Duplication and divergence in humans and chimpanzees

It has become a truism that we humans are genetically about 99% identical to chimpanzees. The origins of this assertion are clear: among early studies of DNA sequences, nucleotide identity between humans and chimpanzees was found to average around 98.9%.(1) However, this figure is correct only with respect to regions of the genome that are shared between humans and chimpanzees. Often ignored are the many parts of their genomes that are not shared. Genomic rearrangements, including insertions, deletions, translocations and duplications, have long been recognized as potentially important sources of novel genomic material(2,3) and are known to account for major genomic differences between humans and chimpanzees.(4) Further, such changes have been implicated in a number of genetic disorders, such as DiGeorge, Angelman/Prader-Willi and Charcot-Marie-Tooth syndromes.(5)     

Innexin and pannexin channels and their signaling

Innexins are bifunctional membrane proteins in invertebrates, forming gap junctions as well as non-junctional membrane channels (innexons). Their vertebrate analogues, the pannexins, have not only lost the ability to form gap junctions but are also prevented from it by glycosylation. Pannexins appear to form only non-junctional membrane channels (pannexons). The membrane channels formed by pannexins and innexins are similar in their biophysical and pharmacological properties. Innexons and pannexons are permeable to ATP, are present in glial cells, and are involved in activation of microglia by calcium waves in glia. Directional movement and accumulation of microglia following nerve injury, which has been studied in the leech which has unusually large glial cells, involves at least 3 signals: ATP is the “go” signal, NO is the “where” signal and arachidonic acid is a “stop” signal.     

Hereditary stability and variation in evolution and development

Evolution and development are both lineage processes but are often conceptualized as occurring by different and mutually exclusive mechanisms. It is conventionally asserted that evolution occurs via the random generation of diversity and the subsequent survival of those that pass selection. On the other hand, development is too often presented as proceeding via the unfolding of a deterministic program encoded in the DNA sequence. In biology, universal generalizations are rare and dogmas are often wrong for particular cases. Deterministic mechanisms contribute some of the new DNA sequences that subsequently become substrates for natural selection. Conversely, stochastic and selective mechanisms are intrinsic to development, and also to maintenance of the immune, and possibly, nervous systems. Cancer appears to be another process that straddles distinctions between evolutionary and developmental modes of hereditary change and stabilization. DNA sequence changes are an essential feature of many cancers, but there are also aspects of the disease similar to developmental lineage gone awry. The literature suggests that the cellular changes that give rise to cancer occur by mechanisms commonly associated with both evolutionary and developmental lineage pathways.     

A link between helper and suppressor factors and the lymphokines migration inhibition factor and migration stimulation factor

The immunogenic and tolerogenic activities of solubilized T2 phage antigens in a primary in vitro response are augmented when these antigens are presented in cell-bound form. This enhancement is shown to be effected equally by an antigen adsorbed to autologous cells, to cells matched or mismatched with respect to major histocompatibility antigens, or to xenogeneic cells. Spleen or lymph node cells are more effective carriers of adsorbed T2 antigens than are thymocytes or erythrocytes. Among lymphocytes, T cells are more effective than B cells. Erythrocytes and B lymphocytes also are shown to bind significantly less solubilized T2 proteins than do T lymphocytes or thymocytes.     

Uses,abuses and management of lakes and rivers

Freshwater basins are vulnerable to human-induced change for a number of reasons. They lie at the bottoms of catchments and therefore are subject to the run-off of a large variety of dissolved and particulate substances; shallow basins provide fertile agricultural soils if drained; and public perception, particularly of wetland basins, is of inhospitable places, so that lobbies for drainage are more likely to be effective than those seeking to preserve the habitat. On the other hand, water is so important to human life that there is also strong concern about the fate of freshwater habitats. Freshwater systems are also often open systems capable of faster recovery from disturbance than their terrestrial counterparts.Three lake, river and wetland ecosystems, the Sudd in the Sudan, the Everglades and adjacent swamplands of southern Florida, USA, and the Norfolk Broadland in the UK are examined from the viewpoints of how they are or were used by their indigenous human populations, and the problems they may face or already face. This sites are used to suggest a general model of human impact and to establish approaches to the wise future use and conservation of these and other similar systems.     

Similar and divergent features in mammalian and yeast prions

Mammalian transmissible spongiform encephalopathies are likely due to the propagation of an abnormal form of a constitutive protein instead of traditional genetic material (nucleic acids). Such infectious proteins, which are termed prions, exist in yeast. They are at the origin of a number of phenotypes that are inherited in a non-Mendelian manner. These prions are very useful to dissect the molecular events at the origin of this structure-based inheritance. The properties of mammalian and yeast prions are presented and compared. This review highlights a number of similarities and differences.     

Localization and organization of microfilaments and related proteins in normal and virus-transformed cells

The localization and organization of actin-like microfilaments in normal, SV-40 and adenovirus transformed cells are determined by the coordinated use of light optical, electron optical and biochemical techniques. In adenovirus-type 5 transformed hamster embryo cells, microfilament meshworks appear to be the predominant organizational form of cellular actin, while in normal hamster cells, microfilament bundles are prevalent. Differences between 3T3 and SV-40 transformed 3T3 cells are less apparent and may be related to the packing and intracellular distribution of microfilament bundles. Attempts at relating these ultrastructural changes in transformed cells to the images obtained following reaction with fluorescein-labelled myosin fragments and indirect immunofluorescence with smooth muscle myosin antibody are discussed. In several instances the fluorescence microscope images do not correspond to the ultrastructural observations. The results are discussed in terms of the possible relationships between alterations in cytoplasmic contractile elements and the abnormal behavior of transformed cells.     

DNA polymerases β and λ and their roles in DNA replication and repair

DNA-dependent DNA polymerases are the main enzymes that catalyze DNA replication. Higher eukaryotic cells have 19 DNA polymerases with strikingly different properties [1]. Mitochondrial DNA polymerase γ of the A family and most of the nuclear enzymes of the B family are high-fidelity DNA polymerases that are involved not only in genomic DNA replication but also in DNA repair. Among the other 15 proteins, DNA polymerases belonging to the X and Y families have a special place. The majority of these enzymes are also involved in repair, including base excision repair and nonhomologous end joining. Some of them play a specific role in replication of damaged DNA templates. This process is referred to as translesion synthesis (TLS). DNA polymerases β and λ, which belong to the X structural family, are polyfunctional enzymes; their properties and functions are discussed.     

Antibodies to Lipids and Liposomes: Immunology and Safety

Naturally occurring antibodies to phospholipids and cholesterol are widespread; they occur commonly during the course of acute infections; they are not causally related to the anti-phospholipid syndrome; they have been associated with other clinical entities only as an epiphenomenon; and they have not been implicated as causing any clinical syndrome or disease. There are theoretical and experimental reasons to believe that normal cells and tissues are protected from binding of antibodies to bilayer lipids by steric hindrance due to adjacent larger molecules, such as large or charged adjacent glycolipids or proteins on the cell surface. There are also reasons to believe that certain natural antibodies to lipids can even serve useful normal functions. Antibodies to liposomal lipids induced by liposomes containing lipid A appear to have characteristics that are similar or identical to naturally occurring antibodies to lipids, and it is therefore believed that such antibodies would not cause adverse clinical effects. Numerous Phase I and II human clinical trials of experimental vaccines containing liposomes and lipid A have shown a high level of safety.     

Effects of husbandry and management systems on physiology and behaviour of farmed and laboratory rabbits

The major issues regarding the welfare of both farmed and laboratory rabbits are reviewed, according to husbandry and management systems. The main stressors that can affect welfare and homeostatic responses in rabbits are also reviewed. An overview of the most widespread housing systems for both farmed and laboratory rabbits is presented. The main problems related to housing and management are identified, in particular those related to individual and group housing, space requirements and group size, as well as human-animal interaction. The effects of psychological and physical stressors on physiology and behaviour are illustrated through examples in various rearing conditions. Psychological stressors include social stress and fear, while physical stressors include environmental variables such as housing system and climatic factors, i.e. heat. Welfare indicators are identified that can be monitored to determine the effects of individual and environmental variables on the animals' possible coping strategies. Physiological indicators include the neuro-endocrine and psycho-neuro-immuno-endocrine measurements, while behavioural indicators include the behavioural repertoire and responses to behavioural tests. Some possible ways to enhance welfare are indicated, such as enrichment of the environment and improved handling procedures.     

Antibodies to lipids and liposomes: immunology and safety

Naturally occurring antibodies to phospholipids and cholesterol are widespread; they occur commonly during the course of acute infections; they are not causally related to the anti-phospholipid syndrome; they have been associated with other clinical entities only as an epiphenomenon; and they have not been implicated as causing any clinical syndrome or disease. There are theoretical and experimental reasons to believe that normal cells and tissues are protected from binding of antibodies to bilayer lipids by steric hindrance due to adjacent larger molecules, such as large or charged adjacent glycolipids or proteins on the cell surface. There are also reasons to believe that certain natural antibodies to lipids can even serve useful normal functions. Antibodies to liposomal lipids induced by liposomes containing lipid A appear to have characteristics that are similar or identical to naturally occurring antibodies to lipids, and it is therefore believed that such antibodies would not cause adverse clinical effects. Numerous Phase I and II human clinical trials of experimental vaccines containing liposomes and lipid A have shown a high level of safety.     

Carotenoid actions and their relation to health and disease

Based on extensive epidemiological observation, fruits and vegetables that are a rich source of carotenoids are thought to provide health benefits by decreasing the risk of various diseases, particularly certain cancers and eye diseases. The carotenoids that have been most studied in this regard are β-carotene, lycopene, lutein and zeaxanthin. In part, the beneficial effects of carotenoids are thought to be due to their role as antioxidants. β-Carotene may have added benefits due its ability to be converted to vitamin A. Additionally, lutein and zeaxanthin may be protective in eye disease because they absorb damaging blue light that enters the eye. Food sources of these compounds include a variety of fruits and vegetables, although the primary sources of lycopene are tomato and tomato products. Additionally, egg yolk is a highly bioavailable source of lutein and zeaxanthin. These carotenoids are available in supplement form. However, intervention trials with large doses of β-carotene found an adverse effect on the incidence of lung cancer in smokers and workers exposed to asbestos. Until the efficacy and safety of taking supplements containing these nutrients can be determined, current dietary recommendations of diets high in fruits and vegetables are advised.     

Osteoclast and its roles in calcium metabolism and bone development and remodeling

Osteoclasts are multinucleated cells responsible for bone resorption and play important roles in normal skeletal development, in the maintenance of its integrity throughout life, and in calcium metabolism. During bone resorption, the cytoskeleton of osteoclasts undergoes extensive reorganization, with polarization and formation of ruffled borders to secrete acid and formation of sealing zone to prevent leakage. The differentiation and function of osteoclasts are in turn regulated by osteoblasts, stromal cells, and bone. They are also subjected to negative feedback regulation by extracellular and intracellular calcium concentrations.     

Long-bone circumference and weight in mammals, birds and dinosaurs

The mid-shaft circumferences of the humerus and femur are closely related to body weight in living terrestrial vertebrates. Because these elements are frequently preserved in subfossil and fossil vertebrate skeletal materials, the relationship can be used to estimate body weight in extinct vertebrates. When the allometric equations are applied to the mid-shaft circumferences of these elements in dinosaurs, the weights calculated for some giant sauropods ( Brachiosaurus ) are found to be lighter than previous estimates.     

Phylogeny and taxonomy of Aspicilia and Megasporaceae

Phylogenetic analyses based on nuLSU and mtSSU indicate that Megasporaceae is monophyletic. Aspicilia species were distributed among three main well supported groups and one group with low support that included the type species; a division of the family into five genera is proposed. The old names Circinaria and Sagedia are reintroduced for groups not including A. cinerea, the type of Aspicilia. The monotypic Megaspora is closely related to Circinaria, while Lobothallia is the sister group of the other Megasporaceae genera. Aspicilia recedens and A. farinosa are transferred to Lobothallia. Species of the 'Sphaerothallia group' are nested in Circinaria. Aspilidea is not a member of Megasporaceae but seems to be more closely related to Ochrolechiaceae. Aspilidea myrinii is neotypified, and lectotypes are designated for Aspicilia gibbosa, A. leprosescens and Lecanora gibbosula.     

Biology and Evolution of Beneficial and Detrimental Viruses of Animals, Plants, and Fungi

Virtually every type of organism may serve as a host for viruses. In some hosts, virus presence may be considered beneficial to humans; in other hosts, viruses are considered detrimental. Examples of viruses that are considered beneficial to humans include those that are used for biological control of organisms that themselves are considered detrimental to humans, such as plant pathogenic fungi. Viruses are extremely variable in terms of morphology, structure, and genome organization. However, viruses that attack hosts from different kingdoms may be related, deriving from the same phylogeny. This paper summarizes some of the properties of three related families of viruses that attack hosts in different kingdoms: the animal-infecting Picornaviridae, the plant-infecting Potyviridae, and the fungus-infecting Hypoviridae. Properties of these viruses that set them apart from each other and factors that may affect their evolution are discussed.     

Molecular Systematics and Evolution of Arabidopsis and Arabis

Abstract: We provide a phylogenetic analysis of the genera Arabidopsis and Arabis based on nuclear ribosomal DNA sequences. We show that traditional taxonomical concepts within tribe Ara-bideae, which includes these genera, are highly artificial. Arabis and Arabidopsis are paraphyletic and consist of several different independent lineages. The genus Capsella, originally placed in tribe Lepideae, is related to North American Arabis and the Arabidopsis thaliana lineage. Other genera, including East Asian Yin-shania, North American Halimolobus, cosmopolitan Barbarea and Cardamine, and European Aubrieta are positioned among different Arabis lineages. One Arabis species, Arabis pauciflora, is only distantly related to tribe Arabideae. Base chromosome number reduction from n = 8 to n = 5 to 7 occurred several times, suggesting that lower base chromosome numbers than n = 8 are derived in tribe Arabideae. Current knowledge on the evolution and systematics of the genera Arabis and Arabidopsis and relationships within the mustard family are summarized and discussed in the light of convergent evolution and transfer of knowledge from Arabidopsis thaliana as a molecular model plant to other species of the Cruciferae.     

Phytochemistry and the systematics and ecology of Loasaceae and Gronoviaceae (Loasales)

A screening for iridoid compounds of 78 of 315 species from all major groups in Gronoviaceae and Loasaceae has been carried out. The results were compared to the systematic concepts in the family and distribution and ecology of the taxa. Iridoids are present in at least some species of all genera screened. Some simple, monomeric compounds (e.g., loganin, sweroside) are found in all major groups of the two families and represent the basic iridoid inventory. Other compounds are restricted to certain taxonomic groups: nine-carbon iridoids (e.g., deutzioside) are restricted to Mentzelia (Loasaceae subfam. Mentzelioideae), hetero-oligomeric iridoids (e.g., tricoloroside methyl ester, acerifolioside) are restricted to two small groups in Loasa (Loasa ser. Macrospermae and ser. Floribundae, Loasaceae subfam. Loasoideae), and oleosides (e.g., 10-hydroxyoleoside dimethyl ester) are restricted to the large genus Caiophora sensu Weigend). The distribution of certain iridoid compounds thus confirms some of the generic limits. Iridoid phytochemistry does not correlate with systematic entities above the generic level nor does it in any way correlate with the morphological evolution of taxa. Conversely, the amount and complexity of iridoid compounds present in taxa correlate positively with the aridity of their habitat and the extent of mammalian herbivore pressure.     

Anatomical and molecular systematics of Asteliaceae and Hypoxidaceae

The astelioid group of asparagoid lilies (Lilianae - Asparagales) comprises Hypoxidaceae, Asteliaceae, Blandfordia and Lanaria. New information is presented on astelioid anatomy, together with a review of other systematic characters. These data are analysed in the context of recent evidence from rbc L nucleotide sequences that astelioids are related to orchids, and that astelioids and orchids (plus Alania and Borya ) form a clade that is sister to all other asparagoid taxa. Hypoxidaceae and Asteliaceae differ from each other in several respects, but there are certain characters linking the two families, notably branched hairs and mucilage canals, unusual characters in Lilianae. Family diagnoses are upheld, but the precise relationships of Blandfordia and Lanaria are still poorly supported within the astelioid clade.     

Distribution and Functions of Sterols and Sphingolipids

Sterols and sphingolipids are considered mainly eukaryotic lipids even though both are present in some prokaryotes, with sphingolipids being more widespread than sterols. Both sterols and sphingolipids differ in their structural features in vertebrates, plants, and fungi. Interestingly, some invertebrates cannot synthesize sterols de novo and seem to have a reduced dependence on sterols. Sphingolipids and sterols are found in the plasma membrane, but we do not have a clear picture of their precise intracellular localization. Advances in lipidomics and subcellular fractionation should help to improve this situation. Genetic approaches have provided insights into the diversity of sterol and sphingolipid functions in eukaryotes providing evidence that these two lipid classes function together. Intermediates in sphingolipid biosynthesis and degradation are involved in signaling pathways, whereas sterol structures are converted to hormones. Both lipids have been implicated in regulating membrane trafficking.Typical examples of eukaryotic lipids, sterols, and sphingolipids can both be found in membranes from simple unicellular fungi and protists to multicellular animals and plants. Their versatile use as structural elements but also as signaling molecules has probably played an important role during the evolution of this large and diverse group of organisms. There are also many eukaryotes that have lost the ability to synthesize sterols de novo including nematodes, insects, and marine invertebrates, which have to take up sterols with their diet. Sterol biosynthesis has also been reported in a number of bacteria. Sphingolipids are more widely spread among prokaryotes than sterols and also show a greater variety of structures among the different eukaryotes.In this short review we will first give an overview about the diversity of sterol and sphingolipid structures and their distribution in nature. Then we will discuss their subcellular distribution. A brief technical section will add some information on the separation and detection of these lipid molecules. Subsequently, we will summarize different genetic approaches to study the functions of sterols and sphingolipids, and finally, we will discuss the functional and possible physical interactions of the two lipid classes within the cell. Far from being comprehensive, we will focus only on a few interesting aspects and try to give new view points, which are less frequently discussed.