An alternate method of classifying allergic bronchopulmonary aspergillosis based on high-attenuation mucus

Background and Aim

Allergic bronchopulmonary aspergillosis (ABPA) is classified radiologically based on the findings of central bronchiectasis (CB) and other radiologic features (ORF). However, the long-term clinical significance of these classifications remains unknown. We hypothesized that the immunological activity and outcomes of ABPA could be predicted on HRCT chest finding of high-attenuation mucus (HAM), a marker of inflammatory activity. In this study, we evaluate the severity and clinical outcomes of ABPA with different radiological classifications.

Methods

Patients were classified based on CT chest findings as: (a) serologic ABPA (ABPA-S) and ABPA-CB; (b) ABPA-S, ABPA-CB, and ABPA-CB-ORF; and, (c) ABPA-S, ABPA-CB and ABPA-CB-HAM. The clinical, spirometric and serological (total and A fumigatus specific IgE levels, eosinophil count) severity of the disease and clinical outcomes in various classifications were analyzed.

Results

Of the 234 (123 males, 111 females; mean age, 34.1 years) patients, 55 (23.5%) had normal HRCT, 179 (76.5%) had CB, 49 (20.9%) had HAM, and 27 (11.5%) had ORF. All immunological markers were consistently higher in the HAM classification, while in other classifications these findings were inconsistent. On multivariate analysis, the factors predicting frequent relapses were presence of HAM (OR 7.38; 95% CI, 3.21–17.0) and CB (OR 3.93; 95% CI, 1.63–9.48) after adjusting for ORF.

Conclusions

The classification scheme based on HAM most consistently predicts immunological severity in ABPA. Central bronchiectasis and HAM are independent predictors of recurrent relapses in ABPA. Hence, HAM should be employed in the radiological classification of ABPA.     

Influence of salinity and temperature on the germination of Kochia scoparia

Kochia scoparia is one of the most common annual halophytes foundin the Great Basin. Seeds were collected from a population growing in asalt playa at Faust, Utah and were germinated at 5 temperature regimes(12 h night/12 h day, 5–15 ^°C, 10–20 ^°C, 15–25 ^°C,20–30 ^°C and 25–35 ^°C) and 6 salinities (0, 200, 400,600, 800 and 1000 mM NaCl) to determine optimal conditions forgermination and recovery of germination from saline conditions after beingtransferred to distilled water. Maximum germination occurred in distilledwater, and an increase in NaCl concentration progressively inhibited seedgermination. Few seeds germinated at 1000 mM NaCl. A temperatureregime of 25 ^°C night and 35 ^°C day yielded maximumgermination. Cooler temperature 5–15 ^°C significantly inhibited seedgermination. Rate of germination decreased with increase in salinity.Germination rate was highest at 25–35 ^°C and lowest at5–15 ^°C. Seeds were transferred from salt solutions to distilled waterafter 20 days and those from high salinities recovered quickly at warmertemperature regimes. Final recovery germination percentages in high salttreatments were high, indicating that exposure to high concentration ofNaCl did not inhibit germination permanently.     

Bionanotechnology approach for FAD-dependent enzymes with nanomaterials sensor

We have reported the modification of biomolecule with nanomaterials. In this paper, the electrochemical response of different FAD-dependent enzymes at carbon nanomaterials modified electrode. The modified electrode also exhibits a promising enhanced electrocatalytic activity toward the oxidation of substrate. Different methods were used for fabrication of modified electrode. The presence of nanomaterials enhances the enzyme loading and stability. Cyclic voltammograms (CVs) were used for the determination of substrate and the apparent coefficient values for these compounds at different electrodes. Finally, we have studied the surface morphology of the modified electrode using scanning electron microscopy (SEM), which revealed that enzyme is coated on nanomaterials.     

Risk Factors for Loss to Follow-Up among People Who Inject Drugs in a Risk Reduction Program at Karachi,Pakistan. A Case-Cohort Study

Introduction

Retention of male people who inject drugs (PWIDs) is a major challenge for harm reduction programs that include sterile needle/syringe exchange in resource-limited settings like Pakistan. We assessed the risk factors for loss to follow-up among male PWIDs enrolled in a risk reduction program in Karachi, Pakistan.

Methods

We conducted a prospective cohort study among 636 HIV-uninfected male PWIDs enrolled during March-June 2009 in a harm reduction program for the estimation of incidence rate. At 24 months post-enrollment, clients who had dropped out of the program were defined as lost to follow-up and included as cases for case-cohort study.

Results

The median age of the participants was 29 years (interquartile range: 23–36). Active outreach accounted for 76% (483/636) of cohort recruits. Loss to follow-up at 24 months was 25.5% (162/636). In multivariable logistic regression, younger age (AOR: 0.97, 95% CI: 0.92–0.99, p = 0.028), clients from other provinces than Sindh (AOR: 1.49, 95% CI: 1.01–2.22, p = 0.046), having no formal education (AOR: 3.44, 95% CI: 2.35–4.90, p<0.001), a history of incarceration (AOR: 1.68, 95% CI: 1.14–2.46, p<0.008), and being homeless (AOR: 1.47, 95% CI: 1.00–2.19, p<0.049) were associated with loss to follow-up.

Conclusions

Our cohort retained 74.5% of male PWIDs in Karachi for 24 months. Its loss to follow up rate suggested substantial ongoing programmatic challenges. Programmatic enhancements are needed for the highest risk male PWIDs, i.e., younger men, men not from Sindh Province, men who are poorly educated, formerly incarcerated, and/or homeless.     

16S rDNA sequence analysis of culturable marine biofilm forming bacteria from a ship's hull

Marine bacteria from the hull of a ship in the form of biofilms or microfouling were isolated, cultured, and identified by phylogenetic analysis using 16S rDNA sequences. With an average length of 946 bp, all the 16 sequences were classified using the Ribosomal database project (RDP) and were submitted to the National Center for Biotechnology Information. Phylogenetic analysis using 16S rDNA sequences indicated that the 16 strains belonged to the Firmicutes (IK-MB6 Exiguobacterium aurantiacum, IK-MB7 Exiguobacterium arabatum, IK-MB8 Exiguobacterium arabatum, IK-MB9 Jeotgalibacillus alimentarius, IK-MB10 Bacillus megaterium, IK-MB11 Bacillus pumilus, IK-MB12 Bacillus pumilus, IK-MB13 Bacillus pumilus, IK-MB14 Bacillus megaterium), High GC, Gram-positive bacteria (IK-MB2 Micrococcus luteus, IK-MB5 Micrococcus luteus, IK-MB16 Arthrobacter mysorens), G-Proteobacteria (IK-MB3 Halomonas aquamarina, IK-MB15 Halotalea alkalilenta), CFB group bacteria (IK-MB1 Myroides odoratimimus), and Enterobacteria (IK-MB4 Proteus mirabilis). Among the 16 strains, representatives of the Firmicutes were dominant (56.25%) compared to the high GC, Gram-positive bacteria (18.75%), G-Proteobacteria (12.5%), CFB group bacteria (6.25%), and Enterobacteria (6.25%). Analysis revealed that majority of marine species found in marine biofilm are of anthropogenic origin.     

Homozygosity Mapping and Targeted Sanger Sequencing Reveal Genetic Defects Underlying Inherited Retinal Disease in Families from Pakistan

Background

Homozygosity mapping has facilitated the identification of the genetic causes underlying inherited diseases, particularly in consanguineous families with multiple affected individuals. This knowledge has also resulted in a mutation dataset that can be used in a cost and time effective manner to screen frequent population-specific genetic variations associated with diseases such as inherited retinal disease (IRD).

Methods

We genetically screened 13 families from a cohort of 81 Pakistani IRD families diagnosed with Leber congenital amaurosis (LCA), retinitis pigmentosa (RP), congenital stationary night blindness (CSNB), or cone dystrophy (CD). We employed genome-wide single nucleotide polymorphism (SNP) array analysis to identify homozygous regions shared by affected individuals and performed Sanger sequencing of IRD-associated genes located in the sizeable homozygous regions. In addition, based on population specific mutation data we performed targeted Sanger sequencing (TSS) of frequent variants in AIPL1, CEP290, CRB1, GUCY2D, LCA5, RPGRIP1 and TULP1, in probands from 28 LCA families.

Results

Homozygosity mapping and Sanger sequencing of IRD-associated genes revealed the underlying mutations in 10 families. TSS revealed causative variants in three families. In these 13 families four novel mutations were identified in CNGA1, CNGB1, GUCY2D, and RPGRIP1.

Conclusions

Homozygosity mapping and TSS revealed the underlying genetic cause in 13 IRD families, which is useful for genetic counseling as well as therapeutic interventions that are likely to become available in the near future.     

Phytotoxic analysis of coastal medicinal plants and quantification of phenolic compounds using HPLC

Abstract

Medicinal plants are rich sources of bioactive phytochemicals. Production of such chemicals usually increased under unfavorable conditions. This study investigated the phytotoxic potential of 105 medicinal plants distributed in arid/semiarid areas along Arabian Sea coast of Pakistan. Total polyphenols, flavonoids, tannins and composition of individual phenolic compounds were also determined in species which showed high phytotoxic potential. Sandwich method was used to determine the phytotoxicity of medicinal plants on the growth of lettuce seedlings. Radicle growth was inhibited more than the hypocotyl growth. In general, halophytes showed higher phytotoxic potential than non-halophytes. Capparis cartilaginea, Indigofera hochstetteri, Parkinsonia aculeata and Prosopis glandulosa showed highest degree of inhibition. Higher amount of total phenols (16.35–25.33?mg GAE g^?1), flavonoids (3.32-6.41?mg QE g^?1) and tannins (1.54–2.54?mg TAE g^?1) were found in these species. Pyrocatechol, quercetin, gallic, hydroxybenzoic and ferulic acids were detected as major phytotoxins, of which, gallic acid, pyrocatechol and quercetin were most abundant. These phytochemicals could be used for the production of natural, safe, healthy and eco-friendly agro-chemicals. Furthermore, these plants can be grown without encroaching agricultural lands, and can convert vast areas of arid/saline lands into economically viable resources, which also helps to halt climate change and desertification.     

Plastome of Saraca asoca (Detarioideae,Fabaceae): Annotation,comparison among subfamily and molecular typing

Saraca asoca (Roxb.) Willd. (subfamily Detarioideae, family Fabaceae) is a perennial evergreen sacred medicinal tree classified under ‘vulnerable’ by the IUCN. The chloroplast (cp) genome/plastome which follows uniparental inheritance contains many useful genetic information because of its conservative rate of evolution. The assembled cp genome of S. asoca which maps as a conserved circular structure revealed extensive rearrangement in gene organization, comprising total length 160,003 bp including LSC, SSC, IRa, and IRb, and GC content was 35.26%. Herein a set of rbcL and matK gene were established using molecular phylogenetic analyses for molecular typing of S. asoca.     

Contents of Volume 9 (2001)

Volume Contents

Contents of Volume 9 (2001)     

Dormancy and germination responses of halophyte seeds to the application of ethylene

Ethylene is invariably produced during seed germination but its role in regulating seed dormancy and germination is poorly understood. Seeds of 22 halophytic species having different life forms – salt secreting dicots, salt secreting monocots, stem succulents and leaf succulents were germinated in Petri dishes kept in a growth chamber set at 20/30 °C (night/day) temperature and a 12 hr light period. Sodium chloride and ethephon were added to the medium from the beginning of the experiment. Seed germination was recorded every other day for twenty days. Application of ethylene did not have any significant effect on releasing seeds from innate dormancy. However, it appeared to have a role in alleviation of salinity effects which varied from negative in certain species to almost complete alleviation of high salinity effects in others.Our data indicates that ethylene appears to have little role in breaking innate seed dormancy however, in most halophyte seeds studied, application of ethylene alleviate the salinity effect to various degrees. Halophyte seeds which could germinate under saline conditions approaching twice the salinity of seawater may offer clues to understand management of seed germination under highly saline conditions. To cite this article: M.A. Khan et al., C. R. Biologies 332 (2009).