Cloning: questions answered and unsolved

Cloning by the transfer of adult somatic cell nuclei to oocytes has produced viable offspring in a variety of mammalian species. The technology is still in its initial stages of development. Studies to date have answered several basic questions related to such issues as genome potency, life expectancy of clones, mitochondrial fates, and feasibility of inter-species nuclear transfer. They have also raised new questions related to the control of nuclear reprogramming and function. These questions are reviewed here.     

Comparison of genomic DNA sequences: solved and unsolved problems

MOTIVATION: The DNA sequences of entire genomes are being determined at a rapid rate. Whereas initial genome sequencing efforts were for organisms chosen to be widely spaced in the tree of life, there is a growing emphasis on projects to sequence a species that is sufficiently similar to an already-sequenced species to allow direct comparison of those two DNA sequences. This and other changes in genome sequencing strategies have created a strong need for new methods to compare genomic sequences. RESULTS: We sketch the current state of software for comparing genomic DNA sequences and outline research directions that we believe are likely to result in important advances in practice.     

The paraflagellar rod of kinetoplastid parasites: From structure to components and function

The role of the eukaryotic flagellum in cell motility is well established but its importance in many other aspects of cell biology, from cell signalling to developmental regulation, is becoming increasingly apparent. In addition to this diversity of function the core structure of the flagellum, which has been inherited from the earliest ancestor of all eukaryotes, is embellished with a range of extra-axonemal structures in many organisms. One of the best studied of these structures is the paraflagellar rod of kinetoplastid protozoa in which the morphological characteristics have been well defined and some of the major protein constituents have been identified. Here we discuss recent advances in the identification of further molecular components of the paraflagellar rod, how these impact on our understanding of its function and regulation and the implications for therapeutic intervention in a number of devastating human pathologies.     

Flagellar morphogenesis: protein targeting and assembly in the paraflagellar rod of trypanosomes

The paraflagellar rod (PFR) of the African trypanosome Trypanosoma brucei represents an excellent model to study flagellum assembly. The PFR is an intraflagellar structure present alongside the axoneme and is composed of two major proteins, PFRA and PFRC. By inducible expression of a functional epitope-tagged PFRA protein, we have been able to monitor PFR assembly in vivo. As T. brucei cells progress through their cell cycle, they possess both an old and a new flagellum. The induction of expression of tagged PFRA in trypanosomes growing a new flagellum provided an excellent marker of newly synthesized subunits. This procedure showed two different sites of addition: a major, polar site at the distal tip of the flagellum and a minor, nonpolar site along the length of the partially assembled PFR. Moreover, we have observed turnover of epitope-tagged PFRA in old flagella that takes place throughout the length of the PFR structure. Expression of truncated PFRA mutant proteins identified a sequence necessary for flagellum localization by import or binding. This sequence was not sufficient to confer full flagellum localization to a green fluorescent protein reporter. A second sequence, necessary for the addition of PFRA protein to the distal tip, was also identified. In the absence of this sequence, the mutant PFRA proteins were localized both in the cytosol and in the flagellum where they could still be added along the length of the PFR. This seven-amino-acid sequence is conserved in all PFRA and PFRC proteins and shows homology to a sequence in the flagellar dynein heavy chain of Chlamydomonas reinhardtii.     

Molecular aspects of atherogenesis: new insights and unsolved questions

Summary The development of atherosclerotic disease results from the interaction between environment and genetic make up. A key factor in atherogenesis is the oxidative modification of lipids, which is involved in the recruitment of mononuclear leukocytes to the arterial intima – a process regulated by several groups of adhesion molecules and cytokines. Activated leukocytes, as well as endothelial mitochondria, can produce reactive oxygen species (ROS) that are associated with endothelial dysfunction, a cause of reduced nitric oxide (NO) bioactivity and further ROS production. Peroxisome proliferator-activated receptors (PPAR) and liver X receptors (LXR) are nuclear receptors significantly involved in the control of lipid metabolism, inflammation and insulin sensitivity. Also, an emerging role has been suggested for G protein coupled receptors and for the small Ras and Rho GTPases in the regulation of the expression of endothelial NO synthase (eNOS) and of tissue factor, which are involved in thrombus formation and modulation of vascular tone. Further, the interactions among eNOS, cholesterol, oxidated LDL and caveola membranes are probably involved in some molecular changes observed in vascular diseases. Despite the relevance of oxidative processes in atherogenesis, anti-oxidants have failed to significantly improve atherosclerosis (ATS) prevention, while statins have proved to be the most successful drugs.     

Mammalian O-mannosylation: unsolved questions of structure/function

Post-translational modification of polypeptides with glycans increases the diversity of the structures of proteins and imparts increased functional diversity. Here, we review the current literature on a relatively new O-glycosylation pathway, the mammalian O-mannosylation pathway. The importance of O-mannosylation is illustrated by the fact that O-mannose glycan structures play roles in a variety of processes including viral entry into cells, metastasis, cell adhesion, and neuronal development. Furthermore, mutations in the enzymes of this pathway are causal for a variety of congenital muscular dystrophies. Here we highlight the protein substrates, glycan structures, and enzymes involved in O-mannosylation as well as our gaps in understanding structure/function relationships in this biosynthetic pathway.     

Morphological relationship between paraflagellar swelling and paraxial rod in Euglena Gracilis

euglena is a mobile photosynthetic and photosensitive cell which dwells in fresh water. Euglena has an important evolutionary role, therefore its morphology has been and still is a subject of interest. The structures in Euglena which are involved in photoreception and signal transduction and transmission have been well studied. In this paper morphological and ultrastructural evidence of a single stable structure formed by the photoreceptor (paraflagellar swelling) and the other specialized flagellar structures of Euglena gracilis (paraxial rod) is provided using conventional and non-conventional SEM and TEM, on detergent treated cells, and on isolated flagella retaining their photoreceptor.     

Sex, outcrossing and mating types: unsolved questions in fungi and beyond

Variability in the way organisms reproduce raises numerous, and still unsolved, questions in evolutionary biology. In this study, we emphasize that fungi deserve a much greater emphasis in efforts to address these questions because of their multiple advantages as model eukaryotes. A tremendous diversity of reproductive modes and mating systems can be found in fungi, with many evolutionary transitions among closely related species. In addition, fungi show some peculiarities in their mating systems that have received little attention so far, despite the potential for providing insights into important evolutionary questions. In particular, selfing can occur at the haploid stage in addition to the diploid stage in many fungi, which is generally not possible in animals and plants but has a dramatic influence upon the structure of genetic systems. Fungi also present several advantages that make them tractable models for studies in experimental evolution. Here, we briefly review the unsolved questions and extant hypotheses about the evolution and maintenance of asexual vs. sexual reproduction and of selfing vs. outcrossing, focusing on fungal life cycles. We then propose how fungi can be used to address these long-standing questions and advance our understanding of sexual reproduction and mating systems across all eukaryotes.     

Homologies between paraflagellar rod proteins from trypanosomes and euglenoids revealed by a monoclonal antibody

A Nonidet P 40 insoluble fraction was isolated from Trypanosoma brucei and was used to raise a monoclonal antibody (5E9). The antigen was localized by indirect immunofluorescence in the flagellum of T. brucei and of two species of euglenoids, Euglena gracilis and Distigma proteus. In immunoblot analysis, 5E9 appeared to bind to paraflagellar rod proteins PFR1 and PFR2 of T. brucei (72000 and 75000 mol. wt.) and of E. gracilis (67000 and 76000 mol. wt.). The presence of a common epitope in paraflagellar rod proteins from species of trypanosomes and euglenoids shows that despite distinct structures of the rods some identical domain exists in the proteins that could be involved in their supramolecular assembly into a similar organelle. The antigenic determinant defined by 5E9 was also shown to be present in a 87000 molecular weight polypeptide located in the proximal part of the flagellum of Crithidia oncopelti in which a paraflagellar rod is not detectable at the ultrastructural level.     

The structure-function correlates of mammalian rod and cone photoreceptor mitochondria: observations and unanswered questions

Our previous work suggests that cone photoreceptor inner segment (CIS) mitochondria demand and produce more ATP than rods. The CISs utilize two complimentary strategies to increase ATP production: increase the absolute number of mitochondria and their cristae surface membrane area. In this treatise, we ask: How are crista junctions formed and regulated? Once formed, are there physical mechanisms that constrain their diameter? How are the constrictions in cristae regulated and is this key for cytochrome c release during apoptosis? What are their differences in rod and cone susceptibility to apoptotic cell death during calcium overload and oxidative stress?     

Three-dimensional structure of the Trypanosome flagellum suggests that the paraflagellar rod functions as a biomechanical spring

Flagellum motility is critical for normal human development and for transmission of pathogenic protozoa that cause tremendous human suffering worldwide. Biophysical principles underlying motility of eukaryotic flagella are conserved from protists to vertebrates. However, individual cells exhibit diverse waveforms that depend on cell-specific elaborations on basic flagellum architecture. Trypanosoma brucei is a uniflagellated protozoan parasite that causes African sleeping sickness. The T. brucei flagellum is comprised of a 9+2 axoneme and an extra-axonemal paraflagellar rod (PFR), but the three-dimensional (3D) arrangement of the underlying structural units is poorly defined. Here, we use dual-axis electron tomography to determine the 3D architecture of the T. brucei flagellum. We define the T. brucei axonemal repeating unit. We observe direct connections between the PFR and axonemal dyneins, suggesting a mechanism by which mechanochemical signals may be transmitted from the PFR to axonemal dyneins. We find that the PFR itself is comprised of overlapping laths organized into distinct zones that are connected through twisting elements at the zonal interfaces. The overall structure has an underlying 57 nm repeating unit. Biomechanical properties inferred from PFR structure lead us to propose that the PFR functions as a biomechanical spring that may store and transmit energy derived from axonemal beating. These findings provide insight into the structural foundations that underlie the distinctive flagellar waveform that is a hallmark of T. brucei cell motility.     

The morphology of ovine Trypanosoma melophagium (zoomastigophorea: kinetoplastida)

Morphologic and biometric data on bloodstream stages of Trypanosoma melophagium are presented. An increasing parasitemia with 111 trypomastigote stages of T. melophagium were found in Giemsa-stained thin blood smears taken from a splenectomized, cortisone-treated sheep recently infested with Melophagus ovinus infected with T. melophagium . The arithmetic mean and standard deviation in micron of the distances between posterior end and kinetoplast were 14.7 and 2.9, from the kinetoplastic to the center of the nucleus 5.1 and 1.1, and from there to the anterior end 19.5 and 1.9. The free flagellum measured 6.0 microns +/- 1.6 microns. The median and the range of the central 70% of values (median +/- 35%) of the nuclear index were 1.1 and 0.9-1.2 and of the kinetoplastic index 3.8 and 3.3-4.9. The same data in microns for the maximal width were 3.1 and 2.1-4.6, and for the width at the level of the nucleus 2.9 and 2.2-4.6. The larger and smaller diameters of the nucleus measured 2.6 (2.2-3.7) micron and 1.7 (1.3-1.7) micron, respectively. The corresponding kinetoplast diameters were 1.1 (0.9-1.3) microns and 0.9 (0.6-0.9) micron, respectively.     

The structure–function correlates of mammalian rod and cone photoreceptor mitochondria: observations and unanswered questions

Our previous work suggests that cone photoreceptor inner segment (CIS) mitochondria demand and produce more ATP than rods. The CISs utilize two complimentary strategies to increase ATP production: increase the absolute number of mitochondria and their cristae surface membrane area. In this treatise, we ask: How are crista junctions formed and regulated? Once formed, are there physical mechanisms that constrain their diameter? How are the constrictions in cristae regulated and is this key for cytochrome c release during apoptosis? What are their differences in rod and cone susceptibility to apoptotic cell death during calcium overload and oxidative stress?     

The unsolved mystery of vision

Vision looms large in neuroscience--it is the subject of a gigantic literature and four Nobel prizes--but there is a growing realization that there are problems with the textbook explanation of how mammalian vision works. Here we will summarize the evidence behind this disquiet. In effect, we shall present a portrait of a field that is 'stuck'. Our initial focus, because it is our area of expertise, is on evidence that the early steps of mammalian vision are more diverse and more interesting than is usually imagined, so that our understanding of the later stages is in trouble right from the start. But we will also summarize problems, raised by others, with the later stages themselves.     

The major component of the paraflagellar rod of Trypanosoma brucei is a helical protein that is encoded by two identical,tandemly linked genes

The flagellum of the parasitic hemoflagellate Trypanosoma brucei contains two major structures: (a) the microtubule axoneme, and (b) a highly ordered, filamentous array, the paraflagellar rod (PFR). This is a complex, three-dimensional structure, of yet unknown function, that extends along most of the axoneme and is closely linked to it. Its major structural component is a single protein of 600 amino acids. This PFR protein can assume two different conformations, resulting in two distinct bands of apparent molecular masses of 73 and 69 kD in SDS-gel electrophoresis. Secondary structure predictions indicate a very high helix content. Despite its biochemical similarity to the intermediate filament proteins (solubility properties, amino acid composition, and high degree of helicity), the PFR protein does not belong in this class of cytoskeletal proteins. The PFR protein is coded for by two tandemly linked genes of identical nucleotide sequence. Both genes are transcribed into stable mRNAs of very similar length that carry the mini-exon sequence at their 5'' termini.     

The endocytic apparatus of the kinetoplastida. Part II: machinery and components of the system

Endocytic systems within eukaryotic cells are a diverse set of intracellular transport pathways responsible for uptake, recycling, interaction with the exocytic system and degradation of molecules. Each of these pathways requires the interaction of distinct protein components that function in macromolecule sorting, control of transport rates and in membrane biogenesis. In the second of two articles on kinetoplastida endocytosis, the endocytic system in Trypanosoma brucei is considered as a model, and the molecules that control this system and the protein components of the endocytic pathway are discussed. We also consider novel mechanisms for sorting that have been proposed to operate in trypanosomes.     

The kinetoplastida endocytic apparatus. Part I: a dynamic system for nutrition and evasion of host defences

The endocytic system of kinetoplastid parasites is a highly polarized membrane network focused on the flagellar pocket localized at one end of the cell. When first characterized, the endosomal network was envisioned as a simple system for uptake of extracellular material by fluid-phase or receptor-mediated mechanisms. Subsequently, it has become clear that the kinetoplastid endosomal system has an active and vital role in avoiding the host immune system and virulence, as well as providing the basic functions to fulfil cellular nutritional requirements. In two reviews, recent advances in the definition and comprehension of kinetoplastida endocytosis are discussed and, in Trypanosoma brucei in particular as the more developed experimental system. In Part 1, the endocytic system is considered in context of the surface molecules and their potential roles in virulence.