Intratypic recombination among lineages of type 1 vaccine-derived poliovirus emerging during chronic infection of an immunodeficient patient

We determined the complete genomic sequences of nine type 1 immunodeficient vaccine-derived poliovirus (iVDPV) isolates obtained over a 337-day period from a poliomyelitis patient from Taiwan with common variable immunodeficiency. The iVDPV isolates differed from the Sabin type 1 oral poliovirus vaccine (OPV) strain at 1.84% to 3.15% of total open reading frame positions and had diverged into at least five distinct lineages. Phylogenetic analysis suggested that the chronic infection was initiated by the fifth and last OPV dose, given 567 days before onset of paralysis, and that divergence of major lineages began very early in the chronic infection. Key determinants of attenuation in Sabin 1 had reverted in the iVDPV isolates, and representative isolates of each lineage showed increased neurovirulence for PVR-Tg21 transgenic mice. None of the isolates had retained the temperature-sensitive phenotype of Sabin 1. All isolates were antigenic variants of Sabin 1, having multiple amino acid substitutions within or near neutralizing antigenic sites 1, 2, and 3a. Antigenic divergence of the iVDPV variants from Sabin 1 followed two major independent evolutionary pathways. The emergence of distinct coreplicating lineages suggests that iVDPVs can replicate for many months at separate sites in the gastrointestinal tract. Some isolates had mosaic genome structures indicative of recombination across and within lineages. iVDPV excretion apparently ceased after 30 to 35 months of chronic infection. The appearance of a chronic VDPV excretor in a tropical, developing country has important implications for the strategy to stop OPV immunization after eradication of wild polioviruses.     

Identification and characterization of the RNA helicase activity of Japanese encephalitis virus NS3 protein

The NS3 protein of Japanese encephalitis virus (JEV) contains motifs typical of RNA helicase/NTPase but no RNA helicase activity has been reported for this protein. To identify and characterize the RNA helicase activity of JEV NS3, a truncated form of the protein with a His-tag was expressed in Escherichia coli and purified. The purified JEV NS3 protein showed an RNA helicase activity, which was dependent on divalent cations and ATP. An Asp-285-to-Ala substitution in motif II of the JEV NS3 protein abolished the ATPase and RNA helicase activities. These results indicate that the C-terminal 457 residues are sufficient to exhibit the RNA helicase activity of JEV NS3.     

Ant communities on small tropical islands: effects of island size and isolation are obscured by habitat disturbance and ‘tramp’ ant species

Aim Comparisons among islands offer an opportunity to study the effects of biotic and abiotic factors on small, replicated biological communities. Smaller population sizes on islands accelerate some ecological processes, which may decrease the time needed for perturbations to affect community composition. We surveyed ants on 18 small tropical islands to determine the effects of island size, isolation from the mainland, and habitat disturbance on ant community composition. Location Thousand Islands Archipelago (Indonesian name: Kepulauan Seribu) off Jakarta, West Java, Indonesia. Methods Ants were sampled from the soil surface, leaf litter and vegetation in all habitat types on each island. Island size, isolation from the mainland, and land‐use patterns were quantified using GIS software. The presence of settlements and of boat docks were used as indicators of anthropogenic disturbance. The richness of ant communities and non‐tramp ant species on each island were analysed in relation to the islands’ physical characteristics and indicators of human disturbance. Results Forty‐eight ant species from 5 subfamilies and 28 genera were recorded from the archipelago, and approximately 20% of the ant species were well‐known human‐commensal ‘tramp’ species. Islands with boat docks or human settlements had significantly more tramp species than did islands lacking these indicators of anthropogenic disturbance, and the diversity of non‐tramp species decreased with habitat disturbance. Main conclusions Human disturbance on islands in the Thousand Islands Archipelago promotes the introduction and/or establishment of tramp species. Tramp species affect the composition of insular ant communities, and expected biogeographical patterns of ant richness are masked. The island with the greatest estimated species richness and the greatest number of unique ant species, Rambut Island, is a forested bird sanctuary, highlighting the importance of protected areas in preserving the diversity of species‐rich invertebrate faunas.     

Effect of water-soluble fraction of cigarette smoke on human aortic endothelial cells – a proteomic approach

Proteomic analysis is an important investigative tool used to systematically explore cellular proteins that are responsive to adverse environmental challenges. Tobacco smoking is the second major cause of death in the world. In this study, we utilized two-dimensional electrophoresis (2-DE) and mass spectrometry (MS) technologies to explore protein changes in human aortic endothelial cells (HAECs) in response to cigarette smoke extracts (CSE). Among 389 individual proteins resolved using 2-DE, 43 had a 2- to 3-fold change in levels as measured by spot intensity and 32 had more than a 3-fold change. Sixteen of the 32 spots with sufficient amount of proteins were excised for identification by performing matrix-assisted laser desorption/ionization (MALDI)-MS analysis. Using a peptide mass fingerprinting (PMF) to search the nrNCBI database, we identified all these 16 proteins, which were either increased (n = 9) or decreased (n = 7) after CSE treatment. All these proteins have known functions, however, none have been reported to be altered after CSE treatment. The findings from our study suggest that utilizing a systemic investigative tool, such as the proteomic approach using 2-DE, may play an important role in discovering novel molecular mechanisms for cigarette smoking-induced pathological changes. Further investigation following the systemic discoveries must be further examined as they may potentially lead to new therapeutic approaches to smoking-induced diseases – a health issue affecting everyone in the world.     

Genetically modified soybeans: false-positive detection in fermented natural soybean (tempe)

Tempe was prepared using mixtures of natural soybean and genetically modified Roundup Ready (RUR) soybean fermented with natural Rhizopus sp. The amount of RUR soybean was quantified using an ELISA plate test. The RUR signal decreased during fermentation. In the control experiments on fermentation of non-RUR soybean, the tempe gave a false-positive RUR signal. The cross-reacting substance was generated only in non-RUR soybean during fermentation by Rhizopus sp., Rhizopus oligosporus, R. oryzae, Mucor rouxii and Aspergillus awamori.     

Enaptin, a giant actin-binding protein, is an element of the nuclear membrane and the actin cytoskeleton

Enaptin belongs to a family of recently identified giant proteins that associate with the F-actin cytoskeleton as well as the nuclear membrane. It is composed of an N-terminal alpha-actinin type actin-binding domain (ABD) followed by a long coiled coil rod and a transmembrane domain at the C-terminus. The ABD binds to F-actin in vivo and in vitro and leads to bundle formation. The human Enaptin gene spreads over 515 kb and gives rise to several splicing isoforms (Nesprin-1, Myne-1, Syne-1, CPG2). The longest assembled cDNA encompasses 27,669 bp and predicts a 1014 kDa protein. Antibodies against the ABD of Enaptin localise the protein at F-actin-rich structures throughout the cell and in focal contacts as well as at the nuclear envelope. In COS7 cells, the protein is also present within the nuclear compartment. With the discovery of the actin-binding properties of Enaptin and the highly homologous Nuance, we define a family of proteins that integrate the cytoskeleton with the nucleoskeleton.     

Ultrasound measurement of the volume of musculus quadriceps after knee joint injury

The monitoring of the recovery of femoral muscles, after the knee-joint injury, is possible by the method of ultrasound measurement of the muscular volume. In a clearly defined longitudinal study, our object was to standardize the method of ultrasound measurement of muscular volume and to evaluate its adequacy in practical application in quadriceps muscle rehabilitation. The ultrasound measurements of m. rectus femoris and m. vastus intermedius were conducted in three intervals: in the first 24 hours after the injury; after 1 week, when immobilization was removed; and after 6 weeks, when rehabilitation was finished. The study comprised 30 patients with knee-joint injury, and 30 asymptomatic subjects, who formed the control group. The results showed significant decrease of muscular volume (mm3) after joint immobilization on injured leg and a significant increase of volume after rehabilitation. The same differences were observed on healthy legs, but without significance. Within the same intervals, there were no changes in the muscular mass in the control group. M. rectus femoris was completely recovered in greater number of patients (54.1%), comparing to m. vastus intermedius (25.4%). We conclude that the ultrasound is an appropriate method for monitoring the process of muscular atrophy during immobilization, as well as the course of muscular restitution during the physical therapy.     

Configuration and localization of the nipple-areola complex in men.

The causes of bilateral absence of the nipple-areola complex in men are seldom congenital, but attributable rather to destruction as a result of trauma, or after mastectomy in female-to-male transsexuals and in male breast cancer, or after the correction of extreme bilateral gynecomastia. Such a bilateral loss becomes a major reconstructive challenge with respect to the configuration and localization of a new nipple-areola complex. Because there is very little information available in the literature, we carried out a cross-sectional study on the configuration and localization of the nipple-areola complex in men.A total of 100 healthy men aged 20 to 36 years were examined under standardized conditions. The first part of the study dealt with the configuration of the nipple-areola complex (dimensions, round or oval shape). The second part concentrated on the localization of the complex on the thoracic wall with respect to anatomic landmarks and in correlation to various parameters such as weight and height of the body, circumference of the thorax, length of sternum, and position in the intercostal space.Of the 100 subjects examined, 91 had oval and seven had a round nipple-areola complex. An asymmetry between the right and the left side was found in two cases. The mean ratio of the horizontal/vertical diameter of an oval nipple-areola complex was 27:20 mm and the mean diameter for a round nipple-areola complex was 23 mm. The center of the nipple-areola complex was in the fourth intercostal space in 75 percent and in the fifth intercostal space in 23 percent of the subjects. To localize the nipple-areola complex on the thoracic wall de novo, at least two reproducible measurements proved to be necessary, composed of a horizontal line (distance from the midsternal line to the nipple = A) and a vertical line (distance from the sternal notch to the intersection of line A, = B). The closest correlation for the horizontal distance A was given by the circumference of the thorax: A = 2.4 cm + [0.09 x circumference of thorax (cm)], (r = 0.68). The best correlation to calculate the vertical distance B was found using the distance A and the length of the sternum: B = 1.2 cm + [0.28 x length of sternum (cm)] + [0.1 x circumference of thorax (cm)], (R = 0.50).In cases of bilateral absence, we recommend creating an oval nipple-areola complex in men. The appropriate localization can be calculated by means of two simple equations derived from the circumference of the thorax and the length of the sternum.