The evolution of birds: an overview of the avian tree of life

The author provides a general overview of the molecular data used to reconstruct the avian tree of life, summarizes some highlights of the ensuing controversies, and reveals those taxonomic relationships that remain largely unchanged by molecular data.     

The tree of life: introduction to an evolutionary debate

The ‘Tree of Life’ is intended to represent the pattern of evolutionary processes that result in bifurcating species lineages. Often justified in reference to Darwin’s discussions of trees, the Tree of Life has run up against numerous challenges especially in regard to prokaryote evolution. This special issue examines scientific, historical and philosophical aspects of debates about the Tree of Life, with the aim of turning these criticisms towards a reconstruction of prokaryote phylogeny and even some aspects of the standard evolutionary understanding of eukaryotes. These discussions have arisen out of a multidisciplinary collaboration of people with an interest in the Tree of Life, and we suggest that this sort of focused engagement enables a practical understanding of the relationships between biology, philosophy and history.     

Selenium and thyroid hormone axis in critical ill states: An overview of conflicting view points

In critical ill states the plasma selenium levels are low and inversely correlated with the severity and outcome of the disease. The plasma selenium levels indicate the amount of circulating selenoproteins and selenoenzymes. These are important for the maintenance of the redox system, modulating the immune system and also for thyroid hormone metabolism. Not only all three deiodinases (D1-3) are selenoenzymes, but within the thyroid gland there are several other selenoenzymes, which are important for the maintenance of normal thyroid function. In critical ill states also triodothyronine (T3) is low and reverse T3 elevated, and also TSH and thyroxin (T4) are low, correlating like low plasma selenium with the severity of the disease. Subsequently, several intervention trials had been performed to evaluate whether an adjuvant selenium supplementation might attenuate the course of the disease and improve outcome. The selenium supplementation improved outcome and even reduced mortality in some but not all prospective randomized trials. A few prospective randomized intervention trials with selenium supplementation had also been performed to evaluate the hypothesis, whether low selenium is the cause of low-T3-syndrome, however, with conflicting results and no clear evidence that low D1 activity is due to the selenium deficiency in critical illness.Because D1 catalyses the conversion of T4 to T3 and also the clearance of reverse T3, low D1 activity would sufficiently explain low plasma T3 and elevated reverse T3. It had been, however, clearly shown that cytokines are responsible for the inhibition of D1 activity, but D2 and D3 are even higher during acute inflammation in critically ill patients. One of the most important effects of selenium on the immune system seems to be the reduction of cytokine release and therefore an indirect connection between low selenium and low D1 activity has to be postulated and not a lower D1 activity due to lower availability of selenium for the D1 expression.     

Plant neurobiology: an integrated view of plant signaling

Plant neurobiology is a newly focused field of plant biology research that aims to understand how plants process the information they obtain from their environment to develop, prosper and reproduce optimally. The behavior plants exhibit is coordinated across the whole organism by some form of integrated signaling, communication and response system. This system includes long-distance electrical signals, vesicle-mediated transport of auxin in specialized vascular tissues, and production of chemicals known to be neuronal in animals. Here we review how plant neurobiology is being directed toward discovering the mechanisms of signaling in whole plants, as well as among plants and their neighbors.     

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.     

New insights into plant somatic embryogenesis: an epigenetic view

Somatic embryogenesis plays a significant role in plant regeneration and requires complex cellular, molecular, and biochemical processes for embryo initiation and development associated with plant epigenetics. Epigenetic regulation encompasses many sensitive events and plays a vital role in gene expression through DNA methylation, chromatin remodelling, and small RNAs. Recently, regulation of epigenetic mechanisms has been recognized as the most promising occurrences during somatic embryogenesis in plants. A few reports demonstrated that the level of DNA methylation can alter in embryogenic cells under in vitro environments. Changes or modification in DNA methylation patterns is linked with regulatory mechanisms of various candidate marker genes, involved in the initiation and development of somatic embryogenesis in plants. This review summarizes the current scenario of the role of epigenetic mechanisms as candidate markers during somatic embryogenesis. It also delivers a comprehensive and systematic analysis of more recent discoveries on expression of embryogenic-regulating genes during somatic embryogenesis, epigenetic variation. Biotechnological applications of epigenetics as well as new opportunities or future perspectives in the development of somatic embryogenesis studies are covered. Further research on such strategies may serve as exciting interaction models of epigenetic regulation in plant embryogenesis and designing novel approaches for plant productivity and crop improvement at molecular levels.     

Towards an integrated view of monocarpic plant senescence

After the flowering of an annual plant, the whole plant will senesce and die. For the process to go to completion, this monocarpic senescence must include three coordinated processes, which have not previously been considered as a total syndrome: (1) the arrest of growth and senescence of the shoot apical meristem; (2) senescence of the leaves; and (3) the suppression of axillary bud growth. Concurrently there is a shift in resource allocation from continued vegetative growth to reproductive growth, combined with a withdrawal of nutrients, especially nitrogen compounds, from the leaves and the transfer of these nutrients to the developing seeds. The start of the senescence process is caused by a shift, almost certainly in gene expression, very early in the reproductive phase. Continuation of the resource transfer and senescence of the vegetative plant involves hormonal regulation and continued changes in gene expression. Each of these processes is examined, especially with reference to the transfer of resources from vegetative to reproductive growth.     

The eukaryotic tree of life: endosymbiosis takes its TOL

Resolving the structure of the eukaryotic tree of life remains one of the most important and challenging tasks facing biologists. The notion of six eukaryotic 'supergroups' has recently gained some acceptance, and several papers in 2007 suggest that resolution of higher taxonomic levels is possible. However, in organisms that acquired photosynthesis via secondary (i.e. eukaryote-eukaryote) endosymbiosis, the host nuclear genome is a mosaic of genes derived from two (or more) nuclei, a fact that is often overlooked in studies attempting to reconstruct the deep evolutionary history of eukaryotes. Accurate identification of gene transfers and replacements involving eukaryotic donor and recipient genomes represents a potentially formidable challenge for the phylogenomics community as more protist genomes are sequenced and concatenated data sets grow.     

Bacopa monniera, a reputed nootropic plant: an overview

Bacopa monniera (BM), a traditional Ayurvedic medicine, used for centuries as a memory enhancing, anti-inflammatory, analgesic, antipyretic, sedative and antiepileptic agent. The plant, plant extract and isolated bacosides (the major active principles) have been extensively investigated in several laboratories for their neuropharmacological effects and a number of reports are available confirming their nootropic action. In addition, researchers have evaluated the anti-inflammatory, cardiotonic and other pharmacological effects of BM preparations/extracts. Therefore, in view of the important activities performed by this plant, investigation must be continued in the recently observed actions described in this paper. Moreover, other clinical studies have to be encouraged, also to evidence any side effects and possible interactions between this herbal medicine and synthetic drugs.     

The evolution of plant life span: facts and hypotheses

There are two different views on the evolution of life forms in Cormophyta: from woody plants to herbaceous ones or in opposite direction - from herbs to trees. In accordance with these views it is supposed that life span in plants changed in the course of evolution from many years (perennials) to few years (annuals, biennials), or went in reverse - from few years to many years. The author discusses the problems of senescence and longevity in Cormophyta in the context of various hypotheses of ageing (programmed death theory, mutation accumulation, antagonistic pleiotropy, disposable soma, genes of ageing, genes of longevity). Special attention is given to bio-morphological aspects of longevity and cases of non-ageing plants ("negative senescence", "potential immortality"). It is proposed to distinguish seven models of simple ontogenesis in Cormophyta that can exemplify the diversity of mechanisms of ageing and longevity. The evolution of life span in plants is considered as an indirect result of natural selection of other characteristics of organisms or as a consequence of fixation of modifications (episelectional evolution). It seems that short life span could emerge several times during evolution of one group of plants, thus favoring its adaptive radiation.