Characterization of mariner transposon from the genome of Himasthla elongata fluke

A novel DNA-transposon Hemar1 has been identified and characterized in the genome of the flatworm Himasthla elongata. This transposon is a representative of the mariner family, which is widely spread in eukaryotes; it belongs to the capitata subfamily and is highly homologous to the mariner element of the freshwater turbellarian worm Dugesia tigrina. The Hemar1 transposon has been established as a dispersed repeat and accounts for about 0.01% of the H. elongata genome. The identified Hemar1 element is a convenient tool for the further study of the functioning of mobile elements in the H. elongata genome.     

A new species of Tunga perforating the osteoderms of its armadillo host in Argentina and redescription of the male of Tunga terasma

A new species of Tunga (Siphonaptera: Tungidae) collected from armadillos in Argentina is described. The new species is characterized by large and pigmented eyes, the presence of two bristles on antennal segment II, two bristles at the base of the maxilla, and a discoid neosome compressed anteroposteriorly. The gravid female is located in the carapace of the host, perforating the osteoderms. The new species resembles Tunga penetrans and Tunga terasma in general appearance. However, it differs by the greater anteroposterior compression of the neosome, a more angular head, and a manubrium with a pointed proximal end and convex ventral margin (the proximal end of the manubrium is rounded or slightly pointed in T. terasma, and the ventral margin is straight in both T. penetrans and T. terasma). In addition, specimens of T. penetrans have more bristles in antennal segments II and III, and lack bristles in the posterior tibia. This is the first report of a species of Tunga perforating the osteoderms of its host and thereby showing a high degree of specialization. Tunga terasma is recorded for the first time in Argentina; the male is described again and the characteristics of the species amended. This information may be useful in epidemiological studies of diseases caused by species of Tunga.     

A note on the structure of system state spaces and its implications on the existence of non-repeatable experiments

The implication of state space structure on the existence of a repeatable experimentE designed to determine if a states∈L has propertyP or notP is investigated. It is shown that if a state spaceL is connected, then no experimentE is repeatable. This formalism is used to demonstrate that if a propertyP has an associated set of points inL which is dense with dense complement inL, then there exists no repeatable experimentE which can be used to test whethers has propertyP or notP. Other consequences of this formalization are discussed.     

Molecular phylogeny of Macrolycus (Coleoptera: Lycidae) with description of new species from China

Macrolycus is a genus of net‐winged beetles with 69 species distributed in the eastern Palearctic and northernmost part of the Oriental region. The first molecular phylogeny of Macrolycus was produced using an rrnL + tRNA‐Leu + nad1 mtDNA fragment. The major lineages and species limits were identified with morphology and molecular data. We propose that Cerceros is a subgenus of Macrolycus to enable identification of all adult specimens in the genus without DNA sequencing. Two species groups are proposed in Macrolycus s. str. and six in Cerceros. Additionally, twelve Macrolycus species are newly described from China: M. aquilinus, M. baihualingensis, M. bicolor, M. guangxiensis, M. jianfenglingensis, M. kuatunensis, M. lizipingensis, M. parvus, M. phoeniceus, M. rhodoneurus, M. rosaceus and M. sichuanensis. Macrolycus holzschuhi is proposed to be a junior subjective synonym of M. jeanvoinei. The highest diversity of Macrolycus is found in southern China. The species from the main islands of Japan are placed in two species groups: M. excellens is a sister to remaining species of the M. murzini group and the M. flabellatus group is a monophylum of closely related species in a sister position to the M. bicolor group.     

Analysis of a case of somatic instability in a strain of maize from India

A case of somatic instability affecting aleurone colour in a strain of maize from India with flint background was analysed. The somatic instability is localized to theC ¹ (Inhibitor) allele ofC locus on the short arm of chromosome 9. Molecular tests indicated thatAc is not present in the Indian stock and the evidence is consistent with the involvement of theEn (Spm) transposable element in the instability. The presence of theEn (Spm)-like element in the stock would suggest that these elements have been present in the maize genome for a long time. A new allele ofshrunken (sh1) gene with a somewhat unorthodox breeding behaviour is also described.     

The phylogenetic position of the bumble bee inquiline Bombus inexspectatus and implications for the evolution of social parasitism

The high alpine European bumble bee Bombus (Thoracobombus) inexspectatus is one of three taxa in which obligate social parasitism has evolved in bumble bees. Until now, the phylogenetic placement of this species has not been analyzed quantitatively because it is rare in nature. Here a specimen of B. inexspectatus is sequenced for five genes to assess its phylogenetic position relative to other bumble bee species. Phylogenetic estimation of B. inexspectatus places this species within the subgenus Thoracobombus, as expected based on morphology. This provides strong support for the acquisition of social parasitism in B. inexspectatus separate from that found in the bumble bees of the subgenus Psithyrus and B. (Alpinobombus) hyperboreus. Furthermore, B. inexspectatus is not the sister taxon of its host but is a near relative, suggesting a loose but not strict adherence to Emery’s rule. B. inexspectatus is a sister taxon to a clade including B. veteranus, a frequent nest usurper that has been suggested to be a facultative social parasite. The phylogenetic placement of all bumble bee social parasites relative to their hosts is discussed.     

Molecular phylogeny of Dipterocarpaceae in Southeast Asia using RFLP of PCR-amplified chloroplast genes

Dipterocarpaceae is the dominant family of Southeast Asia's climax tropical rain forest region, and it contains the region's most important commercial timber species. A molecular phylogeny of the Dipterocarpaceae subfamily Dipterocapoideae was constructed using restriction fragment length polymorphisms of polymerase chain reaction-amplified specific genes in chloroplast DNA. A total of 141 site changes were detected among ten genera and 30 species in 11 different genes: rbcL, psbA, psbD, rpoB, rpoC, petB, atpH, 16S, psaA, petA and trnK. Phylogenetic trees constructed by Wanger parsimony and neighbor-joining methods, using Upuna as the outgroup, displayed five monophytelic groups that included Upuna: HopeaShorea-Parashorea-Neobalanocarpus; Dryobalanops; Dipterocarpus; Anisoptera-Vatica-Cotylelobium; and Upuna. The phylogenetic trees clearly separate species with two different base chromosome numbers: the first group is x=7, and the other is x=11. The x=7 group is thought to be in a synapomorphic character state. Parashorea lucida is a sister to most Shorea species. Neobalanocarpus heimii and Hopea from a clade of a sister to two Shorea species, and Cotylelobium and Vatica are closely related species. Our conclusions agree with a phylogeny derived from wood anatomy data analysis, and with Symington's and Ashton's taxonomic classifications.The raw data of the PCR-RFLP analysis can be obtained from the authors     

A critical conspectus of Italian Lycopodiaceae

As a result of our work on the Lycopodiaceae account for the Critical Flora of Italy, a new, synonymic inventory of Italian taxa is presented, based on herbarium studies and critical re-examination of extant literature. Three genera with eight species are accepted: Huperzia (1 species), Lycopodiella (1), and Lycopodium (6). An additional, ninth species (Lycopodiella cernua) is listed as a casual alien. The genus Diphasiastrum, accepted in several recent works, is treated at sectional level within Lycopodium (three species and their three hybrids). Lycopodium lagopus ( = L. clavatum subsp. monostachyon) is a recent addition to the Italian flora. Images of five types and Internet URI of other six types are supplied. Dot distribution maps and a dichotomous key to Italian species are provided. It is shown that the family name Urostachyaceae (a family here not separated from Lycopodiaceae) was validly published and has priority over Huperziaceae, for which the oldest name, however, would be Phylloglossaceae.     

Expression of the nmpC gene of Escherichia coli K-12 is modulated by external pH. Identification of cis-acting regulatory sequences involved in this regulation

Using a set of gene fusions generated with TnphoA, we previously identified the phmA locus, whose expression is modulated as a function of external pH (pHo). The phmA::phoA fusion was cloned and sequenced and the phmA locus was identified with the nmpC gene. This gene lies within the defective lambdoid prophage qsr′ and NmpC is an outer membrane protein which functions as a porin. We demonstrated that nmpC is sensitive to catabotite repression and dependent on the CRP—cAMP complex. However, cAMP is not a signal for the pHo-dependent expression of nmpC. By generating step deletions in the sequence 5′ to the nmpC coding region, we identified a DNA region in position —345 to —127 which is involved in nmpC repression, mainly during growth at acid pHo. Four regions with strong homologies and a very well-conserved organization of the functional sequence were found in the nmpC and ompF promoters. We propose that the negative regulation of nmpC during growth at low pHo might involve DNA looping of the nmpC promoter.     

An update on the status of native and exotic freshwater fishes of Italy

An updated, corrected checklist of both native and established alien freshwater fish species in Italy is given based on molecular, morphological and biogeographical data. Some 12 native species, reported as conspecific with transalpine species in official Italian ichthylogical literature, are in fact endemics. Previous taxonomic confusion has resulted in the introduction of several alien species, either with official stockings or mixed in as impurities. Rehabilitated species include the cyprinids Scardinius hesperidicus, Scardinius scardafa and Telestes savigny from northern Italy, as well as Squalius ruffoi and the Telestes comes from southern Italy. Squalius albus is a junior synonym of S. squalus. The endemic gudgeon, previously assigned to the genus Romanogobio, is returned to the genus Gobio (G. benacensis). Phoxinus lumaireul is a junior synonym of P. phoxinus. Among the Salmonidae, Salmo cenerinus is a junior synonym of S. marmoratus, while Salmo farioides represents the trout species of the Adriatic lineage for which a neotype is designated. Thymallus aeliani represents the endemic lineage of grayling of the Adriatic populations. The esocid Esox cisalpinus is an endemic pike species and Esox flaviae is a junior synonym; the extensive exportation as well as the presence of this species throughout Europe is possibly due to humans. Among sculpins, Cottus scaturigo and C. ferrugineus are junior synonyms of C. gobio. The International Union for Conservation of Nature (IUCN) categories for native species of Italy are updated. At present, 52 native freshwater fish species are listed: 2 are extinct (Acipenser sturio and Huso huso), 12 are critically endangered, 7 endangered, 10 vulnerable, 3 near‐threatened, 15 low concern and 3 data‐deficient; 35 species are the result of human transfers. Among the 51 introduced species, 6 are recently established (Leuciscus leuciscus, Oreochromis niloticus, Poecilia reticulata, Xiphophorus helleri, Amatitlania nigrofasciatus, Hemichromis sp.), 37 are already established, 5 are probably established and 3 are non‐established Chinese carp, maintained in the wild by intensive stockings. The family most involved is the Cyprinidae, with 22 alien and 20 native species.     

The regulation of urease activity in Aspergillus nidulans

Aspergillus nidulans can utilize urea as a sole source of nitrogen but not as a carbon source. Urea is degraded by a urease. Mutation at any one of three genes, ureB, ureC, and ureD, may result in deficient urease activity. The ureB gene is closely linked to ureA, the structural gene for the urea transport protein. The heat lability of a ureB ^– revertant strain, intragenic complementation tests, and the linkage of ureB to ureA suggest that ureB is the urease structural gene. The ureD gene is probably involved in the synthesis or incorporation of a nickel cofactor essential for urease activity. The function of the ureC gene is not known. Urease is not induced but is subject to nitrogen regulation. The urease activities of ammonium-derepressed mutants show that the effector of nitrogen regulation is more likely to be glutamine than ammonium. When glutamine is present in the medium, urease appears to be inactivated by some means which does not involve a newly synthesized protease or a direct interaction between glutamine and urease.     

Characterization of the pleiotropic phenotype of an ompR strain of Xenorhabdus nematophila

Xenorhabdus nematophila is an insect pathogen that forms a symbiotic association with the nematode, Steinernema carpocapsae. Xenorhabdus is carried into the insect host by the nematode, is released into the hemolymph and participates in killing the insect. The bacteria grow to high concentrations supporting the development of the nematode in the hemolymph. OmpR is a global regulatory protein involved in the regulation of porin genes, motility, acid tolerance and virulence in several enteric bacteria. To study the role of ompR in the lifecyle of Xenorhabdus, an ompR -minus strain was constructed. The ompR strain produced markedly reduced levels of the porin protein, OpnP and was both hypermotile and exhibited a hyperhemolysis phenotype. Inactivation of flhDC, the master regulator for flagella synthesis, eliminated hemolysin production in the ompR strain, suggesting that ompR regulates hemolysin production via flhDC. The ompR mutant strain was virulent towards insect hosts. However, when nematodes were grown on a mixture of the wild-type and the ompR strain, only the wild-type strain was recovered indicating that ompR is required for competitive symbiotic interaction with the nematode. The role of ompR in the symbiosis between the bacterium and the nematode is under investigation. This revised version was published online in August 2006 with corrections to the Cover Date.     

Interactions between enhancer of rudimentary and Notch and deltex reveal a regulatory function of enhancer of rudimentary in the Notch signaling pathway in Drosophila melanogaster

Enhancer of rudimentary, e(r), encodes a small nuclear protein, ER, that has been implicated in the regulation of pyrimidine metabolism, DNA replication, and cell proliferation. In Drosophila melanogaster, a new recessive Notch allele, N^nd-p, was isolated as a lethal in combination with an e(r) allele, e(r)^p2. Both mutants are viable as single mutants. N^nd-p is caused by a P-element insertion in the 5' UTR, 378-bp upstream of the start of translation. Together the molecular and genetic data argue that N^nd-p is a hypomorphic allele of N. The three viable notchoid alleles, N^nd-p, N^nd-1, and N^nd-3, are lethal in combination with e(r)^- alleles. Our present hypothesis is that e(r) is a positive regulator of the Notch signaling pathway and that the lethality of the Ne(r) double mutants is caused by a reduction in the expression of the pathway. This is supported by the rescue of the lethality by a mutation in Hairless, a negative regulator of N, and by the synthetic lethality of dxe(r) double mutants. Further support for the hypothesis is a reduction in E(spl) expression in an e(r)^- mutant. Immunostaining localizes ER to the nucleus, suggesting a nuclear function for ER. A role in the Notch signaling pathway, suggests that e(r) may be expressed in the nervous system. This turns out to be the case, as immunostaining of ER shows that ER is localized to the developing CNS.     

Identification and DNA sequence of tdcR, a positive regulatory gene of the tdc operon of Escherichia coli

Summary Efficient in vivo expression of the biodegradative threonine dehydratase (tdc) operon of Escherichia coli is dependent on a regulatory gene, tdcR. The tdcR gene is located 198 base pairs upstream of the tdc operon and is transcribed divergently from this operon. The nucleotide sequence of tdcR and two unrelated reading frames has been determined. The deduced amino acid sequence of TdcR indicates that is is a polypeptide of M_r 12000 with 99 amino acid residues and contains a potential helix-turnhelix DNA binding motif. Deletion analysis and minicell expression of the tdcR gene suggest that TdcR may serve as a trans-acting positive activator for the tdc operon.     

The Evolution of RecD Outside of the RecBCD Complex

The common understanding of the function of RecD, as derived predominantly from studies in Escherichia coli, is that RecD is one of three enzymes in the RecBCD double-stranded break repair DNA recombination complex. However, comparative genomics has revealed that many organisms possess a recD gene even though the other members of the complex, recB and recC, are not present. Further, bioinformatic analyses have shown that there is substantial sequence dissimilarity between recD genes associated with recB and recC (recD1), and those that are not associated with recBC (recD2). Deinococcus radiodurans, known for its extraordinary DNA repair capability, is one such organism that does not possess either recB or recC, and yet does possess a recD gene. The recD of D. radiodurans was deleted and this mutant was shown to have a capacity to repair double-stranded DNA breaks equivalent to wild-type. The phylogenetic history of recD was studied using a dataset of 120 recD genes from 91 fully sequenced species. The analysis focused upon the role of gene duplication and functional genomic context in the evolution of recD2, which appears to have undergone numerous independent events resulting in duplicate recD2 genes. The role of RecD as part of the RecBCD complex appears to have a divergence from an earlier ancestral RecD function still preserved in many species including D. radiodurans.     

Isolation and Properties of Flagella of Trypanosomatids*

SYNOPSIS. A procedure is described for the isolation of flagella of Crithidia fasciculata. Herpetomonas samuelpessoai and Leishmania tarentolae in a highly purified state and giving reasonably good yield. The 3 types of flagella give a similar electrophoretic pattern of proteins. It is shown that H. samuelpessoai and, to a lesser extent, C. fasciculata flagella confer protection against Trypanosoma cruzi infection.