Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade

The SAR11 clade, here represented by Candidatus Pelagibacter ubique, is the most successful group of bacteria in the upper surface waters of the oceans. In contrast to previous studies that have associated the 1.3 Mb genome of Ca. Pelagibacter ubique with the less than 1.5 Mb genomes of the Rickettsiales, our phylogenetic analysis suggests that Ca. Pelagibacter ubique is most closely related to soil and aquatic Alphaproteobacteria with large genomes. This implies that the SAR11 clade and the Rickettsiales have undergone genome reduction independently. A gene flux analysis of 46 representative alphaproteobacterial genomes indicates the loss of more than 800 genes in each of Ca. Pelagibacter ubique and the Rickettsiales. Consistent with their different phylogenetic affiliations, the pattern of gene loss differs with a higher loss of genes for repair and recombination processes in Ca. Pelagibacter ubique as compared with a more extensive loss of genes for biosynthetic functions in the Rickettsiales. Some of the lost genes in Ca. Pelagibacter ubique, such as mutLS, recFN, and ruvABC, are conserved in all other alphaproteobacterial genomes including the small genomes of the Rickettsiales. The mismatch repair genes mutLS are absent from all currently sequenced SAR11 genomes and also underrepresented in the global ocean metagenome data set. We hypothesize that the unique loss of genes involved in repair and recombination processes in Ca. Pelagibacter ubique has been driven by selection and that this helps explain many of the characteristics of the SAR11 population, such as the streamlined genomes, the long branch lengths, the high recombination frequencies, and the extensive sequence divergence within the population.     

The mechanism of γ-Secretase dysfunction in familial Alzheimer disease

The mechanisms by which mutations in the presenilins (PSEN) or the amyloid precursor protein (APP) genes cause familial Alzheimer disease (FAD) are controversial. FAD mutations increase the release of amyloid β (Aβ)42 relative to Aβ40 by an unknown, possibly gain‐of‐toxic‐function, mechanism. However, many PSEN mutations paradoxically impair γ‐secretase and ‘loss‐of‐function’ mechanisms have also been postulated. Here, we use kinetic studies to demonstrate that FAD mutations affect Aβ generation via three different mechanisms, resulting in qualitative changes in the Aβ profiles, which are not limited to Aβ42. Loss of ε‐cleavage function is not generally observed among FAD mutants. On the other hand, γ‐secretase inhibitors used in the clinic appear to block the initial ε‐cleavage step, but unexpectedly affect more selectively Notch than APP processing, while modulators act as activators of the carboxypeptidase‐like (γ) activity. Overall, we provide a coherent explanation for the effect of different FAD mutations, demonstrating the importance of qualitative rather than quantitative changes in the Aβ products, and suggest fundamental improvements for current drug development efforts.     

Peripheral "chicken" obestatin administration does not affect feed intake and gut muscle contractility of meat-type and layer-type chicks (Gallus gallus domesticus)

Obestatin has recently been discovered in the rat stomach. As for ghrelin, the 23-amino acid obestatin is also derived from post-translational processing of the prepro-ghrelin gene but seems to have opposite effects on feed intake. In avian species, ghrelin is mainly present in the proventriculus and decreases feed intake, as opposed to its orexigenic properties in mammals. An obestatin-like sequence was also found in the avian ghrelin precursor protein but the potential involvement of this peptide in appetite regulation of chickens is unclear. We therefore investigated the effects of a single peripheral administration of this predicted "chicken" obestatin peptide on voluntary feed intake of 7- to 9-day-old meat-type and layer-type chicks. "Chicken" obestatin was injected intraperitoneally or intravenously at a dose of 1 nmol or 10 nmol/100 g body weight and feed intake was measured up to 4 h post injection. None of these treatments did reveal any effect of the putative "chicken" obestatin on appetite of either meat-type of layer-type chicks. Furthermore, "chicken" obestatin also failed to affect the in vitro contractility of muscle strips from crop and proventriculus. In conclusion, in the given experimental settings, the putative "chicken" obestatin has indistinctive physiological effects on feed intake and in vitro muscle contractility of gut segments, and hence its functional properties in ingestive behavior of avian species remain obscure.     

Ontogenetic changes in leaf traits of tropical rainforest trees differing in juvenile light requirement

Relationships between leaf traits and the gap dependence for regeneration, and ontogenetic changes therein, were investigated in juvenile and adult tropical rainforest tree species. The juveniles of the 17 species included in the study were grown in high light, similar to the exposed crowns of the adult trees. The traits were structural, biomechanical, chemical and photosynthetic. With increasing species gap dependence, leaf mass per area (LMA) decreased only slightly in juveniles and remained constant in adults, whereas punch strength together with tissue density decreased, and photosynthetic capacity and chlorophyll increased. Contrary to what has been mostly found in evergreen tropical rainforest, the trade-off between investment in longevity and in productivity was evident at an essentially constant LMA. Of the traits pertaining to the chloroplast level, photosynthetic capacity per unit chlorophyll increased with gap dependence, but the chlorophyll a/b ratio showed no relationship. Adults had a twofold higher LMA, but leaf strength was on average only about 50% larger. Leaf tissue density, and chlorophyll and leaf N per area were also higher, whereas chlorophyll and leaf N per unit dry mass were lower. Ranking of the species, relationships between traits and with the gap dependence of the species were similar for juveniles and adults. However, the magnitudes of most ontogenetic changes were not clearly related to a species’ gap dependence. The adaptive value of the leaf traits for juveniles and adults is discussed.     

The influence of acclimation, endosymbionts and diet on the supercooling capacity of the predatory bug Macrolophus pygmaeus

The generalist predator Macrolophus pygmaeus Rambur (Hemiptera: Miridae) is a key biological control agent in European greenhouses. The influence of acclimation, infection with endosymbiotic bacteria and diet on the cold tolerance of the Mediterranean biocontrol population was assessed by determining the supercooling point, i.e. the temperature at which the insect’s body fluids freeze. This parameter provides a first indication of an insect’s establishment potential in a new region and of its possible geographical range. Allowing the predatory bugs to adapt to lower temperatures resulted in an increase in supercooling ability. Macrolophus pygmaeus bugs exposed to antibiotics in their artificial diet and hence cured from their infection with the endosymbiotic bacteria Wolbachia pipientis, Rickettsia bellii and R. limoniae were more tolerant to freezing than infected bugs. The diet of the predators also affected the freezing temperature of the body fluids. Predators fed an artificial diet based on egg yolk were less resistant to freezing than those fed Ephestia kuehniella Zeller (Lepidoptera: Pyralidae) eggs. These findings illustrate that several factors may affect the cold hardiness of a biocontrol agent and may thus complicate the evaluation of its establishment potential in the framework of an environmental risk assessment.     

Pronounced seasonal dynamics of freshwater chitinase genes and chitin processing

Seasonal variation in activity of enzymes involved in polymer degradation, including chitinases, has been observed previously in freshwater environments. However, it is not known whether the seasonal dynamics are due to shifts in the activity of bacteria already present, or shifts in community structure towards emergence or disappearance of chitinolytic organisms. We traced seasonal shifts in the chitinase gene assemblage in a temperate lake and linked these communities to variation in chitinase activity. Chitinase genes from 20 samples collected over a full yearly cycle were characterized by pyrosequencing. Pronounced temporal shifts in composition of the chitinase gene pool (beta diversity) occurred along with distinct shifts in richness (alpha diversity) as well as chitin processing. Changes in the chitinase gene pool correlated mainly with temperature, abundance of crustacean zooplankton and phytoplankton blooms. Also changes in the physical structure of the lake, e.g. stratification and mixing were associated with changes in the chitinolytic community, while differences were minor between surface and suboxic hypolimnetic water. The lake characteristics influencing the chitinolytic community are all linked to changes in organic particles and we suggest that seasonal changes in particle quality and availability foster microbial communities adapted to efficiently degrade them.     

Progress report on the first sub-Saharan trial of newer versus older antihypertensive drugs in native black patients

ABSTRACT: BACKGROUND: The epidemic surge in hypertension in sub-Saharan Africa is not matched by clinical trials of antihypertensive agents in Black patients recruited in this area of the world. We mounted the Newer versus Older Antihypertensive agents in African Hypertensive patients (NOAAH) trial to compare, in native African patients, a single-pill combination of newer drugs, not involving a diuretic, with a combination of older drugs including a diuretic. METHODS: Patients aged 30 to 69 years with uncomplicated hypertension (140 to 179/90 to 109 mmHg) and [less than or equal to]2 associated risk factors are eligible. After a four week run-in period off treatment, 180 patients have to be randomized to once daily bisoprolol/hydrochlorothiazide 5/6.25 mg (R) or amlodipine/valsartan 5/160 mg (E). To attain blood pressure <140/<90 mmHg during six months, the doses of bisoprolol and amlodipine should be increased to 10 mg/day with the possible addition of up to 2 g/day alpha-methyldopa. RESULTS: At the time of writing of this progress report, of 206 patients enrolled in the run-in period, 140 had been randomized. At randomization, the R and E groups were similar (P [greater than or equal to]0.11) with respect to mean age (50.7 years), body mass index (28.2 kg/m2), blood pressure (153.9/91.5 mmHg) and the proportions of women (53.6%) and treatment naive patients (72.7%). After randomization, in the R and E groups combined, blood pressure dropped by 18.2/10.1 mmHg, 19.4/11.2 mmHg, 22.4/12.2 mmHg and 25.8/15.2 mmHg at weeks two (n = 122), four (n = 109), eight (n = 57), and 12 (n = 49), respectively. The control rate was >65% already at two weeks. At 12 weeks, 12 patients (24.5%) had progressed to the higher dose of R or E and/or had alpha-methyldopa added. Cohort analyses of 49 patients up to 12 weeks were confirmatory. Only two patients dropped out of the study. CONCLUSIONS: NOAAH (NCT01030458) demonstrated that blood pressure control can be achieved fast in Black patients born and living in Africa with a simple regimen consisting of a single-pill combination of two antihypertensive agents. NOAAH proves that randomized clinical trials of cardiovascular drugs in the indigenous populations of sub-Saharan Africa are feasible.     

The Role of the Suprachiasmatic Nucleus in Cardiac Autonomic Control during Sleep

Background

The suprachiasmatic nucleus (SCN) may play an important role in central autonomic control, since its projections connect to (para)sympathetic relay stations in the brainstem and spinal cord. The cardiac autonomic modifications during nighttime may therefore not only result from direct effects of the sleep-related changes in the central autonomic network, but also from endogenous circadian factors as directed by the SCN. To explore the influence of the SCN on autonomic fluctuations during nighttime, we studied heart rate and its variability (HRV) in a clinical model of SCN damage.

Methods

Fifteen patients in follow-up after surgical treatment for nonfunctioning pituitary macroadenoma (NFMA) compressing the optic chiasm (8 females, 26–65 years old) and fifteen age-matched healthy controls (5 females, 30–63 years) underwent overnight ambulatory polysomnography. Eleven patients had hypopituitarism and received adequate replacement therapy. HRV was calculated for each 30-second epoch and corrected for sleep stage, arousals, and gender using mixed effect regression models.

Results

Compared to controls, patients spent more time awake after sleep onset and in NREM1-sleep, and less in REM-sleep. Heart rate, low (LF) and high frequency (HF) power components and the LF/HF ratio across sleep stages were not significantly different between groups.

Conclusions

These findings suggest that the SCN does not play a dominant role in cardiac autonomic control during sleep.     

Direct Observation of α-Synuclein Amyloid Aggregates in Endocytic Vesicles of Neuroblastoma Cells

Aggregation of α-synuclein has been linked to both familial and sporadic Parkinson’s disease. Recent studies suggest that α-synuclein aggregates may spread from cell to cell and raise questions about the propagation of neurodegeneration. While continuous progress has been made characterizing α-synuclein aggregates in vitro, there is a lack of information regarding the structure of these species inside the cells. Here, we use confocal fluorescence microscopy in combination with direct stochastic optical reconstruction microscopy, dSTORM, to investigate α-synuclein uptake when added exogenously to SH-SY5Y neuroblastoma cells, and to probe in situ morphological features of α-synuclein aggregates with near nanometer resolution. We demonstrate that using dSTORM, it is possible to follow noninvasively the uptake of extracellularly added α-synuclein aggregates by the cells. Once the aggregates are internalized, they move through the endosomal pathway and accumulate in lysosomes to be degraded. Our dSTORM data show that α-synuclein aggregates remain assembled after internalization and they are shortened as they move through the endosomal pathway. No further aggregation was observed inside the lysosomes as speculated in the literature, nor in the cytoplasm of the cells. Our study thus highlights the super-resolution capability of dSTORM to follow directly the endocytotic uptake of extracellularly added amyloid aggregates and to probe the morphology of in situ protein aggregates even when they accumulate in small vesicular compartments.     

Microbial diversity and dynamics in multi- and single-compartment anaerobic bioreactors processing sulfate-rich waste streams

We investigated bacterial and archaeal community structures and population dynamics in two anaerobic bioreactors processing a carbohydrate- and sulfate-rich synthetic wastewater. A five-compartment anaerobic migrating blanket reactor (AMBR) was designed to promote biomass and substrate staging, which partially separates the processes of methanogenesis and sulfidogenesis in the middle and outer compartment(s) respectively. The second reactor was a conventional, single-compartment upflow anaerobic sludge blanket (UASB) reactor. Both reactors, which were seeded with the same inoculum, performed well when the influent chemical oxygen demand (COD)/SO(4) (2-) mass ratio was 24.4. The AMBR performed worse than the UASB reactor when the influent COD/SO(4) (2-) mass ratio was decreased to 5.0 by raising the sulfate load. Terminal restriction fragment length polymorphism analyses of bacterial 16S rRNA genes showed that the increase in sulfate load had a greater impact on bacterial diversity and community structure for the five AMBR compartments than for the UASB reactor. Moreover, bacterial community profiles across AMBR compartments became more similar through time, indicating a converging, rather than a staged community. While similar populations were abundant in both reactors at the beginning of the experiment, fermenting bacteria (clostridia, streptococci), and sulfate-reducing bacteria became more abundant in the AMBR, after shifting to a higher sulfate load, while a novel Thermotogales-like population eventually became predominant in the UASB reactor. A similar shift in the community structure of the hydrogenotrophic methanogens in the AMBR occurred: representatives of the Methanobacteriaceae out-competed the Methanospirillaceae after increasing the sulfate load in the AMBR, while the archaeal community structure was maintained in the UASB.