A test of Chargaff's second rule

In 1968, Chargaff and his colleagues discovered a rule in Bacillus subtilis: in single stranded DNA, A=T and C=G. This rule has since been confirmed many times in other bacterial and eukaryotic genomes. To the best of our knowledge, this rule has not been tested before in either single stranded DNA or RNA genomes. Over 3400 genomic sequences were examined here and included for the first time both double and single stranded DNA and RNA genomes. We found that: (1) with the exception of the organellar DNA, this parity rule holds for all types of double stranded DNA genomes and (2) that this rule fails to hold for other types of genomes. The parity rule appears to be a selective force on genome evolution and codon use.     

Neutralism and selectionism: a network-based reconciliation

Neutralism and selectionism are extremes of an explanatory spectrum for understanding patterns of molecular evolution and the emergence of evolutionary innovation. Although recent genome-scale data from protein-coding genes argue against neutralism, molecular engineering and protein evolution data argue that neutral mutations and mutational robustness are important for evolutionary innovation. Here I propose a reconciliation in which neutral mutations prepare the ground for later evolutionary adaptation. Key to this perspective is an explicit understanding of molecular phenotypes that has only become accessible in recent years.     

Microsatellites that violate Chargaff's second parity rule have base order-dependent asymmetries in the folding energies of complementary DNA strands and may not drive speciation

Models for meiotic recombination based on Crick's “unpairing postulate” require symmetrical extrusion of stem-loop structures from homologous DNA duplexes. The potential for such extrusion is abundant in many species and, for a given single-strand segment, can be quantitated as the “folding of natural sequence” (FONS) energy value. This, in turn, can be decomposed into base order-dependent and base composition-dependent components. The FONS values of top and bottom strands in most Caenorhabditis elegans segments are close, as are the corresponding base order-dependent and base composition-dependent components; any discrepancies are in the base composition-dependent component. This suggests that the strands would extrude with similar kinetics. However, interspersed among these segments and at the ends of chromosomes (telomeres) are segments containing short tandem repeats (microsatellites) which, by virtue of their high variability, have been postulated to inhibit the pairing of homologous chromosomes and hence drive speciation. In these segments, there are usually wide discrepancies between the FONS values of top and bottom strands, mainly attributable to differences in base order-dependent components. Analyses of artificial microsatellites of different unit sizes and base compositions show that this asymmetrical distribution of folding potential is greatest for microsatellites when the units are short and violate Chargaff's second parity rule. It is proposed that when there is folding asymmetry, recombination proceeds by special, strand-biased, somatic mechanisms analogous to those operating with Chi sequences in Escherichia coli. If meiotic recombination in the germ-line requires extrusion symmetry, then a general inhibitory influence of microsatellite-containing segments could mask the antirecombinational influence of their variability. Thus, microsatellites may not have driven speciation.     

The evolution of altruism between siblings: Hamilton's rule revisited

This paper explores the validity of Hamilton's rule in the case of other-only altruism in which the benefits are shared by other members of the sibling group excluding the donor. It presents a model of competition between two alleles which code for different kinds of altruism. It derives a simple replicator equation for allele frequencies under conditions of strong selection. This equation does not depend on the size of the sibling group. In mathematical form, the equation is similar to Hamilton's original rule in the case of inbreeding, although the causal mechanism is different. The paper derives a simple criterion to determine whether there will be a polymorphism in which both alleles coexist permanently. Such an event is rare and victory will normally go to the allele with the higher value of 1/2b-c, where b is the total benefit which an offspring confers on its siblings and c is the cost to the donor. The paper also considers how an offspring will behave in particular circumstances. Using a specialized version of the basic model, it shows how, in the absence of polymorphism, natural selection should take the system towards the point of 50% marginal altruism. With this type of altruism, an offspring will perform any act for which the expected cost to the donor is at most half the expected benefit to its siblings. Acts which do not satisfy this criterion are not performed. This accords with Haldane's quip that he would sacrifice his own life for two of his brothers, but not for less. Numerical simulation is used to explore these issues in greater depth. The paper also examines briefly the implications of heterozygote advantage for Hamilton's rule. It concludes with a brief discussion of the connection between other-only altruism and whole-group altruism, in which the donor gains some benefit from its actions.     

Bioreporters: gfp versus lux revisited and single-cell response

Genetically engineered organisms expressing spectroscopically active reporter molecules in response to chemical effectors display great potential as living transducers in sensing applications. Green fluorescent protein (gfp gene) bioreporters have distinct advantages over luminescent couterparts (lux gene), including applicability at the single-cell level, but are typically less sensitive. Here we describe a gfp-bearing bioreporter that is sensitive to naphthalene (a poorly water soluble pollutant behaving like a large class of hydrophobic compounds), is suitable for use in chemical assays and bioavailability studies, and has detection limits comparable to lux-bearing bioreporters for higher efficiency detection strategies. Simultaneously, we find that the exploitation of population response data from single-cell analysis is not an algorithmic conduit to enhanced signal detection and hence lower effector detection limits, as normally assumed. The assay reported functions to equal effect with or without biocide.     

ATP versus pyrophosphate: glycolysis revisited in parasitic protists

It is generally assumed that glycolysis is remarkably similar among all organisms, prokaryotic and eukaryotic. This view has been extended to protists. However, there is growing evidence that significant deviations from conventional glycolysis occur in protists. Very different species, some parasitic, rely on peculiar enzymes that use pyrophosphate as substrate. In this review, Emmanuel Mertens describes such unusual pyrophosphate metabolism in parasitic protists.     

The "A" rule revisited: polymerases as determinants of mutational specificity

Organisms control the specificity and frequency with which they mutate via their complement of proteins. The mismatch repair (MMR) proteins correct errors after they are made. The DNA polymerases of the cell determine the response to damaged DNA which has not been repaired by excision. Polymerase action can be considered as consisting of three main steps: addition of a base, proofreading of the added nucleotide and elongation. Each of these steps is kinetically complex and can be modulated. The modulation accounts for different behaviors of organisms in response to stress. The recent findings of DNA polymerases with properties appropriate for dealing with damaged DNA may help to account for the phenomenon of spontaneous mutation and for the hypermutability associated with immunoglobulin maturation and carcinogenesis.     

Rationing mental health care: parity,disparity, and justice

Recent policy debates in the US over access to mental health care have raised several philosophically complex ethical and conceptual issues. The defeat of mental health parity legislation in the US Congress has brought new urgency and relevance to theoretical and empirical investigations into the nature of mental illness and its relation to other forms of sickness and disability. Manifold, nebulous, and often competing conceptions of mental illness make the creation of coherent public policy exceedingly difficult. Referencing a variety of approaches to ethical reflection on health care, and drawing from the empirical literature on therapeutic efficacy and economic efficiency, we argue that differential rationing, 'disparity,' is unjustifiable.     

Allen's rule revisited: quantitative genetics of extremity length in the common frog along a latitudinal gradient

Ecogeographical rules linking climate to morphology have gained renewed interest because of climate change. Yet few studies have evaluated to what extent geographical trends ascribed to these rules have a genetic, rather than environmentally determined, basis. This applies especially to Allen's rule, which states that the relative extremity length decreases with increasing latitude. We studied leg length in the common frog (Rana temporaria) along a 1500 km latitudinal gradient utilizing wild and common garden data. In the wild, the body size-corrected femur and tibia lengths did not conform to Allen's rule but peaked at mid-latitudes. However, the ratio of femur to tibia length increased in the north, and the common garden data revealed a genetic cline consistent with Allen's rule in some trait and treatment combinations. While selection may have shortened the leg length in the north, the genetic trend seems to be partially masked by environmental effects.     

Effects of dietary energy intake during gestation and lactation on milk yield and composition of first,second and fourth parity sows

Abstract

In order to determine the effects of a varied level of dietary energy intake during pregnancy and lactation on milk yield and composition, first, second and fourth parity sows (Large White × German Landrace) were provided with energy at a level of either: (i) 100% of ME requirement (MEreq) during pregnancy and lactation, (ii) 120% MEreq during pregnancy and 80% during lactation, and (iii) 80% MEreq during pregnancy and 120% during lactation. In spite of equal target levels feed analysis revealed that gestating first parity sows with 120/80 treatment combination and lactating sows of 80/120 treatment combination received 25, and 11 – 17% more digestible N than in the respective 100/100 treatment combination. Irrespective of this 120/80 sows responded with the highest milk DM, fat, and energy contents, and the lowest lactose concentrations whereas protein levels where not affected, irrespective of parity (p < 0.05). Milk yield of sows in 1st and 4th lactation was 85 and 106% of that in 2nd lactation, respectively. Average milk composition was 18.1% DM, 4.9% protein, 6.8% fat, 5.6% lactose, and 0.8% ash. Milk composition changes ceased at day 7 of lactation with a reduction of milk GE and protein, and an increase of lactose content. Concentrations of threonine, arginine, valine, leucine, tyrosine, phenylalanine, cystine, and tryptophan, as well as stearic, oleic, and linoleic acid were higher in colostrum than in milk at later lactation stages. In contrast, laurine, myristic, palmitic, and palmitoleic acids were lower concentrated in colostrum. In conclusion, these results illustrate the importance of body reserve mobilization for milk production in sows and indicate that low energy supply during gestation cannot be compensated by higher energy supply during lactation.     

Effects of dietary energy intake during gestation and lactation on milk yield and composition of first, second and fourth parity sows

In order to determine the effects of a varied level of dietary energy intake during pregnancy and lactation on milk yield and composition, first, second and fourth parity sows (Large White x German Landrace) were provided with energy at a level of either: (i) 100% of ME requirement (MEreq) during pregnancy and lactation, (ii) 120% MEreq during pregnancy and 80% during lactation, and (iii) 80% MEreq during pregnancy and 120% during lactation. In spite of equal target levels feed analysis revealed that gestating first parity sows with 120/80 treatment combination and lactating sows of 80/120 treatment combination received 25, and 11-17% more digestible N than in the respective 100/100 treatment combination. Irrespective of this 120/80 sows responded with the highest milk DM, fat, and energy contents, and the lowest lactose concentrations whereas protein levels where not affected, irrespective of parity (p < 0.05). Milk yield of sows in 1st and 4th lactation was 85 and 106% of that in 2nd lactation, respectively. Average milk composition was 18.1% DM, 4.9% protein, 6.8% fat, 5.6% lactose, and 0.8% ash. Milk composition changes ceased at day 7 of lactation with a reduction of milk GE and protein, and an increase of lactose content. Concentrations of threonine, arginine, valine, leucine, tyrosine, phenylalanine, cystine, and tryptophan, as well as stearic, oleic, and linoleic acid were higher in colostrum than in milk at later lactation stages. In contrast, laurine, myristic, palmitic, and palmitoleic acids were lower concentrated in colostrum. In conclusion, these results illustrate the importance of body reserve mobilization for milk production in sows and indicate that low energy supply during gestation cannot be compensated by higher energy supply during lactation.     

Phylogenetic hypotheses: Cladoniaceae,Stereocaulaceae, Baeomycetaceae,and Icmadophilaceae revisited

Parsimony analyses of SSU rDNA sequences were conducted to examine phylogenetic relationships of selected genera within the families Cladoniaceae, Stereocaulaceae, Icmadophilaceae and Baeomycetaceae (lichen-forming ascomycetes). The analyses included 93 taxa (84 species) representing various groups of ascomycetous fungi. Analyses of the matrix with pre-aligned sequences were performed using heuristic and parsimony ratchet searches, and support values for the same matrix were calculated using parsimony jackknifing. The results support the recognition of the four families. Cladoniaceae are recircumscribed to accommodate Cladia, Cladonia, Heterodea, Metus, Pilophorus, Pycnothelia, Ramalea, Thysanothecium and the newly erected genus Carassea. Myelorrhiza is excluded from the family, while the status of other potential members, Calathaspis, Gymnoderma s.str. and Squamella, remains unresolved. Baeomycetaceae include Baeomyces and Phyllobaeis. Stereocaulaceae include Stereocaulon only, although the status of Muhria is still unclear. Finally, Icmadophilaceae include Dibaeis, Endocena, Knightiella, Icmadophila, Siphula and Thamnolia, while the status of Pseudobaeomyces and Siphulella requires further elucidation. The genus Cladonia appeared to be a polyphyletic assemblage, and accordingly, a new genus Carassea S. Stenroos, gen. nov., represented by C. connexa (Vain.) S. Stenroos, comb. nov., is described. Carassea is most closely related to Pycnothelia and Metus in the Cladoniaceae. Siphula, represented in the present analysis by six species, is not monophyletic, and is in need of reclassification.     

Sequential aspects of spontaneous abortion: maternal age, parity, and pregnancy compensation artifact

At least 3 hypotheses predict that spontaneous abortion risk differs during reporductive history: genuine maternal age effects change individual risks; genuine birth order effects change individual risks; and variant individual risks, which are really independent of both age and parity, produce an artifactual association of risk with age in populations of women. The availability of large numbers of reproductive histories recorded on magnetic tape by the Collaborative Study on Cerebral Palsy provides an opportunity to weigh these hypotheses. Information was gathered between mid-1959 and mid-1966 by 13 hospitals, mostly east of the Mississippi. Random samples of essentially all women registering in the obstetric clinics of the collaborating institutions entered the study. Generally, these women came from poorer urban areas. Data are taken from the interviews at 1st registrations only. At this time, women had prior reproductive histories of varying lengths. The data are analyzed to yield broad comparative evaluations of the maternal age, parity, and artifact hypotheses. When the logit transforms of abortion risks were regressed on maternal age, the linear component was positive and significant at the 1% level in every ethnic group. In all categories except blacks, the fit to such a simple model was quite adequate. Fit in the case of the blacks was disturbed by the high rate among 13-year olds and the low rate among 37-year olds. The 37-year old black sample was the only one to depart markedly from the trend of increased risk at high age. Primary analysis of birth order defects used Slater's (1962) rank order statistic on a group of histories. In every ethnic category the observed mean value of Slater's statistic exceeds its expected value of 0.5; every standardized deviation has a negligibly small probability when tested against the normal distribution. The conclusin is that spontaneous abortions tend to come late in a reproductive history. The white data showed a definite trend contrary to expectation under the pregnancy compensation hypothesis. Although not significant in the "o" (liveborn) versus "x" (abortion) contrast, the lowering trent in maternal age with prior abortion experience was signifixant for the longer histories. Equally surprising was the apparent positive finding in the black data. In sum, the data clearly showed that among women with histories mixing spontaneous abortions and live births, risk of abortion was greater at higher parity. Although the women sampled tended to be young, and increase of risk with age was demonstrated in the white sample. These effects were not because of sample biases. Black age effects were possibly confounded with pregnancy compensation artifact which can mimic aging influence in unselected samples.     

Chemoaffinity revisited: dscams, protocadherins, and neural circuit assembly

The chemoaffinity hypothesis for neural circuit assembly posits that axons and their targets bear matching molecular labels that endow neurons with unique identities and specify synapses between appropriate partners. Here, we focus on two intriguing candidates for fulfilling this role, Drosophila Dscams and vertebrate clustered protocadherins (Pcdhs). In each, a complex genomic locus encodes large numbers of neuronal transmembrane proteins with homophilic binding specificity, individual members of which are expressed combinatorially. Although these properties suggest that Dscams and Pcdhs could act as specificity molecules, they may do so in ways that challenge traditional views of how neural circuits assemble.     

25R,26-Hydroxycholesterol revisited: synthesis, metabolism, and biologic roles

The CYP27 gene is expressed in arterial endothelium, macrophages, and other tissues. The gene product generates sterol intermediates that function as ligands for nuclear receptors prior to their transport to the liver for metabolism, mostly to bile acids. Most attention has been given to 27-hydroxycholesterol as a ligand for LXR activated receptors and to chenodeoxycholic acid as a ligand for farnesoid X activated receptors (FXRs). Expression of the pathway in macrophages is essential for normal reverse cholesterol transport. Thus, ABC transporter activity is upregulated, which enhances cholesterol efflux. Absence of these mechanisms probably accounts for the accelerated atherosclerosis that occurs in cerebrotendinous xanthomatosis. Accumulation of 27-hydroxycholesterol in human atheroma is puzzling and may reflect low levels of oxysterol 7alpha-hydroxylase activity in human macrophages. The same enzyme determines the proportion of mono-, di-, and tri-hydroxy bile acids synthesized in the liver. Oxysterol 7alpha-hydroxylase deficiency is a molecular basis for cholestatic liver disease. Chenodeoxycholic acid, the major normal end product, downregulates expression of cholesterol 7alpha-hydroxylase via the FXR/short heterodimer protein nuclear receptor and thus limits total bile acid production. The challenge is to quantify in a physiologic setting the magnitude of the pathway in different tissues and to further evaluate the biologic roles of all the intermediates that may function as ligands for orphan nuclear receptors or via other regulatory mechanisms.