Phylogenetic relationships among ferns and gymnosperms; an overview

Ferns and gymnosperms are two of the most important traditionally recognized groups of vascular plants, but both are unnatural when viewed in terms of phylogenetic systematics. That is to say that neither consists of a monophyletic group. Nevertheless, both continue to be recognized as informal groupings of plants because representatives of each have similar grades of structural and reproductive features, and because many aspects of their natural relationships remain equivocal. Monophylesis for some traditionally recognized groups of pteridophytes and gymnosperms is fairly well established, but is unresolved or highly suspect for others. The latter include fernssensu lato, filicalean ferns, seed ferns and coniferophytes. Some recent studies also question whether conifers represent an unnatural assemblage. However, a taxon that includes the Marsileales and Salviniales recently has been interpreted to be monophyletic. Comparisons of results from phylogenetic analyses using either morphological or molecular characters provide a basis for assessing the strengths of systematic hypotheses and suggest fruitful avenues for future study. It is clear from all approaches that the greatest impediment to resolution of phylogenetic relationships in the inadequate rate at which new data are being developed.     

Auxin and Monocot Development

Monocots are known to respond differently to auxinic herbicides; hence, certain herbicides kill broadleaf (i.e., dicot) weeds while leaving lawns (i.e., monocot grasses) intact. In addition, the characters that distinguish monocots from dicots involve structures whose development is controlled by auxin. However, the molecular mechanisms controlling auxin biosynthesis, homeostasis, transport, and signal transduction appear, so far, to be conserved between monocots and dicots, although there are differences in gene copy number and expression leading to diversification in function. This article provides an update on the conservation and diversification of the roles of genes controlling auxin biosynthesis, transport, and signal transduction in root, shoot, and reproductive development in rice and maize.Auxinic herbicides have been used for decades to control dicot weeds in domestic lawns (Fig. 1A), commercial golf courses, and acres of corn, wheat, and barley, yet it is not understand how auxinic herbicides selectively kill dicots and spare monocots (Grossmann 2000; Kelley and Reichers 2007). Monocots, in particular grasses, must perceive or respond differently to exogenous synthetic auxin than dicots. It has been proposed that this selectivity is because of either limited translocation or rapid degradation of exogenous auxin (Gauvrit and Gaillardon 1991; Monaco et al. 2002), altered vascular anatomy (Monaco et al. 2002), or altered perception of auxin in monocots (Kelley and Reichers 2007). To explain these differences, there is a need to further understand the molecular basis of auxin metabolism, transport, and signaling in monocots.Open in a separate windowFigure 1.Differences between monocots and dicots. (A) A dicot weed in a lawn of grasses. Note the difference in morphology of the leaves. (B) Germinating dicot (bean) seedling. Dicots have two cotyledons (cot). Reticulate venation is apparent in the leaves. The stem below the cotyledons is called the hypocotyl (hyp). (C) Germinating monocot (maize) seedling. Monocots have a single cotyledon called the coleoptile (col) in grasses. Parallel venation is apparent in the leaves. The stem below the coleoptile is called the mesocotyl (mes).Auxin, as we have seen in previous articles, plays a major role in vegetative, reproductive, and root development in the model dicot, Arabidopsis. However, monocots have a very different anatomy from dicots (Raven et al. 2005). Many of the characters that distinguish monocots and dicots involve structures whose development is controlled by auxin: (1) As the name implies, monocots have single cotyledons, whereas dicots have two cotyledons (Fig. 1B,C). Auxin transport during embryogenesis may play a role in this difference as cotyledon number defects are often seen in auxin transport mutants (reviewed in Chandler 2008). (2) The vasculature in leaves of dicots is reticulate, whereas the vasculature in monocots is parallel (Fig. 1). Auxin functions in vascular development because many mutants defective in auxin transport, biosynthesis, or signaling have vasculature defects (Scarpella and Meijer 2004). (3) Dicots often produce a primary tap root that produces lateral roots, whereas, in monocots, especially grasses, shoot-borne adventitious roots are the most prominent component of the root system leading to the characteristic fibrous root system (Fig. 2). Auxin induces lateral-root formation in dicots and adventitious root formation in grasses (Hochholdinger and Zimmermann 2008).Open in a separate windowFigure 2.The root system in monocots. (A) Maize seedling showing the primary root (1yR), which has many lateral roots (LR). The seminal roots (SR) are a type of adventitious root produced during embryonic development. Crown roots (CR) are produced from stem tissue. (B) The base of a maize plant showing prop roots (PR), which are adventitious roots produced from basal nodes of the stem later in development.It is not yet clear if auxin controls the differences in morphology seen in dicots versus monocots. However, both conservation and diversification of mechanisms of auxin biosynthesis, homeostasis, transport, and signal transduction have been discovered so far. This article highlights the similarities and the differences in the role of auxin in monocots compared with dicots. First, the genes in each of the pathways are introduced (Part I, Table I) and then the function of these genes in development is discussed with examples from the monocot grasses, maize, and rice (Part II).     

Calmodulin: an overview

Calmodulin is a 16,700-dalton Ca2+-binding protein ubiquitous in the eukaryotes. It has no intrinsic enzymatic activity, but it regulates a wide spectrum of enzymes that control many basic cellular processes, ranging from the metabolism of cyclic nucleotides, Ca2+, and glycogen to contractile activity and stimulus-secretion coupling. Mounting evidence now indicates that calmodulin is the major intracellular Ca2+ receptor that remained elusive despite three decades of extensive work by many investigators.     

Hantaviruses: an overview

Hantaviruses are a newly emerging group of rodent-borne viruses that have significant zoonotic potential. Human infection by hantaviruses can result in profound morbidity and mortality, with death rates as high as 50%, and potentially long-term cardiovascular consequences. Hantaviruses are carried by peridomestic and wild rodents worldwide and have occasionally been linked to infections in laboratory rodents. Because these viruses have been associated with significant human disease, they have become the subject of intense scientific investigation. In this review the reader is introduced to the hantaviruses, including hantavirus diseases and their pathogenesis. A review of the biology, morphology, and molecular biology of the hantaviruses with a brief overview of the ecology and biology of hantavirus-rodent pairs is also included. The risks of occupational exposure to hantaviruses, diagnosis of hantavirus infections, and methods for handling potentially infected rodents and tissues are discussed as well.     

Hydroxyurea: an overview

Hydroxyurea has been a compound of scientific and clinical interest for over 100 years. A small molecule with many biological properties, hydroxyurea is used in a number of myeloproliferative, neoplastic, and non-hematological diseases. Recently, the agent has been investigated for use in the treatment of Human Immunodeficiency Virus (HIV) disease. Hydroxyurea is associated with dose related bone marrow suppression, crosses the placenta, and is excreted in breast milk. Toxicity is often managed through dose titration. Although adequate attention must be paid to the drug's use in pregnancy and during breast feeding, hydroxyurea's ease of administration, multiplicity of clinical effects, and low cost ensure the drug a place in therapy for years to come.     

Monocot Xylem Revisited: New Information,New Paradigms

Five sources of data force extensive revision of ideas about the nature and evolution of monocot xylem: scanning electron microscopy (SEM) studies of thick sections; availability of molecular phylogenies covering a relatively large number of families and genera; information on ecology and habitat; data concerning habit; and observations from xylem physiology. These five new sources of data, absent from the studies of Cheadle, plus added information from light microscopy, lead to a fresh understanding of how xylem has evolved in monocots. Tracheary elements hitherto recorded as vessel elements with scalariform end walls prove in a number of instances, to retain pit membranes (often porous or reticulate) in the end walls. There is not an inexorable progression from "primitive" to "specialized" xylem in monocots; apparent accelerations or reversions are also possible. The latter include such changes as the result of production of narrower vessel elements; or production of less metaxylem, which is probably heterochronic in nature (an extreme form of juvenilism). Tracheary elements intermediate between vessel elements and tracheids must be recognized for what they are, and not forced into mutually exclusive categories. Original data on tracheids and various types of vessel elements is related here to ecology and habit of groups such as Asteliaceae, Boryaceae, Cyclanthaceae, Orchidaceae, Pandanaceae, Taccaceae, Typhaceae, dracaenoid Asparagaceae, and Zingiberales. Data from palm xylem shows a nearly unique syndrome of features that can be explained with the aid of information from physiology and ecology. Vessellessness of stems and leaves characterizes a large number of monocot species; the physiological and ecological significance of these is highlighted. An understanding of how non-palm arborescent monocots combine an all-tracheid stem xylem with addition of bundles and vegetative modifications is attempted. The effect of the disjunction between xylems of adventitious roots and stems, providing a physiologically demonstrated valve ("rectifier") effect is discussed. "Ecological iteration" has occurred in some monocot lineages, so that early-departing branches in some cases may have more "specialized" xylem because of entry into xeric habitats, whereas nearby crown groups, which may have retained "primitive" xylem, probably represent long occupation of mesic habitats. Cheadle's use of xylem for "negations" of phyletic pathways can no longer be accepted. Symplesiomorphic mesomorphic xylem patterns do characterize many of the earlier-departing branches in the monocots as a whole, however. Cheadle's idea that monocots and non-monocot angiosperms attained vessels independently is improbable in the light of molecular trees for angiosperms. Vessels in roots seem an adaptation to major swings in moisture availability to adventitious roots as compared to taproots. The commonness of all-tracheid plans in stems and leaves in earlier-departing monocot clades is a feature that requires further clarification but is primarily related to the xylem disjunction that adventitious roots have. Secondary vessellessness or something very close to it can be hypothesized for Campynemataceae, Philesiaceae, Taccaceae, and some Orchidaceae. Eleven salient shifts in our conceptual views of monocot xylem are proposed and conclude the paper. Monocot xylem is not a collection of historical information, but a rigorously parsimonious system related to contemporary habits and habitats.     

Chikungunya: an overview

Chikungunya (CHIK), a mosquito borne debilitating disease, is caused by CHIK virus, an alphavirus belonging to the family Togaviridae. The sudden onset of very high fever along with rash, and severe arthralgia especially in the small joints of hands and toes are the characteristics of the disease. It was first reported from Tanzania in 1952–53 and spread subsequently to sub-Saharan Africa, South East Asia and Pacific causing large epidemics. The virus exists in three genotypes, the Asian, West African and East Central South African that are responsible for outbreaks in the respective areas. The first outbreak in Asia was in Bangkok in 1958 followed by other Asian countries. India experienced massive outbreaks of CHIK in the 1960s and early 70s mainly in cities. After a gap of 32 years an explosive outbreak of CHIK devastated the country affecting more than 1.4 million people in 13 states. The epidemic also witnessed many unusual clinico-pathological complications including CHIK associated deaths and mother to child transmission. High morbidity with severe arthralgia persisted for several months made the people mentally and physically weak. This review describes CHIK in general and highlights the various clinico-pathological aspects observed during the recent outbreak.     

Polyhydroxyalkanoates: an overview

Polyhydroxyalkanoates have gained major importance due to their structural diversity and close analogy to plastics. These are gaining more and more importance world over. Different sources (natural isolates, recombinant bacteria, plants) and other methods are being investigated to exert more control over the quality, quantity and economics of poly(3-hydroxybutyrate) (PHB) production. Their biodegradability makes them extremely desirable substitutes for synthetic plastics. The PHB biosynthetic genes phbA, phbB and phbC are clustered and organized in one phbCAB operon. The PHB pathway is highly divergent in the bacterial genera with regard to orientation and clustering of genes involved. Inspite of this the enzymes display a high degree of sequence conservation. But how similar are the mechanisms of regulation of these divergent operons is as yet unknown. Structural studies will further improve our understanding of the mechanism of action of these enzymes and aid us in improving and selecting better candidates for increased production. Metabolic engineering thereafter promises to bring a feasible solution for the production of "green plastic".     

Genetic ecotoxicology: an overview

The techniques currently available for detecting genotoxin exposure are briefly described and evaluated with regard to the goals of genetic ecotoxicology. The occurrence and significance of genotoxin-induced neoplasia in marine organisms is described. Although there are numerous examples of hotspots where tumour incidences in fish and shellfish have been correlated with raised concentrations of anthropogenic chemicals, causal mechanisms are seldom established. Insufficient information is available to gauge the seriousness of genotoxicity for marine organisms on regional or global scales. The possibility of using marine organisms as sentinels to provide early warning of potential threats to Man is examined. Recognition of the genotoxic disease syndrome in lower animals highlights the need to explore the relationships between DNA damage (adduct formation, gene mutations, etc.) and its phenotypic consequences. Within a given population, not all individuals are equally susceptible to pollutant toxicity (including genotoxicity). The potential for using similarities in phenotypic traits to recognise subsets of individuals within populations possessing similar genotypes is discussed. Changes in heterozygosity and the evolution of genetically resistant populations following exposure to pollution are evaluated in the context of genetic ecotoxicology. Risk assessment procedures are required which enable genotoxin exposure to be related to specific consequences at the community and ecosystem levels. This necessitates both a sound scientific understanding of the mechanisms involved and the development of pragmatic ecotoxicological tools that can be employed by environmental managers.     

Phagocyte migration: an overview

Phagocytes are the first line of host defense thanks to their capacity to infiltrate infected and wounded tissues, where they exert their bactericidal and tissue repair functions. However, tissue infiltration of phagocytes also stimulates the progression of pathologies such as cancer and chronic inflammatory diseases. It is therefore necessary to identify the molecular and cellular mechanisms that control this process to identify new therapeutic targets. Phagocytes leave the blood stream by crossing the vascular wall and infiltrate interstitial tissues, a three-dimensional environment. A state-of-the-art of the different steps of phagocyte tissue recruitment in vivo and of the different in vitro models is developed in this synthesis. We focus on recent data concerning the migration of phagocytes in three-dimensional environments. The use of two different migration modes, amoeboid and mesenchymal, by macrophages and the role of podosomes and proteases in the mesenchymal migration are discussed.     

Chitin whiskers: an overview

Chitin is the second most abundant semicrystalline polysaccharide. Like cellulose, the amorphous domains of chitin can also be removed under certain conditions such as acidolysis to give rise to crystallites in nanoscale, which are the so-called chitin nanocrystals or chitin whiskers (CHWs). CHW together with other organic nanoparticles such as cellulose whisker (CW) and starch nanocrystal show many advantages over traditional inorganic nanoparticles such as easy availability, nontoxicity, biodegradability, low density, and easy modification. They have been widely used as substitutes for inorganic nanoparticles in reinforcing polymer nanocomposites. The research and development of CHW related areas are much slower than those of CW. However, CHWs are still of strategic importance in the resource scarcity periods because of their abundant availability and special properties. During the past decade, increasing studies have been done on preparation of CHWs and their application in reinforcing polymer nanocomposites. Some other applications such as being used as feedstock to prepare chitosan nanoscaffolds have also been investigated. This Article is to review the recent development on CHW related studies.     

Agave biotechnology: an overview

Agaves are plants of importance both in Mexican culture and economy and in other Latin-American countries. Mexico is reported to be the place of Agave origin, where today, scientists are looking for different industrial applications without compromising its sustainability and preserving the environment. To make it possible, a deep knowledge of all aspects involved in production process, agro-ecological management and plant biochemistry and physiology is required. Agave biotechnology research has been focusing on bio-fuels, beverages, foods, fibers, saponins among others. In this review, we present the advances and challenges of Agave biotechnology.     

Enzyme technology: an overview

Enzymes are being used in numerous new applications in the food, feed, agriculture, paper, leather, and textiles industries, resulting in significant cost reductions. At the same time, rapid technological developments are now stimulating the chemistry and pharma industries to embrace enzyme technology, a trend strengthened by concerns regarding health, energy, raw materials, and the environment.