Cap-dependent translation without base-by-base scanning of an messenger ribonucleic acid

'Ribosome scanning' is the generally accepted mechanism for explaining how a ribosome finds an initiation codon located far removed from the ribosome recruiting site (cap structure). However, the molecular characteristics of ribosome scanning along 5' untranslated regions (UTRs) remain obscure. Herein, using a rabbit reticulocyte lysate (RRL) system and artificial ribonucleic acid (RNA) constructs composed of a capped leader RNA and an uncapped reporter RNA annealed through a double-stranded RNA (dsRNA) bridge, we show that the ribosome can efficiently bypass a stable, dsRNA region without melting the structure. The insertion of an upstream open reading frame in the capped leader RNA impaired the translation of reporter RNA, indicating that a ribosome associated with the 5'-end explores the regions upstream of the dsRNA bridge in search of the initiation codon. These data indicate that a ribosome may skip part(s) of an messenger RNA 5'UTR without thoroughly scanning it.     

The intracrine hypothesis: an update

The intracellular actions of peptide hormones, growth factors, as well as of extracellular-signaling enzymes and DNA-binding proteins, either within target cells or within their cells of synthesis has been called intracrine action. Although these intracrine moieties are structurally diverse, they share certain characteristics of synthesis and function. This has given rise to the development of a theory of intracrine action which permits testable predictions to be made regarding the functioning of these peptides/proteins. Here the intracrine hypothesis is briefly described and then recent experimental findings which bear on predictions made earlier on the basis of the theory are discussed. These findings provide new support for the intracrine hypothesis.     

The new mycobacteria: an update

The continuous evolution of mycobacterial taxonomy may represent a source of confusion for laboratories and clinicians. Apart from the obvious pathogenic strains of the Mycobacterium tuberculosis complex, Mycobacterium leprae and Mycobacterium ulcerans, the role of other mycobacteria may be associated with varying conditions ranging from contamination to specific disease processes. Of the more than 120 mycobacterial species recognized currently, very few have not been reported as pathogenic in humans or animals. Although the attempt to keep pace with the steadily increasing number of mycobacterial species seems hopeless, a careful review of the recent literature relevant to the newly described species may be advantageous. The aim of this present update is to provide epidemiological and clinical information along with major phenotypic and genotypic characteristics of the species described in the last 3 years.     

The freemartin syndrome: an update

The freemartin condition represents the most frequent form of intersexuality found in cattle, and occasionally other species. This review considers the current state of knowledge of freemartin biology, incidence, experimental models, diagnosis, uses for freemartins in cattle herds, occurrence in non-bovine species, effects on the male, and highlights potential new research areas. Freemartins arise when vascular connections form between the placentae of developing heterosexual twin foeti, XX/XY chimerism develops, and ultimately there is masculinisation of the female tubular reproductive tract to varying degrees. With twinning rates in Holstein cows increasing, there will be greater economic importance to establish early diagnosis of the freemartin and the detection of the less common single born freemartin. New diagnostic methods based on the detection of Y-chromosome DNA segments by polymerase chain reaction (PCR) show improved assay sensitivity and efficiency over karyotyping and clinical examination. The implications for the chimeric male animal born co-twin to the freemartin are contentious as to whether fertility is affected; if germ cell chimerism does indeed occur; and, if there are any real effects on the sex ratio of offspring produced. In beef cattle, the freemartin carcass has similar characteristics to normal herdmates. Hormonal treatment of freemartins for use as oestrous detectors has been used to obtain salvage value. The biology of freemartin sheep has recently been studied in detail, and the condition may be increasing in prevalence with the introduction of high fecundity genes into flocks. Potential new research areas are discussed, such as detection of foetal DNA in maternal circulation for prenatal diagnosis and investigation of the anti-tumour properties of Mullerian inhibiting substance (MIS). The freemartin syndrome will always be a limiting factor in cattle and to a lesser extent in sheep production systems that have the goal to produce multiple reproductively normal female offspring from a single dam without using sex predetermination.     

Recognizing translation initiation sites of eukaryotic genes based on the cooperatively scanning model

MOTIVATION: Translation initiation sites (TISs) of genes are the key points of protein synthesis. Exact recognition of TISs in eukaryotic genes is one of the most important tasks in gene-finding algorithms. However, the task has not been satisfactorily fulfilled up to the present. Here, we propose a cooperatively scanning model for recognizing TISs and the first exons of eukaryotic genes on the basis of the structural characteristics of multi-exon genes. RESULTS: The model was employed to cooperatively scan the TISs and 3' splicing sites in eukaryotic genes, and the TISs and the first exons of 132 mammalian gene sequences are identified to evaluate the model. Accuracy of exactly recognizing the TISs and the first exons has been found to amount respectively to 64.4 and 51.5%. We believe that the model will be a useful tool for genome annotation and that it can be easily incorporated into other algorithms to achieve higher accuracy in recognizing TISs and the first exons. AVAILABILITY: The program is available upon request.     

The antibiotic R&D pipeline: an update

There is an urgent need for new antibacterials to target emerging multidrug-resistant bacteria. The need for such agents is rising while the efforts in antibacterial research have declined dramatically in the past few decades with the result of only four compounds belonging to new chemical classes being approved for clinical use. The main reasons that led to this critical situation are shortly described. A renewed interest in the research of new effective antimicrobials is nonetheless delivering compounds deriving mainly from modification of existing drugs, yet new chemical classes are appearing. Because many of these activities have started relatively recently, we should expect a long period before new antibiotics are added to the medical armamentarium.     

The reductive hotspot hypothesis: an update

The mitochondrial free radical theory of aging is seriously challenged by the finding that mutant mtDNA never becomes abundant in vivo, a result disputed only in experiments using novel PCR variants whose quantitative accuracy is widely doubted. However, evidence continues to mount that mitochondria are the crucial site of free radical damage in vivo, most notably that mice lacking the nonmitochondrial isoforms of superoxide dismutase are healthy. It is thus important to determine whether a low level of mutant mtDNA could have serious systemic effects. This possibility exists because of the observed mosaic distribution of mutant mtDNA: some cells (or muscle fiber segments) lack any aerobic respiration. Such cells are presumed to satisfy their ATP needs by glycolysis. In vitro, however, NADH recycling by transmembrane pyruvate/lactate exchange does not suffice: cells only survive if they can up-regulate the plasma membrane oxidoreductase (PMOR). The PMOR's physiological electron acceptor is unknown. It was proposed recently (de Grey, A. D. N. J. (1998) J. Anti-Aging Med. 1(1), 53-66) that a prominent in vivo acceptor from these mitochondrially mutant cells may be oxygen, forming extracellular superoxide. The mosaic ("hotspot") distribution of this superoxide would limit its dismutation by extracellular superoxide dismutase; it may thus reduce transition metals leading to oxidation of circulating material, such as LDL. This would raise systemic oxidative stress, greatly amplifying the damage done by the originating mitochondrially mutant cells. This model, now known as the "reductive hotspot hypothesis," has recently gained much indirect experimental support; several direct tests of it are also feasible.