Natural and synthetic alleles provide complementary insights into the nature of selection acting on the Men polymorphism of Drosophila melanogaster

Two malic enzyme alleles, Men^113A and Men^113G, occur at approximately equal frequency in North American populations of Drosophila melanogaster, while only Men^113A occurs in African populations. We investigated the population genetics, biochemical characteristics, and selective potential of these alleles. Comparable levels of nucleotide polymorphism in both alleles suggest that the Men^113G allele is not recently derived, but we find no evidence in the DNA sequence data for selection maintaining the polymorphism. Interestingly, the alleles differ in both V_max and K_m for the substrate malate. Triglyceride concentration and isocitrate dehydrogenase (IDH) and glucose-6-phosphate dehydrogenase (G6PD) activities are negatively correlated with the in vivo activities of the Men alleles. We examined the causality of the observed correlations using P-element excision-derived knockout alleles of the Men gene and found significant changes in the maximum activities of both IDH and G6PD, but not in triglyceride concentration, suggesting compensatory interactions between MEN, IDH, and G6PD. Additionally, we found significantly higher than expected levels of MEN activity in knockout heterozygotes, which we attribute to transvection effects. The distinct differences in biochemistry and physiology between the naturally occurring alleles and between the engineered alleles suggest the potential for selection on the Men locus.     

A Combination of Structural and Cis-Regulatory Factors Drives Biochemical Differences in Drosophila melanogaster Malic Enzyme

The evolutionary significance of molecular variation is still contentious, with much current interest focusing on the relative contribution of structural changes in proteins versus regulatory variation in gene expression. We present a population genetic and biochemical study of molecular variation at the malic enzyme locus (Men) in Drosophila melanogaster. Two amino acid polymorphisms appear to affect substrate-binding kinetics, while only one appears to affect thermal stability. Interestingly, we find that enzyme activity differences previously assigned to one of the polymorphisms may, instead, be a function of linked regulatory differences. These results suggest that both regulatory and structural changes contribute to differences in protein function. Our examination of the Men coding sequences reveals no evidence for selection acting on the polymorphisms, but earlier work on this enzyme indicates that the biochemical variation observed has physiological repercussions and therefore could potentially be under natural selection.     

Comments on some taxonomic changes affecting marine Bivalvia of the New Zealand region recently introduced in Huber's Compendium of bivalves,with some additional taxonomic changes

The recent Compendium of bivalves by Huber [(2010) Compendium of bivalves. ConchBooks, Hackenheim] introduces a large number of taxonomic and nomenclatural changes across the Bivalvia, worldwide. In this paper, we discuss a number of these changes that pertain to the New Zealand fauna. Although many of Huber's changes are justified, we find that there are a significant number with which we disagree, noting that many of them have been made in poorly understood groups with what seems to us rather weak evidence for the change. We have been guided by the belief that, in such cases, one should opt for taxonomic stability and await stronger data. We also argue that in a number of these difficult groups such data are likely to be molecular. We note also that in reviewing some of these cases, it has been convenient to make a small number of original changes. Recent records of Lima mestayerae Marwick, 1924 are based on mislocalised specimens of Lima nimbifer Iredale, 1924 from eastern Australia. Specimens from the New Zealand region identified as Pteria avicula [sic] (Holten, 1802) are Pteria levitata (Iredale, 1939). We suggest also that Semele brambleyae Powell, 1967 is adventive, probably the Asian Semele vestalis (A. Adams in Reeve, 1853).     

Yeast strains from the Schirmacher Oasis,Antarctica

Summary Soil samples from the Schirmacher Oasis of Antarctica were examined for the presence of yeasts. The number of yeast cells in the samples varied between 600 and 3000 g of wet soil. Eight pure cultures were obtained. All of the eight isolates were nonfermentative and all but one was Diazonium Blue B (DBB)-positive, indicating their basidiomycetous affinity. Based on their morphology, reproductive behavior, growth at different temperatures and salt concentrations, nutritional characteristies and various biochemical tests, all the eight cultures have been identified. Three of them are red yeasts, Rhodotorula rubra, one Bullera alba, one a dimorphic, Candida humicola and one Candida famata. The remaining two cultures have been tentatively identified as Candida ingeniosa and Candida auriculariae.     

A comparative structural and functional analysis of cyanobacterial plastocyanin and cytochrome c 6 as alternative electron donors to Photosystem I

Plastocyanin and cytochrome c ₆ are two soluble metalloproteins that act as alternative electron carriers between the membrane-embedded complexes cytochromes b ₆ f and Photosystem I. Despite plastocyanin and cytochrome c ₆ differing in the nature of their redox center (one is a copper protein, the other is a heme protein) and folding pattern (one is a β-barrel, the other consists of α-helices), they are exchangeable in green algae and cyanobacteria. In fact, the two proteins share a number of structural similarities that allow them to interact with the same membrane complexes in a similar way. The kinetic and thermodynamic analysis of Photosystem I reduction by plastocyanin and cytochrome c ₆ reveals that the same factors govern the reaction mechanism within the same organism, but differ from one another. In cyanobacteria, in particular, the electrostatic and hydrophobic interactions between Photosystem I and its electron donors have been analyzed using the wild-type protein species and site-directed mutants. A number of residues similarly conserved in the two proteins have been shown to be critical for the electron transfer reaction. Cytochrome c ₆ does contain two functional areas that are equivalent to those previously described in plastocyanin: one is a hydrophobic patch for electron transfer (site 1), and the other is an electrically charged area for complex formation (site 2). Each cyanobacterial protein contains just one arginyl residue, similarly located between sites 1 and 2, that is essential for the redox interaction with Photosystem I. This revised version was published online in June 2006 with corrections to the Cover Date.     

Transformation of Mycoplasma capricolum and Examination of DNA Restriction Modification in M. capricolum and Mycoplasma mycoides subsp. mycoides

Plasmids pIKΔ and pIKΔ-erm have recently been developed as mycoplasmal cloning vectors. In this report, we demonstrate that these plasmids can replicate in Mycoplasma capricolum, a mycoplasmal species for which transformation had not previously been characterized. Both plasmids are stably maintained at a higher copy number than in their parental species, Mycoplasma mycoides subsp. mycoides. We have also examined the possibility of one or more restriction-modification systems affecting transformation frequencies in both species.     

Rusophycus carleyi (James, 1885), Trace Fossils from the Lower Ordovician of Southern Morocco,and the Trilobites that Made Them

Thin-bedded, pyrite-rich, fine sandstones and mudstones of the Floian-Dapingian Upper Fezouata Formation contain abundant trace fossils Rusophycus carleyi in close association with a species of the asaphid trilobite Asaphellus. The sizes and shapes of this trilobite and the traces match closely. Five specimens have even been found where an articulated specimen of Asaphellus appears to be directly located over a specimen of Rusophycus carleyi within a thin bed of sandstone, suggesting that the trilobite animal may have been trapped on top of a trace that it had just made. Such intimate associations between a putative tracemaker and a trace are rare in the fossil record and particularly rare for Trilobita. The number of coxal impressions that form part of R. carleyi, eleven, matches the number expected for an asaphid trilobite (one for each of eight thoracic segments and one for each of three post-oral cephalic appendages). Impressions of the hypostome, thoracic tip impressions, cephalic margin, and pygidial margin in a few of the traces also match those of this asaphid trilobite. R. carleyi has been found in Ordovician strata of other parts of the world in association with asaphid trilobites.     

Changes in butterfly communities over a 10‐year period in Geum river basin in Korea

One conclusion of this study is that as the road network expands in rural and remote areas the surrounding butterfly populations are generally noted to be decreasing or even disappearing. However, there is one exception, Libythea celtis. This common species, living close to forested areas, have actually increased while thier competing species have decreased according to this study. The endangered species of Korea, Parnassius bremeri, Sinia divina and Argynnis nerippe, which inhabit the area of the study have also decreased or disappeared. Another result of this study is that, while the number of species which inhabit the grasslands have decreased, no similar changes have been noted in the number for the species which inhabit the shrubs. Furthermore, there has been a growth in the numbers of the species that inhabit trees. In addition, the number of individuals has decreased in the grasslands and shrubs but increased in the trees. Overall, the general conclusion of this study is that, while the development of rural and remote areas showed a decrease in the number of specific butterfly species, they are being replaced by more common species.     

Evolutionary changes in the integument of the onychophoran Plicatoperipatus jamaicensis (Peripatidae)

The dorsal integument of nearly all species of Peripatidae—one of the two major subgroups of Onychophora (velvet worms)—typically exhibits 12 plicae (=annuli) per segment. The only exception might occur in Plicatoperipatus jamaicensis, from which 24 putative plicae per segment have been reported. Hence, the number of plicae might have been duplicated in this species. If so, one would expect that the structure of the duplicated plicae would resemble that of all other onychophoran species, and that the structures commonly associated with the plicae, including crater‐shaped papillae and hyaline organs, would also have been duplicated. To clarify whether there was indeed such duplication, we compared the structure of the integument in embryos and adults of Pl. jamaicensis (with the putative number of 24 plicae per segment) and Principapillatus hitoyensis (with the common number of 12 plicae per segment). Our scanning electron microscopic data revealed that embryos of both species have 12 plicae per segment. While this number persists in adults of Pr. hitoyensis, 12 additional rows of papillae (=pseudoplicae) occur in the dorsal integument in adults of Pl. jamaicensis. These pseudoplicae differ from the typical plicae of other onychophorans in that they are not equipped with primary papillae and are situated in furrows between the true plicae, as evidenced by the position of hyaline organs and crater‐shaped papillae. Our data further show that the number of the ventrolateral plicae, crater‐shaped papillae, and hyaline organs is similar in the two species studied. This suggests that the plicae have not been duplicated in the integument of Pl. jamaicensis, but rather that additional pseudoplicae have been inserted between the 12 original plicae. These pseudoplicae might have led to a denser package of dermal papillae in the dorsal integument of Pl. jamaicensis, but the functional significance of this evolutionary change is unknown.     

CHROMOSOME NUMBERS IN PERITYLE AND RELATED GENERA (PERITYLANAE-COMPOSITAE)

Chromosome numbers are presented for 28 species of the genus Perityle, one putative inter-sectional hybrid, two species of Amauria, one species of Eutetras, and one species of Pericome. For Perityle, initial counts are recorded for 12 species of sect. Laphamia (n = 16, 17, 18, 36, ca. 102) and 11 species of sect. Perityle (n = 11, 12, 13, 16, 17, 18, 19, 34, 51). Chromosome numbers for the two species of Amauria (n = 18) are first reports for the genus. Including the current information, chromosome numbers have been recorded for 37 of the approximately 50 species recognized for Perityle. At least 24 taxa have numbers of n = 17, suggesting a base chromosome number of x = 17 for Perityle.     

The invasion of Biomphalaria pfeifferi by Schistosoma mansoni miracidia and the development of daughter sporocysts

Laboratory experiments have been carried out to determine the susceptibility of Gezira Biomphalaria pfeifferi snails to S. mansoni miracidia and the relationship between miracidia and daughter sporocyst production at the 10–17 day development stage. The relationship between snail numbers, miracidia numbers and water volume has also been studied. Two non susceptible snails, Bulinus truncatus and Cleopatra bulimoides, both of which occur naturally in Gezira canals, were tested to see if they act as decoys for S. mansoni miracidia.The results showed that the B. pfeifferi are 100% susceptible to S. mansoni invasion, at least to the daughter sporocyst development stage. The more miracidia that penetrated the more daughter sporocysts were produced, however individual variation and overlap were great. When one miracidium was released to find one snail it succeeded in low water volumes (5 m, 50 ml), but failed in 5 litres. When 100 miracidia were released mortality of snails was high suggesting superinfection particularly when only one or five snails were available. Among survivors daughter sporocyst counts were very high. Cleopatra and Bulinus snails do have a decoy effect when present in large numbers. In their presence the number of infected snails was marginally reduced and the number of daughter sporocysts greatly reduced. However, if superinfection is reduced by decoy effect, it is conceivable that Biomphalaria may be protected by decoy snails in circumstances where miracidia counts are high.     

Multiple paternity in <Emphasis Type="Italic">Rhipicephalus</Emphasis> (<Emphasis Type="Italic">Boophilus</Emphasis>) <Emphasis Type="Italic">microplus</Emphasis> confirmed by microsatellite analysis

The aim of this study was to determine if individual ticks among the progeny of a single female Rhipicephalus (Boophilus) microplus tick removed from cattle under natural conditions are the result of mating with one or several males. To this end, simulations were run using an existing dataset of genotypes from 8 microsatellite loci to predict the number of samples required and the best locus. Subsequently, 14–22 progeny from each of 15 engorged female ticks removed from three cows, and the engorged females themselves, were genotyped for the BmM1 locus and the minimum number of potential male parents was determined for each progeny group. Of the 15 progeny groups, 10 must have been sired by more than one male, as indicated by the presence of five unique alleles among the progeny or three unique alleles that could not have been contributed by the female. This finding demonstrates multiple paternity in R. microplus.     

Biochemistry and Genetics of Actinomycete Cellulases

Abstract

The order Actinomycetales includes a number of genera that contain species that actively degrade cellulose and these include both mesophilic and facultative thermophilic species. Cellulases produced by strains from two of the genera containing thermophilic organisms have been studied extensively: Microbispora bispora and Thermomonospora fusca. Fractionation of M. bispora cellulases has identified six different enzymes, all of which were purified to near homogeneity and partially characterized. Two of these enzymes appear to be exocellulases and gave synergism with each other and with the endocellulases. The structural genes of five M. bispora cellulases have been cloned and one was sequenced. Fractionation of T. fusca cellulases has identified five different enzymes, all of which were purified to near homogeneity and partially characterized. One of the T. fusca enzymes gives synergism in the hydrolysis of crystalline cellulose with several T. fusca endocellulases and with Trichoderma reesei CBHI but not with T. reesei CBHII. Each T. fusca cellulase contains distinct catalytic and cellulose binding domains. The structural genes of four of the T. fusca endoglucanases have been cloned and sequenced, while three cellulase genes have been cloned from “T. curvata”. The T. fusca cellulase genes are expressed at a low level in Escherichia coli, but at a high level in Streptomyces lividans. Sequence comparisons have shown that there are no significant amino acid homologies between any of the catalytic domains of the four T. fusca cellulases, but each of them shows extensive homology to several other cellulases and fits in one of the five existing cellulase gene families. There have been extensive studies of the regulation of the synthesis of these cellulases and a number of regulatory mutants have been isolated. This work has shown that the different T. fusca cellulases are coordinately regulated over a 100-fold range by two independent controls; induction by cellobiose and repression by any good carbon source.     

Cytotaxonomy and evolution in Cryptocoryne (Araceae)

A hypothetical phylogeny is presented for the genus Cryptocoryne (Araceae, Cryptocoryninae). This scheme is based on both geographical and cytological data. Therefore the geography of S. E. Asia, the distribution of the various base numbers and the possible relationships between the base numbers are discussed.In the resulting phylogeny the various base numbers of Cryptocoryne (and the one of Lagenandra) are thought to have been derived from a hypothetical primary base number x₁=9. As a consequence of the scheme, Cryptocoryne is assumed to have a diphyletic character.     

Automatic Cell Counting in Continuous Flow Cultures of Tetrahymena pyriformis*

This report describes an electronic cell counter constructed for determining cell number in cultures of the ciliate, Tetrahymena pyriformis. The culture chamber has been equipped with a device which determines the number of cells per unit volume and records the number automatically. As cell multiplication is unaffected by the counting procedure the cells are returned to the culture. Furthermore, keeping the culture volume constant we have arranged a continuous flow of fresh nutrient medium through the culture chamber and thus established conditions under which cell multiplication has continued for months while determinations of cell concentrations have been recorded every 10 min. Since the culture volume has been small, ～25 ml, growth studies utilizing this method require less than one liter of fresh medium per week in spite of the fast multiplication (9 generations per 24 hr) occurring in cultures of Tetrahymena pyriformis under optimal conditions.     

Transitions in the evolution of meiosis

Meiosis may have evolved gradually within the eukaryotes with the earliest forms having a one‐step meiosis. It has been speculated that the putative transition from a one‐step meiosis without recombination to one with recombination may have been stimulated by the invasion of Killer alleles. These imaginary selfish elements are considered to act prior to recombination. They prime for destruction (which occurs after cell division) the half of the cell on the opposite side of the meiotic spindle. Likewise the transition from one‐step to two‐step meiosis might have been stimulated by a subtly different sort of imaginary distorter allele, a SisterKiller. These are proposed to act after recombination. It has yet to be established that the presence of such distorter alleles could induce the transitions in question. To investigate these issues we have analysed the dynamics of a modifier (1) of recombination and (2) of the number of steps of meiosis, as they enter a population with one‐step meiosis. For the modifier of recombination, we find that invasion conditions are very broad and that persistence of Killer and modifier is likely through most parameter space, even when the recombination rate is low. However, if we allow a Killer element to mutate into one that is self‐tolerant, the modifier and the nonself‐tolerant alleles are typically both lost from the population. The modifier of the number of steps can invade if the SisterKiller acts at meiosis II. However, a SisterKiller acting at meiosis I, far from promoting the modifier’s spread, actually impedes it. In the former case the invasion is easiest if there is no recombination. The SisterKiller hypothesis therefore fails to provide a reasonable account of the evolution of two‐step meiosis with recombination. As before, the evolution of self‐tolerance on the part of the selfish element destroys the process. We conclude that the conditions under which SisterKillers promote the evolution of two‐step meiosis are very much more limited than originally considered. We also conclude that there is no universal agreement between ESS and modifier analyses of the same transitions.     

Biochemistry of Entamoeba: A review

Entamoeba histolytica, the protozoan parasite causing amoebiasis, is carried by approximately 10% of the world's population although only a minority of carriers of the organism present active clinical symptoms. Although Entamoeba are classified as eukaryotes, the biochemistry of these organisms has a number of unusual facets which are reminiscent of prokaryotes. It has indeed been suggested that these cells represent early evolutionary forms that have been successful in surviving unchanged in the protected environment in which they reproduce (the intestine). Glycolysis in Entamoeba lacks several of the typical eukaryotic glycolytic enzymes. The pentose phosphate shunt enzymes are missing completely. Another unusual feature of the glycolytic path is the utilization of PP_i instead of ATP in a number of enzyme reactions e.g. phosphofructokinase. Entamoeba is the only eukaryote in which one of these PP_i utilizing enzymes, phosphoenolpyruvate carboxytransferase, has been found. The respiratory pathway is also an unusual one. Entamoeba are classified as anaerobes but the cells do have an affinity for oxygen. The oxygen is reduced to water at the end of a respiratory chain which is not well understood but which operates withough cytochromes or mitochondria. The nucleic acid, protein and lipid metabolic pathways have not been well studied and interest has mainly focused on the proteolytic processes of the amoeba which have been implicated in the pathogenic, histolytic behaviour of the parasite. Despite these efforts the mechanism of attack of the parasite and the stimuli that cause it to invade the host are not yet clear. This understandably is the goal of much of the present studies concerning E. histolytica but the organism also deserves study in its own right as an example of an organism that has an unusual biochemistry and may represent an early stage in the evolution of eukaryotic cells.     

New chromosome number inRutaceae

Detailed chromosome counts have been made in 61 species, belonging to 33 genera ofRutaceae. 30 of these species are reported here for the first time. For 18 species at least one previous publication gives a chromosome number differing from that reported here. Such discrepancies are, in most cases, due to errors in counting or identification of the material. By critically reviewing the literature on each particular case, it appears possible to eliminate most of the false data. On the basis of the present results, the base number x = 10 is proposed for the genusRuta. Cytogenetics ofRutaceae, I.     

Identification and characterization of a second copy number control gene in mini-F plasmids

Summary We previously reported the existence of a series of chemically induced trans recessive copy-number mutations (cop) for mini-F plasmids and the existence of a similar series of cop mutations induced by insertion of the ampicillin resistance transposon Tn3. In this paper we describe the experiments showing that these two series of mutations are in different genes. Briefly, the experiments show that the one mutant series can complement the other, that the mutations map in distinct but adjacent regions, that the copy numbers of double mutants are the products of the copy numbers determined by the single mutations, and that Tn3 does not elevate copy number by a polar effect on the adjacent cop gene defined by chemical mutagenesis. We term the latter gene copA and the gene mutated by Tn3, copB. We also demonstrate here that copB mutations are recessive to the wild type allele. Further, we have characterized copB by deletion and recombinational analysis as the series of five 19- to 22-base-pair directly repeated sequences that had previously been designated incC-that is, one of the incompatibility genes. The evidence for this conclusion is that plasmids lacking two, three or five direct repeats have their copy number elevated proportionately. Possible mechanisms for copB control of replication are discussed.     

Analysis of Mitochondrial DNA Variation as an Approach to Systematic Relationships in the Genus Acanthamoeba1

Classification at the species level has been difficult in the genus Acanthamoeba. The taxonomic designations of a number of strains are in doubt and new approaches to classification are needed. We describe the use of electrophoretic patterns obtained with restriction enzyme digests of mitochondrial DNA as a basis for one new approach. Results from analysis of ten strains of A. castellanii, two of A. polyphaga and one of A. astronyxis are discussed. Examples both of nucleotide sequence diversity and of sequence conservation have been found among strains with the same species designation. Five strains from Europe, North America and New Zealand had identical digestion phenotypes with five enzymes; consequently, very similar nucleotide sequences are predicted. All are pathogenic to humans or mice. The mtDNA sequences of eight remaining strains are predicted to differ from this cluster and, in most cases, from each other at least as much as in sibling species of Paramecium aurelia.