The mitochondrial genome of Chlamydomonas. II. Genetic analysis of non-mendelian obligate photautotrophic mutants

Summary Among a collection of obligate photoautotrophic (dark-dier,dk) mutants isolated inChlamydomonas reinhardtii, two have been found which are inherited in crosses to wild type in a non-Mendelian, biparental and apparently random fashion. F₁ progeny include not only cells which show thedk and wildtype parental phenotypes but also many which possess intermediate phenotypes between wild type anddk. When F₁ progeny withdk, intermediate or wild-type phenotype were backcrossed to wild type, thedk phenotype continued to be inherited in a biparental and random fashion. Upon selection, neither mutant formed stable clones producing onlydk progeny, suggesting that the two mutants segregatedk and wild-type progeny somatically and that the homozygousdk condition may be lethal. The biparental transmission of these two non-Mendeliandk mutations resembles the transmission of acriflavin-inducedminute mutations ofChlamydomonas and is distinct from the uniparentally inherited chloroplast mutations of this alga. Both thedk andminute mutations may alter mitochondrial DNA and thereby alter mitochondrial functions.     

Frequency distributions for chloroplast genes in Chlamydomonas zygote clones: Evidence for random drift

Mitochondria and chloroplasts of eucaryotic cells contain populations of DNA molecules. In certain cases, e.g., the chloroplasts of Chlamydomonas reinhardtii and the mitochondria of Saccharomyces cerevisiae, organelles contributed by the two parents are known to fuse in the zygote, creating a single population of DNA molecules. In a cross, this population will include molecules of both parental genotypes. There is reason to suspect that organelle DNA molecules in this population are selected randomly for replication and recombination. This would result in random changes in the frequency of a particular allele or genotype within the organelle gene pool of a single zygote and also within its clone of progeny cells. A given gene frequency would increase in some zygote clones and decrease in others, analogous to random drift of gene frequencies in small Mendelian populations. To test this, we have examined the distribution of chloroplast gene frequencies among the zygote clones produced in each of a number of crosses of Chlamydomonas. These distributions are typically U or L shaped as predicted by the random drift hypothesis. They include uniparental zygote clones, in which a chloroplast allele from one parent has been fixed (frequency 100%) and the alternative allele from the other parent has been lost (frequency 0%). Among the remaining (biparental) zygote clones, there is a linear distribution of allele frequencies, showing a great increase in variance over the input frequencies. In these experiments both biparental and uniparental zygotes show a bias favoring chloroplast alleles from the mt⁺ (maternal) parent, and there is no statistically significant mode at the allele frequency of 0.5 corresponding to the equal input of alleles from the maternal and paternal (mt^?) parents. The observed distributions support the hypothesis that both uniparental inheritance and the high variance of allele frequencies among zygote clones are due to random drift of allele frequencies, coupled with a directional force which favors fixation of the maternal allele. In addition, statistical analysis of the data shows a strong but incomplete tendency for linked chloroplast markers to be fixed or lost together in uniparental zygotes. Possible cellular and molecular mechanisms for these observations are discussed.     

Calcium-dependent stimulation of BALB/c 3T3 mouse cell DNA synthesis by a tumor-promoting phorbol ester (PMA).

During the first six passages after their arrival in this laboratory, BALB/c 3T3 mouse cells did not proliferate in serum containing-medium having an ionic calcium concentration of 0.05 mM or less, but by the ninth passage they had become able to multiply in the presence of these lower calcium levels. In low calcium (e.g., 0.02 mM) medium, passage 1-6, cells in sparse cultures were blocked at the Gl/S boundary of their cycle. These blocked cells could be induced to start making DNA within only one hour either by returning the ionic calcium level to a normal range of values (1.25 mM), or by adding 0.05 mug/ml of PMA (12-O-tetradecanoyl-phorbol-13-acetate). PMA probably acted by sensitizing the blocked cells to calcium rather than replacing the ion, because it was ineffective in ionic calcium-free medium. Finally, PMA did not by itself induce proliferation of cells (regardless of the number of passages) which had been proliferatively inactivated by density-dependent factors in confluent cultures. However, PMA did promote DNA synthesis by these cells during their brief transition to the "cycling" state caused by exposure to fresh serum-containing medium.     

A limited survey of aflatoxins and fumonisins in retail maizebased products in the UK using immunoassay detection

A total of 27 maize-based products destined for human consumption were collected from retail outlets within the city of Glasgow in the UK and were analysed for the presence of aflatoxins using immunoaftinity column chromatography with fluorescence detection and for fumonisins by competitive ELISA. Aflatoxins were detected at a trace level below 4 in eight (30%) of the 27 samples tested, no sample contained aflatoxins at a high level although one sample of sweetcorn did contain aflatoxins at a level of 5-10 Fumonisins were detected in eight (30%) of the samples at levels from 1 to 8mgkg^-1 and a further eight samples contained fumonisin at a level below 1 mgkg^-1 but above the detectable level. The highest concentration of fumonisins was found in a sample of fine corn meal at 8-12mgkg^-1.     

Stimulation of DNA synthesis by an inositol polyphosphate-activated protein phosphatase in calcium-deprived rat liver cells

Specific stages of the prereplicative G1 phase of the cell cycle in nonneoplastic cells requires extracellular Ca2+ for successful transition. These are the G0-G1 and the G1-S transitions. A variety of agents are able to replace Ca2+ and to at least partially stimulate cells to replicate their chromosomes. One of these agonist, inositol 1,3,4,5-tetrakisphosphate [Ins(1,3,4,5)P4], has been demonstrated by us to also stimulate the activity of a phosphoprotein phosphatase. The addition of a purified preparation of the protein phosphatase to Ca2(+)-deprived G1-S-blocked T51B rat liver cells stimulates a rapidly responding fraction of cells to enter their S phase, and this effect is blocked by protein phosphatase inhibitors heparin and inhibitor 2.     

Mechanical coupling of the rib cage, abdomen, and diaphragm through their area of apposition

Although volumetric displacements of the chest wall are often analyzed in terms of two independent parallel pathways (rib cage and abdomen), Loring and Mead have argued that these pathways are not mechanically independent (J. Appl. Physiol. 53: 756-760, 1982). Because of its apposition with the diaphragm, the rib cage is exposed to two distinct pressure differences, one of which depends on abdominal pressure. Using the analysis of Loring and Mead as a point of departure, we developed a complementary analysis in which mechanical coupling of the rib cage, abdomen, and diaphragm is modeled by a linear translational transformer. This model has the advantage that it possesses a precise electrical analogue. Pressure differences and compartmental displacements are related by the transformation ratio (n), which is the mechanical advantage of abdominal over pleural pressure changes in displacing the rib cage. In the limiting case of very high lung volume, n----0 and the pathways uncouple. In the limit of very small lung volume, n----infinity and the pathways remain coupled; both rib cage and abdomen are driven by abdominal pressure alone, in accord with the Goldman-Mead hypothesis. A good fit was obtained between the model and the previously reported data for the human chest wall from 0.5 to 4 Hz (J. Appl. Physiol. 66:350-359, 1989). The model was then used to estimate rib cage, diaphragm, and abdominal elastance, resistance, and inertance. The abdomen was a high-elastance high-inertance highly damped compartment, and the rib cage a low-elastance low-inertance more lightly damped compartment. Our estimate that n = 1.9 is consistent with the findings of Loring and Mead and suggests substantial pathway coupling.     

Partial protein domains: evolutionary insights and bioinformatics challenges

Protein domains are generally thought to correspond to units of evolution. New research raises questions about how such domains are defined with bioinformatics tools and sheds light on how evolution has enabled partial domains to be viable.With the rapid expansion in the number of determined protein sequences - over 92 million in UniProt in March 2015 - an ever-increasing number of biologists are using bioinformatics tools for annotation of these sequences. One widely used strategy is to identify occurrences of Pfam families within the sequence of interest [1]. A Pfam family is a multiple sequence alignment of the occurrences of a particular domain both in different species and in different regions of the same protein. The concept underpinning Pfam is that proteins typically comprise one or more domains (regions), each of which is an evolutionary unit that generally has a well-defined biological function. A significant sequence similarity between a query protein and a Pfam family provides the basis for annotations. Two recent articles [2,3] in Genome Biology evaluate the implications of having the query sequence only matching part of a Pfam family, which is an intriguing finding, given that a Pfam family is considered to be an evolutionary unit.     

The evolutionary emergence of stochastic phenotype switching in bacteria

Stochastic phenotype switching - or bet hedging - is a pervasive feature of living systems and common in bacteria that experience fluctuating (unpredictable) environmental conditions. Under such conditions, the capacity to generate variable offspring spreads the risk of being maladapted in the present environment, against offspring likely to have some chance of survival in the future. While a rich subject for theoretical studies, little is known about the selective causes responsible for the evolutionary emergence of stochastic phenotype switching. Here we review recent work - both theoretical and experimental - that sheds light on ecological factors that favour switching types over non-switching types. Of particular relevance is an experiment that provided evidence for an adaptive origin of stochastic phenotype switching by subjecting bacterial populations to a selective regime that mimicked essential features of the host immune response. Central to the emergence of switching types was frequent imposition of 'exclusion rules' and 'population bottlenecks' - two complementary faces of frequency dependent selection. While features of the immune response, exclusion rules and bottlenecks are likely to operate in many natural environments. Together these factors define a set of selective conditions relevant to the evolution of stochastic switching, including antigenic variation and bacterial persistence.     

Scats and den contents as indicators of the diet of stoats (Mustela erminea) in the Tasman Valley,South Canterbury,New Zealand

Stoats are significant predators of native fauna in New Zealand. They occur in many habitat types and consume a wide range of prey. The diet of stoats in the Tasman River, South Canterbury, was studied by analysis of scats and den contents. Analysis of 206 scats showed that stoats ate mainly lagomorphs, birds and invertebrates. Minor components included mice, lizards, fish and hedgehogs. Stoats ate more birds in spring than in autumn, and female stoats ate more invertebrates than did males. The contents of 219 dens collected in the same area at the same time provided further information. Birds and lagomorphs occurred at high frequency in dens, and other components were minor. Remains in dens were larger than in scats and allowed identification of many more prey items to species level. Den contents revealed a potentially substantial impact of stoats on threatened shorebirds locally; this impact was not detected by analysis of scats.