Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton

Virioplankton have a significant role in marine ecosystems, yet we know little of the predominant biological characteristics of aquatic viruses that influence the flow of nutrients and energy through microbial communities. Family A DNA polymerases, critical to DNA replication and repair in prokaryotes, are found in many tailed bacteriophages. The essential role of DNA polymerase in viral replication makes it a useful target for connecting viral diversity with an important biological feature of viruses. Capturing the full diversity of this polymorphic gene by targeted approaches has been difficult; thus, full-length DNA polymerase genes were assembled out of virioplankton shotgun metagenomic sequence libraries (viromes). Within the viromes novel DNA polymerases were common and found in both double-stranded (ds) DNA and single-stranded (ss) DNA libraries. Finding DNA polymerase genes in ssDNA viral libraries was unexpected, as no such genes have been previously reported from ssDNA phage. Surprisingly, the most common virioplankton DNA polymerases were related to a siphovirus infecting an α-proteobacterial symbiont of a marine sponge and not the podoviral T7-like polymerases seen in many other studies. Amino acids predictive of catalytic efficiency and fidelity linked perfectly to the environmental clades, indicating that most DNA polymerase-carrying virioplankton utilize a lower efficiency, higher fidelity enzyme. Comparisons with previously reported, PCR-amplified DNA polymerase sequences indicated that the most common virioplankton metagenomic DNA polymerases formed a new group that included siphoviruses. These data indicate that slower-replicating, lytic or lysogenic phage populations rather than fast-replicating, highly lytic phages may predominate within the virioplankton.     

Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent

Viruses that infect marine cyanobacteria–cyanophages–often carry genes with orthologs in their cyanobacterial hosts, and the frequency of these genes can vary with habitat. To explore habitat-influenced genomic diversity more deeply, we used the genomes of 28 cultured cyanomyoviruses as references to identify phage genes in three ocean habitats. Only about 6–11% of genes were consistently observed in the wild, revealing high gene-content variability in these populations. Numerous shared phage/host genes differed in relative frequency between environments, including genes related to phosphorous acquisition, photorespiration, photosynthesis and the pentose phosphate pathway, possibly reflecting environmental selection for these genes in cyanomyovirus genomes. The strongest emergent signal was related to phosphorous availability; a higher fraction of genomes from relatively low-phosphorus environments–the Sargasso and Mediterranean Sea–contained host-like phosphorus assimilation genes compared with those from the N. Pacific Gyre. These genes are known to be upregulated when the host is phosphorous starved, a response mediated by pho box motifs in phage genomes that bind a host regulatory protein. Eleven cyanomyoviruses have predicted pho boxes upstream of the phosphate-acquisition genes pstS and phoA; eight of these have a conserved cyanophage-specific gene (PhCOG173) between the pho box and pstS. PhCOG173 is also found upstream of other shared phage/host genes, suggesting a unique regulatory role. Pho boxes are found upstream of high light-inducible (hli) genes in cyanomyoviruses, suggesting that this motif may have a broader role than regulating phosphorous-stress responses in infected hosts or that these hlis are involved in the phosphorous-stress response.     

Side effects of atypical antipsychotics: a brief overview

This paper reviews the available evidence concerning the side effects of atypical antipsychotics, including weight gain, type II diabetes mellitus, hyperlipidemia, QTc interval prolongation, myocarditis, sexual side effects, extrapyramidal side effects and cataract. Some recommendations about how to prevent and manage these side effects are also provided. It is concluded that atypical antipsychotics do not represent a homogeneous class, and that differences in side effects should be taken into account by clinicians when choosing an antipsychotic for an individual patient.     

Polymeric aspects of protein folding: a brief overview

Regardless of the differences in primary amino acid sequences, protein molecules in a number of conformational states behave as polymer homologues, allowing speculations as to the volume interactions being a driving force in formation of equilibrium structures. For instance, both native and molten globules exhibit key features of polymer globules, where the fluctuations of the molecular density are expected to be much less than the molecular density itself. Protein molecules in the compact denatured (pre-molten globule) states possess properties of squeezed coils. In fact, even high concentrations of strong denaturants (e.g., urea and GdmCl) more likely constitute bad solvents for protein chains. Thus, globular proteins are probably never random coils without positional correlations and biological polypeptide chains represent the macromolecular coils below a critical point even under harsh denaturing conditions. Several implications of these findings to protein folding are discussed.     

Phosphorus budget of a 70-year-old northern hardwood forest

Recent measurements have made it possible to revise and improve the phosphorus budget of the Hubbard Brook Experimental Forest, including partitioning P uptake by vegetation from the forest floor and mineral soil and estimating net P mineralization in the forest floor. Both living biomass and forest floor are accumlating P (at rates of 1.3 and 0.16 kg P ha^-1 yr^-1 respectively) in this 70-yr old northern hardwood forest. About 61% of the P taken up by the vegetation each year comes from the forest floor (5.9 kg P ha^-1 yr^-1 of a total 9.6 kg P ha^-1 yr^-1), even though the P content of this pool is just 5% of that in mineral soil. The turnover rate of P in the forest floor is 7% yr^-1, while that of the mineral soil is 0.3% yr^-1. Recycling of P in the forest floor is very efficient; of the 5.6 kg P ha^-1 yr^-1 net mineralization in the forest floor, only 0.3 kg P ha^-1 leaches into the mineral soil; the rest is taken up by plants. This tight recycling of P is important because P is less readily available in the mineral soil than in the forest floor.     

Cell death and human intestinal protozoa: a brief overview

Protozoan programmed cell death or apoptosis is an important factor in the survival of the parasite and its pathogenicity. The most amazing aspect of protozoan cell death is in its molecular architecture. To date, protozoa lack most of the components of the highly complex cell death machinery studied in multicellular organisms. Hence the unique apoptotic machinery in protozoa can be exploited for the development of therapeutic drugs and diagnostic markers. This review focuses on human intestinal protozoa undergoing cell death and inducing or inhibiting host cell apoptosis. The first part of this review focuses on intestinal protozoa that undergo PCD under various stress conditions. The second part focuses on protozoa that induce or inhibit PCD in their host cell. Although these intestinal parasites differ in their mechanism of infection and intracellular localization, they may activate conserved cell death pathways within themselves and in the host cell. Understanding conserved cell death pathways in the intestinal protozoa and their host-parasite PCD relationship may lead to drug targets which can be used for a broad range of parasitic diseases.     

In vitro fertilization and embryo transfer: a brief overview

The in vitro fertilization process breaks down into three essential components: induction of ovulation, fertilization of the oocyte, and development of embryos that are transferred into the uterus. Problems may arise resulting in failure at any one of these junctions. In 1984, the World Congress on In Vitro Fertilization was held, looking at 9,641 laparoscopies yielding 1,101 clinical pregnancies, with an overall pregnancy rate of 11 percent--clearly indicating that in vitro fertilization/embryo transfer (IVF/ET) was an idea whose time had come. Ovulation induction is monitored by both the use of ultrasound and daily estradiol levels, ultrasound indicating the number of oocytes that will be available for capture, and estradiol indicating in an indirect way the quality of those oocytes. It is a major aim in each patient to obtain at least four embryos, since this optimizes success rates. Ovulation induction at Yale is carried out with a high-dose human menopausal gonadotropin (HMG)/human chorionic gonadotropin (HCG) regimen. This regimen has insured us a success rate of 17 percent clinical pregnancies per laparoscopy. In the future, modification will occur in the process with cryopreservation of oocytes and embryos, and gamete manipulation. The modifications will be effected primarily to increase pregnancy rates. Research will continue mainly to delineate better biochemical markers for oocyte quality, but also to further explain the mystery of implantation.     

Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses

Viruses influence oceanic ecosystems by causing mortality of microorganisms, altering nutrient and organic matter flux via lysis and auxiliary metabolic gene expression and changing the trajectory of microbial evolution through horizontal gene transfer. Limited host range and differing genetic potential of individual virus types mean that investigations into the types of viruses that exist in the ocean and their spatial distribution throughout the world''s oceans are critical to understanding the global impacts of marine viruses. Here we evaluate viral morphological characteristics (morphotype, capsid diameter and tail length) using a quantitative transmission electron microscopy (qTEM) method across six of the world''s oceans and seas sampled through the Tara Oceans Expedition. Extensive experimental validation of the qTEM method shows that neither sample preservation nor preparation significantly alters natural viral morphological characteristics. The global sampling analysis demonstrated that morphological characteristics did not vary consistently with depth (surface versus deep chlorophyll maximum waters) or oceanic region. Instead, temperature, salinity and oxygen concentration, but not chlorophyll a concentration, were more explanatory in evaluating differences in viral assemblage morphological characteristics. Surprisingly, given that the majority of cultivated bacterial viruses are tailed, non-tailed viruses appear to numerically dominate the upper oceans as they comprised 51–92% of the viral particles observed. Together, these results document global marine viral morphological characteristics, show that their minimal variability is more explained by environmental conditions than geography and suggest that non-tailed viruses might represent the most ecologically important targets for future research.     

Prenatal effects of alcohol on growth: a brief overview

Intrauterine growth retardation is the most reliable consequence of prenatal exposure to alcohol in both humans and animals. The decrease in fetal growth is caused by alcohol, not by congeners present in alcoholic beverages. The most likely hypothesis whereby alcohol decreases growth is via hypoxia, which interferes with cellular processes that require oxygen to function adequately, e.g., placental transport and protein synthesis. The third trimester of pregnancy is when alcohol exerts its greatest impact on fetal growth.     

Genetic regulation of cholesterol absorption and plasma plant sterol levels: commonalities and differences

The molecular basis of the processes that control two closely related traits, the absorption of cholesterol from the intestines and plasma plant sterol levels, are only partially understood. The discovery that mutations in two novel hemitransporters, ATP binding cassette transporter G5 (ABCG5) and ABCG8, underlie a rare inborn error in plant sterol metabolism, beta-sitosterolemia, represents a major breakthrough in this field. More recently, genetic studies in the mouse that mapped loci in linkage with cholesterol absorption and plasma plant sterol levels and studies in humans that examined the relationship of plasma plant sterol levels to sequence variation in the ABCG5/ABCG8 locus suggested the involvement of other genes. Moreover, studies in beta-sitosterolemic patients, in ABCG5/ABCG8-targeted animals, and on a newly developed cholesterol absorption inhibitor, ezetimibe, suggest commonalities and differences in the regulation of the two traits. This review summarizes the evidence for genetic control of cholesterol absorption and plasma plant sterol levels, presents the evidence for commonalities and differences between the two traits, and discusses recent developments and future perspectives in this field.     

Photosystem 2 and the oxygen evolving complex: a brief overview

These special issues of photosynthesis research present papers documenting progress in revealing the many aspects of photosystem 2, a unique, one-of-a-kind complex system that can reduce a plastoquinone to a plastoquinol on every second flash of light and oxidize 2 H₂O to an O₂ on every fourth flash. This overview is a brief personal assessment of the progress observed by the author over a four-decade research career, including a discussion of some remaining unsolved issues. It will come as no surprise to readers that there are remaining questions given the complexity of PS2, and the efforts that have been needed so far to uncover its secrets. In fact, most readers will have their own lists of outstanding questions.

     

Role of hydroxycinnamic acids in food flavor: a brief overview

The influence of hydroxycinnamic acids (HCAs) on food flavor is reviewed. In coffee, whole-grain foods and related model systems, the HCAs have been reported to contribute to the flavor profile by multiple mechanisms, such as to impart taste attributes, to generate aroma and taste-active compounds by phenolic degradation, as well as to alter the mechanisms of the Maillard reaction and related flavor development. Consequently the role of HCAs on the flavor properties of food products is complex, multifaceted and can be related to the chemistry and fate of HCAs during thermal processing.     

Life cycles and distribution of atherinids in the marine and estuarine waters of southern Australia

New and published data have been collated for the biology and distribution of atherinid species abundant in the coastal saline waters of Australia below 30°S. This information has been used to determine whether these species typically spawn at sea or pass through the whole of their life cycle in estuaries, and in one case, also lagoons and saline lakes. Length-frequency data, gonadosomatic indices and distribution records indicate that in south-eastern AustraliaCraterocephalus honoriae andAtherinosoma microstoma typically reach total lengths less than 90 mm, have a one-year life cycle and breed within estuaries. This parallels the situation recently described forAtherinosoma elongata, Atherinosoma wallacei andAllanetta mugiloides in south-western Australia (Princeet al., 1982a; Prince & Potter, 1983). The marine speciesAtherinosoma presbyteroides, which reaches a similar size and has a one year life cycle in both south-western and south-eastern mainland Australia, only enters estuaries in large numbers in the former region. WhileAtherinomorus ogilbyi is also found in estuaries and typically breeds at sea, it reaches total lengths as great as 189 mm and has a longer life thanA. presbyteroides. The limited data forAtherinason esox andAtherinason hepsetoides demonstrate that both these marine atherinids can attain total lengths of 139 and 108 mm respectively and live for longer than a year but do not enter estuaries in large numbers. The latter species is unique amongst southern Australian atherinids in having a distribution which extends into deeper water. It is suggested that landlocking may have played a role in the evolution and success of the estuarine mode of lifesensu stricto ofA. wallacei, A. elongata, A. microstoma, A. honoriae andA. mugiloides in southern Australian waters.     

Distribution and Abundance of Zooplankton in an Alkaline Freshwater Marsh in Northumberland County,Pennsylvania

The zooplankton community of two ponds in an alkaline marsh in central Pennsylvania were studied. The ponds were found to be distinctly different from one another with regard to species but similar when only zooplankton types are considered. The ponds were quite similar with respect to a number of physico-chemical characteristics but differed significantly with respect to alkalinity, conductivity, habitat type, vegetation, depth, and predation pressure.     

Isolation and characterization of a bacteriophage with an unusually large genome from the Great Salt Plains National Wildlife Refuge, Oklahoma, USA

In this study we present a bacteriophage isolated from the Great Salt Plains National Wildlife Refuge (GSP) that is shown to have a genome size of 340 kb, unusually large for a bacterial virus. Transmission electron microscopy analysis of the virion showed this to be a Myoviridae, the first reported to infect the genus Halomonas. This temperate phage, PhigspC, exhibits a broad host range, displaying the ability to infect two different Halomonas spp. also isolated from the GSP. The phage infection process demonstrates a high level of tolerance towards temperature, pH and salinity; however, free virions are rapidly inactivated in water unless supplemented with salt. We show that susceptibility to osmotic shock is correlated with the density of the packaged DNA (rho(pack)). Lysogens of Halomonas salina GSP21 were detrimental to host fitness at 10% salinity, but the lysogen was able to grow faster than the wild type at 20% salinity. From these results we propose that the extensive genome of PhigspC may encode environmentally relevant genes (ERGs); genes that are perhaps not essential for the phage life cycle but increase host and phage fitness in some environmental conditions.     

Adenosine in the local regulation of blood flow: a brief overview

Based on data from a variety of experiments from several laboratories, adenosine appears to play an important role in the adjustment of blood flow to the metabolic requirements of the tissue. This has been shown to be true for heart, brain, and skeletal muscle in several different species. A reduction in oxygen supply or an increase in oxygen demand results in vasodilation and adenosine release. However, adenosine is also coupled to blood flow increments with enhanced metabolic activity and in the presence of an adequate oxygen supply. To what extent other vasoactive agents participate with adenosine in producing vasodilation under a variety of conditions is not known.     

The voyage of stem cell toward terminal differentiation: a brief overview

Presently, worldwide attempts are being made to apply stem cells and stem cell-derived products to a wide range of clinical applications and for the development of cell-based therapies. In order to harness stem cells and manipulate them for therapeutic application, it is very important to understand the basic biology of stem cells and identify the factors that govern the dynamics of these cells in the body. Several signaling pathways have emerged as key regulators of stem cells. Some of these signaling pathways regulate the stem cell's proliferative capacity and therefore act as direct regulators of the stem cell, whereas others are involved in shaping and maintaining the stem cell niche and therefore act as indirect regulators of the stem cell. It is difficult to identify which signaling pathways critically affect the stem cell's behavior and which are important for maintaining the quiescent population. A stem cell receives different extrinsic signals compared with the bulk population and responds to them differently. In order to manipulate these adult cells for therapeutic approaches it is crucial to identify how signaling pathways regulate stem cells either directly by regulating proliferative status or indirectly by influencing the niche. The main challenge is to identify whether different factors provide diverse extrinsic signals to the stem cell and its daughter cell population, or whether there are intrinsic differences in stem cell and daughter cell populations that is reflected in their behavior. In this study, we will focus on the various aspects of stem cell biology and differentiation, as well as exploring the potential strategies to intervene the differentiation process in order to obtain the desired yield of cells applicable in regenerative medicine.     

The Freshwater Animal Diversity Assessment: an overview of the results

The geographic genetic structure of two common encrusting sponges, Hymeniacidon sinapium and Hymeniacidon flavia (family Halichondriidae), was investigated using two DNA markers, Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA and NADH dehydrogenase subunit 5 (nad5) of mitochondrial DNA. In the ITS analyses, multiple sequence types were identified within each species. Geographic distribution patterns of sequence types showed higher diversity in the western than eastern areas in both species. However, intraspecific genetic diversity of the two species in Japan differed markedly. Hymeniacidon flavia had far more diverse sequence types, and several genetic differentiations between localities were detected. In contrast, H. sinapium had only four sequence types in Japan, and two Atlantic Hymeniacidon species had sequence types similar to this species. In comparison to ITS, nad5 showed very low genetic diversity in both species, with two haplotypes identified in each species. In H. flavia, frequency of haplotype changed gradually from north to south. In H. sinapium, one haplotype was predominant in most regions, and another haplotype was minor and distributed only in the Korean and Tsushima populations. Based on the unique distribution patterns of sequence types around Shikoku and Kyushu, geographical history and ocean currents were assumed to affect the generation of genetic structure. The geographic genetic structure of H. flavia suggests low dispersal ability of pelagic larvae, whereas higher larval dispersal ability and a far broader distribution range are suggested in H. sinapium. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: C. Sturmbauer