AmpliBASE MT: a Mycobacterium tuberculosis diversity knowledgebase

AmpliBASE MT is an online databank of high-resolution DNA fingerprints representing fluorescent amplified fragment length polymorphism (FAFLP) profiles or amplitypes developed for the Mycobacterium tuberculosis complex strains from 48 different countries. AmpliBASE MT is based on a relational database management system that is hyperlinked to visualize genotyping results in the form of DNA fingerprint images for individual strains. A flexible search system based on systematic comparisons of fragment sizes in base pairs allows inter-laboratory comparison of FAFLP profiles. Besides this, the database also displays previously published data on IS6110 profiles, spoligotypes, MIRU-VNTRs and large sequence polymorphisms along with the FAFLP records that will give the overall comparisons. Being the first of its kind, AmpliBASE MT is expected to be a very helpful tool in strengthening the concept of 'geographic genomics' and will be very helpful to molecular epidemiologists and those interested in diagnostic development for tuberculosis.     

Degradation of different hydrocarbons and production of biosurfactant byPseudomonas aeruginosa isolated from coastal waters

Summary A bacterium isolated from an oil spillage sample and identified asPseudomonas aeruginosa degraded hexadecane and heptadecane by 47% and 58% with 9% and 12% of total carbon from the respective substrates being liberated as CO₂. With octadecane and nonadecane as substrates, 73% and 60% were biodegraded while 27% and 25% of total carbon was evolved as CO², respectively. Production of biosurfactant by this bacterium was studied using hexadecane 5% (v/v) as substrate. The surface tension of spent culture medium, as well as the supernatant, was 30 mN/m compared to 71 mN/m for water. When the supernatant was mixed with hexadecane (15, v/v) a stable emulsion was formed which deteriorated only by 10% after one month.

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Dégradation de différents hydrocarbures et production de biosurfactants parPseudomonas aeruginosa isolé d'eaux côtières

Résumé Une bactérie, isolée d'un échantillon d'hydrocarbures épandus, et identifiée commePseudomonas aeruginosa, dégrade l'hexaet l'heptadécane à raison respective de 47 et de 58% du carbone total avec 9 et 12% des substrats respectifs libérés sous la forme de CO₂. Avec l'octa- et le nonadécane comme substrats, la biodégradation atteint respectivement 73 et 60% avec 27 et 25% du carbone total transformé en CO₂. On a étudié la production de biosurfactant par cette bactérie en utilisant l'hexadécane à 5% (v/v) comme substrat. La tension superficielle de la liqueur mixte, comme celle de son surnageant atteint 30 mN/m par comparaison à 71 mN/m pour l'eau. Lorsque le surnageant est mélangé à l'hexadécane (15, v/v), on forme une émulsion stable qui ne se détériore que de 10% au bout d'un mois.

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This work was carried out at the Biotechnology Laboratories of the Nuclear Institute for Agriculture & Biology (NIAB), Faisalabad.     

Leaching of chalcopyrite byThiobacillus thiooxidans and oxidized copper ore byThiobacillus ferrooxidans isolated from local environments

Summary Feasibility for bacterial leaching of two different copper ores from Pakistan was investigated with locally isolated, acidophilic thiobacilli in shake flask culture at 28±2°C. After a lag period of 16 d,Thiobacillus thiooxidans solubilized up to 19% of copper present in chalcopyrite ore in 14 d before entering stationary phase. In oxidized copper ore amended with chalcopyrite ore and supplemented with sulphur to provide an energy source forT. ferrooxidans, the pH dropped as a result of bacterial growth and was accompanied by copper solubilization. The highest copper release, 61% of total, occurred in flasks having oxidized copper ore, sulphur and calcopyrite (111, by weight) and inoculated withT. ferrooxidans. Supplementation used in these tests resulted in nearly six times more solubilization as compared to tests conducted without supplementation.

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Resumen Se ha estudiado la posibilidad de realizar un lixiviado mediante bacterias de dos minerales de cobre del Pakistan. Las bacterias utilizadas son cepas, aísladas localmente, de tiobacilos acidófilos que se hacen crecer en un medio líquido en agitación a 28±2°C. Después de una fase lag de 16 dThiobacillus thiooxidans solubilizó hasta 19% del cobre presente en la calcopirita en 14 d, antes de alcanzar la fase estacionaria. El mineral de cobre oxidado se modificó con calcopirita y se suplementó con azufre afín de sumministrar una fuente de energía paraT. ferrooxidans, a resultas del crecimiento bacteriano el pH disminuyó solubilizándose cobre. La mayor cantidad de cobre sulubilizado se cencontró en frascos con mineral de cobre oxidado, azufre y calcopirita (111 en peso) e inoculados conT. ferrooxidans. La adición de suplementos incrementó 6 veces la solubilización comparada con la obtenida en ensayos sin adición de suplementos.

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Résumé On a testé la faisabilité de la lixiviation bactérienne de deux minerais différents de cuivre du Pakistan au moyen de thiobacilli acidophiles,isolés localement, en culture en flaçons agités à 28 ±2°C. Après une période de latence de 16 jours,Thiobacillus thiooxidans a solubilisé jusqu'à 19% du cuivre présent dans le minerai de chalcopyrite en 14 jours avant d'entrer en phase stationnaire de croissance. Dans un minerai de cuivre amendé par le minerai de chalcopyrite et additionné de soufre de manière à fournir une source d'énergie pourT. ferrooxidans, le pH a baissé comme suite de la croissance bactérienne, ce qui a entraîné la solubilisation du cuivre. La libération la plus élevée de cuivre, 61% au total, a eu lieu dans les flaçons qui avaient à oxyder le minerai de cuivre, le soufre et la chalcopyrite oans les proportions de 111 en poids, et qui avaient été inoculés parT. ferrooxydans. La supplémentation effectuée dans ces tests a eu pour effet de dissoudre six fois plus de cuivre que dans les tests conduits sans supplémentation.

     

Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome

The rhizosphere microbiome plays a significant role in the life of plants in promoting plant survival under adverse conditions. However, limited information is available about microbial diversity in saline environments. In the current study, we compared the composition of the rhizosphere microbiomes of the halophytes Urochloa, Kochia, Salsola, and Atriplex living in moderate and high salinity environments (Khewra salt mines; Pakistan) with that of the non-halophyte Triticum. Soil microbiomes analysis using pyrosequencing of 16S rRNA gene indicated that Actinobacteria were dominant in saline soil samples whereas Proteobacteria predominated in non-saline soil samples. Firmicutes, Acidobacteria, Bacteriodetes and Thaumarchaeota were predominant phyla in saline and non-saline soils, whereas Cyanobacteria, Verrucomicrobia, Gemmatimonadetes and the unclassified WPS-2 were less abundant. Sequences from Euryarchaeota, Ignavibacteriae, and Nanohaloarchaeota were identified only from the rhizosphere of halophytes. Dominant halophilic bacteria and archaea identified in this study included Agrococcus, Armatimonadetes gp4, Halalkalicoccus, Haloferula and Halobacterium. Our analysis showed that increases in soil salinity correlated with significant differences in the alpha and beta diversity of the microbial communities across saline and non-saline soil samples. Having a complete inventory of the soil bacteria from different saline environments in Pakistan will help in the discovery of potential inoculants for crops growing on salt-affected land.     

Phytochemical profile,enzyme inhibition activity and molecular docking analysis of Feijoa sellowiana O. Berg

Feijoa sellowiana leaves and fruits have been investigated as a source of diverse bioactive metabolites. Extract and eight metabolites isolated from F. sellowiana leaves were evaluated for their enzymatic inhibitory activity against α-glucosidase, amylase, tyrosinase, acetylcholinestrerase and butyrylcholinesterase both in vitro and in silico. Feijoa leaves’ extract showed strong antioxidant activity and variable levels of inhibitions against target enzymes with a strong anti-tyrosinase activity (115.85 mg Kojic acid equivalent/g). Additionally, α-tocopherol emerged as a potent inhibitor of AChE and BChE (5.40 & 10.38 mmol galantamine equivalent/g, respectively). Which was further investigated through molecular docking and found to develop key enzymatic interactions in AChE and BChE active sites. Also, primetin showed good anti BChE (11.70 mmol galantamine equivalent/g) and anti-tyrosinase inhibition (90.06 mmol Kojic acid equivalent/g) which was also investigated by molecular docking studies.

Highlights

• Isolation of eight bioactive constituents from Feijoa sellowiana leaves.
• In vitro assays using different enzymatic drug targets were investigated.
• In silico study was performed to define compound interactions with target proteins.
• Feijoa leaf is an excellent source of anti-AChE and antityrosinase bioactives.

     

Pharmacological and pharmacognostical valuation of Canna indica leaves extract by quantifying safety profile and neuroprotective potential

The current study primarily focused on the pharmacognostical and phytochemical screening of Canna indica and further analyzing the leaves extract for toxicological profile and neuroprotective potential. The microscopic, dry powder properties of the leaf material and phytochemical, physicochemical analysis was evaluated for pharmacognostical assessment. Dry leaves of C. indica were extracted using methanol and then further studied for both in vitro and in vivo toxicological study. The acute toxicity was measured by estimating the antioxidant defense system and anatomical impairment in the rat's organs. Also, the neuroprotective activity of the plant extract was assessed using anticholinesterase enzymatic inhibitory assay. The extract was found to be hemocompatible and showed absences of induction of behavioural changes. Likewise, no changes were seen on the anatomical structure of the rat’s organs. The methanolic extract portrayed a significant upsurge in the reduced glutathione level and showed a comparable acetylcholinesterase inhibition in a dosedependent manner with an IC50 value of 14.53 μg/mL compared to the standard Donepezil with an IC50 value of 13.31 μg/mL. C. indica has compelling pharmacognostical characteristics, good safety reports, and significant antioxidant as well as the neuroprotective potential that shows great potential for its further in-depth research for pharmacological use.     

Decomposition of organic matter by fungi in saline soils

The object of the present investigation was to study the fungal decomposition of organic matter from different sources, added to the saline soils. The organic matter added was in the form of fresh cuttings of two salt tolerant harbaceous plants namelyDiplachne fusca (Kallar grass) andSesbania aculeata (Dhancha). In addition to these treatments, farm yard manure and press mud (waste of sugar industry) were also used as a source of organic matter. Twelve combinations of these treatments were studied. A number of fungi were isolated from differently treated saline soils incubated at 30 °C. Among the fungi isolatedAspergillus spp. andFusarium solani had the highest frequency of occurrence. The relative cellulolytic ability of 10 fungal species was also estimated.Alternaria humicola andNigrospora sp. were found to be the most cellulolytic among the fungi isolated. The decrease in organic matter due to microbial decomposition was found to be most rapid during first two weeks of incubation. Among the treatments with one organic matter source, press mud produced maximum humus equal to 0.28 %. The pH and electrical conductivity increased slightly due to the closed system where no leaching took place.     

Regulation of cardiac and renal mineralocorticoid receptor expression by captopril following myocardial infarction in rats

Myocardial infarction (MI) activates the renin-angiotensin system in the heart and increases local production of aldosterone. This hormone may increase reactive fibrosis in the myocardium favoring heart failure development. To elucidate the potential contribution of aldosterone to cardiac remodeling following MI, we evaluated the expression of mineralocorticoid receptors (MCR) in the left ventricle (LV) and kidney of rats after MI and captopril treatment. MI was induced by ligation of the coronary artery in Wistar rats, which were separated into (1) sham-operated group, (2) MI group, (3) MI-captopril treated group (cap, 50 mg kg(-1) day(-1)). One month later angiotensin converting enzyme (ACE) activity was assayed in the plasma, LV and kidney. Cardiac and renal angiotensin II (Ang II) levels were determined by ELISA and MCR mRNA expression and protein were measured by Taqman RT-PCR and Western blot, respectively. Cardiac MCR mRNA and protein levels increased nearly by 80% after MI and Cap treatment normalized cardiac MCR protein and mRNA expression. Kidney MCR expression was not affected. ACE activity increased 34% in the plasma and 83% in the LV after MI. This increase was prevented by Cap. Ang II concentration increased 225% in the LV and 193% in kidney, which was partially attenuated by Cap. Our data demonstrate upregulation of MCR in the heart following MI what may facilitate the effects of aldosterone in the ventricular remodeling process. ACE inhibitors may reduce reactive fibrosis not only by decreasing Ang II production but also by attenuating the aldosterone-signaling pathway by decreasing the expression of MCR receptors.     

Mutations in C12orf57 Cause a Syndromic Form of Colobomatous Microphthalmia

Microphthalmia is an important developmental eye disorder. Although mutations in several genes have been linked to this condition, they only account for a minority of cases. We performed autozygome analysis and exome sequencing on a multiplex consanguineous family in which colobomatous microphthalmia is associated with profound global developmental delay, intractable seizures, and corpus callosum abnormalities, and we identified a homozygous truncating mutation in C12orf57 [c.1A>G; p.Met1?]. In a simplex case with a similar phenotype, we identified compound heterozygosity for the same mutation and another missense mutation [c.152T>A; p.Leu51Gln]. Little is known about C12orf57 but we show that it is expressed in several mouse tissues, including the eye and brain. Our data strongly implicate mutations in C12orf57 in the pathogenesis of a clinically distinct autosomal-recessive syndromic form of colobomatous microphthalmia.