Structural Co-Evolution of Viruses and Cells in the Primordial World

Viruses and cells co-evolve due to the parasitic nature of viruses. Yet there are no models suggesting how the unicellular organisms and their viruses might co-evolve structurally. Here, in this study, we plunge into this unexplored field from a wide perspective and try to describe some of the intriguing ways in which viruses may have shaped the cellular life forms on the ancient Earth. At first we propose a scenario where viruses act as a driving force in the emergence of bacterial cell walls by providing favorable intermediates for the otherwise improbable steps in the cell wall generation. We also discuss the role of viruses in the evolution of cell surface components such as receptors and second membranes. Finally we focus on hypothetical proto-viruses, the selfish abusers of the RNA-world, in explaining some of the very early stages in the origin and evolution of life. Proto-viruses may be responsible for creating the first true cells in order to support their selfish needs. In this model we also suggest a logical pathway to explaining the emergence of modern viruses.     

Isolation of Legionella from water samples using various culture methods

The efficacy of a non-selective medium and two selective media were compared for the isolation of legionellas from water samples. The effect of acid wash treatment for decontamination of the water samples on the isolation frequency of legionellas was also studied. The 236 samples were taken from cooling, humidifying and drinking water systems; 21% were legionella-positive when inoculated directly on modified Wadowsky-Yee (MWY) medium and 26% were positive when concentrated (x 200) before cultivation on MWY or CCVC media. Inoculation on MWY medium after concentration followed by decontamination by the acid-wash technique gave the highest isolation frequency (31%). The lowest frequency (8%) was found with the non-selective BCYEα medium. An isolation frequency of 28% was achieved with the BCYEα medium after concentration and acid-wash treatment of the samples. Forty per cent of the samples were positive for legionellas when the results from all the culture methods were combined. Not all the legionella-positive samples were identified by a single culture method. Ninety-three of the 95 positive samples were detected with the two best combinations of three culture methods. The best culture method for detecting legionellas depended on the source of the water sample. Some water quality characteristics, like temperature and organic matter content, affected the isolation frequency of Legionella spp.     

Making and marketing Chambira hammocks and bags in the village of Brillo Nuevo, Northeastern Peru

Astrocaryum chambira Burret is a palm that provides edible fruits and fibers for making handicrafts. This study focused on the fiber products (hammocks and bags) made by the Bora in the Peruvian Amazonia. Making chambira handicrafts consists of several different phases. Handicrafts are marketed to tourists, river traders, or shopkeepers in the city of Iquitos. Villagers travel actively to sell their products because of the remote location of the village from the market. The prices received by producers were extremely low when considering the amount of work, but the prices were low also in other steps (middleman, tourist). Still, chambira works provide an important source of income for villagers. The greater abundance ofA. chambira in secondary forest compared with the primary forest indicates that it has potential for agroforestry. Agroforestry systems can provide a sustainable way to use land in the rainforest areas in NE Peru, and in this system nontimber forest products may have an important role.     

Somatic polyploidy examined by flow cytometry in Daphnia

Flow cytometry was used to examine the patterns of somatic polyploidyand to determine the haploid genome sizes in Daphnia. The averageproportions of polyploid nuclei among adult animals of D.pulex,D.longispina, D.pulex x D.longispina and D.magna equalled 27,24, 24 and 24%, respectively. Both interclonal and developmentallyregulated variation were observed in the level of somatic polyploidy.Adult animals expressed more extensive polyploidy than did juveniles.The estimates of the haploid genome sizes (C values) of D.pulex,D.longispina, D.pulex x D.longispina and D.magna equalled 0.32,0.27, 0.26 and 0.37 pg, respectively. These are the smallestgenomes reported in crustaceans. Apparently, somatic polyploidycompensates for the loss of genetic material and gives riseto genetic plasticity which may contribute to the considerablelevel of phenotypic plasticity observed in Daphina.     

The role of MatP,ZapA and ZapB in chromosomal organization and dynamics in Escherichia coli

Despite extensive research over several decades, a comprehensive view of how the Escherichia coli chromosome is organized within the nucleoid, and how two daughter chromosomes segregate has yet to emerge. Here we investigate the role of the MatP, ZapA and ZapB proteins in organizing the replication terminus (Ter) region and in the chromosomal segregation process. Quantitative image analysis of the fluorescently labeled Ter region shows that the replication terminus attaches to the divisome in a single segment along the perimeter of the cell in a MatP, ZapA and ZapB-dependent manner. The attachment does not significantly affect the bulk chromosome segregation in slow growth conditions. With or without the attachment, two chromosomal masses separate from each other at a speed comparable to the cell growth. The separation starts even before the replication terminus region positions itself at the center of the nucleoid. Modeling of the segregation based on conformational entropy correctly predicts the positioning of the replication terminus region within the nucleoid. However, the model produces a distinctly different chromosomal density distribution than the experiment, indicating that the conformational entropy plays a limited role in segregating the chromosomes in the late stages of replication.     

Isolation of Cellular Lipid Droplets: Two Purification Techniques Starting from Yeast Cells and Human Placentas

Lipid droplets are dynamic organelles that can be found in most eukaryotic and certain prokaryotic cells. Structurally, the droplets consist of a core of neutral lipids surrounded by a phospholipid monolayer. One of the most useful techniques in determining the cellular roles of droplets has been proteomic identification of bound proteins, which can be isolated along with the droplets. Here, two methods are described to isolate lipid droplets and their bound proteins from two wide-ranging eukaryotes: fission yeast and human placental villous cells. Although both techniques have differences, the main method - density gradient centrifugation - is shared by both preparations. This shows the wide applicability of the presented droplet isolation techniques.In the first protocol, yeast cells are converted into spheroplasts by enzymatic digestion of their cell walls. The resulting spheroplasts are then gently lysed in a loose-fitting homogenizer. Ficoll is added to the lysate to provide a density gradient, and the mixture is centrifuged three times. After the first spin, the lipid droplets are localized to the white-colored floating layer of the centrifuge tubes along with the endoplasmic reticulum (ER), the plasma membrane, and vacuoles. Two subsequent spins are used to remove these other three organelles. The result is a layer that has only droplets and bound proteins.In the second protocol, placental villous cells are isolated from human term placentas by enzymatic digestion with trypsin and DNase I. The cells are homogenized in a loose-fitting homogenizer. Low-speed and medium-speed centrifugation steps are used to remove unbroken cells, cellular debris, nuclei, and mitochondria. Sucrose is added to the homogenate to provide a density gradient and the mixture is centrifuged to separate the lipid droplets from the other cellular fractions.The purity of the lipid droplets in both protocols is confirmed by Western Blot analysis. The droplet fractions from both preps are suitable for subsequent proteomic and lipidomic analysis.     

Complete nucleotide mtDNA sequence of Barbary sheep (Ammotragus lervia).

In this report we describe the complete sequence of the mtDNA genome of Ammotragus lervia (Barbary sheep or aoudad) as obtained by PCR and sequencing with primer walking using flanking sequences. The molecule is 16,530 base pairs in length, resulting similar to those of goat and sheep. The genome organization matches to those of other mammalian mitochondrial genomes. The phylogenetic position of the Ammotragus relative to twelve other mammalian species was assessed based on protein-coding sequences. A goat-aoudad split of 9.9-8.9 MYBP has been estimated, whereas the divergence ancestor/caprines was dated at 12.1-10.8 MYBP.