

The present communication deals with the adsorption of tyramine neurotransmitter over the surface of pristine, Boron (B) and Silicon (Si) doped fullerenes. Density functional theory (DFT) calculations have been used to investigate tyramine adsorption on the surface of fullerenes in terms of stability, shape, work function, electronic characteristics, and density of state spectra. The most favourable adsorption configurations for tyramine have been computed to have adsorption energies of - 1.486, - 30.889, and - 31.166 kcal/mol, respectively whereas for the rest three configurations, it has been computed to be - 0.991, - 6.999, and - 8.796 kcal/mol, respectively. The band gaps for all six configurations are computed to be 2.68, 2.67, 2.06, 2.17, 2.07, and 2.14 eV, respectively. The band gap of pristine, B and Si doped fullerenes shows changes in their band gaps after adsorption of tyramine neurotransmitters. However, the change in band gaps reveals more in B doped fullerene rather than pristine and Si doped fullerenes. The change in band gaps of B and Si doped fullerenes leads a change in the electrical conductivity which helps to detect tyramine. Furthermore, natural bond orbital (NBO) computations demonstrated a net charge transfer of 0.006, 0.394, and 0.257e from tynamine to pristine, B and Si doped fullerenes.

Coexistence of fast photodarkening and slow photobleaching in Ge19As21Se60 thin films.

We experimentally demonstrate the coexistence of two opposite photo-effects, viz. fast photodarkening (PD) and slow photobleaching (PB) in Ge(19)As(21)Se(60) thin films, when illuminated with a laser of wavelength 671 nm. PD appears to begin instantaneously upon light illumination and saturates in tens of seconds. By comparison, PB is a slower process that starts only after PD has saturated. Both PD and PB follow stretched exponential dependence on time. Modeling of overall change as a linear sum of two contributions suggests that the changes in As and Ge parts of glass network respond to light effectively independent of each other.

Melanin, a promising radioprotector: mechanisms of actions in a mice model.

The radioprotective effect of extracellular melanin, a naturally occurring pigment, isolated from the fungus Gliocephalotrichum simplex was examined in BALB/C mice, and the probable mechanism of action was established. At an effective dose of 50mg/kg body weight, melanin exhibited both prophylactic and mitigative activities, increasing the 30-day survival of mice by 100% and 60%, respectively, after exposure to radiation (7Gy, whole body irradiation (WBI)). The protective activity of melanin was primarily due to inhibition of radiation-induced hematopoietic damages as evidenced by improvement in spleen parameters such as index, total cellularity, endogenous colony forming units, and maintenance of circulatory white blood cells and platelet counts. Melanin also reversed the radiation-induced decrease in ERK phosphorylation in splenic tissue, which may be the key feature in its radioprotective action. Additionally, our results indicated that the sustained activation of AKT, JNK and P38 proteins in splenic tissue of melanin pre-treated group may also play a secondary role. This was also supported by the fact that melanin could prevent apoptosis in splenic tissue by decreasing BAX/Bcl-XL ratio, and increasing the expressions of the proliferation markers (PCNA and Cyclin D1), compared to the radiation control group. Melanin also reduced the oxidative stress in hepatic tissue and abrogated immune imbalance by reducing the production of pro-inflammatory cytokines (IL6 and TNFα). In conclusion, our results confirmed that fungal melanin is a very effective radioprotector against WBI and the probable mechanisms of radioprotection are due to modulation in pro-survival (ERK) signaling, prevention of oxidative stress and immunomodulation.

Role of rigidity and temperature in the kinetics of photodarkening in Ge(x)As(45-x)Se55 thin films.

We present insightful results on the kinetics of photodarkening (PD) in Ge(x)As(45-x)Se55 glasses at the ambient and liquid helium temperatures when the network rigidity is increased by varying x from 0 to 16. We observe a many fold change in PD and its kinetics with decreasing network flexibility and temperature. Moreover, temporal evolution of PD shows a dramatic change with increasing x.

Effect of pre-freeze addition of cysteine hydrochloride and reduced glutathione in semen of crossbred Jersey bulls on sperm parameters and conception rates.

This study was aimed to assess the effect of pre-freeze addition of cysteine hydrochloride and glutathione (GSH) on post-thaw sperm functional parameters and field fertility. The experimental bulls (n = 6) aged 4-6 years were used for this study. A total of 36 ejaculates (six ejaculates per bull) were collected and divided into three groups, group I (control), group II (5 mm cysteine hydrochloride) and group III (5 mm GSH). The extended semen samples with and without additives were filled in mini straw using automatic filling and sealing machine and cryopreserved in liquid nitrogen. Post-freeze seminal traits were recorded after thawing at 37°C for 30 s. The curvilinear velocity (VCL) and amplitude of lateral head displacement values were significantly (p < 0.05) higher in GSH than the cysteine and control groups. Post-thaw plasmalemma integrity was significantly (p < 0.01) higher in GSH group when compared to cysteine and control groups. The loss of acrosomal integrity was significantly (p < 0.01) lower in GSH than in cysteine and control groups. Addition of GSH non-significantly (p = 0.1) improved mitochondrial membrane potential (MMP) (per cent) than control group. This study indicates that the addition of cysteine and GSH suggestive (p = 0.08) of reducing lipid peroxide levels. The conception rate (%) in glutathione group was significantly (p < 0.05) higher than that in cysteine (68 vs 58) and control (49) groups. The post-thaw sperm progressive forward motility (r = 0.4) had moderate, but no significant correlation with conception rate. However, post-thaw straight-line velocity (r = 0.7), loss of acrosomal integrity (r = -0.8) and MMP (r = 0.9) had significant (p < 0.05) correlation with field fertility. This study indicates that the use of glutathione as semen additive may be used for improving post-thaw semen quality and overall augmentation of pregnancy in cows.

Development of an in-house capture ELISA: An attempt to detect CagA antigen in sera of Helicobacter pylori infected patients.

The CagA protein one of the key virulence factors of Helicobacter pylori plays an important role in the pathogenesis of peptic ulcer diseases. Unfortunately the cagA gene status can only be determined by PCR while serology is an alternative approach to detect antigens or antibodies. Our aim is to detect the CagA antigen in sera of infected subjects by the development of an in-house capture ELISA test. Gastric antral biopsies and serum samples were collected from 63 patients. PCR was used to determine the cagA status. Our previously developed recombinant CagA protein and monoclonal antibody were used for setting up the capture ELISA test. H. pylori positive [(38 gastritis, 14 duodenal ulcers (DU), 11 gastric ulcer (GU)] patients were determined by PCR. The cagA gene was detected in 21 (55%) of gastritis, 11 (78%) of DU and 7 (60%) of GU patients. The reagents used in setting up the capture ELISA test following optimization displayed high performance. This study showed that our developed in-house capture ELISA has the potential to detect the CagA antigen at very low concentrations even though not detected in our H. pylori infected patients sera but we are also intended to use it in saliva and stool samples.

Quantitative cellular uptake, localization and cytotoxicity of curcumin in normal and tumor cells.

Using absorption and fluorescence spectroscopic methods, quantitative cellular uptake of curcumin, an antioxidant and anti-tumor agent from Curcuma longa, was calculated in two types of normal cells: spleen lymphocytes, and NIH3T3 and two tumor cell lines: EL4 and MCF7. Both the uptake and fluorescence intensity of curcumin were significantly higher in tumor cells compared to the normal cells. A linear dependency on the uptake was observed with treatment concentration of curcumin. Using laser confocal microscopy, intracellular localization of curcumin was monitored and the results indicated that curcumin is located both in the cell membrane and the nucleus. Sub-cellular fractionation of curcumin-loaded MCF7 cells supported the differential distribution of curcumin in membrane, cytoplasm and nuclear compartments of cell with maximum localization in the membrane. Cytotoxicity studies in different cell lines indicated that the toxicity of curcumin increased with increasing uptake.

A preliminary study on the genetic profile of cag pathogenicity-island and other virulent gene loci of Helicobacter pylori strains from Turkey.

Helicobacter pylori genetic diversity affects the function and antigenicity of virulence factors associated with the disease outcome. Gene profile was done to identify the distribution of gene loci within and outside the cag pathogenicity-island (PAI). H. pylori strains from 35 patients [21 gastritis, 14 peptic ulcer diseases (PUD)] were analyzed using PCR. The profile of the cag PAI was evaluated using primers spanning the 3' end, cagA, promoter region of the cagA, cagE, cagT, 5' end (LEC), extreme right end, plasticity region open reading frames (ORFs), oipA (Hp0638) and vacA alleles. We found few intact cag PAI in the strains examined. Deletions were found in LEC1 (9.5% versus 14.3%), LEC2 (4.8% versus 14.3%), cagT (33.3% versus 28.6%), cagE (28.6% versus 28.6%) and the promoter region of the cagA (19.0% versus 42.9%) of gastritis and PUD strains, respectively. The cagA gene was detectable in 57.1% of gastritis and 92.9% of PUD-associated strains. The cagRJ region also showed deletions for many of its genes. The oipA (Hp0638) gene was detected in 80.9% of gastritis and in 92.9% of PUD strains. The plasticity region ORFs JHP912 and JHP931 were predominant in PUD strains. The vacA-s1a-m1a genotype was predominant in PUD, while s2m2 in gastritis strains. This comprehensive analysis showed deletions in several genes within and outside the cag PAI. However, cagA, oipA, JHP912, JHP931 and vacA-s1a-m1a were more predominant in PUD strains than gastritis-associated strains, suggesting the importance of genetic diversity on the disease progression and clinical outcome.

Genotyping of Helicobacter pylori strains from gastric biopsies by multiplex polymerase chain reaction. How advantageous is it?

Recent application of multiplex polymerase chain reaction (PCR) for genotyping Helicobacter pylori direct from biopsies revealed variable results (detection of amplicons from DNA extracted by boiling biopsies, variable size amplicons and deletions, uniform intensity of amplicon bands). We aimed to look at how applicable the technique is for determining cagA and vacA genotypes and to correlate the results with the severity of the disease. H. pylori strains from 52 patients (35 duodenal ulcers [DUs], 7 gastric ulcers [GUs], 10 gastritis) were included. Three antral biopsies were obtained for Campylobacter-like organism (CLO) and PCR. Primers for cagA, vacA s1s2, and m1m2 alleles were used. No PCR amplicons were detected from boiling biopsies; thus, DNA was extracted by QIAamp kit. H. pylori was positive in 84.6% of the patients (85.7% DU, 100% GU, and 70% gastritis). The cagA gene was detected in 86.6% DU, 71.4% GU, and 57.0% gastritis patients. The vacA allelic distribution among cagA-positive strains was 80.7% s1m1 in DU and 60.0% in GU patients, whereas 75.0% of gastritis had s1m2. No variability in the amplicon sizes was found, and the intensity of the amplicon bands was not uniform. A deleted band of approximately 420 bp below the m1 band was detected in strains from 2 DU and 1 GU patients. Although the multiplex PCR is a rapid and an effective tool for detecting several genes in a single-step system, one has to adjust for optimization of the technique when genotyping H. pylori direct from biopsies. A significant association was found between the cagA-positive vacA-s1m1 genotype and peptic ulcers.