Long-range correlations in nucleotide sequences.

DNA sequences have been analysed using models, such as an n-step Markov chain, that incorporate the possibility of short-range nucleotide correlations. We propose here a method for studying the stochastic properties of nucleotide sequences by constructing a 1:1 map of the nucleotide sequence onto a walk, which we term a 'DNA walk'. We then use the mapping to provide a quantitative measure of the correlation between nucleotides over long distances along the DNA chain. Thus we uncover in the nucleotide sequence a remarkably long-range power law correlation that implies a new scale-invariant property of DNA. We find such long-range correlations in intron-containing genes and in nontranscribed regulatory DNA sequences, but not in complementary DNA sequences or intron-less genes.     

Preliminary index of authors of Utah plant names

Presented herein is an index to approximately 800 authors of vascular plant names of Utah. A standardized abbreviation is presented for each author. These are listed alphabetically. Following each abbreviation is the full name and birth and death dates (where available) of each individual. In some cases the date of publication is given when biographical information is not known.     

Materialism: Replies to Comments from Readers

The canonical developmental trajectory (CDT), as represented in this paper is both conservative and emergentist. Emerging modes of existence, as new informational constraints, require the material continuation of prior modes upon which they are launched. Informational constraints are material configurations. The paper is not meant to be a direct critique of existing views within science, but an oblique one presented as an alternative, developmental model.     

Development and maintenance of B and T lymphocytes requires antiapoptotic MCL-1

Regulated apoptosis is essential for both the development and the subsequent maintenance of the immune system. Interleukins, including IL-2, IL-4, IL-7 and IL-15, heavily influence lymphocyte survival during the vulnerable stages of VDJ rearrangement and later in ensuring cellular homeostasis, but the genes specifically responsible for the development and maintenance of lymphocytes have not been identified. The antiapoptotic protein MCL-1 is an attractive candidate, as it is highly regulated, appears to enhance short-term survival and functions at an apical step in genotoxic deaths. However, Mcl-1 deficiency results in peri-implantation lethality. Here we show that mice conditional for Mcl-1 display a profound reduction in B and T lymphocytes when MCL-1 is removed. Deletion of Mcl-1 during early lymphocyte differentiation increased apoptosis and arrested the development at pro-B-cell and double-negative T-cell stages. Induced deletion of Mcl-1 in peripheral B- and T-cell populations resulted in their rapid loss. Moreover, IL-7 both induced and required MCL-1 to mediate lymphocyte survival. Thus, MCL-1, which selectively inhibits the proapoptotic protein BIM, is essential both early in lymphoid development and later on in the maintenance of mature lymphocytes.     

cdx4 mutants fail to specify blood progenitors and can be rescued by multiple hox genes

Organogenesis is dependent on the formation of distinct cell types within the embryo. Important to this process are the hox genes, which are believed to confer positional identities to cells along the anteroposterior axis. Here, we have identified the caudal-related gene cdx4 as the locus mutated in kugelig (kgg), a zebrafish mutant with an early defect in haematopoiesis that is associated with abnormal anteroposterior patterning and aberrant hox gene expression. The blood deficiency in kgg embryos can be rescued by overexpressing hoxb7a or hoxa9a but not hoxb8a, indicating that the haematopoietic defect results from perturbations in specific hox genes. Furthermore, the haematopoietic defect in kgg mutants is not rescued by scl overexpression, suggesting that cdx4 and hox genes act to make the posterior mesoderm competent for blood development. Overexpression of cdx4 during zebrafish development or in mouse embryonic stem cells induces blood formation and alters hox gene expression. Taken together, these findings demonstrate that cdx4 regulates hox genes and is necessary for the specification of haematopoietic cell fate during vertebrate embryogenesis.     

BAD and glucokinase reside in a mitochondrial complex that integrates glycolysis and apoptosis

Glycolysis and apoptosis are considered major but independent pathways that are critical for cell survival. The activity of BAD, a pro-apoptotic BCL-2 family member, is regulated by phosphorylation in response to growth/survival factors. Here we undertook a proteomic analysis to assess whether BAD might also participate in mitochondrial physiology. In liver mitochondria, BAD resides in a functional holoenzyme complex together with protein kinase A and protein phosphatase 1 (PP1) catalytic units, Wiskott-Aldrich family member WAVE-1 as an A kinase anchoring protein, and glucokinase (hexokinase IV). BAD is required to assemble the complex in that Bad-deficient hepatocytes lack this complex, resulting in diminished mitochondria-based glucokinase activity and blunted mitochondrial respiration in response to glucose. Glucose deprivation results in dephosphorylation of BAD, and BAD-dependent cell death. Moreover, the phosphorylation status of BAD helps regulate glucokinase activity. Mice deficient for BAD or bearing a non-phosphorylatable BAD(3SA) mutant display abnormal glucose homeostasis including profound defects in glucose tolerance. This combination of proteomics, genetics and physiology indicates an unanticipated role for BAD in integrating pathways of glucose metabolism and apoptosis.     

Extreme deuterium enrichment in stratospheric hydrogen and the global atmospheric budget of H2

Molecular hydrogen (H2) is the second most abundant trace gas in the atmosphere after methane (CH4). In the troposphere, the D/H ratio of H2 is enriched by 120 per thousand relative to the world's oceans. This cannot be explained by the sources of H2 for which the D/H ratio has been measured to date (for example, fossil fuels and biomass burning). But the isotopic composition of H2 from its single largest source--the photochemical oxidation of methane--has yet to be determined. Here we show that the D/H ratio of stratospheric H2 develops enrichments greater than 440 per thousand, the most extreme D/H enrichment observed in a terrestrial material. We estimate the D/H ratio of H2 produced from CH4 in the stratosphere, where production is isolated from the influences of non-photochemical sources and sinks, showing that the chain of reactions producing H2 from CH4 concentrates D in the product H2. This enrichment, which we estimate is similar on a global average in the troposphere, contributes substantially to the D/H ratio of tropospheric H2.     

Utah plant types—historical perspective 1840 to 1981—annotated list, and bibliography

New taxa include: Cryptantha cinerea (Torr.) Cronq. var. arenicola Higgins & Welsh; Physaria chambersii Rollins var. sobolifera Welsh (Cruciferae); Phacelia demissa Gray var. minor N. D. Atwood (Hydrophyllaceae); Iris pariensis Welsh (Iridaceae); Astragalus preussii var. cutleri Barneby and Pediomelum aromaticum (Payson) Welsh var. tuhyi Welsh (Leguminosae); Abronia nana Wats. var. harrisii Welsh (Nyctaginaceae); Camissonia atwoodii Cronq. (Onagraceae); Habenaria zothecina Higgins & Welsh (Orchidaceae); Aqiiilegia formosa Fisch. in DC. var. fosteri Welsh (Ranunculaceae). New nomenclatural combinations include: Rhus aromatica Ait. var. simplicifolia (Greene) Cronq. (Anacardiaceae); Lomatium kingii (Wats.) Cronq., L. kingii var. alpinum (Wats.) Cronq. (Apiaceae); Cryptantha cinerea (Torr.) Cronq. var. laxa (Macbr.) Higgins; Mertensia lanceolata (Pursh) DC. var. nivalis (Wats.) Higgins (Boraginaceae); Opuntia erinacea Engelm. var. aurea (Baxter) Welsh (Cactaceae); Arenaria fendleri Gray var. aculeata (Wats.) Welsh, A. fendleri var. eastwoodiae (Rydb.) Welsh, Lychnis apetala L. var. kingii (Wats.) Welsh, Stellaria longipes Goldie var. monantha (Hulten) Welsh (Caryophyllaceae); Draba densifolia Nutt. ex T. & G. var. apiculata (C. L. Hitchc.) Welsh, D. oligosperma Hook. var. juniperina (Dorn) Welsh, Physaria acutifolia Rydb. var. stylosa (Rollins) Welsh, Thelypodiopsis sagittata (Nutt.) Schulz var. ovalifolia (Rydb.) Welsh (Cruciferae); Lotus plebeius (T. Brandg.) Barneby, Lupinus polyphyllus Lindl. in Edwards var. ammophilus (Greene) Barneby, L polyphyllus var. humicola (A. Nels.) Barneby, L. argenteus Pursh var. fulvomaculatus (Payson) Barneby, L. argenteus var. palmeri (Wats.) Barneby, Pediomelum aromaticum (Payson) Welsh, P. epipsilum (Barneby) Welsh, Psoralidium lanceolatum (Pursh) Rydb. var. stenophyllum (Rydb.) Welsh, and P. lanceolatum var. stenostachys (Rydb.) Welsh (Leguminosae); Mirabilis linearis (Pursh) Hiemerl var. decipiens (Standl.) Welsh (Nyctaginaceae); Camissonia boothii var. condensata (Munz) Cronq., C. boothii var. villosa (Wats.) Cronq., C. clavaeformis (Torr. & Frem.) Raven var. purpurascens (Wats.) Cronq., C. scapoidea (T. & G.) var. utahensis (Raven) Welsh, Oenothera caespitosa var. macroglottis (Rydb.) Cronq., Oe. caespitosa var. navajoensis (Wagner, Stockhouse, & Klein) Cronq., Oe. flava (A. Nels.) Garrett var. acutissima (W. L. Wagner) Welsh, and Oe. primiveris Gray var. bufonis (Jones) Cronq. (Onagraceae); Papaver radicatum Rottb. var. pygmaeum (Rydb.) Welsh (Papaveraceae); Dodecatheon pulchellum (Raf.) Merr. var. zionense (Eastw.) Welsh (Primulaceae); Aquilegia flavescens Wats. var. rubicunda (Tidestr.) Welsh, Delphinium andersonii Gray var. scaposum (Greene) Welsh, D. occidentalis (Wats.) Wats. var. barbeyi (Huth) Welsh, and Ranunculus andersonii Gray var. juniperinus (Jones) Welsh (Ranunculaceae); Purshia mexicana (D. Don) Welsh and P. mexicana var. stansburyi (Torr.) Welsh (Rosaceae); Galium mexicanum H.B.K. var. asperrimum (Gray) Higgins & Welsh (Rubiaceae); Castilleja parvula Rydb. var. revealii (N. Holmgren) N. D. Atwood and C. rhexifolia Rydb. var. sulphurea (Rydb.) N. D. Atwood (Scrophulariaceae).