Novel filamentous spore-forming iron bacteria causes bulking in activated sludge

Several Gram-positive iron bacteria were isolated from bulking sludge. They were filamentous and had false branching. They had sheaths with iron deposits and formed spores on modified sucrose casitone yeast extract agar. They did not grow on influsion agar for longer than 1 month but could withstand 80°C for 1 h on the same medium. Adding them to sewage before aeration increased the biochemical oxygen demand of waste water and caused poor settling properties of activated sludges. They were the predominant filamentous micro-organisms in bulking activated sludges. At present, these strains cannot be assigned to recognized taxa of Bacillus spp. or sheathed iron bacteria.     

Evaluation of some genes and proteins involved in apoptosis on human chronic myeloid leukemia cells (K562 cells) by datura innoxia leaves aqueous extract

Abstract

Datura innoxia (D. innoxia) has an extensive usage in traditional medicine and can also be used for intervention therapy in order to treat cancer. Despite of accomplishing some researches on D. innoxia mechanism, still our knowledge is very little about exact D. innoxia apoptotic mechanism on human chronic myeloid leukemia cells (K562 cells). This study purpose was to clarify the molecular mechanism of apoptosis, which was mediated by D. innoxia leaves aqueous extract in K562 cells. MTT assay and flow cytometry was applied in order to assess the viability and apoptosis induction of K562 cells and normal human lymphoid B cells in the D. innoxia presence. Finally, the expression of the apoptotic related genes (p53, BAX, BCL2, Caspases 3, 6, 7 and 9) were evaluated using quantitative Real-Time PCR. Western blot analysis was applied for assessing the protein expression. MTT results indicated that D. innoxia could inhibit the viability of K562 cells in a dose- and time-dependent manner. In parallel, D. innoxia inhibitory effect on normal human lymphoid B cells was lower in comparison with its effect on K562 cells at the same concentrations and same incubation time. Apoptosis induction in K562 cells after D. innoxia exposure was determined by flow cytometry. Apoptosis was activated by D. innoxia in K562 cells throughout increasing the expression of P53, BAX/BCL2 ratio, caspase 9, 3, 6, 7. Western blot analysis demonstrated significant increase in cleaved PARP-1 and cleaved caspase 3 in treated K562 cells with high D. innoxia leaves aqueous extract concentration. D. innoxia leaves trigger apoptosis in K562 cells throughout intrinsic apoptotic pathway.

Communicated by Ramaswamy H. Sarma     

Phylogenetic Analysis of Glycerol 3-Phosphate Acyltransferases in Opisthokonts Reveals Unexpected Ancestral Complexity and Novel Modern Biosynthetic Components

Glycerolipid synthesis represents a central metabolic process of all forms of life. In the last decade multiple genes coding for enzymes responsible for the first step of the pathway, catalyzed by glycerol 3-phosphate acyltransferase (GPAT), have been described, and characterized primarily in model organisms like Saccharomyces cerevisiae and mice. Notoriously, the fungal enzymes share low sequence identity with their known animal counterparts, and the nature of their homology is unclear. Furthermore, two mitochondrial GPAT isoforms have been described in animal cells, while no such enzymes have been identified in Fungi. In order to determine if the yeast and mammalian GPATs are representative of the set of enzymes present in their respective groups, and to test the hypothesis that metazoan orthologues are indeed absent from the fungal clade, a comparative genomic and phylogenetic analysis was performed including organisms spanning the breadth of the Opisthokonta supergroup. Surprisingly, our study unveiled the presence of ‘fungal’ orthologs in the basal taxa of the holozoa and ‘animal’ orthologues in the basal holomycetes. This includes a novel clade of fungal homologues, with putative peroxisomal targeting signals, of the mitochondrial/peroxisomal acyltransferases in Metazoa, thus potentially representing an undescribed metabolic capacity in the Fungi. The overall distribution of GPAT homologues is suggestive of high relative complexity in the ancestors of the opisthokont clade, followed by loss and sculpting of the complement in the descendent lineages. Divergence from a general versatile metabolic model, present in ancestrally deduced GPAT complements, points to distinctive contributions of each GPAT isoform to lipid metabolism and homeostasis in contemporary organisms like humans and their fungal pathogens.     

Applying a neural network to predict the thermodynamic parameters for an expanded nearest-neighbor model

Predicting the secondary and tertiary structure of RNAs largely depends on our capabilities in estimating the thermodynamics of RNA duplexes. In this work, an expanded nearest-neighbor model, designated INN-48, is established. The thermodynamic parameters of this model are predicted using both multiple linear regression analysis and neural network analysis. It is suggested that due to the increase in the number of parameters and the insufficiency of the existing data, neural network analysis results in more reliable predictions. Furthermore, it is suggested that INN-48 can be used to estimate the thermodynamics of RNA duplex formation for longer sequences, whereas INN-HB, the previous model on which INN-48 is based, can be used for short sequences.     

Genome-wide linkage analysis of a Parkinsonian-pyramidal syndrome pedigree by 500 K SNP arrays

Robust SNP genotyping technologies and data analysis programs have encouraged researchers in recent years to use SNPs for linkage studies. Platforms used to date have been 10 K chip arrays, but the possible value of interrogating SNPs at higher densities has been considered. Here, we present a genome-wide linkage analysis by means of a 500 K SNP platform. The analysis was done on a large pedigree affected with Parkinsonian-pyramidal syndrome (PPS), and the results showed linkage to chromosome 22. Sequencing of candidate genes revealed a disease-associated homozygous variation (R378G) in FBXO7. FBXO7 codes for a member of the F-box family of proteins, all of which may have a role in the ubiquitin-proteosome protein-degradation pathway. This pathway has been implicated in various neurodegenerative diseases, and identification of FBXO7 as the causative gene of PPS is expected to shed new light on its role. The performance of the array was assessed and systematic analysis of effects of SNP density reduction was performed with the real experimental data. Our results suggest that linkage in our pedigree may have been missed had we used chips containing less than 100,000 SNPs across the genome.     

Increasing the expression of calcium-permeable TRPC3 and TRPC7 channels enhances constitutive secretion

The hTRPC [human TRPC (canonical transient receptor potential)] family of non-selective cation channels is proposed to mediate calcium influx across the plasma membrane via PLC (phospholipase C)-coupled receptors. Heterologously expressed hTRPC3 and hTRPC7 have been localized at the cell surface; however, a large intracellular component has also been noted but not characterized. In the present study, we have investigated the intracellular pool in COS-7 cells and have shown co-localization with markers for both the TGN (trans-Golgi network) and the cis-Golgi cisternae by immunofluorescence microscopy. Addition of BFA (Brefeldin A) to cells expressing hTRPC3 or hTRPC7 resulted in the redistribution of the Golgi component to the endoplasmic reticulum, indicating that this pool is present in both the Golgi stack and the TGN. Expression of either TRPC3 or TRPC7, but not TRPC1 or the cell surface marker CD8, resulted in a 2-4-fold increase in secreted alkaline phosphatase in the extracellular medium. Based on these results, we propose that an additional function of these members of the hTRPC family may be to enhance secretion either by affecting transport through the Golgi stack or by increasing fusion at the plasma membrane.