Discovering simple DNA sequences by the algorithmic significance method

A new method, ‘algorithmic significance’, is proposedas a tool for discovery of patterns in DNA sequences. The mainidea is that patterns can be discovered by finding ways to encodethe observed data concisely. In this sense, the method can beviewed as a formal version of the Occam's Razor principle. Inthis paper the method is applied to discover significantly simpleDNA sequences. We define DNA sequences to be simple if theycontain repeated occurrences of certain ‘words’and thus can be encoded in a small number of bits. Such definitionincludes minisatellites and microsatellites. A standard dynamicprogramming algorithm for data compression is applied to computethe minimal encoding lengths of sequences in linear time. Anelectronic mail server for identification of simple sequencesbased on the proposed method has been installed at the Internetaddress pythia@anl.gov.     

βs Haplotypes in various world populations

Summary We have determined the ^s haplotypes in 709 patients with sickle cell anemia, 30 with SC disease, 91 with S--thalassemia, and in 322 Hb S heterozygotes from different countries. The methodology concerned the detection of mutations in the promoter sequences of the ^G- and ^A-globin genes through dot blot analysis of amplified DNA with ³²P-labeled probes, and an analysis of isolated Hb F by reversed phase high performance liquid chromatography to detect the presence of the ^AT chain [^A75 (E19) IleThr] that is characteristic for haplotype 17 (Cameroon). The results support previously published data obtained with conventional methodology that indicates that the ^s gene arose separately in different locations. The present methodology has the advantage of being relatively inexpensive and fast, allowing the collection of a vast body of data in a short period of time. It also offers the opportunity of identifying unusual ^s haplotypes that may be associated with a milder expression of the disease. The numerous blood samples obtained from many SS patients living in different countries made it possible to compare their hematological data. Such information is included (as average values) for 395 SS patients with haplotype 19/19, for 2 with haplotype 17/17, for 50 with haplotype 20/20, for 2 with haplotype 3/3, and for 37 with haplotype 31/31. Some information on haplotype characteristics of normal ^A chromosomes is also presented.     

Sexual dimorphism of skull shape in a lacertid lizard species (Podarcis spp., Dalmatolacerta sp., Dinarolacerta sp.) revealed by geometric morphometrics

Geometric morphometric techniques were used to examine allometric and non-allometric influences on sexual shape dimorphism (SShD) in the ventral cranium (skull base, palate and upper jaw) of four species of lacertid lizards (Podarcis muralis, Podarcis melisellensis, Dalmatolacerta oxycephala, Dinarolacerta mosorensis). These species differ in body shape, ecology and degree of phylogenetic relatedness. The structures of the ventral cranium that were studied are directly involved in the mechanics of feeding and are connected to the jaw musculature; these structures are potentially subject to both sexual and natural selection. Allometry accounted for a considerable degree of cranial shape variation between the sexes. Allometric shape changes between individuals with smaller cranium size and individuals with larger cranium size are mostly related to changes in the skull base showing pronounced negative allometry. The rostral part, however, either scaled isometrically or showed less pronounced negative allometry than the skull base. Non-allometric intersexual shape variation predominantly involved changes related to the jaw adductor muscle chamber, i.e., changes that are associated with biomechanically relevant traits of the jaw system in females and males. Both allometric and non-allometric shape changes appeared to be species-specific. Our results indicate that natural and sexual selection may be involved in the evolution of SShD.     

Direct interaction between SNAP-23 and L-type Ca2+ channel

During secretion, membrane-bound secretory vesicles dock and fuse at the base of porosomes in the cell plasma membrane. Among other proteins, the porosome is composed of SNAREs and Ca2+-channels. Ca2+-channels and SNAREs have been implicated in cell secretion. Several immunoprecipitation and binding studies suggest the physical interaction of the t-SNARE proteins, Syntaxin-1 and SNAP-25 with various Ca2+-channels. In this study, using yeast two-hybrid and immunoanalysis, we demonstrate for the first time, direct interaction of SNAP-23 and a L-type Ca2+-channel at the plasma membrane in pancreas.     

Structure, isolation, composition and reconstitution of the neuronal fusion pore

Neuronal communication is dependent on the fusion of 40-50 nm in diameter synaptic vesicles containing neurotransmitters, at the presynaptic membrane. Here we report for the first time at 5-8A resolution, the presence of 8-10 nm in diameter cup-shaped neuronal fusion pores or porosomes at the presynaptic membrane, where synaptic vesicles dock and fuse to release neurotransmitters. The structure, isolation, composition, and functional reconstitution of porosomes present at the nerve terminal are described. These findings reveal the molecular mechanism of neurotransmitter release at the presynaptic membrane of nerve terminals.     

Abbreviated Exposure to Hypoxia Is Sufficient to Induce CNS Dysmyelination,Modulate Spinal Motor Neuron Composition,and Impair Motor Development in Neonatal Mice

Neonatal white matter injury (nWMI) is an increasingly common cause of cerebral palsy that results predominantly from hypoxic injury to progenitor cells including those of the oligodendrocyte lineage. Existing mouse models of nWMI utilize prolonged periods of hypoxia during the neonatal period, require complex cross-fostering and exhibit poor growth and high mortality rates. Abnormal CNS myelin composition serves as the major explanation for persistent neuro-motor deficits. Here we developed a simplified model of nWMI with low mortality rates and improved growth without cross-fostering. Neonatal mice are exposed to low oxygen from postnatal day (P) 3 to P7, which roughly corresponds to the period of human brain development between gestational weeks 32 and 36. CNS hypomyelination is detectable for 2–3 weeks post injury and strongly correlates with levels of body and brain weight loss. Immediately following hypoxia treatment, cell death was evident in multiple brain regions, most notably in superficial and deep cortical layers as well as the subventricular zone progenitor compartment. PDGFαR, Nkx2.2, and Olig2 positive oligodendrocyte progenitor cell were significantly reduced until postnatal day 27. In addition to CNS dysmyelination we identified a novel pathological marker for adult hypoxic animals that strongly correlates with life-long neuro-motor deficits. Mice reared under hypoxia reveal an abnormal spinal neuron composition with increased small and medium diameter axons and decreased large diameter axons in thoracic lateral and anterior funiculi. Differences were particularly pronounced in white matter motor tracts left and right of the anterior median fissure. Our findings suggest that 4 days of exposure to hypoxia are sufficient to induce experimental nWMI in CD1 mice, thus providing a model to test new therapeutics. Pathological hallmarks of this model include early cell death, decreased OPCs and hypomyelination in early postnatal life, followed by dysmyelination, abnormal spinal neuron composition, and neuro-motor deficits in adulthood.