Organization of the nar genes at the chlZ locus

The two membrane-bound respiratory nitrate reductases of Escherichia coli are encoded by distinct operons at two different loci, chlC and chlZ, on the chromosome. The chlZ locus includes a narK homologue, narU, encoding a nitrite extrusion protein, and narZYWV encoding nitrate reductase Z. No apparent homologue to the narXL operon has been found. Homology between narU and narK on the one hand and narZYWV and narGHJI on the other hand is limited to the coding regions.     

On the systematic position of the lichen genus Heppia

The systematic position of the lichen genus Heppia in the order Lichinales was investigated. 18S rDNA sequence data were analyzed using a Bayesian approach to infer phylogeny using Markov chain Monte Carlo methods. The Lichinales are divided at family level into the sister groups Lichinaceae and Peltulaceae. The genus Heppia forms a highly supported clade in the family Lichinaceae. It is shown that the genus Heppia is morphologically well circumscribed within the Lichinaceae. As a nomenclatural consequence, the family name Heppiaceae is placed into synonymy under the older name Lichinaceae.     

Importance of the galE gene on the virulence of Pasteurella multocida

The galE gene of Pasteurella multocida has been isolated by complementing galE-defective mutants of Salmonella typhimurium with a plasmid library of this organism. The complete nucleotide sequence of the P. multocida galE gene consists of 1017 nucleotides, encoding a predicted polypeptide of 339 amino acids. The deduced amino acid sequence displayed the highest identity (85%) to the GalE protein of Haemophilus influenzae. However, the gene organization surrounding the galE locus was different from that of H. influenzae. A galE-defective mutant of P. multocida was obtained by replacement of the active galE gene by a copy inactivated in vitro. The resulting galE mutant was highly attenuated as seen in a biological test carried out in a mouse model.     

Characterizing the effects of the protein environment on the reduction potentials of metalloproteins

The reduction potentials of electron transfer proteins are critically determined by the degree of burial of the redox site within the protein and the degree of permanent polarization of the polypeptide around the redox site. Although continuum electrostatics calculations of protein structures can predict the net effect of these factors, quantifying each individual contribution is a difficult task. Here, the burial of the redox site is characterized by a dielectric radius R _p (a Born-type radius for the protein), the polarization of the polypeptide is characterized by an electret potential ? _p (the average electrostatic potential at the metal atoms), and an electret-dielectric spheres (EDS) model of the entire protein is then defined in terms of R _p and ? _p. The EDS model shows that for a protein with a redox site of charge Q, the dielectric response free energy is a function of Q ², while the electret energy is a function of Q. In addition, R _p and ? _p are shown to be characteristics of the fold of a protein and are predictive of the most likely redox couple for redox sites that undergo different redox couples.     

Studies of the transmissibility of the agent of bovine spongiform encephalopathy to the domestic chicken

Background

Escherichia coli O157:H7 is the most common serovar of enterohemorrhagic E. coli associated with serious human disease outbreaks. Cattle are the main reservoir with E. coli O157:H7 inducing hemorrhagic enteritis in persistent shedding beef cattle, however little is known about how this pathogen affects cattle health. Jejunal Hemorrhage Syndrome (JHS) has unclear etiology but the pathology is similar to that described for E. coli O157:H7 challenged beef cattle suggestive that E. coli O157:H7 could be involved. There are no effective treatments for JHS however new approaches to managing pathogen issues in livestock using prebiotics and probiotics are gaining support. The first objective of the current study was to characterize pathogen colonization in hemorrhaged jejunum of dairy cattle during natural JHS outbreaks. The second objective was to confirm the association of mycotoxigenic fungi in feeds with the development of JHS and also to identify the presence of potential mycotoxins. The third objective was to determine the impact of a prebiotic, Celmanax?, or probiotic, Dairyman's Choice? paste, on the cytotoxicity associated with feed extracts in vitro. The fourth objective was to determine the impact of a prebiotic or a probiotic on E. coli O157:H7 colonization of mucosal explants and a bovine colonic cell line in vitro. The final objective was to determine if prebiotic and probiotic feed additives could modify the symptoms that preceded JHS losses and the development of new JHS cases.

Findings

Dairy cattle developed JHS after consuming feed containing several types of mycotoxigenic fungi including Fusarium culmorum, F. poae, F. verticillioides, F. sporotrichioides, Aspergillus flavus, Penicillium roqueforti, P. crustosum, P. paneum and P. citrinum. Mixtures of Shiga toxin - producing Escherichia coli (STEC) colonized the mucosa in the hemorrhaged tissues of the cattle and no other pathogen was identified. The STECs expressed Stx1 and Stx2, but more significantly, Stxs were also present in the blood clot blocking the jejunum. Mycotoxin analysis of the corn crop confirmed the presence of fumonisin, NIV, ZEAR, DON, 15-ADON, 3-ADON, NEO, DAS, HT-2 and T-2. Feed extracts were toxic to enterocytes and 0.1% Celmanax? removed the cytotoxicity in vitro. There was no effect of Dairyman's Choice? paste on feed-extract activity in vitro. Fumonisin, T-2, ZEAR and DON were toxic to bovine cells and 0.1% Celmanax? removed the cytotoxicity in vitro. Celmanax? also directly decreased E. coli O157:H7 colonization of mucosal explants and a colonic cell line in a dose-dependent manner. There was no effect of Dairyman's Choice? paste on E. coli O157:H7 colonization in vitro. The inclusion of the prebiotic and probiotic in the feed was associated with a decline in disease.

Conclusion

The current study confirmed an association between mycotoxigenic fungi in the feed and the development of JHS in cattle. This association was further expanded to include mycotoxins in the feed and mixtures of STECs colonizing the severely hemorrhaged tissues. Future studies should examine the extent of involvement of the different STEC in the infection process. The prebiotic, Celmanax?, acted as an anti-adhesive for STEC colonization and a mycotoxin binder in vitro. Future studies should determine the extent of involvement of the prebiotic in altering disease.     

Identification of the Dictyostelium discoideum homolog of the N-ethylmaleimide-sensitive fusion protein

The N-ethylmaleimide-sensitive fusion protein (NSF) is required for vesicular membrane fusion in multiple cellular functions. We have cloned a cDNA encoding the Dictyostelium discoideum homolog of the NSF protein. This cDNA hybridizes with a single fragment in Southern blots suggesting that NSF is encoded by a single gene in the amoeba. It is expressed constitutively during vegetative growth and throughout the differentiation cycle. The encoded gene product comprises 738 aa with a predicted molecular mass of 82 kDa. It shows the characteristic three-domain structure of NSF proteins. A more divergent amino-terminal part is followed by two highly conserved ATP-binding domains featuring Walker A and B signature sequences. The D. discoideum protein presents an overall aa sequence identity of 44% when compared to known NSF homologs. The monoclonal antibody 2E5 directed against Cricetellus griseus NSF recognizes a protein with a molecular weight of approx. 80 000 in a D. discoideum crude extract and the recombinant D. discoideum His₆-NSF expressed in Escherichia coli.     

Three highly divergent subfamilies of the impala transposable element coexist in the genome of the fungus Fusarium oxysporum

The transposable element impala is a member of the widespread superfamily of Tc1-mariner transposons, identified in the genome of the plant pathogenic fungus Fusarium oxysporum. This element is present in a low copy number and is actively transposed in the F.?oxysporum strain F24 that is pathogenic for melons. The structure of the impala family was investigated by cloning and sequencing all the genomic copies. The analysis revealed that this family is composed of full-length and truncated copies. Four copies contained a long open reading frame that could potentially encode a transposase of 340 amino acids. The presence of conserved functional domains (a nuclear localisation signal, a catalytic DDE domain and a DNA-binding domain) suggests that these four copies may be autonomous elements. Sequence comparisons and phylogenetic analysis of the impala copies defined three subfamilies, which differ by a high level of nucleotide polymorphism (around 20%). The coexistence of these divergent subfamilies in the same genome may indicate that the impala family is of ancient origin and/or that it arose by successive horizontal transmission events.     

Reassessment of the Morphology and Taxonomic Status of the Earliest Herpetotheriid Marsupials of Europe

The earliest Eocene locality of Dormaal (Belgium) has provided the oldest Cenozoic herpetotheriid marsupials of Europe. No herpetotheriid has ever been reported earlier than the Eocene in Europe, except for a questionable single upper molar from the Upper Cretaceous of the Belgian/Dutch border. The systematics of the herpetotheriids of Dormaal was formerly based on only a dozen dental specimens, which were assigned, after several revisions, to two species Peratherium constans and Amphiperatherium brabantense. Most importantly, these two species were considered at the root of most of the hepetotheriid lineages of the European Paleogene. Here we report a large sample of about 400 new dental remains that allow a better definition of both species as well as a testing of their systematic status. The evidence of significant morphological variability leads us to reconsider the diagnosis of Peratherium constans and to question the validity of Amphiperatherium brabantense. This study highlights that the primitive species Peratherium constans and Amphiperatherium brabantense are hardly distinguishable from each other, and therefore conclude that Peratherium constans was the only marsupial present at Dormaal. The important morphological variation exhibited by this herpetotheriid is similar to the variability observed in the type-species Peratherium elegans and in other fossil and extant metatherians. Consequently, our results suggest that several Amphiperatherium species from the Eocene could represent variants of the genus Peratherium. The question of the Amphiperatherium presence in Europe is therefore raised and a thorough discriminate analysis of both genera should be conducted in later works.     

Contents of the exocrine glands of the ant subfamily Cerapachyinae

The chemistry of the exocrine glands of three species of the small and little-known ant subfamily Cerapachyinae has been examined for the first time. The mandibular glands of Cerapachys jacobsoni contained acetophenone and skatole, but some individuals contained, in addition, 4-methyl-3-heptanone and 3-octanol. The mandibular glands of the new species, presently known as Cerapachys sp. 15 of FI contained 4-methyl-3-heptanone, as the major substance but also 4-methyl-3-heptanol, methyl 6-ethylsalicylate, and traces of 4,5-dimethyl-4-hexen-3-one and homomanicone. The Dufour glands of C. jacobsoni contained a mixture of higher aldehydes, acetates and other esters, with a small amount of hydrocarbons, all in the range C₁₁–C₂₀. The Dufour glands of Cylindromyrmex whymperi contained a mixture of long-chain epoxides, the second ant species to display them. The sternal glands of C. whymperi contain a recruitment pheromone, but only partial identification of the contents was possible. The venom glands of all three species were devoid of volatile material. The Dufour glands of Cerapachys sp. 15 of FI and the mandibular glands of C. whymperi had no detectable volatile contents.     

Role of the parCBA Operon of the Broad-Host-Range Plasmid RK2 in Stable Plasmid Maintenance

The par region of the stably maintained broad-host-range plasmid RK2 is organized as two divergent operons, parCBA and parDE, and a cis-acting site. parDE encodes a postsegregational killing system, and parCBA encodes a resolvase (ParA), a nuclease (ParB), and a protein of unknown function (ParC). The present study was undertaken to further delineate the role of the parCBA region in the stable maintenance of RK2 by first introducing precise deletions in the three genes and then assessing the abilities of the different constructs to stabilize RK2 in three strains of Escherichia coli and two strains of Pseudomonas aeruginosa. The intact parCBA operon was effective in stabilizing a conjugation-defective RK2 derivative in E. coli MC1061K and RR1 but was relatively ineffective in E. coli MV10Δlac. In the two strains in which the parCBA operon was effective, deletions in parB, parC, or both parB and parC caused an approximately twofold reduction in the stabilizing ability of the operon, while a deletion in the parA gene resulted in a much greater loss of parCBA activity. For P. aeruginosa PAO1161Rif^r, the parCBA operon provided little if any plasmid stability, but for P. aeruginosa PAC452Rif^r, the RK2 plasmid was stabilized to a substantial extent by parCBA. With this latter strain, parA and res alone were sufficient for stabilization. The cer resolvase system of plasmid ColE1 and the loxP/Cre system of plasmid P1 were tested in comparison with the parCBA operon. We found that, not unlike what was previously observed with MC1061K, cer failed to stabilize the RK2 plasmid with par deletions in strain MV10Δlac, but this multimer resolution system was effective in stabilizing the plasmid in strain RR1. The loxP/Cre system, on the other hand, was very effective in stabilizing the plasmid in all three E. coli strains. These observations indicate that the parA gene, along with its res site, exhibits a significant level of plasmid stabilization in the absence of the parC and parB genes but that in at least one E. coli strain, all three genes are required for maximum stabilization. It cannot be determined from these results whether or not the stabilization effects seen with parCBA or the cer and loxP/Cre systems are strictly due to a reduction in the level of RK2 dimers and an increase in the number of plasmid monomer units or if these systems play a role in a more complex process of plasmid stabilization that requires as an essential step the resolution of plasmid dimers.     

A study of the mechanism of the antiarrhythmic action of Allapinin

Allapinin (lappaconitine hydrobromide) is a drug used for the treatment of cardiac rhythm disturbances; its properties are characteristic of class IC antiarrhythmics. The mechanism of its electrophysiological action involves the blockade of Na⁺ channels with a subsequent decrease of depolarization rate leading to a slowing of impulse propagation and a decrease of excitability in the conductive system of the heart. Factors underlying the side effects of Allapinin (tachycardia, arterial hypertension, impaired coordination, etc.) are currently unknown, and therefore a study of the molecular mechanisms of its action seems relevant. The target genes of the drug were identified in rats with induced aconitine arrhythmia using the commercially available Rat Neuroscience Ion Channels & Transporters RT² Profiler? PCR Array kit (SA Biosciences). A comparison of expression levels of 84 genes in rats treated with Allapinin, after the induction of arrhythmia by aconitine (experiment) and in physiological saline-treated arrhythmic rats (control), revealed 18 mRNAs which were up- or downregulated twofold or more in the experiment relative to the control. Allapinin was shown to stimulate the expression of genes coding for various types of K⁺ channels (kcna6, kcnj1, kcnj4, kcnq2, and kcnq4), Ca²⁺ channel (cacna1g), and vesicular acetylcholine transporter (slc18a3). A decrease in mRNA levels was detected for genes coding for K⁺ channels (kcne1, kcns1), a Na⁺ channel (scn8a), and membrane transporter genes (atp4a, slc6a9). Our data shows that Allapinin administered to animals with aconitine arrhythmia modulates the expression of genes accounting for ion current conductances involved in the formation of various phases of action potential (I _Na , I _to , I _Ks , I _K1 , I _CaT ). The effect of the drug on the levels of mRNAs coding for acetylcholine and glycine transporters suggests the involvement of these neuromediators in the mechanisms underlying the antiarrhythmic effect of Allapinin.     

Effect of atoms evaporated from the anode on the structure of the vacuum arc space charge sheath

The structure of the anode space charge sheath of a vacuum arc is studied with allowance for the dependence of the negative anode fall on the ratio of the directed electron velocity v ₀ to the electron thermal velocity v _T for different values of the flux density of atoms evaporated from the anode. Poisson’s equation for the sheath potential is solved taking into account the electron space charge, fast cathode ions, and slow ions produced due to the ionization of atoms evaporated from the anode. The kinetic equation for atoms and slow anode ions is solved with allowance for ionization in the collision integral. Analytic solutions for the velocity distribution functions of atoms and slow ions and the density of slow ions are obtained. It is shown that the flux of slow ions substantially affects the spatial distribution of the electric field E(z) in the sheath. As the flux density increases, the nonmonotonic dependence E(z) transforms into a monotonic one and the sheath narrows. For a given flux of evaporated atoms Πa, the increase in the ratio of the directed electron velocity to the electron thermal velocity leads again to a nonmonotonic dependence E(z). As z increases, the electric field first increases, passes through the maximum, decreases, passes through the minimum E _min, and then again increases toward the anode. There is a limiting value of the ratio (v ₀/v _T )* at which E _min(z) vanishes. At v ₀/v _T > (v ₀/V _T )*, the condition for the existence of a steady-state sheath is violated and the profiles of the field and potential in the sheath become oscillating. The dependence of (v ₀/v _T )* on the flux density of evaporated atoms Π _a is obtained. It is shown that the domain of existence of steady-state solutions in the sheath broadens with increasing Π _a .     

Revision of trilobites of the genus Paraphillipsia Tumanskaya from the Permian Olistoliths of Crimea

The genus Paraphillipsia Tumanskaya, 1935 is revised and the species P. taurica Tumanskaya, 1935 from the Middle Permian of Crimea is redescribed. The age distribution of species of the genus Paraphillipsia from Crimea is emended based on new stratigraphic data on the locality (species previously considered Artinskian became Roadian). As a result of analysis of a rather large number of new records of trilobites, the species P. kussicum, P. tauricum var. anfensis, and P. netschaewi are synonymized under P. taurica.     

The product of the retroviral transforming gene v-myb is a truncated version of the protein encoded by the cellular oncogene c-myb

Avian myeloblastosis virus (AMV) is an oncogenic retrovirus that rapidly causes myeloblastic leukemia in chickens and transforms myeloid cells in culture. AMV carries an oncogene, v-myb, that is derived from a cellular gene, c-myb, found in the genomes of vertebrate species. We constructed a plasmid vector that allows expression of a portion of the coding region for v-myb in a procaryotic host. We then used the myb-encoded protein produced in bacteria to immunize rabbits. The antisera obtained permitted identification of the proteins encoded by both v-myb and chicken c-myb. The molecular weights of the products of v-myb and c-myb (45,000 and 75,000 respectively) indicate that the v-myb protein is an appreciably truncated version of the c-myb protein.     

Causes of differences in the distribution of the invasive plants Ambrosia artemisiifolia and Ambrosia trifida in the Yili Valley,China

Ambrosia artemisiifolia and Ambrosia trifida are two species of very harmful and invasive plants of the same genus. However, it remains unclear why A. artemisiifolia is more widely distributed than A. trifida worldwide. Distribution and abundance of these two species were surveyed and measured from 2010 to 2017 in the Yili Valley, Xinjiang, China. Soil temperature and humidity, main companion species, the biological characteristics in farmland ecotone, residential area, roadside and grassland, and water demand of the two species were determined and studied from 2017 to 2018. The area occupied by A. artemisiifolia in the Yili Valley was more extensive than that of A. trifida, while the abundance of A. artemisiifolia in grassland was less than that of A. trifida at eight years after invasion. The interspecific competitive ability of two species was stronger than those of companion species in farmland ecotone, residential, and roadside. In addition, A. trifida had greater interspecific competitive ability than other plant species in grassland. The seed size and seed weight of A. trifida were five times or eight times those of A. artemisiifolia. When comparing the changes under simulated annual precipitation of 840 mm versus 280 mm, the seed yield per m² of A. trifida decreased from 50,185 to 19, while that of A. artemisiifolia decreased from 15,579 to 530.

The differences in the distribution of the two species are mainly due to differences in interspecific competitive ability, seed size, and water dependence. The two species have stronger interspecific competitive ability than that of companion species, but A. artemisiifolia has a smaller seed size and stronger drought tolerance, which allows A. artemisiifolia to spread farther than A. trifida. The reason for wider distribution of A. trifida in grassland is that A. trifida has stronger interspecific competitive ability than A. artemisiifolia under sufficient water.     

The evolutionary history of the genes involved in the biosynthesis of the antioxidant ergothioneine

Ergothioneine (EGT) is a histidine betaine derivative that exhibits antioxidant action in humans. EGT is primarily synthesized by fungal species and a number of bacterial species. A five-gene cluster (egtA, egtB, egtC, egtD & egtE) responsible for EGT production in Mycobacteria smegmatis has recently been identified. The first fungal biosynthetic EGT gene (NcEgt-1) has also been identified in Neurospora crassa. NcEgt-1 contains domains similar to those found in M. smegmatis egtB and egtD. EGT is biomembrane impermeable. Here we inferred the evolutionary history of the EGT cluster in prokaryotes as well as examining the phyletic distribution of Egt-1 in the fungal kingdom. A genomic survey of 2509 prokaryotes showed that the five-gene EGT cluster is only found in the Actinobacteria. Our survey identified more than 400 diverse prokaryotes that contain genetically linked orthologs of egtB and egtD. Phylogenetic analyses of Egt proteins show a complex evolutionary history and multiple incidences of horizontal gene transfer. Our analysis also identified two independent incidences of a fusion event of egtB and egtD in bacterial species. A genomic survey of over 100 fungal genomes shows that Egt-1 is found in all fungal phyla, except species that belong to the Saccharomycotina subphylum. This analysis provides a comprehensive analysis of the distribution of the key genes involved in the synthesis of EGT in prokaryotes and fungi. Our phylogenetic inferences illuminate the complex evolutionary history of the genes involved in EGT synthesis in prokaryotes. The potential to synthesize EGT is a fungal trait except for species belonging to the Saccharomycotina subphylum.     

Diversification of the Genus Anopheles and a Neotropical Clade from the Late Cretaceous

The Anopheles genus is a member of the Culicidae family and consists of approximately 460 recognized species. The genus is composed of 7 subgenera with diverse geographical distributions. Despite its huge medical importance, a consensus has not been reached on the phylogenetic relationships among Anopheles subgenera. We assembled a comprehensive dataset comprising the COI, COII and 5.8S rRNA genes and used maximum likelihood and Bayesian inference to estimate the phylogeny and divergence times of six out of the seven Anopheles subgenera. Our analysis reveals a monophyletic group composed of the three exclusively Neotropical subgenera, Stethomyia, Kerteszia and Nyssorhynchus, which began to diversify in the Late Cretaceous, at approximately 90 Ma. The inferred age of the last common ancestor of the Anopheles genus was ca. 110 Ma. The monophyly of all Anopheles subgenera was supported, although we failed to recover a significant level of statistical support for the monophyly of the Anopheles genus. The ages of the last common ancestors of the Neotropical clade and the Anopheles and Cellia subgenera were inferred to be at the Late Cretaceous (ca. 90 Ma). Our analysis failed to statistically support the monophyly of the Anopheles genus because of an unresolved polytomy between Bironella and A. squamifemur.