The Revised Classification of Eukaryotes

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re‐introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under‐sampled areas and from environmental genomic information.     

Studies of H3K4me3 demethylation by KDM5B/Jarid1B/PLU1 reveals strong substrate recognition in vitro and identifies 2,4-pyridine-dicarboxylic acid as an in vitro and in cell inhibitor

Dynamic methylations and demethylations of histone lysine residues are important for gene regulation and are facilitated by histone methyltransferases and histone demethylases (HDMs). KDM5B/Jarid1B/PLU1 is an H3K4me3/me2-specific lysine demethylase belonging to the JmjC domain-containing family of histone demethylases (JHDMs). Several studies have linked KDM5B to breast, prostate and skin cancer, highlighting its potential as a drug target. However, most inhibitor studies have focused on other JHDMs, and inhibitors for KDM5B remain to be explored. Here, we report the expression, purification and characterization of the catalytic core of recombinant KDM5B (ccKDM5B, residues 1-769). We show that ccKDM5B, recombinantly expressed in insect cells, demethylates H3K4me3 and H3K4me2 in vitro. The kinetic characterization showed that ccKDM5B has an apparent Michaelis constant (K(m) (app) ) value of 0.5 μm for its trimethylated substrate H3(1-15)K4me3, a considerably increased apparent substrate affinity than reported for related HDMs. Despite the presence of a PHD domain, the catalytic activity was not affected by additional methylation at the H3K9 position, suggesting that in vitro chromatin cross-talk between H3K4 and H3K9 does not occur for ccKDM5B. Inhibition studies of ccKDM5B showed both in vitro and in cell inhibition of ccKDM5B by 2,4-pyridinedicarboxylic acid (2,4-PDCA) with a potency similar to that reported for the HDM KDM4C. Structure-guided sequence alignment indicated that the binding mode of 2,4-PDCA is conserved between KDM4A/C and KDM5B.     

Perioperative oxygen fraction – effect on surgical site infection and pulmonary complications after abdominal surgery: a randomized clinical trial. Rationale and design of the PROXI-Trial

Background

Infants born at extreme prematurity (below 28 weeks' gestation) are at high risk of developmental disability. A major risk factor for disability is having a low level of thyroid hormone which is recognised to be a frequent phenomenon in these infants. At present it is unclear whether low levels of thyroid hormone are a cause of disability, or a consequence of concurrent adversity.

Methods

We propose an explanatory multi-centre double blind randomised controlled trial of thyroid hormone supplementation in babies born below 28 weeks' gestation. All infants will receive either levothyroxine or placebo until 32 weeks' corrected gestational age. The primary outcome will be brain growth. This will be assessed by the width of the sub-arachnoid space measured using cranial ultrasound and head circumference at 36 weeks' corrected gestational. The secondary outcomes will be (a) thyroid hormone concentrations measured at increasing postnatal age, (b) status of the hypothalamic pituitary axis, (c) auxological data between birth and 36 weeks' corrected gestational age, (d) thyroid gland volume, (e) volumes of brain structures (measured by magnetic resonance imaging), (f) determination of the extent of myelination and white matter integrity (measured by diffusion weighted MRI) and brain vessel morphology (measured by magnetic resonance angiography) at expected date of delivery and (g) markers of morbidity including duration of mechanical ventilation and chronic lung disease. We will also examine how activity of the hypothalamic-pituitary-adrenal axis modulates the effects of thyroid supplementation. This will contribute to decisions about which confounding variables to assess in large-scale studies.

Trial registration

Current Controlled Trials ISRCTN89493983     

Development of nine microsatellite markers for Pomacentrus amboinensis

The relatively long pelagic larval duration of Pomacentrus amboinensis, a tropical fish, suggests the potential for long-distance dispersal; however, several nongenetic studies have found substantial self-recruitment at one location. To analyse patterns of connectivity of this species, primers for nine independent microsatellite loci were developed for P. amboinensis using a magnetic bead enrichment protocol. Twenty individuals from one location were analysed and observed heterozygosities ranged from 0.7 to 0.95. Eight of nine loci were in Hardy-Weinberg equilibrium and no evidence of linkage or null alleles were found.     

Copepods act as a switch between alternative trophic cascades in marine pelagic food webs

A recent meta‐analysis indicates that trophic cascades (indirect effects of predators on plants via herbivores) are weak in marine plankton in striking contrast to freshwater plankton ( Shurin et al. 2002 , Ecol. Lett., 5, 785–791). Here we show that in a marine plankton community consisting of jellyfish, calanoid copepods and algae, jellyfish predation consistently reduced copepods but produced two distinct, opposite responses of algal biomass. Calanoid copepods act as a switch between alternative trophic cascades along food chains of different length and with counteracting effects on algal biomass. Copepods reduced large algae but simultaneously promoted small algae by feeding on ciliates. The net effect of jellyfish on total algal biomass was positive when large algae were initially abundant in the phytoplankton, negative when small algae were dominant, but zero when experiments were analysed in combination. In contrast to marine systems, major pathways of energy flow in Daphnia‐dominated freshwater systems are of similar chain length. Thus, differences in the length of alternative, parallel food chains may explain the apparent discrepancy in trophic cascade strength between freshwater and marine planktonic systems.     

Composition and diversity of the spider fauna in the canopy of a montane forest in Tanzania

Spiders were sampled using insecticide knockdown in an African montane forest in the Uzungwa Mountains of Tanzania. The results are used to discuss the faunal composition at the site and in comparison to other sites, and the implications of the results for estimating spider diversity in Africa are discussed. A total of 5233 adults comprising 149 species were collected from 11 samples covering a total of 906 m² of projected area. Three species contributed 45% of the sample. Previous insecticide knockdown studies of tropical lowland forest canopies have shown a dominance of Theridiidae, Salticidae and Araneidae. In the present study Linyphiidae dominated in abundance and were the second most diverse in terms of species richness. Other abundant families were Oonopidae and Pholcidae, while Theridiidae, Salticidae and Araneidae were rich in species. This supports a previous study, which indicated that the importance of linyphiids increases with altitude. Species richness was predicted using a number of estimators, which produced relatively similar results. Using the abundance-based estimator, Chao 1, the predicted richness for the total area sampled is 183 ± 15 species. This indicates that at least 20% of the area's spider community remains unsampled. A high ratio of undescribed species (approximately 80%) and a relatively high species turnover compared to a site 20 km away within the same forest complex suggests that the number of spiders in Africa could well be much higher than the current, published estimate of 20000 species.     

The crystal structure of human Delta4-3-ketosteroid 5beta-reductase defines the functional role of the residues of the catalytic tetrad in the steroid double bond reduction mechanism

The 5beta-reductases (AKR1D1-3) are unique enzymes able to catalyze efficiently and in a stereospecific manner the 5beta-reduction of the C4-C5 double bond found into Delta4-3-ketosteroids, including steroid hormones and bile acids. Multiple-sequence alignments and mutagenic studies have already identified one of the residues presumably located at their active site, Glu 120, as the major molecular determinant for the unique activity displayed by 5beta-reductases. To define the exact role played by this glutamate in the catalytic activity of these enzymes, biochemical and structural studies on human 5beta-reductase (h5beta-red) have been undertaken. The crystal structure of h5beta-red in a ternary complex with NADP (+) and 5beta-dihydroprogesterone (5beta-DHP), the product of the 5beta-reduction of progesterone (Prog), revealed that Glu 120 does not interact directly with the other catalytic residues, as previously hypothesized, thus suggesting that this residue is not directly involved in catalysis but could instead be important for the proper positioning of the steroid substrate in the catalytic site. On the basis of our structural results, we thus propose a realistic scheme for the catalytic mechanism of the C4-C5 double bond reduction. We also propose that bile acid precursors such as 7alpha-hydroxy-4-cholesten-3-one and 7alpha,12alpha-dihydroxy-4-cholesten-3-one, when bound to the active site of h5beta-red, can establish supplementary contacts with Tyr 26 and Tyr 132, two residues delineating the steroid-binding cavity. These additional contacts very likely account for the higher activity of h5beta-red toward the bile acid intermediates versus steroid hormones. Finally, in light of the structural data now available, we attempt to interpret the likely consequences of mutations already identified in the gene encoding the h5beta-red enzyme which lead to a reduction of its enzymatic activity and which can progress to severe liver function failure.     

Molecular strategies in the evolution of mammalian dental patterning

The acquisition of masticatory capability by mammals allowed a better processing of food and a consequent increase in the efficiency of nutrients intake by the digestive system. The development of tooth classes and variations in tooth number can be considered intrinsic characteristics of mammalian dentition. These features allowed species to develop specialized dentitions, creating new adaptive zones. Comparative developmental data from knockout mutant mice and human tooth agenesis present new insights on the molecular strategies that permitted rapid phenotypic differentiation, adaptation and speciation of mammalian dentition.     

Peatland restoration: A brief assessment with special reference to Sphagnum bogs

Recent literature on peatland restorationindicates as a general goal repairing orrebuilding ecosystems by restoringecosystem structure, trophic organization,biodiversity, and functions to thosecharacteristic of the type of peatland towhich the damaged ecosystem belonged, or atleast to an earlier successional stage.Attainment requires provision of anappropriate hydrological regime,manipulating surface topography, improvingmicroclimate, adding appropriate diaspores,manipulating base status where necessary,fertilizing in some cases, excludinginappropriate invaders, adaptively managingthrough at least one flood/drought cycle toensure sustainability, and monitoring on ascale of decades. Several matchingconditions favoring or opposing restorationare suggested.In the restoration of peatlands, successeshave generally been those of short-termrepair. Periods of restoration have beenmuch too short to ensure progression to, oreven well toward, a fully functionalpeatland reasonably compatible with thepristine state of similar peatlandselsewhere, although with altered surfacepatterns.Long-term monitoring ofpeatland-restoration projects is essentialfor a better understanding of how to carryout such restoration successfully.Paleoecology is suggested as anunderutilized tool in peatlandrestoration.     

Wild Atlantic salmon Salmo salar L. strains have greater growth potential than a domesticated strain selected for fast growth

A study was undertaken to examine the responses of three Atlantic salmon Salmo salar strains to growth hormone (GH) treatment. A positive growth response to sustained-release GH implants was found in two wild strains (Namsen and Imsa) as well as one domesticated strain (AquaGen). The data revealed that the growth-selected AquaGen strain has further growth potential, however, a stronger growth response was observed in the wild strains which outgrew the domesticated strain after GH treatment. These observations suggest that some growth potential may have been lost during the selection for rapid growth in the AquaGen strain. In September, the parr were GH implanted and in December sampled for plasma GH and insulin-like growth factor I (IGF-I) levels, liver, muscle and gill GH receptor, IGF-I mRNA levels, gill Na⁺,K⁺-ATPase activity, muscle and liver lipid content and body silvering. Low temperature and seasonal growth cessation probably explains the relatively limited GH effects found. Body silvering in all strains was positively correlated to size. GH increased IGF-I plasma levels in the Namsen strain inspite of liver IGF-I mRNA levels being lower in GH-treated fish.