Ribosomal DNA: molecular evolution and phylogenetic inference.

Ribosomal DNA (rDNA) sequences have been aligned and compared in a number of living organisms, and this approach has provided a wealth of information about phylogenetic relationships. Studies of rDNA sequences have been used to infer phylogenetic history across a very broad spectrum, from studies among the basal lineages of life to relationships among closely related species and populations. The reasons for the systematic versatility of rDNA include the numerous rates of evolution among different regions of rDNA (both among and within genes), the presence of many copies of most rDNA sequences per genome, and the pattern of concerted evolution that occurs among repeated copies. These features facilitate the analysis of rDNA by direct RNA sequencing, DNA sequencing (either by cloning or amplification), and restriction enzyme methodologies. Constraints imposed by secondary structure of rRNA and concerted evolution need to be considered in phylogenetic analyses, but these constraints do not appear to impede seriously the usefulness of rDNA. An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence. In general, the small subunit nuclear sequences appear to be best for elucidating Precambrian divergences, the large subunit nuclear sequences for Paleozoic and Mesozoic divergences, and the organellar sequences of both subunits for Cenozoic divergences. Primer sequences were designed for use in amplifying the entire nuclear rDNA array in 15 sections by use of the polymerase chain reaction; these "universal" primers complement previously described primers for the mitochondrial rRNA genes. Pairs of primers can be selected in conjunction with the analysis of divergence of the rRNA genes to address systematic problems throughout the hierarchy of life.     

Phylogenetic relationships of the pipid frogs Xenopus and Silurana: an integration of ribosomal DNA and morphology

Relationships of the pipid frog genus Silurana (= Xenopus tropicalis group of some authors) are of particular interest to developmental and molecular biologists because of the purported ancestral (i.e., unduplicated) karyotype of S. tropicalis relative to the genus Xenopus. Although most previous studies have assumed that Silurana is the sister group of Xenopus, recent morphological work suggests that Silurana is more closely related both to the South American genus Pipa and to the African genera Hymenochirus and Pseudhymenochirus than it is to Xenopus. We examined 1,486 bp of relatively variable regions of the ribosomal DNA array (including portions of the 18S and 28S genes, as well as part of an internal transcribed spacer) in Hymenochirus, Silurana, and Xenopus, as well as the outgroup genus Spea, in order to test the alternative hypotheses of relationships for Silurana. Maximum-parsimony analysis using bootstrapping and an analysis using Lake's method of invariants both significantly support the sister-group relationship between Xenopus and Silurana rather than the relationship suggested by morphology. Analysis of the combined morphological/molecular data matrix also significantly supports the Xenopus-Silurana relationship. Although our results are not inconsistent with the recognition of the genus Silurana to accommodate the species formerly called X. tropicalis and X. epitropicalis, the proposed relationships do not require the recognition of this genus in order to render Xenopus monophyletic.     

Identification of viruses in the urine of renal transplant recipients by cytomorphology

This study was designed to reassess the cytomorphology of viral infections in urinary cells obtained from renal transplant patients and to examine the association, if any, between these cytologic changes and the transplant rejection. A total of 2,354 cytologic specimens obtained from 91 renal transplant recipients was evaluated. A combination of techniques, including cellulosic filters, immunofluorescence, hemagglutination inhibition and electron microscopy, was utilized. Cytologic observations were correlated with the patient's clinical history. Thirty-eight patients revealed cytologic evidence of viral infections (herpes simplex, cytomegalovirus and papovavirus). These viral infections had distinct cytomorphology. Cytomegalovirus infection may manifest as intracytoplasmic, orangeophilic inclusions, in addition to the classical intranuclear inclusion. In the majority of renal transplant patients there appeared to be no relationship between the viral infection and the renal transplant rejection episodes.     

Phosphorus Deposition in a Low-Phosphorus Landscape: Sources,Accuracy and Contribution to Declines in Surface Water P

Atmospheric deposition can be an important source of phosphorus (P) to watersheds in geologically low-P landscapes like the Precambrian Shield, in south-central Ontario. Recent observations in this region of declining total P (TP) concentrations in streams and lakes, as well as P limitation in vegetation, prompted this investigation into the potential contributing role of atmospheric deposition. Long-term (1980–2014) measurements of bulk TP deposition at four monitoring stations, as well as wet-only deposition at one of the sites (2012–2014) and pollen measurements in 2014, were used to assess the potential contribution of biogenic sources to TP deposition in the region. Ratios of phosphorus to potassium (P:K) in historical bulk deposition and variability in P deposition among the four sites indicated that continuously open, bulk deposition collectors are enriched in ‘local’ biogenic sources of P, particularly in the summer, fall and spring months. Furthermore, in 2014 pollen could account for as much as 30% of bulk TP deposition, and pine trees (Pinus strobus) were the most important source of pollen (>75% of collected pollen). In contrast, winter bulk deposition was the least affected by local, biogenic sources, and likely best reflects net P inputs to this region from long-range (that is, external to the watershed) sources. Catchment input–output budgets for P that use measured annual bulk deposition totals as inputs are generally strongly positive (indicating net retention/accumulation of P within watersheds), whereas annual budgets calculated using extrapolated winter deposition are in approximate balance. Balanced P budgets are more consistent with regional observations of declining surface water TP and P limitation in terrestrial vegetation. Importantly, there was no significant decline in winter TP deposition over the period of record (1980–2014), which suggests that changes in regional deposition are not responsible for declines in surface water TP. Although we recommend extrapolating winter bulk deposition measurements to approximate annual atmospheric TP input to terrestrial ecosystems in non-dusty, oligotrophic landscapes such as this, local sources of P, particularly pollen, are likely important seasonal sources of P nutrition to lakes.     

Formation and properties of some wood extractives

Chemical and other data concerning the location and site of formation of heartwood extractives are discussed. The biological conditions in the transition zone adjacent to the heartwood boundary are briefly described and some properties of extractives are given. The classes of polyphenolic compounds found in the wood of Eucalyptus species are listed together with the details of ellagic acid derivatives which are the most common class in this genus.     

Catchments catch all: long-term population history of a giant springtail from the southeast Australian highlands--a multigene approach

Phylogeography can reveal evolutionary processes driving natural genetic-geographical patterns in biota, providing an empirical framework for optimizing conservation strategies. The long-term population history of a rotting-log-adapted giant springtail (Collembola) from montane southeast Australia was inferred via joint analysis of mitochondrial and multiple nuclear gene genealogies. Contemporary populations were identified using multilocus nuclear genotype clustering. Very fine-scale sampling combined with nested clade and coalescent-based analyses of sequences from mitochondrial cytochrome oxidase I and three unlinked nuclear loci uncovered marked population structure, deep molecular divergences, and abrupt phylogeographical breaks over distances on the order of tens of kilometres or less. Despite adaptations that confer low mobility, rare long-distance gene flow was implicated: novel computer simulations that jointly modelled stochasticity inherent in coalescent processes and that of DNA sequence evolution showed that incomplete lineage sorting alone was unable to explain the observed spatial-genetic patterns. Impacts of Pleistocene or earlier climatic cycles were detected on multiple timescales, and at least three putative moist forest refuges were identified. Water catchment divisions predict phylogeographical patterning and present-day population structure with high precision, and may serve as an excellent surrogate for biodiversity indication in sedentary arthropods from topographically heterogeneous montane temperate forests.     

Wood polyphenols of Eucalyptus polyanthemos

Sixteen major components have been detected in woody tissues of Eucalyptus polyanthemos. The components identified include 2,3- and 4,6-(hexahydroxydiphenoyl)-glucose, a di-(hexahydroxydiphenoyl)-glucose known as pedunculagin, an ellagitannin which appears to be a cyclic di-(hexahydroxydiphenoyl)-diglucose, 3,4,3′-tri-O-methylellagic acid and its 4′-glucoside, 3,4,3′,4′-tetra-O- and 3,3′-di-O-methylellagic acids. A 3,3′-di-O-methylellagic acid glucoside and 2 gallotannins are possibly present in addition to the unidentified ellagitannin D-13. The distribution of these components in the woody tissues is discussed in relation to heartwood formation. The trimethylellagic acid glucoside was also present in the heartwood of other members of the red-box group of eucalypts.     

Fluorescent antibody study of diseased, end-stage human kidneys.

Forty cases of diseased kidneys at end-stage were studied by fluorescent antibody technique in search for viral etiology of glomerulonephritis and other renal diseases. Among these 40 cases, 12 (30%) were ascribed to immune complex disease because of detection of immunoglobulins and complement in glomeruli of the same kidney specimen. In 8 cases (20%) only complement was detected in glomeruli. In the remaining 50% neither complement nor immunoglobulin deposit was found in glomeruli. The etiologies of the latter cases remain unknown. Of 12 cases of kidney disease of immune complex origin, hepatitis virus type B surface antigen was detected in 2 cases. In these 2 cases the magnitude of immune complex deposits with complement was greater than that of other cases. Other than hepatitis B virus antigen, no other viruses including Coxsackieviruses, ECHO viruses, and HSV-1 could be detected by indirect fluorescent antibody techniques. The proportion of complement deposit to the deposition of complement with immune complex in the diseased kidneys at end-stage was calculated and statistically analyzed.     

Effects of Intensive Blood Pressure Lowering on Cardiovascular and Renal Outcomes: A Systematic Review and Meta-Analysis

Background

Guidelines recommend intensive blood pressure (BP) lowering in patients at high risk. While placebo-controlled trials have demonstrated 22% reductions in coronary heart disease (CHD) and stroke associated with a 10-mmHg difference in systolic BP, it is unclear if more intensive BP lowering strategies are associated with greater reductions in risk of CHD and stroke. We did a systematic review to assess the effects of intensive BP lowering on vascular, eye, and renal outcomes.

Methods and Findings

We systematically searched Medline, Embase, and the Cochrane Library for trials published between 1950 and July 2011. We included trials that randomly assigned individuals to different target BP levels.We identified 15 trials including a total of 37,348 participants. On average there was a 7.5/4.5-mmHg BP difference. Intensive BP lowering achieved relative risk (RR) reductions of 11% for major cardiovascular events (95% CI 1%–21%), 13% for myocardial infarction (0%–25%), 24% for stroke (8%–37%), and 11% for end stage kidney disease (3%–18%). Intensive BP lowering regimens also produced a 10% reduction in the risk of albuminuria (4%–16%), and a trend towards benefit for retinopathy (19%, 0%–34%, p = 0.051) in patients with diabetes. There was no clear effect on cardiovascular or noncardiovascular death. Intensive BP lowering was well tolerated; with serious adverse events uncommon and not significantly increased, except for hypotension (RR 4.16, 95% CI 2.25 to 7.70), which occurred infrequently (0.4% per 100 person-years).

Conclusions

Intensive BP lowering regimens provided greater vascular protection than standard regimens that was proportional to the achieved difference in systolic BP, but did not have any clear impact on the risk of death or serious adverse events. Further trials are required to more clearly define the risks and benefits of BP targets below those currently recommended, given the benefits suggested by the currently available data. Please see later in the article for the Editors'' Summary.