Environmental Determination of Selective Significance or Neutrality of Amylase Variants in DROSOPHILA MELANOGASTER

Strains homozygous at the amylase locus were derived from a polymorphic laboratory population of Drosophila melanogaster. The Amy ^4,6 strain has higher enzyme activity than the Amy¹ strain.——Maltose has the same nutritional value as starch.——The effect of starch in pure culture depends on the yeast level. At low yeast level increasing starch increases survival, at high yeast level increasing starch increases mean dry weight. The strains do not differ in survival or mean dry weight in pure culture.——In mixed cultures at 50% input of Amy ^4,6 and Amy¹ as larvae the percentage Amy^4,6 in adults increases with increasing starch at low yeast levels, but equals input frequency at high yeast levels. No increase in percentage Amy^4,6 in adults is present with increasing maltose at low yeast levels in mixed culture. The increase in percentage Amy^4,6 with increasing starch must be due to selection on the amylase locus working by competition for food in the larval stage. The single locus selection coefficient is determined by the environment and can reach quite high values.——Viability selection in the presence of starch is in the direction indicated by the enzyme activities.     

Genetic Analysis of the Dumpy Complex Locus in DROSOPHILA MELANOGASTER: Complementation, Fine Structure and Function

An extensive genetic analysis of the dumpy locus is presented. This study includes complementation, fine structure mapping and allelic interaction. A number of complementing recessive lethals of the dp complex have been genetically mapped. Two alleles of the ol(v) type that complement l alleles map to the left portion of the locus. A number of olv alleles that complement both l and lv lethals map within the right portion of the locus.——Fine-structure analysis demonstrated that both olv and o alleles are distributed among various subloci. Evidence for spacer regions between subloci is presented.——An extensive discussion of the data considers whether the locus is unicistronic or multicistronic. The conclusion reached is that the locus is not a single functional cistron. The possibility of a single cistron encoding a multifunctional polypeptide is discussed.——The hypothesis is proposed that the left portion of the map and the l mutations function as regulatory sequences and that the right portion of the map encodes structural sequences.     

BASE: A novel workflow to integrate nonubiquitous genes in comparative genomics analyses for selection

Inferring the selective forces that orthologous genes underwent across different lineages can help us understand the evolutionary processes that have shaped their extant diversity and the phenotypes they underlie. The most widespread metric to estimate the selection regimes of coding genes—across sites and phylogenies—is the ratio of nonsynonymous to synonymous substitutions (dN/dS, also known as ω). Nowadays, modern sequencing technologies and the large amount of already available sequence data allow the retrieval of thousands of orthologous genes across large numbers of species. Nonetheless, the tools available to explore selection regimes are not designed to automatically process all genes, and their practical usage is often restricted to the single‐copy ones which are found across all species considered (i.e., ubiquitous genes). This approach limits the scale of the analysis to a fraction of single‐copy genes, which can be as low as an order of magnitude in respect to those which are not consistently found in all species considered (i.e., nonubiquitous genes). Here, we present a workflow named BASE that—leveraging the CodeML framework—eases the inference and interpretation of gene selection regimes in the context of comparative genomics. Although a number of bioinformatics tools have already been developed to facilitate this kind of analyses, BASE is the first to be specifically designed to allow the integration of nonubiquitous genes in a straightforward and reproducible manner. The workflow—along with all relevant documentation—is available at github.com/for‐giobbe/BASE.     

Microbial Degradation of Natural Rubber Vulcanizates

An actinomycete, Nocardia sp. strain 835A, grows well on unvulcanized natural rubber and synthetic isoprene rubber, but not on other types of synthetic rubber. Not only unvulcanized but also various kinds of vulcanized natural rubber products were more or less utilized by the organism as the sole source of carbon and energy. The thin film from a latex glove was rapidly degraded, and the weight loss reached 75% after a 2-week cultivation period. Oligomers with molecular weights from 10⁴ to 10³ were accumulated during microbial growth on the latex glove. The partially purified oligomers were examined by infrared and ¹H nuclear magnetic resonance and ¹³C nuclear magnetic resonance spectroscopy, and the spectra were those expected of cis-1, 4-polyisoprene with the structure, OHC—CH₂—[—CH₂—C(—CH₃)=CH —CH₂—]_n—CH₂—C(=O)— CH₃, with average values of n of about 114 and 19 for the two oligomers.     

Proportionality: A Valid Alternative to Correlation for Relative Data

In the life sciences, many measurement methods yield only the relative abundances of different components in a sample. With such relative—or compositional—data, differential expression needs careful interpretation, and correlation—a statistical workhorse for analyzing pairwise relationships—is an inappropriate measure of association. Using yeast gene expression data we show how correlation can be misleading and present proportionality as a valid alternative for relative data. We show how the strength of proportionality between two variables can be meaningfully and interpretably described by a new statistic ϕ which can be used instead of correlation as the basis of familiar analyses and visualisation methods, including co-expression networks and clustered heatmaps. While the main aim of this study is to present proportionality as a means to analyse relative data, it also raises intriguing questions about the molecular mechanisms underlying the proportional regulation of a range of yeast genes.     

Two Chromosomal Genes Required for Killing Expression in Killer Strains of SACCHAROMYCES CEREVISIAE

The killer character of yeast is determined by a 1.4 x 10⁶ molecular weight double-stranded RNA plasmid and at least 12 chromosomal genes. Wild-type strains of yeast that carry this plasmid (killers) secrete a toxin which is lethal only to strains not carrying this plasmid (sensitives). ——— We have isolated 28 independent recessive chromosomal mutants of a killer strain that have lost the ability to secrete an active toxin but remain resistant to the effects of the toxin and continue to carry the complete cytoplasmic killer genome. These mutants define two complementation groups, kex1 and kex2. Kex1 is located on chromosome VII between ade5 and lys5. Kex2 is located on chromosome XIV, but it does not show meiotic linkage to any gene previously located on this chromosome. ——— When the killer plasmid of kex1 or kex2 strains is eliminated by curing with heat or cycloheximide, the strains become sensitive to killing. The mutant phenotype reappears among the meiotic segregants in a cross with a normal killer. Thus, the kex phenotype does not require an alteration of the killer plasmid. ——— Kex1 and kex2 strains each contain near-normal levels of the 1.4 x 10⁶ molecular weight double-stranded RNA, whose presence is correlated with the presence of the killer genome.     

Developmental Analysis of the Wing Disc in the Mutant Engrailed of DROSOPHILA MELANOGASTER

The engrailed (en) mutation leads to the transformation of the posterior structures of the dorsal mesothoracic disc into those characteristic of the anterior region of the same disc. Similar posterior-anterior duplications have been detected in dorsal as well as ventral structures of all the thoracic segments. —Genetic combinations of en with other pattern mutants have shown their synergistic effect on the posterior wing pattern.—A clonal analysis of the en wing disc shows that en affects its development in a characteristic way. The genetic change, by induced mitotic recombination, of en⁺ into en cells is followed by the corresponding transformation, except when it takes place some cell divisions prior to differentiation.—The en posterior wing disc cells show positive affinities with normal anterior wing disc cells in aggregates.—The mode of action of the en⁺ locus controlling wing disc development is discussed.     

Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication

Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex duplication—inverted triplication—duplication (DUP-TRP/INV-DUP) rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals—16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homology—or homeology—driven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication and potentially higher order amplification of a genomic interval can occur in a manner consistent with rolling circle amplification as predicted by the microhomology-mediated break induced replication (MMBIR) model.     

PARENT DEVELOPMENT

Today''s parents tend to be overwhelmed with advice from many sources. In his role as family counselor, the pediatrician must understand and consider the emotional development of parents in relation to their child''s development; otherwise, his advice and counsel do not “take” and he becomes tired and frustrated and angry.Parents progress through definite stages of development: Stage 1: Learning the cues—the struggle of the parents to interpret the infant''s needs. Stage 2: Learning to accept growth and development—the parent learning to accept some loss of control of the toddler. Stage 3: Learning to separate—the parent learning to allow the child to develop independently. Stage 4: Learning to accept rejection, without deserting—the struggle of the parents not to intrude and yet to be there when needed. Stage 5: Learning to build a new life having been thoroughly discredited by one''s teenager—the parent learning to live independently while the teenager struggles to develop his own identity.The pediatrician who is accepting, sensitive and a good listener and who keeps in mind that parents as well as children have capacities for growth and development, will be a potent factor in promoting good parent-child relationships and many times more effective in dealing with the child in health and disease.     

Nutritional biology: a neglected basic discipline of nutritional science

On the basis of a scientific-philosophical analysis, this paper tries to show that the approaches in current nutritional science—including its subdisciplines which focus on molecular aspects—are predominantly application-oriented. This becomes particularly evident through a number of conceptual problems characterized by the triad of ‘dearth of theoretical foundation,’ ‘particularist research questions,’ and ‘reductionist understanding of nutrition.’ The thesis presented here is that an interpretive framework based on nutritional biology is able to shed constructive light on the fundamental problems of nutritional science. In this context, the establishment of ‘nutritional biology’ as a basic discipline in research and education would be a first step toward recognizing the phenomenon of ‘nutrition’ as an oecic process as a special case of an organism–environment interaction. Modern nutritional science should be substantively grounded on ecological—and therefore systems biology as well as organismic—principles. The aim of nutritional biology, then, should be to develop near-universal ‘law statements’ in nutritional science—a task which presents a major challenge for the current science system.     

Effect of Mating Structure on Variation in Linkage Disequilibrium

Measurement of linkage disequilibrium involves two sampling processes. First, there is the sampling of gametes in the population to form successive generations, and this generates disequilibrium dependent on the effective population size (N_e) and the mating structure. Second, there is sampling of a finite number (n) of individuals to estimate the population disequilibrium.——Two-locus descent measures are used to describe the mating system and are transformed to disequilibrium moments at the final sampling. Approximate eigenvectors for the transition matrix of descent measures are used to obtain formulae for the variance of the observed disequilibria as a function of N_e, mating structure, n, and linkage or recombination parameter.——The variance of disequilibrium is the same for monoecious populations with or without random selfing and for dioecious populations with random pairing for each progeny. With monogamy, the variance is slightly higher, the proportional difference being greater for unlinked loci.     

Use of a Novel Fluorinated Organosulfur Compound To Isolate Bacteria Capable of Carbon-Sulfur Bond Cleavage

The vacuum residue fraction of heavy crudes contributes to the viscosity of these oils. Specific microbial cleavage of C—S bonds in alkylsulfide bridges that form linkages in this fraction may result in dramatic viscosity reduction. To date, no bacterial strains have been shown conclusively to cleave C—S bonds within alkyl chains. Screening for microbes that can perform this activity was greatly facilitated by the use of a newly synthesized compound, bis-(3-pentafluorophenylpropyl)-sulfide (PFPS), as a novel sulfur source. The terminal pentafluorinated aromatic rings of PFPS preclude growth of aromatic ring-degrading bacteria but allow for selective enrichment of strains capable of cleaving C—S bonds. A unique bacterial strain, Rhodococcus sp. strain JVH1, that used PFPS as a sole sulfur source was isolated from an oil-contaminated environment. Gas chromatography-mass spectrometry analysis revealed that JVH1 oxidized PFPS to a sulfoxide and then a sulfone prior to cleaving the C—S bond to form an alcohol and, presumably, a sulfinate from which sulfur could be extracted for growth. Four known dibenzothiophene-desulfurizing strains, including Rhodococcus sp. strain IGTS8, were all unable to cleave the C—S bond in PFPS but could oxidize PFPS to the sulfone via the sulfoxide. Conversely, JVH1 was unable to oxidize dibenzothiophene but was able to use a variety of alkyl sulfides, in addition to PFPS, as sole sulfur sources. Overall, PFPS is an excellent tool for isolating bacteria capable of cleaving subterminal C—S bonds within alkyl chains. The type of desulfurization displayed by JVH1 differs significantly from previously described reaction results.     

Characteristics of the process of enzyme release from secretory plant cells

Secretion—the outward movement of molecules across the plasmalemma—of α-amylase by barley (Hordeum vulgare L. cv. Himalaya) aleurone layers is an energy-dependent process that is not directly dependent upon protein synthesis or RNA synthesis and does not appear to be under the direct control of gibberellic acid or abscisic acid. Release—the movement of the secreted α-amylase molecules through the walls into the surrounding medium—is apparently diffusion limited and is markedly dependent upon the presence of ions.     

Entrainment of Lemna CO(2) Output Through Phytochrome

The entrainability of Lemna perpusilla CO₂ output by periodic 15 minute red (R) and far red (F) illuminations was tested in low nitrate medium. R every 8 hour, symbolized R/R/R, gives a flat output (no entrainment) as does F/F/F. However, R/—/— (R every 24 hour) entrains rapidly, and F/—/— does so as well, in a similar manner. The effects of R/R/— and F/F/— also resemble each other closely. Entrainment by R/F/F or R/R/F is rapid and indifferent to order of presentation, e.g., R/F/F and F/R/F lead to the same steady state. Typical phytochrome reversals occur, e.g., R,F/F/F holds output flat, while F,R/F/F entrains in the manner of R/F/F. Blue (B) light acts like R in schedules such as B/F/F but like F in schedules such as B/R/R. In all schedules studied, the zeitgeber (primary synchronizer) appears to be the sharpest transition from a low to a high level of far red-absorbing phytochrome that occurs with a 24-hr periodicity. Thus in entrainment, and by inference in photoperiodic timing, the level of far red-absorbing phytochrome at any time may be less significant than the succession of levels of which it is a part, a conclusion that implies the existence of a “scanning” mechanism that compares levels of far red-absorbing phytochrome at various times of day.     

Predicting distributions of Wolbachia strains through host ecological contact—Who's manipulating whom?

Reproductive isolation in response to divergent selection is often mediated via third‐party interactions. Under these conditions, speciation is inextricably linked to ecological context. We present a novel framework for understanding arthropod speciation as mediated by Wolbachia, a microbial endosymbiont capable of causing host cytoplasmic incompatibility (CI). We predict that sympatric host sister‐species harbor paraphyletic Wolbachia strains that provide CI, while well‐defined congeners in ecological contact and recently diverged noninteracting congeners are uninfected due to Wolbachia redundancy. We argue that Wolbachia provides an adaptive advantage when coupled with reduced hybrid fitness, facilitating assortative mating between co‐occurring divergent phenotypes—the contact contingency hypothesis. To test this, we applied a predictive algorithm to empirical pollinating fig wasp data, achieving up to 91.60% accuracy. We further postulate that observed temporal decay of Wolbachia incidence results from adaptive host purging—adaptive decay hypothesis—but implementation failed to predict systematic patterns. We then account for post‐zygotic offspring mortality during CI mating, modeling fitness clines across developmental resources—the fecundity trade‐off hypothesis. This model regularly favored CI despite fecundity losses. We demonstrate that a rules‐based algorithm accurately predicts Wolbachia infection status. This has implications among other systems where closely related sympatric species encounter adaptive disadvantage through hybridization.     

Rate of Gene Silencing at Duplicate Loci: A Theoretical Study and Interpretation of Data from Tetraploid Fishes

A large-scale simulation has been conducted on the rate of gene loss at duplicate loci under irreversible mutation. It is found that tight linkage does not provide a strong sheltering effect, as thought by previous authors; indeed, the mean loss time for the case of tight linkage is of the same order of magnitude as that for no linkage, as long as Nu is not much larger than 1, where N is the effective population size and u the mutation rate. When Nu is 0.01 or less, the two loci behave almost as neutral loci, regardless of linkage, and the mean loss time is about only half the mean extinction time for a neutral allele under irreversible mutation. However, the former becomes two or more times larger than the latter when Nu ≥ 1.——In the simulation, the sojourn times in the frequency intervals (0, 0.01) and (0.99, 1) and the time for the frequency of the null allele to reach 0.99 at one of the two loci have also been recorded. The results show that the population is monomorphic for the normal allele most of the time if Nu ≤ 0.01, but polymorphic for the null and the normal alleles most of the time if Nu ≥ 0.1.——The distribution of the frequency of the null allele in an equilibrium tetraploid population has been studied analytically. The present results have been applied to interpret data from some fish groups that are of tetraploid origin, and a model for explaining the slow rate of gene loss in these fishes is proposed.     

Mobilization and utilization of cyanogenic glycosides: the linustatin pathway

In the seeds of Hevea brasiliensis, the cyanogenic monoglucoside linamarin (2-β-d-glucopyranosyloxy-2-methylpropionitrile) is accumulated in the endosperm. After onset of germination, the cyanogenic diglucoside linustatin (2-[6-β-d-glucosyl-β-d-glucopyranosyloxy]-2- methylpropionitrile) is formed and exuded from the endosperm of Hevea seedlings. At the same time the content of cyanogenic monoglucosides decreases. The linustatin-splitting diglucosidase and the β-cyanoalanine synthase that assimilates HCN, exhibit their highest activities in the young seedling at this time. Based on these observations the following pathway for the in vivo mobilization and metabolism of cyanogenic glucosides is proposed: storage of monoglucosides (in the endosperm)—glucosylation—transport of the diglucoside (out of the endosperm into the seedling)—cleavage by diglucosidase—reassimilation of HCN to noncyanogenic compounds. The presence of this pathway demonstrates that cyanogenic glucosides, typical secondary plant products serve in the metabolism of developing plants as N-storage compounds and do not exclusively exhibit protective functions due to their repellent effect.