A nuclear gene for higher level phylogenetics: phosphoenolpyruvate carboxykinase tracks mesozoic-age divergences within Lepidoptera (Insecta)

The sequence of phosphoenolpyruvate carboxykinase (PEPCK) has been previously identified as a promising candidate for reconstructing Mesozoic-age divergences (Friedlander, Regier, and Mitter 1992, 1994). To test this hypothesis more rigorously, 597 nucleotides of aligned PEPCK coding sequence (approximately 30% of the coding region) were generated from 18 species representing Mesozoic-age lineages of moths (Insecta: Lepidoptera) and outgroup taxa. Relationships among basal Lepidoptera are well established by morphological analysis, providing a strong test for the utility of a gene which has not previously been used in systematics. Parsimony and other phylogenetic analyses were conducted on nucleotides by codon positions (nt1, nt2, nt3) separately and in combination, and on amino acids, for comparison to the test phylogeny. The highest concordance was achieved with nt1 + nt2, for which one of two most-parsimonious trees was identical to the test phylogeny, and with all nucleotides when nt3 was down-weighted sevenfold or higher, for which a single most-parsimonious tree identical to the test phylogeny resulted. Substitutions in nt3 approached saturation in many, but not all, pairwise comparisons and their exclusion or severe downweighting greatly increased the degree of concordance with the test phylogeny. Neighbor-joining analysis confirms this finding. The utility of PEPCK for phylogenetics is demonstrated over a time span for which few other suitable genes are currently available.      

Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals

Differential rates of nucleotide substitution among different gene segments and between distinct evolutionary lineages is well documented among mitochondrial genes and is likely a consequence of locus-specific selective constraints that delimit mutational divergence over evolutionary time. We compared sequence variation of 18 homologous loci (15 coding genes and 3 parts of the control region) among 10 mammalian mitochondrial DNA genomes which allowed us to describe different mitochondrial evolutionary patterns and to produce an estimation of the relative order of gene divergence. The relative rates of divergence of mitochondrial DNA genes in the family Felidae were estimated by comparing their divergence from homologous counterpart genes included in nuclear mitochondrial DNA (Numt, pronounced "new might"), a genomic fossil that represents an ancient transfer of 7.9 kb of mitochondrial DNA to the nuclear genome of an ancestral species of the domestic cat (Felis catus). Phylogenetic analyses of mitochondrial (mtDNA) sequences with multiple outgroup species were conducted to date the ancestral node common to the Numt and the cytoplasmic (Cymt) mtDNA genes and to calibrate the rate of sequence divergence of mitochondrial genes relative to nuclear homologous counterparts. By setting the fastest substitution rate as strictly mutational, an empirical "selective retardation index" is computed to quantify the sum of all constraints, selective and otherwise, that limit sequence divergence of mitochondrial gene sequences over time.      

Rapid evolution in a conserved gene family. Evolution of the actin gene family in the sea urchin genus Heliocidaris and related genera

Camarodont sea urchins possess a rapidly evolving actin gene family whose members are expressed in distinct cell lineages in a developmentally regulated fashion. Evolutionary changes in the actin gene family of echinoids include alterations in number of family members, site of expression, and gene linkage, and a dichotomy between rapidly and slowly evolving isoform-specific 3' untranslated regions. We present sequence comparisons and an analysis of the actin gene family in two congeneric sea urchins that develop in radically different modes, Heliocidaris erythrogramma and H. tuberculata. The sequences of several actin genes from the related species Lytechinus variegatus are also presented. We compare the features of the Heliocidaris and Lytechinus actin genes to those of the the actin gene families of other closely related sea urchins and discuss the nature of the evolutionary changes among sea urchin actins and their relationship to developmental mode.      

Bacterioplankton Dynamics in the McMurdo Dry Valley Lakes, Antarctica: Production and Biomass Loss over Four Seasons

Abstract Research of the microbial ecology of McMurdo Dry Valley lakes has concentrated primarily on phototrophs; relatively little is known about the heterotrophic bacterioplankton. Bacteria represent a substantial proportion of water column biomass in these lakes, comprising 30 to 60% of total microplankton biomass. Bacterial production and cell numbers were measured 3 to 5 times, within four Antarctic seasons (October to January), in Lakes Fryxell, Hoare, and Bonney. The winter-spring transition (September to October) was included during one year. Lake Fryxell was the most productive, but variable, lake, followed by Lakes Bonney and Hoare. Bacterial production ranged from 0 to 0.009 μg C ml-1 d-1; bacterial populations ranged from 3.2 x 10(4) to 4.4 x 10(7) cells ml-1. Bacterial production was always greatest just below the ice cover at the beginning of the season. A second maximum developed just above the chemocline of all the lakes, as the season progressed. Total bacterioplankton biomass in the lakes decreased as much as 88% between successive sampling dates in the summer, as evidenced by areal integration of bacterial populations; the largest decreases in biomass typically occurred in mid-December. A forward difference model of bacterial loss in the trophogenic zone and the entire water column of these lakes showed that loss rates in the summer reached 6.3 x 10(14) cells m-2 d-1 and 4.16 x 10(12) cells m-2 d-1, respectively. These results imply that bacteria may be a source of carbon to higher trophic levels in these lakes, through grazing.     

PCR-based assays of mendelian polymorphisms from anonymous single-copy nuclear DNA: techniques and applications for population genetics

This paper outlines a PCR-based approach for population genetics that offers several advantages over conventional Southern blotting methods for revealing restriction-fragment-length polymorphisms (RFLPs) in nuclear DNA. Primers are constructed from clones isolated from a nuclear DNA library, and these primers subsequently are employed in in vitro syntheses of homologous regions. Amplified products are then screened directly for RFLPs by using gel-staining procedures. Population applications for this PCR-based approach, including potential strengths and weaknesses, are exemplified by two RFLP data sets generated to estimate (a) male-mediated gene flow in the green turtle (Chelonia mydas) and (b) geographic population genetic structure in the American oyster (Crassostrea virginica). Restriction assays of amplified products from 14 or 15 independent primer pairs in each species revealed polymorphisms at several loci that proved highly informative in the population genetic analyses. In general, the Mendelian polymorphisms produced by this PCR-based approach will provide useful genetic markers for population studies, particularly in situations where simpler and less expensive allozyme methods have failed, for whatever reason, to provide adequate information.      

SOSORT 2012 consensus paper: reducing x-ray exposure in pediatric patients with scoliosis

This 2012 Consensus paper reviews the literature on side effects of x-ray exposure in the pediatric population as it relates to scoliosis evaluation and treatment. Alternative methods of spinal assessment and imaging are reviewed, and strategies for reducing the number of radiographs are developed. Using the Delphi technique, SOSORT members developed consensus statements that describe how often radiographs should be taken in each of the pediatric and adolescent sub-populations.     

Heavy metal concentrations in,and human health risk assessment of,three commercially valuable fish species in the lower Niger River,Nigeria

The concentrations of Fe, Mn, Ni, Pb and V in water, sediment and the gill, liver and muscle tissues of Synodontis resupinatus, Heterotis niloticus and Clarias gariepinus, all commercially important fish species of the lower Niger River, were investigated in 2015. Water, sediment and fish samples were collected for six months and heavy metals were determined using an Atomic Absorption Spectrometer. Fe ranked highest in water and sediment, with concentrations of 2.74 mg l^?1 and 61.60 mg kg^?1, respectively. Metals followed the magnitude of Fe > Mn > Ni > V > Pb in the water and Fe > Mn > V > Ni > Pb in the sediments. Metal concentrations were higher in the tissues of S. resupinatus compared with H. niloticus and C. gariepinus. Fe was also highest in the gills, liver and muscle of the three fish species. Its highest concentration of 132.97 mg kg^?1 dry weight was recorded in the gills of S. resupinatus. Bioconcentration factors of metals ranged from 8.79 for Mn in H. niloticus muscle to 67.99 for Ni in S. resupinatus gills. The fish species studied pose no health risk for all metals studied, because the target hazard quotient was less than 1 and the estimated daily intakes of the metals were below the reference doses.