Photoheterotrophic Microbes in the Arctic Ocean in Summer and Winter

Photoheterotrophic microbes, which are capable of utilizing dissolved organic materials and harvesting light energy, include coccoid cyanobacteria (Synechococcus and Prochlorococcus), aerobic anoxygenic phototrophic (AAP) bacteria, and proteorhodopsin (PR)-containing bacteria. Our knowledge of photoheterotrophic microbes is largely incomplete, especially for high-latitude waters such as the Arctic Ocean, where photoheterotrophs may have special ecological relationships and distinct biogeochemical impacts due to extremes in day length and seasonal ice cover. These microbes were examined by epifluorescence microscopy, flow cytometry, and quantitative PCR (QPCR) assays for PR and a gene diagnostic of AAP bacteria (pufM). The abundance of AAP bacteria and PR-containing bacteria decreased from summer to winter, in parallel with a threefold decrease in the total prokaryotic community. In contrast, the abundance of Synechococcus organisms did not decrease in winter, suggesting that their growth was supported by organic substrates. Results from QPCR assays revealed no substantial shifts in the community structure of AAP bacteria and PR-containing bacteria. However, Arctic PR genes were different from those found at lower latitudes, and surprisingly, they were not similar to those in Antarctic coastal waters. Photoheterotrophic microbes appear to compete successfully with strict heterotrophs during winter darkness below the ice, but AAP bacteria and PR-containing bacteria do not behave as superior competitors during the summer.Photoheterotrophy, which is the ability to utilize organic substrates and to harvest light energy, occurs in a broad range of microbes (14). Phototrophic microbes should be included in models of carbon cycling and food web dynamics, which now typically include only photoautotrophs, which produce organic carbon and oxygen, and heterotrophs, which consume organic matter and oxygen via aerobic respiration (55). Photoheterotrophy is potentially an important competitive adaptation, enabling microbes to survive adverse conditions or to outgrow competitors. Photoheterotrophic microbes include proteorhodopsin (PR)-containing bacteria, aerobic anoxygenic phototrophic (AAP) bacteria, and cyanobacteria.PR is a membrane protein that binds retinal and functions as a light-driven proton pump that can have several physiological functions, including ATP generation (15). The actual role of PR in the environment is uncertain, however. Light enhances the growth of some PR-containing bacteria, such as Dokdonia sp. (17), but has no effect on the growth of others, including Pelagibacter ubique (16) and the SAR92-like strain HTCC2207 (44). Similarly, Campbell et al. (4) found no significant correlation with light intensity for three of four PR gene types examined in the North Atlantic Ocean. Nevertheless, emerging biogeographic patterns of PR genes are providing clues about what controls the distribution and abundance of PR-containing photoheterotrophs in oceanic systems. One of the first oceanic environments to be examined for PR was the coastal waters near Palmer Station, Antarctica (2). Sequence analysis revealed that the Antarctic PRs differed from those isolated from Monterey Bay and surface waters in the central North Pacific (2). In spite of this early report, there has been no work on PR-containing bacteria in Arctic waters. PR-containing bacteria may have unique responses to the continuous summer light, winter darkness, and shading by seasonal ice cover that occur in high-latitude environments.The diversity and abundance of AAP bacteria have been examined by sequencing of the pufM gene (20, 51, 58), which is involved in bacteriochlorophyll (BChl a) synthesis, and by counting of BChl a-fluorescing cells by infrared fluorescence microscopy (14). Enumeration by infrared epifluorescence microscopy indicates that the abundance of AAP bacteria in environments such as the North Pacific Gyre and the Northeast Atlantic Ocean ranges from 1% to 10% (12, 13, 42) and can exceed 10% of the total prokaryotic community in estuaries (41, 50). AAP bacteria have been found in freshwater high-latitude waters (20, 35), but sequence analysis of pufM genes indicates that these AAP bacteria are distinct from those found in marine systems (50). The abundance of AAP bacteria decreases with latitude within the North Atlantic Ocean, from the central gyre to the waters near Greenland (13). Although these photoheterotrophic microbes are still present at 65°N, extrapolation of the trend suggests that AAP bacteria might be absent from the high-latitude waters of the Arctic Ocean.Polar waters appear to be an exception to the otherwise widespread distribution of coccoid cyanobacteria in the world oceans (33, 54). The abundance of Synechococcus and Prochlorococcus decreases with latitude, as exemplified by the 4-orders-of-magnitude decline in abundance between 44°S and 62°S in the South Atlantic Ocean (25). The abundance of Synechococcus also decreases with latitude in the North Atlantic Ocean, between the central gyre and the waters near Greenland, to a low level at 65°N (13). The strong correlation between abundance and temperature (25) suggests that coccoid cyanobacteria are not important at high latitudes, although there are scattered reports of Prochlorococcus in waters as far north as 60°N, near Iceland (27), and of Synechococcus in Antarctic coastal waters (53). However, more data are needed on the abundance of Synechococcus and Prochlorococcus in polar waters such as the Arctic Ocean.The goal of this study was to explore the abundance and diversity of photoheterotrophic microbes in the Arctic Ocean in order to develop a better picture of the biogeographic range of these biogeochemically important microbes and to gain insights into their ecology. Coastal waters of the Chukchi Sea and the Beaufort Sea were sampled in summer at the end of 24-h daylight and in winter following the period of 24-h darkness. The abundances of cyanobacteria, PR-containing bacteria, and AAP bacteria were monitored using flow cytometry, infrared epifluorescence microscopy, and real-time quantitative PCR (QPCR). These data provide a unique perspective on the potential impact of photoheterotrophic microbes on food webs and carbon cycling in this high-latitude aquatic system.     

A novel approach to biological control with entomopathogenic nematodes: Prophylactic control of the peachtree borer, Synanthedon exitiosa

Generally, microbial control agents such as entomopathogenic nematodes are applied in a curative manner for achieving pest suppression; prophylactic applications are rare. In this study, we determined the ability of two Steinernema carpocapsae strains (All and Hybrid) to prophylactically protect peach trees from damage caused by the peachtree borer, Synanthedon exitiosa, which is a major pest of stone fruit trees in North America. In prior studies, the entomopathogenic nematodes S. carpocapsae and Heterorhabditis bacteriophora caused field suppression when applied in a curative manner to established S. exitiosa populations. In our current study, nematodes were applied three times (at 150,000–300,000 infective juveniles/tree) during September and October of 2005, 2006, and 2007. A control (water only) and a single application of chlorpyrifos (at the labeled rate) were also made each year. The presence of S. exitiosa damage was assessed each year in the spring following the treatment applications. Following applications in 2006, we did not detect any differences among treatments or the control (possibly due to a low and variable S. exitiosa infestation of that orchard). Following applications in 2005 and 2007, however, the nematode and chemical treatments caused significant damage suppression. The percentage of trees with S. exitiosa damage in treated plots ranged from 0% damage in 2005 to 16% in plots treated with S. carpocapsae (Hybrid) in 2007. In control plots damage ranged from 25% (2005) to 41% (2007). Our results indicate that nematodes applied in a preventative manner during S. exitios’s oviposition period can reduce insect damage to levels similar to what is achieved with recommended chemical insecticide treatments.     

Induced Dimerization of the Amyloid Precursor Protein Leads to Decreased Amyloid-�� Protein Production

The amyloid precursor protein (APP) plays a central role in Alzheimer disease (AD) pathogenesis because sequential cleavages by β- and γ-secretase lead to the generation of the amyloid-β (Aβ) peptide, a key constituent in the amyloid plaques present in brains of AD individuals. In several studies APP has recently been shown to form homodimers, and this event appears to influence Aβ generation. However, these studies have relied on APP mutations within the Aβ sequence itself that may affect APP processing by interfering with secretase cleavages independent of dimerization. Therefore, the impact of APP dimerization on Aβ production remains unclear. To address this question, we compared the approach of constitutive cysteine-induced APP dimerization with a regulatable dimerization system that does not require the introduction of mutations within the Aβ sequence. To this end we generated an APP chimeric molecule by fusing a domain of the FK506-binding protein (FKBP) to the C terminus of APP. The addition of the synthetic membrane-permeant drug AP20187 induces rapid dimerization of the APP-FKBP chimera. Using this system we were able to induce up to 70% APP dimers. Our results showed that controlled homodimerization of APP-FKBP leads to a 50% reduction in total Aβ levels in transfected N2a cells. Similar results were obtained with the direct precursor of β-secretase cleavage, C99/SPA4CT-FKBP. Furthermore, there was no modulation of different Aβ peptide species after APP dimerization in this system. Taken together, our results suggest that APP dimerization can directly affect γ-secretase processing and that dimerization is not required for Aβ production.The mechanism of β-amyloid protein (Aβ)² generation from the amyloid precursor protein is of major interest in Alzheimer disease research because Aβ is the major constituent of senile plaques, one of the neuropathological hallmarks of Alzheimer disease (1, 2). In the amyloidogenic pathway Aβ is released from the amyloid precursor protein (APP) (3) after sequential cleavages by β-secretase BACE1 (4–6) and by the γ-secretase complex (7, 8). BACE1 cleavage releases the large ectodomain of APP while generating the membrane-anchored C-terminal APP fragment (CTF) of 99 amino acids (C99). Cleavage of β-CTF by γ-secretase leads to the secretion of Aβ peptides of various lengths and the release of the APP intracellular domain (AICD) into the cytosol (9–11). The γ-secretase complex consists of at least four proteins: presenilin, nicastrin, Aph-I, and Pen-2 (12). Presenilin is thought to be the catalytic subunit of the enzyme complex (13), but how the intramembrane scission is carried out remains to be elucidated. Alternatively, APP can first be cleaved in the non-amyloidogenic pathway by α-secretase within the Aβ domain between Lys-16 and Leu-17 (14, 15). This cleavage releases the APP ectodomain (APPsα) while generating the membrane-bound C-terminal fragment (α-CTF) of 83 amino acids (C83). The latter can be further processed by the γ-secretase complex, resulting in the secretion of the small 3-kDa fragment p3 and the release of AICD.APP, a type I transmembrane protein (16) of unclear function, may act as a cell surface receptor (3). APP and its two homologues, APLP1 and APLP2, can dimerize in a homotypic or heterotypic manner and, in so doing, promote intercellular adhesion (17). In vivo interaction of APP, APLP1, and APLP2 was demonstrated by cross-linking studies from brain homogenates (18). To date at least four domains have been reported to promote APP dimerization; that is, the E1 domain containing the N-terminal growth factor-like domain and copper binding domain (17), the E2 domain containing the carbohydrate domain in the APP ectodomain (19), the APP juxtamembrane region (20), and the transmembrane domain (21, 22). In the latter domain the dimerization appears to be mediated by the GXXXG motif near the luminal face of the transmembrane region (21, 23). In addition to promoting cell adhesion, APP dimerization has been proposed to increase susceptibility to cell death (20, 24).Interestingly, by introducing cysteine mutations into the APP juxtamembrane region, it was shown that stable dimers through formation of these disulfide linkages result in significantly enhanced Aβ production (25). This finding is consistent with the observation that stable Aβ dimers are found intracellularly in neurons and in vivo in brain (26). Taken together, these results have led to the idea that APP dimerization can positively regulate Aβ production. However, other laboratories have not been able to confirm some of these observations using slightly different approaches (23, 27).To further address the question of how dimerization of APP affects cleavage by α-, β-, and γ-secretase, we chose to test this with a controlled dimerization system. Accordingly, we engineered a chimeric APP molecule by fusing a portion of the FK506-binding protein (FKBP) to the C terminus of APP such that the addition of the synthetic membrane-permeant bifunctional compound, AP20187, will induce dimerization of the APP-FKBP chimera in a controlled manner by binding to the FKBP domains. Using this system, efficient dimerization of APP up to 70% can be achieved in a time and concentration-dependent fashion. Our studies showed that controlled homodimerization of APP-FKBP leads to decreased total Aβ levels in transfected N2a cells. Homodimerization of the β-CTF/C99 fragment, the direct precursor of γ-secretase cleavage, showed comparable results. In addition, induced dimerization of APP did not lead to a modulation of different Aβ peptides as it was reported for GXXXG mutants within the transmembrane domain of APP (21).     

Multiple histone modifications in euchromatin promote heterochromatin formation by redundant mechanisms in Saccharomyces cerevisiae

Background  

Methylation of lysine 79 on histone H3 by Dot1 is required for maintenance of heterochromatin structure in yeast and humans. However, this histone modification occurs predominantly in euchromatin. Thus, Dot1 affects silencing by indirect mechanisms and does not act by the recruitment model commonly proposed for histone modifications. To better understand the role of H3K79 methylation gene silencing, we investigated the silencing function of Dot1 by genetic suppressor and enhancer analysis and examined the relationship between Dot1 and other global euchromatic histone modifiers.     

Extremely short duration high intensity interval training substantially improves insulin action in young healthy males

Background

Impaired glucose tolerance (IGT) is a prediabetic state. If IGT can be prevented from progressing to overt diabetes, hyperglycemia-related complications can be avoided. The purpose of the present study was to examine whether pioglitazone (ACTOS^®) can prevent progression of IGT to type 2 diabetes mellitus (T2DM) in a prospective randomized, double blind, placebo controlled trial.

Methods/Design

602 IGT subjects were identified with OGTT (2-hour plasma glucose = 140–199 mg/dl). In addition, IGT subjects were required to have FPG = 95–125 mg/dl and at least one other high risk characteristic. Prior to randomization all subjects had measurement of ankle-arm blood pressure, systolic/diastolic blood pressure, HbA_1C, lipid profile and a subset had frequently sampled intravenous glucose tolerance test (FSIVGTT), DEXA, and ultrasound determination of carotid intima-media thickness (IMT). Following this, subjects were randomized to receive pioglitazone (45 mg/day) or placebo, and returned every 2–3 months for FPG determination and annually for OGTT. Repeat carotid IMT measurement was performed at 18 months and study end. Recruitment took place over 24 months, and subjects were followed for an additional 24 months. At study end (48 months) or at time of diagnosis of diabetes the OGTT, FSIVGTT, DEXA, carotid IMT, and all other measurements were repeated. Primary endpoint is conversion of IGT to T2DM based upon FPG ≥ 126 or 2-hour PG ≥ 200 mg/dl. Secondary endpoints include whether pioglitazone can: (i) improve glycemic control (ii) enhance insulin sensitivity, (iii) augment beta cell function, (iv) improve risk factors for cardiovascular disease, (v) cause regression/slow progression of carotid IMT, (vi) revert newly diagnosed diabetes to normal glucose tolerance.

Conclusion

ACT NOW is designed to determine if pioglitazone can prevent/delay progression to diabetes in high risk IGT subjects, and to define the mechanisms (improved insulin sensitivity and/or enhanced beta cell function) via which pioglitazone exerts its beneficial effect on glucose metabolism to prevent/delay onset of T2DM.

Trial Registration

clinical trials.gov identifier: NCT00220961     

Dynamic equilibria in an epidemic model with voluntary vaccinations

The dynamics of an epidemic model with voluntary vaccinations are studied. Individual vaccination decisions are modelled using an economic/game-theoretic approach: agents in the model decide whether to vaccinate or not by weighing the cost and benefit of vaccination and choose the action that maximizes their net benefit. It is shown that, when vaccine efficacy is low, there are parameter values for which multiple steady-state equilibria and periodic equilibria coexist. When multiplicity of steady states is obtained, which one the population reaches in some cases depends entirely on agents' expectations concerning the future course of an epidemic and not on the initial conditions of the model. (?)Comments and suggestions from anonymous referees of the journal are gratefully acknowledged. This paper is dedicated to the loving memory of Lucy Hauser.     

Evolutionary dynamics of the kinetochore network in eukaryotes as revealed by comparative genomics

During eukaryotic cell division, the sister chromatids of duplicated chromosomes are pulled apart by microtubules, which connect via kinetochores. The kinetochore is a multiprotein structure that links centromeres to microtubules, and that emits molecular signals in order to safeguard the equal distribution of duplicated chromosomes over daughter cells. Although microtubule‐mediated chromosome segregation is evolutionary conserved, kinetochore compositions seem to have diverged. To systematically inventory kinetochore diversity and to reconstruct its evolution, we determined orthologs of 70 kinetochore proteins in 90 phylogenetically diverse eukaryotes. The resulting ortholog sets imply that the last eukaryotic common ancestor (LECA) possessed a complex kinetochore and highlight that current‐day kinetochores differ substantially. These kinetochores diverged through gene loss, duplication, and, less frequently, invention and displacement. Various kinetochore components co‐evolved with one another, albeit in different manners. These co‐evolutionary patterns improve our understanding of kinetochore function and evolution, which we illustrated with the RZZ complex, TRIP13, the MCC, and some nuclear pore proteins. The extensive diversity of kinetochore compositions in eukaryotes poses numerous questions regarding evolutionary flexibility of essential cellular functions.     

The pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenine

Understanding how self-cleaving ribozymes mediate catalysis is crucial in light of compelling evidence that human and bacterial gene expression can be regulated through RNA self-cleavage. The hairpin ribozyme catalyzes reversible phosphodiester bond cleavage through a mechanism that does not require divalent metal cations. Previous structural and biochemical evidence implicated the amidine group of an active site adenosine, A38, in a pH-dependent step in catalysis. We developed a way to determine microscopic pK(a) values in active ribozymes based on the pH-dependent fluorescence of 8-azaadenosine (8azaA). We compared the microscopic pK(a) for ionization of 8azaA at position 38 with the apparent pK(a) for the self-cleavage reaction in a fully functional hairpin ribozyme with a unique 8azaA at position 38. Microscopic and apparent pK(a) values were virtually the same, evidence that A38 protonation accounts for the decrease in catalytic activity with decreasing pH. These results implicate the neutral unprotonated form of A38 in a transition state that involves formation of the 5'-oxygen-phosphorus bond.