A simple method for studying whole sections of rice grain

We developed a new and simple method to collect sections of a whole brown rice kernel for investigation of histological properties. A single kernel of rice was dehydrated through a graded ethanol series, transferred to xylene, and embedded in paraffin. During sectioning of the blocks using a rotary microtome, we used a special adhesive tape to collect and place the sections on slides so they remained flat. The use of the adhesive tape technique combined with autofluorescence characteristics allowed us to visualize cell walls throughout an entire longitudinal or transverse section of a whole rice kernel. We obtained scanning electron microscopy images of the sections to determine section quality.     

ProLysED

Bacterial proteases are an important group of enzymes that have very diverse biochemical and cellular functions. Proteases from prokaryotic sources also have a wide range of uses, either in medicine as pathogenic factors or in industry and therapeutics. ProLysED (Prokaryotic Lysis Enzymes Database), our meta-server integrated database of bacterial proteases, is a useful, albeit very niche, resource. The features include protease classification browsing and searching, organism-specific protease browsing, molecular information and visualisation of protease structures from the Protein Data Bank (PDB) as well as predicted protease structures. AVAILABILITY: ProLysED is integrated into the ProLysES (Prokaryotic Lysis Enzymes Site) website at http://genome.ukm.my/prolyses/. Access to the ProLysED database is free for academic users upon registration.     

The dynamics of protons,aluminium, and calcium in the rhizosphere of maize cultivated in tropical acid soils: experimental study and modelling

The goals of this work were to understand the dynamics of H⁺, Al and Ca in the rhizosphere of maize cultivated in tropical acid soils, and to evaluate the contribution of the dissolution kinetics of the Al-hydroxides to Al dynamics. The study of the dissolution kinetics was based on a comparison between experimental and simulated data, using a model of the chemical processes in the rhizosphere. Two Oxisols, pH 5.1 and 4.6, and one Ultisol, pH 5.2, were studied. An Al-tolerant maize variety (Zea mays L.) was grown for 14 days on a 3-mm thick soil layer. The composition of the soil and the soil solution, together with the concentration of Al in the roots, were determined throughout the experiment. The results showed that root growth (i) decreased the soil solution pH, up to one pH unit, (ii) increased Al concentration in the soil solution, (iii) increased exchangeable Al, and (iv) decreased exchangeable Ca. Soil solution pH, exchangeable Al, and exchangeable Ca were closely linked. Exchangeable Al increased 1.5 – 3.0 times, due to the dissolution of easily mobilised Al components. In addition, Al accumulation in roots depended mainly on Al in the soil solution. Modelling the interactions between H⁺, Al, and Ca proved that the main factor determining Al in the soil solution was the kinetic reactivity of the easily mobilised Al components. These components, probably poorly crystallised Al-hydroxides, are key players in the functioning of the rhizosphere in tropical acid soils.     

Computed Tomography Structural Lung Changes in Discordant Airflow Limitation

Background

There is increasing evidence that structural lung changes may be present before the occurrence of airflow limitation as assessed by spirometry. This study investigated the prevalence of computed tomography (CT) quantified emphysema, airway wall thickening and gas trapping according to classification of airflow limitation (FEV₁/FVC <70% and/or < the lower limit of normal (LLN)) in (heavy) smokers.

Methods

A total number of 1,140 male former and current smokers participating in a lung cancer screenings trial (NELSON) were included and underwent chest CT scanning and spirometry. Emphysema was quantified by the 15^th percentile, air way wall thickening by the square root of wall area for a theoretical airway with 10mm lumen perimeter (Pi10) and gas trapping by the mean lung density expiratory/inspiratory (E/I)-ratio. Participants were classified by entry FEV₁/FVC: group 1>70%; group 2<70% but >LLN; and group 3<LLN. 32 restricted subjects, i.e. FEV₁/FVC >70% but FEV₁ <80% predicted, were excluded. Multivariate regression analysis correcting for covariates was used to asses the extent of emphysema, airway wall thickening and gas trapping according to three groups of airflow limitation.

Results

Mean (standard deviation) age was 62.5 (5.2) years and packyears smoked was 41.0 (18.0). Group 2 subjects when compared to group 1 had a significantly lower 15^th percentile, −920.6 HU versus −912.2 HU; a higher Pi10, 2.87 mm versus 2.57 mm; and a higher E/I-ratio, 88.6% versus 85.6% (all p<0.001).

Conclusion

Subjects with an FEV₁/FVC<70%, but above the LLN, have a significant greater degree of structural lung changes on CT compared to subjects without airflow limitation.     

Molecular Docking of Known Carcinogen 4- (Methyl-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) with Cyclin Dependent Kinases towards Its Potential Role in Cell Cycle Perturbation

Cell cycle is maintained almost all the times and is controlled by various regulatory proteins and their complexes (Cdk+Cyclin) in different phases of interphase (G₁, S and G₂) and mitosis of cell cycle. A number of mechanisms have been proposed for the initiation and progression of carcinogenesis by abruption in cell cycle process. One of the important features of cancer/carcinogenesis is functional loss of these cell cycle regulatory proteins particularly in CDKs and cyclins. We hypothesize that there is a direct involvement of these cell cycle regulatory proteins not only at the genetic level but also proteins level, during the initiation of carcinogenesis. Therefore, it becomes significant to determine inconsistency in the functioning of regulatory proteins due to interaction with carcinogen 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Hence, we investigated the interaction efficiency of NNK, against cell cycle regulatory proteins. We found a different value of ΔG (free energy of binding) among the studied proteins ranging between -3.29 to -7.25 kcal/mol was observed. To validate the results, we considered Human Oxy-Hemoglobin at 1.25 Å Resolution, [PDB_ID:1HHO] as a +ve control, (binding energy -6.06 kcal/mol). Finally, the CDK8 (PDB_ID:3RGF) and CDK2 (PDB_ID:3DDP) regulatory proteins showing significantly strong molecular interaction with NNK -7.25 kcal/mol, -6.19 kcal/mol respectively were analyzed in details. In this study we predicted that CDK8 protein fails to form functional complex with its complementary partner cyclin C in presence of NNK. Consequently, inconsistency of functioning in regulatory proteins might lead to the abruption in cell cycle progression; contribute to the loss of cell cycle control and subsequently increasing the possibility of carcinogenesis.     

A molecular phylogeny for aplocheiloid fishes (Atherinomorpha, Cyprinodontiformes): the role of vicariance and the origins of annualism

Annual aplocheiloid killifish embryos possess a rare ability among vertebrates to enter stages of developmental arrest (diapause) when subjected to adverse environmental conditions. Previous morphological analyses have presented disparate hypotheses regarding the evolution of the intriguing life history associated with this phenomenon. We present a novel hypothesis of aplocheiloid relationships based on 1,009 bp of sequence data from three mitochondrial genes (cytochrome b, 12S rRNA, and 16S rRNA). Phylogenetic analysis using maximum parsimony, neighbor- joining, and maximum likelihood produce strongly congruent topologies. Our data confirm the monophyly of the Neotropical family Rivulidae, while demonstrating a paraphyletic Old World assemblage. The basal sister group position of Indo-Malaysian and Madagascaran taxa relative to a monophyletic South American/African dichotomy strongly indicates the role of vicariance in the diversification of these fishes in spite of their definition as secondary freshwater fish. The distribution of annualism onto this topology implies a single early origin for this suite of characters, prior to the divergence of South American and African taxa. If so, then annualism has since been lost several times during the evolution of genera now residing in permanent aquatic habitats. Paleoclimatic knowledge complements this scenario based on molecular characters.      

Seasonal occurrence and ecological aspects of Afrodiplozoon polycotyleus (Monogenea: Diplozoidae) from the gills of three cyprinids from the Nwanedi-Luphephe dams,South Africa

The effect of seasonal changes and ecological aspects of Afrodiplozoon polycotyleus (Paperna, 1973) collected on Labeobarbus marequensis (Smith, 1841), Enteromius trimaculatus (Peters, 1852) and Enteromius radiatus (Peters, 1853) was investigated from January to October 2008. Fish were collected at the Nwanedi-Luphephe dams, Limpopo River System, South Africa using gill, cast and seine nets and electrofishing gear. Enteromius radiatus and E. trimaculatus were the most infested compared with L. marequensis. Seasonal changes had an influence on the intensity of A. polycotyleus, with infestation rates higher in spring, summer and autumn. The adults predominantly infected the medial region of the second gill arch, whereas diporpae were mainly found on the first gill. Neither sex nor water quality changes had an influence on the intensity of the parasite. The health condition of the hosts was not affected by the parasite. The different infestation rates of the parasite between the species could be attributed to host characteristics, behaviour and habitat preferences. The selection of a particular gill/region could be attributed to space for attachment organs and food supply, as well as flow and velocity of the water over the gills. The occurrence of A. polycotyleus on E. radiatus constitutes a new host record.     

The development of a novel diagnostic PCR for Madurella mycetomatis using a comparative genome approach

BackgroundEumycetoma is a neglected tropical disease most commonly caused by the fungus Madurella mycetomatis. Identification of eumycetoma causative agents can only be reliably performed by molecular identification, most commonly by species-specific PCR. The current M. mycetomatis specific PCR primers were recently discovered to cross-react with Madurella pseudomycetomatis. Here, we used a comparative genome approach to develop a new M. mycetomatis specific PCR for species identification.MethodologyPredicted-protein coding sequences unique to M. mycetomatis were first identified in BLASTCLUST based on E-value, size and presence of orthologues. Primers were then developed for 16 unique sequences and evaluated against 60 M. mycetomatis isolates and other eumycetoma causing agents including the Madurella sibling species. Out of the 16, only one was found to be specific to M. mycetomatis.ConclusionWe have discovered a predicted-protein coding sequence unique to M. mycetomatis and have developed a new species-specific PCR to be used as a novel diagnostic marker for M. mycetomatis.