Na+ Tolerance and Na+ Transport in Higher Plants

Many types of cells methylate phospholipids using two methyltransferase enzymes that are asymmetrically distributed in membranes. As the phospholipids are successively methylated, they are translocated from the inside to the outside of the membrane. When catecholamine neurotransmitters, lectins, immunoglobulins or chemotaxic peptides bind to the cell surface, they stimulate the methyltransferase enzymes and reduce membrane viscosity. The methylation of phospholipids is coupled to Ca2+ influx and the release of arachidonic acid, lysophosphatidylcholine, and prostaglandins. These closely associated biochemical changes facilitate the transmission of many signals through membranes, resulting in the generation of adenosine 3',5'-monophophate in many cell types, release of histamine in mast cells and basophils, mitogenesis in lymphocytes, and chemotaxis in neutrophils.

https://science.sciencemag.org/content/sci/209/4461/1082.full.pdf

Phospholipid methylation and biological signal transmission

Transposable elements are mobile genetic units that exhibit broad diversity in their structure and transposition mechanisms. Transposable elements occupy a large fraction of many eukaryotic genomes and their movement and accumulation represent a major force shaping the genes and genomes of almost all organisms. This review focuses on DNA-mediated or class 2 transposons and emphasizes how this class of elements is distinguished from other types of mobile elements in terms of their structure, amplification dynamics, and genomic effect. We provide an up-to-date outlook on the diversity and taxonomic distribution of all major types of DNA transposons in eukaryotes, including Helitrons and Mavericks. We discuss some of the evolutionary forces that influence their maintenance and diversification in various genomic environments. Finally, we highlight how the distinctive biological features of DNA transposons have contributed to shape genome architecture and led to the emergence of genetic innovations in different eukaryotic lineages.

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DNA Transposons and the Evolution of Eukaryotic Genomes

http://auburn.edu/academic/agriculture/fisheries/genomics/FISH7660%202006/DNA%20marker%20review%20paper-Aquaculture.pdf

DNA marker technologies and their applications in aquaculture genetics.

/pdf/the-structure-biosynthesis-and-function-of-glycosylated-4rbegebbn2.pdf

The structure, biosynthesis and function of glycosylated phosphatidylinositols in the parasitic protozoa and higher eukaryotes.

Background GNE myopathy is an adult onset recessive genetic disorder that affects distal muscles sparing the quadriceps. GNE gene mutations have been identified in GNE myopathy patients all over the world. Homozygosity is a common feature in GNE myopathy patients worldwide. Objectives The major objective of this study was to investigate the mutation spectrum of GNE myopathy in India in relation to the population diversity in the country. Materials and methods We have collated GNE mutation data of Indian GNE myopathy patients from published literature and from recently identified patients. We also used data of people of Indian subcontinent from 1000 genomes database, South Asian Genome database and Strand Life Science database to determine frequency of GNE mutations in the general population. Results A total of 67 GNE myopathy patients were studied, of whom 21% were homozygous for GNE variants, while the rest were compound heterozygous. Thirty-five different mutations in the GNE gene were recorded, of which 5 have not been reported earlier. The most frequent mutation was p.Val727Met (65%) found mainly in the heterozygous form. Another mutation, p.Ile618Thr was also common (16%) but was found mainly in patients from Rajasthan, while p.Val727Met was more widely distributed. The latter was also seen at a high frequency in general population of Indian subcontinent in all the databases. It was also present in Thailand but was absent in general population elsewhere in the world. Conclusion p.Val727Met is likely to be a founder mutation of Indian subcontinent.

Mutation Spectrum of GNE Myopathy in the Indian Sub-Continent.

Entamoeba histolytica, a protozoan parasite, is the etiologic agent of amoebiasis in humans. It exists in two forms—the trophozoite which is the active, dividing form, and the cyst which is dormant and can survive for prolonged periods outside the host. In most infected individuals the trophozoites exist as commensals. In a small percentage of infections, the trophozoites become invasive and penetrate the intestinal mucosa, causing ulcers. The trophozoites may reach other parts of the body—mainly liver, where they cause tissue necrosis, leading to lifethreatening abscesses. It is thought that pathogenesis of infection byEntamoeba histolytica is governed at several levels, chief among them are (i) adherence of trophozoite to the target cell, (ii) lysis of target cell, and (iii) phagocytosis of target cell. Several molecules which may be involved in these processes have been identified. A lectin inhibitable by galactose and N-acetyl-D-galactosamine is present on the trophozoite surface. This is implicated in adherence of trophozoite to the target cell. Various amoebic poreforming proteins are known, of which 5kDa protein (amoebapore) has been extensively studied. These can insert into the lipid bilayers of target cells, forming ion-channels. The phagocytic potential of trophozoites is directly linked to virulence as measured in animal models. Factors like association of bacteria with trophozoites also influence virulence. Thus, pathogenesis is determined by multiple factors and a unifying picture taking into account the relative contributions of each factor is sought. Recent technical advances, which includes the development of a transfection system to introduce genes into trophozoites, should help to understand the mechanism of pathogenesis in amoebiasis.

/pdf/pathogenesis-of-infection-by-entamoeba-histolytica-4yvw1w9fqz.pdf

Pathogenesis of infection by Entamoeba histolytica

Entamoeba histolytica extrachromosomal circular ribosomal DNA: analysis of clonal variation in a hypervariable region.

A large number of transcriptome-level studies in Entamoeba histolytica, the protozoan parasite that causes amoebiasis, have investigated gene expression patterns to help understand the pathology and biology of the organism. They have compared virulent and avirulent strains in lab culture and after tissue invasion, cells grown under different stress conditions, response to anti-amoebic drug treatments, and gene expression changes during the process of encystation. These studies have revealed interesting molecules/pathways that will help increase our mechanistic understanding of differentially expressed genes during growth perturbations and tissue invasion. Some of the important insights obtained from transcriptome studies include the observations that regulation of carbohydrate metabolism may be an important determinant for tissue invasion, while the novel up-regulated genes during encystation include phospholipase D, and meiotic genes, suggesting the possibility of meiosis during the process. Classification of genes according to expression levels showed that amongst the highly transcribed genes in cultured E. histolytica trophozoites were some virulence factors, raising the question of the role of these factors in normal parasite growth. Promoter motifs associated with differential gene expression and regulation were identified. Some of these motifs associated with high gene expression were located downstream of start codon, and were required for efficient transcription. The listing of E. histolytica genes according to transcript expression levels will help us determine the scale of post-transcriptional regulation, and the possible roles of predicted promoter motifs. The small RNA transcriptome is a valuable resource for detailed structural and functional analysis of these molecules and their regulatory roles. These studies provide new drug targets and enhance our understanding of gene regulation in E. histolytica.

/pdf/advances-in-entamoeba-histolytica-biology-through-4t0v0w4mvy.pdf

Advances in Entamoeba histolytica Biology Through Transcriptomic Analysis.

The major clinical manifestations of Entamoeba histolytica infection include amebic colitis and liver abscess. However the majority of infections remain asymptomatic. Earlier reports have shown that some E. histolytica isolates are more virulent than others, suggesting that virulence may be linked to genotype. Here we have looked at the genomic distribution of the retrotransposable short interspersed nuclear elements EhSINE1 and EhSINE2. Due to their mobile nature, some EhSINE copies may occupy different genomic locations among isolates of E. histolytica possibly affecting adjacent gene expression; this variability in location can be exploited to differentiate strains. We have looked for EhSINE1- and EhSINE2-occupied loci in the genome sequence of Entamoeba histolytica HM-1:IMSS and searched for homologous loci in other strains to determine the insertion status of these elements. A total of 393 EhSINE1 and 119 EhSINE2 loci were analyzed in the available sequenced strains (Rahman, DS4-868, HM1:CA, KU48, KU50, KU27 and MS96-3382. Seventeen loci (13 EhSINE1 and 4 EhSINE2) were identified where a EhSINE1/EhSINE2 sequence was missing from the corresponding locus of other strains. Most of these loci were unoccupied in more than one strain. Some of the loci were analyzed experimentally for SINE occupancy using DNA from strain Rahman. These data helped to correctly assemble the nucleotide sequence at three loci in Rahman. SINE occupancy was also checked at these three loci in 7 other axenically cultivated E. histolytica strains and 16 clinical isolates. Each locus gave a single, specific amplicon with the primer sets used, making this a suitable method for strain typing. Based on presence/absence of SINE and amplification with locus-specific primers, the 23 strains could be divided into eleven genotypes. The results obtained by our method correlated with the data from other typing methods. We also report a bioinformatic analysis of EhSINE2 copies. Our results reveal several loci with extensive polymorphism of SINE occupancy among different strains of E. histolytica and prove the principle that the genomic distribution of SINEs is a valid method for typing of E. histolytica strains.

/pdf/genomic-distribution-of-sines-in-entamoeba-histolytica-452jcn69ut.pdf

Alok Bhattacharya

Papers

Mutation Spectrum of GNE Myopathy in the Indian Sub-Continent.

Pathogenesis of infection by Entamoeba histolytica

Entamoeba histolytica extrachromosomal circular ribosomal DNA: analysis of clonal variation in a hypervariable region.

Advances in Entamoeba histolytica Biology Through Transcriptomic Analysis.

Genomic distribution of SINEs in Entamoeba histolytica strains: implication for genotyping