Effective Sizes for Subdivided Populations

Many derivations of effective population sizes have been suggested in the literature; however, few account for the breeding structure and none can readily be expanded to subdivided populations. Breeding structures influence gene correlations through their effects on the number of breeding individuals of each sex, the mean number of progeny per female, and the variance in the number of progeny produced by males and females. Additionally, hierarchical structuring in a population is determined by the number of breeding groups and the migration rates of males and females among such groups. This study derives analytical solutions for effective sizes that can be applied to subdivided populations. Parameters that encapsulate breeding structure and subdivision are utilized to derive the traditional inbreeding and variance effective sizes. Also, it is shown that effective sizes can be determined for any hierarchical level of population structure for which gene correlations can accrue. Derivations of effective sizes for the accumulation of gene correlations within breeding groups (coancestral effective size) and among breeding groups (intergroup effective size) are given. The results converge to traditional, single population measures when similar assumptions are applied. In particular, inbreeding and intergroup effective sizes are shown to be special cases of the coancestral effective size, and intergroup and variance effective sizes will be equal if the population census remains constant. Instantaneous solutions for effective sizes, at any time after gene correlation begins to accrue, are given in terms of traditional F statistics or transition equations. All effective sizes are shown to converge upon a common asymptotic value when breeding tactics and migration rates are constant. The asymptotic effective size can be expressed in terms of the fixation indices and the number of breeding groups; however, the rate of approach to the asymptote is dependent upon dispersal rates. For accurate assessment of effective sizes, initial, instantaneous or asymptotic, the expressions must be applied at the lowest levels at which migration among breeding groups is nonrandom. Thus, the expressions may be applicable to lineages within socially structured populations, fragmented populations (if random exchange of genes prevails within each population), or combinations of intra- and interpopulation discontinuities of gene flow. Failure to recognize internal structures of populations may lead to considerable overestimates of inbreeding effective size, while usually underestimating variance effective size.     

Airborne pollen characteristics and the influence of temperature and precipitation in Raleigh,North Carolina,USA (1999–2012)

The incidence of allergic diseases has been increasing in recent decades, in part due to increased exposure to aeroallergens, particularly pollen. Allergic diseases have a major burden on the health care system, with annual costs in the USA alone exceeding $30 billion. There is evidence that the production of aeroallergens, including pollen, is increasing in response to environmental and climatic change, which has important implications for the treatment of allergy sufferers. In this study, pollen data from a Rotorod sampler in Raleigh, North Carolina, was used to characterize and examine trends in the atmospheric pollen seasons for trees, grasses, and weeds over the period 1999–2012. The influence of mean monthly antecedent and concurrent temperature and precipitation on the timing, duration, and severity of the pollen seasons was assessed using Pearson’s product-moment correlation coefficients and multiple linear regression models. An increasing trend was noted in seasonal tree pollen concentrations, while seasonal and peak weed pollen concentrations declined over time. The atmospheric pollen seasons for grasses and weeds trended toward earlier start dates and longer durations, while the tree pollen season trended toward an earlier end date. Peak daily tree pollen concentrations were strongly associated with antecedent temperature and precipitation, while peak daily grass pollen concentrations were strongly associated with concurrent precipitation. The strongest relationships between climate and weed pollen were associated with the timing and duration of the pollen season, with drier antecedent and warmer concurrent conditions tied to longer weed pollen seasons.     

Synthesis and structural characterization of charybdotoxin, a potent peptidyl inhibitor of the high conductance Ca2(+)-activated K+ channel.

Charybdotoxin (ChTX), a potent inhibitor of the high conductance Ca2(+)-activated K+ channel (PK,Ca) is a highly basic peptide isolated from venom of the scorpion Leiurus quinquestriatus hebraeus, whose primary structure has been determined (Gimenez-Gallego, G., Navia, M. A., Reuben, J. P., Katz, G. M., Kaczorowski, G. J., and Garcia, M. L. (1988) Proc. Natl. Acad. Sci. U. S. A. 85, 3329-3333). The synthesis of this peptide using continuous flow solid phase fluorenylmethyloxycarbonyl-pentafluorophenyl ester methodology has now been achieved. The 1-37-amino acid hexasulfhydryl peptide oxidizes readily to give the tricyclic disulfide structure in good yield. This folded synthetic material is identical to native toxin based on three criteria: co-migration with ChTX on reversed phase high performance liquid chromatography (HPLC); competitive inhibition of 125I-labeled monoiodotyrosine charybdotoxin binding to bovine aortic sarcolemmal membrane vesicles with a Ki (10 pM) identical to that of native toxin; blockade of PK,Ca activity in excised outside-out patches from bovine aortic smooth muscle with the potency and inhibitory properties characteristic of ChTX (i.e. appearance of silent periods interdispersed with normal bursts of channel activity in single channel recordings). Selective enzymatic digestion of native or synthetic ChTX by simultaneous exposure to chymotrypsin and trypsin yields identical reversed phase HPLC profiles. Analysis of the sequence and amino acid composition of the resulting fragments defines a disulfide bond arrangement (Cys7-Cys28, Cys13-Cys33, Cys17-Cys35) which differs from that previously suggested. This configuration predicts a highly folded tertiary structure for ChTX which, together with observations from electrophysiological and binding experiments, suggests a possible mechanism by which ChTX interacts with PK,Ca to block channel function.     

Cyclic lactam analogues of Ac-[Nle4]alpha-MSH4-11-NH2

Two side-chain cyclic lactam analogues of the 4-11 fragment of alpha-melanocyte-stimulating hormone (alpha-MSH), Ac-[Nle4,D-Orn5,Glu8]alpha-MSH4-11-NH2 and Ac-[Nle4,D-Orn5,D-Phe7,Glu8]alpha-MSH4-11-NH2, were prepared on p-methylbenzhydrylamine resin by using a combination of N alpha-Boc and N alpha-Fmoc synthetic strategies with diphenyl phosphorazidate mediated cyclization. The melanotropin activities of these two analogues were examined and compared relative to those of alpha-MSH, Ac-[Nle4]alpha-MSH4-11-NH2, and Ac-[Nle4,D-Phe7]alpha-MSH4-11-NH2. In the frog (Rana pipiens) skin bioassay, the L-Phe7 17-membered ring cyclic analogue was slightly more potent than the linear Ac-[Nle4]alpha-MSH4-11-NH2 and exhibited prolonged melanotropic bioactivity (greater than or equal to 4 h). In this same assay, the D-Phe7 cyclic analogue was more than 100-fold less potent than the L-Phe cyclic analogue and was 10,000 times less potent than linear Ac-[Nle4,D-Phe7]alpha-MSH4-11-NH2. In the lizard skin (Anolis carolinensis) bioassay, the L-Phe7 cyclic analogue was 100-fold less potent than Ac-[Nle4]alpha-MSH4-11-NH2, while the D-Phe7 cyclic analogue was 10,000-fold less potent than both Ac-[Nle4]alpha-MSH4-11-NH2 and the D-Phe7 linear derivative Ac-[Nle4,D-Phe7]alpha-MSH4-11-NH2. The solution conformation of these two cyclic analogues in dimethyl sulfoxide-d6 was examined by 1D and 2D 500-MHz 1H NMR spectroscopy. Our analysis suggests an H bond stabilized C10 (or C13) turn for the D-Phe7 cyclic structure while the L-Phe7 analogue is more conformationally flexible.(ABSTRACT TRUNCATED AT 250 WORDS)     

The regulation of mitochondrial DNA copy number in glioblastoma cells

As stem cells undergo differentiation, mitochondrial DNA (mtDNA) copy number is strictly regulated in order that specialized cells can generate appropriate levels of adenosine triphosphate (ATP) through oxidative phosphorylation (OXPHOS) to undertake their specific functions. It is not understood whether tumor-initiating cells regulate their mtDNA in a similar manner or whether mtDNA is essential for tumorigenesis. We show that human neural stem cells (hNSCs) increased their mtDNA content during differentiation in a process that was mediated by a synergistic relationship between the nuclear and mitochondrial genomes and results in increased respiratory capacity. Differentiating multipotent glioblastoma cells failed to match the expansion in mtDNA copy number, patterns of gene expression and increased respiratory capacity observed in hNSCs. Partial depletion of glioblastoma cell mtDNA rescued mtDNA replication events and enhanced cell differentiation. However, prolonged depletion resulted in impaired mtDNA replication, reduced proliferation and induced the expression of early developmental and pro-survival markers including POU class 5 homeobox 1 (OCT4) and sonic hedgehog (SHH). The transfer of glioblastoma cells depleted to varying degrees of their mtDNA content into immunocompromised mice resulted in tumors requiring significantly longer to form compared with non-depleted cells. The number of tumors formed and the time to tumor formation was relative to the degree of mtDNA depletion. The tumors derived from mtDNA depleted glioblastoma cells recovered their mtDNA copy number as part of the tumor formation process. These outcomes demonstrate the importance of mtDNA to the initiation and maintenance of tumorigenesis in glioblastoma multiforme.     

Effective Population Sizes with Multiple Paternity

While the concept of effective population size is of obvious applicability to many questions in population genetics and conservation biology, its utility has suffered due to a lack of agreement among its various formulations. Often, mathematical formulations for effective sizes apply restrictive assumptions that limit their applicability. Herein, expressions for effective sizes of populations that account for mating tactics, biases in sex ratios, and differential dispersal rates (among other parameters) are developed. Of primary interest is the influence of multiple paternity on the maintenance of genetic variation in a population. In addition to the standard inbreeding and variance effective sizes, intragroup (coancestral) and intergroup effective sizes also are developed. Expressions for effective sizes are developed for the beginning of nonrandom gene exchanges (initial effective sizes), the transition of gene correlations (instantaneous effective sizes), and the steady-state (asymptotic effective size). Results indicate that systems of mating that incorporate more than one male mate per female increase all effective sizes above those expected from polygyny and monogamy. Instantaneous and asymptotic sizes can be expressed relative to the fixation indices. The parameters presented herein can be utilized in models of effective sizes for the study of evolutionary biology and conservation genetics.     

Host cell-specific growth advantage of pseudorabies virus with a deletion in the genome sequences encoding a structural glycoprotein.

Several attenuated strains of pseudorabies virus contain genomes that carry a deletion in their short unique (Us) component. The sizes of the deletions are different in the various attenuated strains; the deletions may include part of one of the inverted repeats as well as part of the Us region of the genome. In most cases, the deletion includes the gene encoding the glycoprotein gI. The attenuated strains with a deletion in their S component have a common history of having been cultivated in chicken embryo fibroblasts (CEF). We show here that passage of wild-type virus in CEF promotes the emergence of populations of virions with a deletion in their S component. The emergence of these mutants is the result of their growth advantage over the wild type and is related to the lack of expression of gI, as shown by the following. (i) The Norden strain (which has a deletion in the Us) was marker rescued to restore an intact Us. The nonrescued Norden strain had a growth advantage over the rescued Norden strain in CEF. (ii) Passage of wild-type (gI+) virus in CEF but not in rabbit kidney or pig kidney cells resulted invariably in the emergence of virions whose genomes had a deletion in the S component. (iii) Passage of a gI- mutant in CEF did not result in the emergence of such virions. The emergence of virions with a deletion in their S component thus appears to be linked to gI expression. We conclude that gI is deleterious to the growth of pseudorabies virus in CEF and that this effect is cell type specific.     

DO BLACK-TAILED PRAIRIE DOGS MINIMIZE INBREEDING?

Considerable controversy surrounds the importance of inbreeding in natural populations. The rate of natural inbreeding and the influences of behavioral mechanisms that serve to promote or minimize inbreeding (e.g., philopatry vs. dispersal) are poorly understood. We studied inbreeding and social structuring of a population of black-tailed prairie dogs (Cynomys ludovicianus) to assess the influence of dispersal and mating behavior on patterns of genetic variation. We examined 15 years of data on prairie dogs, including survival and reproduction, social behavior, pedigrees, and allozyme alleles. Pedigrees revealed mean inbreeding coefficients (F) of 1–2%. A breeding-group model that incorporated details of prairie dog behavior and demography was used to estimate values of fixation indices (F-statistics). Model predictions were consistent with the minimization of inbreeding within breeding groups (“coteries,” asymptotic F_IL = –0.18) and random mating within the subpopulation (“colony,” asymptotic F_IS = 0.00). Estimates from pedigrees (mean F_IL = –0.23, mean F_IS = 0.00) and allozyme data (mean F_IL = –0.21, mean F_IS = –0.01) were consistent with predictions of the model. The breeding-group model, pedigrees, and allozyme data showed remarkably congruent results, and indicated strong genetic structuring within the colony (F_LS = 0.16, 0.19, and 0.17, respectively). We concluded that although inbreeding occurred in the colony, the rate of inbreeding was strongly minimized at the level of breeding groups, but not at the subpopulation level. The behavioral mechanisms most important to the minimization of inbreeding appeared to be patterns of male-biased dispersal of both subadults and adults, associated with strong philopatry of females. Incest avoidance also occurred, associated with recognition of close kin via direct social learning within the breeding groups.     

Ray Wu’s Golden Rules: How he achieved greatness in work, and in life

Overview When Ray Wu passed away on February 10, 2008, he was 79, working full-time in his lab at Cornell University, and was at or near the top of his long and noteworthy career. He had developed the first method for DNA sequencing and pioneered recombinant DNA technology. He had identified key genes related to stress tolerance in plants and was poised to apply these to boost crop yields of rice and other