A highly specific one-step PCR - assay for the rapid discrimination of enteropathogenic Yersinia enterocolitica from pathogenic Yersinia pseudotuberculosis and Yersinia pestis

Based on differences within the yopT-coding region of Yersinia. enterocolitica, Y pseudotuberculosis and Y pestis, a rapid and sensitive one-step polymerase chain reaction assay with high specificity for pathogenic Y enterocolitica was developed. By this method pathogenic isolates of Y enterocolitica can be easily identified and discriminated from other members of this genus. The entire coding sequence of the yopT effector gene of Y. pseudotuberculosis Y36 was determined.     

Evidence for the pathogenic role of Rhodococcus species in pulmonary diseases

Three hundred expectorated sputa from patients suffering from chest disorders were examined microscopically and cultured on various media. Among other microorganisms isolated there were four strains of Rhodococcus aurantiacus ( Gordona aurantiaca ), one each of Rh. erythropolis, Rh. pellegrino, Rh. rubropertinctus and Rh. rhodnii. Suspensions in 5% hog gastric mucin were virulent for immuno-suppressed white mice and the pathology of their lungs was compatible with those produced in experimental nocardial and rhodococcus infections. The in-vitro antibiogram was similar to that of Nocardia asteroides. Two of the patients from whom Rh. aurantiacus and Rh. pellegrino were isolated responded bacteriologically and clinically to treatment with co-trimoxazole. The frequency with which these rhodococci were isolated and the clinical conditions of the patients strongly indicated a pathogenic role for some Rhodococcus species. It is suggested that rhodococci should be sought in chronic pulmonary infections, particularly in those who are immuno-compromised or debilitated, and their aetiologic role determined.     

Evidence for the pathogenic role of Rhodococcus species in pulmonary diseases

Three hundred expectorated sputa from patients suffering from chest disorders were examined microscopically and cultured on various media. Among other micro-organisms isolated there were four strains of Rhodococcus aurantiacus (Gordona aurantiaca), one each of Rh. erythropolis, Rh. pellegrino, Rh. rubropertinctus and Rh. rhodnii. Suspensions in 5% hog gastric mucin were virulent for immuno-suppressed white mice and the pathology of their lungs was compatible with those produced in experimental nocardial and rhodococcus infections. The in-vitro antibiogram was similar to that of Nocardia asteroides. Two of the patients from whom Rh. aurantiacus and Rh. pellegrino were isolated responded bacteriologically and clinically to treatment with co-trimoxazole. The frequency with which these rhodococci were isolated and the clinical conditions of the patients strongly indicated a pathogenic role for some Rhodococcus species. It is suggested that rhodococci should be sought in chronic pulmonary infections, particularly in those who are immuno-compromised or debilitated, and their aetiologic role determined.     

Evidence for evolutionary convergence at MHC in two broadly distributed mesocarnivores

Variation within major histocompatibility complex (MHC) genes is important in recognizing pathogens and initiating an immune response. These genes are relevant in enhancing our understanding of how species cope with rapid environmental changes and concomitant fluctuations in selective pressures such as invasive, infectious diseases. Disease-based models suggest that diversity at MHC is maintained through balancing selection arising from the coevolution of hosts and pathogens. Despite intensive balancing selection, sequence motifs or even identical MHC alleles can be shared across multiple species; three potential mechanisms have been put forth to explain this phenomenon: common ancestry, convergent evolution, and random chance. To understand the processes that maintain MHC similarity across divergent species, we examined the variation at two orthologous MHC-DRB genes in widespread North American Musteloid species, striped skunks (Mephitis mephitis), and raccoons (Procyon lotor). These species are often sympatric and exposed to a similar suite of diseases (e.g., rabies, canine distemper, and parvovirus). Given their exposure to similar selective pressures from pathogens, we postulated that similar DRB alleles may be present in both species. Our results indicated that similar motifs are present within both species, at functionally relevant polymorphic sites. However, based on phylogenetic analyses that included previously published MHC sequences of several closely related carnivores, the respective MHC-DRB alleles do not appear to have been maintained through common ancestry and unlikely through random chance. Instead, the similarities observed between the two mesocarnivore species may rather be due to evolutionary convergence.     

Evidence for two distinctive species of Pseudorchis (Orchidaceae) in Scandinavia.

Reinhammar, L.-G. 1995. Evidence for two distinct species of Pseudorchis (Orchidaceae) in Scandinavia. - Nord. J. Bot. 15: 469–481. Copenhagen. ISSN 0107–055X.
Nordic populations of Pseudorchis albida s.l. were studied for variation in morphological characters. Canonical variates analysis (CVA) arrange populations in two discrete groups, corresponding to P. albida S.S. and P. straminea , respectively. In principal component analysis (PCA) of the total material a small overlap could be seen. However, separate PCA:s on members of the two taxa from the same geographic region show perfect separation. Since the two taxa are distinct in morphology as well as in additional characters, e.g. habitat preference in the area of sympatry, they are best treated as separate species. The generic name Pseudorchis is considered to be validly published and is then preferred over the later Leucorchis . A lectotype is selected for Gymnadenia albida f. subalpina .     

Parallel origins of apomixis in two diverged evolutionary lineages in tribe Potentilleae (Rosaceae)

We synthesized the results from a flow cytometric seed screen and the literature to infer the phylogenetic origin and the geographical and taxonomic distribution of apomixis in tribe Potentilleae (Rosaceae). We distinguished between regular sexuality and apomixis, the zygotic and parthenogenetic origin of the embryo, and the pseudogamous (i.e. sexual) versus autonomous origin of the endosperm. The combined evidence provides information on reproductive modes for 11 genera and 120 species. For the first time records on reproductive mode are provided for the genus Farinopsis, 29 species (from five genera), and seven series of Potentilla. Regular sexuality was observed in Aphanes, Argentina, Comarum, Dasiphora, Drymocallis, Farinopsis, Fragaria, Horkeliella, Potentilla, and Sibbaldia. Reliable evidence for apomixis is restricted to two evolutionary lineages of Potentilleae: the Potentilla core group and Alchemilla/Aphanes. Early evolutionary divergence of these lineages (approximately 50 Mya), characterized by pseudogamous and autonomous apomictic seed formation, respectively, suggests parallel origins of apomixis. Apomixis is shown to be taxonomically widespread in the whole Northern Hemisphere distribution range of Potentilla, a pattern that is explained by hybrid transfer and repeated intercontinental dispersals. Taxonomic and geographical coverage is discussed with reference to species diversity centres of genera. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 214–229.     

Evidence for two species of glutamate dehydrogenases in Thiobacillus novellus

When grown autotrophically in a thiosulfate-mineral salts medium, cells of the facultative chemoautotrophic bacterium, Thiobacillus novellus, produced two distinct glutamate dehydrogenases, one specific for nicotinamide adenine dinucleotide phosphate (NADP) and the other specific for nicotinamide adenine dinucleotide (NAD). When glutamate was supplied exogenously as the sole carbon source, the NAD-specific glutamate dehydrogenase was fully induced. Lower levels of the enzyme were found in bacteria grown in l-arginine, l-alanine, glucose, glycerol, lactate, citrate, or succinate. Arginine, histidine, and aspartate, on the other hand, caused a marked repression of the NADP-specific glutamate dehydrogenase activity. The NAD-dependent glutamate dehydrogenase was allosteric. Adenosine-5'-monophosphate and adenosine-5'-diphosphate acted as positive effectors. Both glutamate dehydrogenases were purified about 250-fold and were shown to be distinct protein with different physical properties.     

Evidence for cryptic hybridization between different evolutionary lineages of the invasive clam genus Corbicula (Veneroida,Bivalvia)

We studied two Corbicula morphotypes in a syntopic population in the Rhine River in order to reveal their taxonomic, reproductive and phylogenetic relationship, using morphometrics, DAF‐fingerprinting, mitochondrial COI and nuclear ITS1 sequence variation. Morphometric analysis showed that two statistically distinguishable morphotypes with few intermediates were present.Mitochondrial sequence analysis detected two divergent clades. DAF‐fingerprinting revealed three highly distinctive multilocus genotypes. Two of the multilocus genotypes were significantly associated with different morphotypes and mitochondrial lineages. The third genotype B, however, was found in both morphotypes, intermediates and mitochondrial lineages. Conclusive evidence for hybridization came from RFLP analysis of the nuclear ITS1 locus. We interpret the hybrids as F1 hybrids between different evolutionary lineages. Integration of Corbicula sequences from all over the world into Maximum Parsimony analysis suggested a simultaneous radiation resulting in several evolutionary lineages whose species status remained doubtful. An unequivocal taxonomic assignment of the two evolutionary lineages in the Rhine population was therefore not possible.     

Evidence for social enhancement of reproduction in two Eulemur species

Across the past 20 years, captive reproduction has declined steeply in mongoose lemurs (Eulemur mongoz) and has been only moderately successful in black lemurs (E. macaco). At the same time, reproduction has been so successful in brown lemurs (E. fulvus) that contraception has been used since 1987 to limit captive numbers. No obvious cause for the differential reproductive success has been identified. Our experience with a pair of unrelated mongoose lemurs at the Philadelphia Zoological Garden suggested that they reproduced in only those years when they were caged in close proximity to another nonreproductive, full-sibling pair of mongoose lemurs. Examination of the worldwide pattern of captive reproduction by Eulemur species during the past two decades revealed that female black and mongoose lemurs housed in institutions with either additional conspecific males or additional conspecific pairs had a higher rate of reproduction than those maintained as an isolated pair. Black lemurs also had higher rates of reproduction when additional conspecific females were present. No similar pattern was found for brown lemurs or for two comparable mammals, the pudu (Pudu pudu) and the okapi (Okapia johnstoni). The evidence presented for the black and mongoose lemurs supports the existence of the Allee effect in these two species, namely, that reproduction is enhanced by the presence of conspecifics. © 1996 Wiley-Liss, Inc.     

Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis

Molecular Biology Reports - A significant proportion of plant genomes is consists of transposable elements (TEs), especially LTR retrotransposons (LTR-RTs) which are known to drive genome...     

Diverse lineages of pathogenic Leptospira species are widespread in the environment in Puerto Rico,USA

BackgroundLeptospirosis, caused by Leptospira bacteria, is a common zoonosis worldwide, especially in the tropics. Reservoir species and risk factors have been identified but surveys for environmental sources are rare. Furthermore, understanding of environmental Leptospira containing virulence associated genes and possibly capable of causing disease is incomplete, which may convolute leptospirosis diagnosis, prevention, and epidemiology.Methodology/Principal findingsWe collected environmental samples from 22 sites in Puerto Rico during three sampling periods over 14-months (Dec 2018-Feb 2020); 10 water and 10 soil samples were collected at each site. Samples were screened for DNA from potentially pathogenic Leptospira using the lipL32 PCR assay and positive samples were sequenced to assess genetic diversity. One urban site in San Juan was sampled three times over 14 months to assess persistence in soil; live leptospires were obtained during the last sampling period. Isolates were whole genome sequenced and LipL32 expression was assessed in vitro.We detected pathogenic Leptospira DNA at 15/22 sites; both soil and water were positive at 5/15 sites. We recovered lipL32 sequences from 83/86 positive samples (15/15 positive sites) and secY sequences from 32/86 (10/15 sites); multiple genotypes were identified at 12 sites. These sequences revealed significant diversity across samples, including four novel lipL32 phylogenetic clades within the pathogenic P1 group. Most samples from the serially sampled site were lipL32 positive at each time point. We sequenced the genomes of six saprophytic and two pathogenic Leptospira isolates; the latter represent a novel pathogenic Leptospira species likely belonging to a new serogroup.Conclusions/SignificanceDiverse and novel pathogenic Leptospira are widespread in the environment in Puerto Rico. The disease potential of these lineages is unknown but several were consistently detected for >1 year in soil, which could contaminate water. This work increases understanding of environmental Leptospira diversity and should improve leptospirosis surveillance and diagnostics.     

Divergent evolutionary histories of two sympatric spruce bark beetle species

Ips typographus and Pityogenes chalcographus are two sympatric Palearctic bark beetle species with wide distribution ranges. As both species are comparable in biology, life history, and habitat, including sharing the same host, Picea abies, they provide excellent models for applying a comparative approach in which to identify common historical patterns of population differentiation and the influence of species-specific ecological characteristics. We analysed patterns of genetic diversity, genetic structure and demographic history of ten I. typographus and P. chalcographus populations co-distributed across Europe using both COI and ITS2 markers. Rather than similarities, our results revealed striking differences. Ips typographus was characterised by low genetic diversity, shallow population structure and strong evidence that all extant haplogroups arose via a single Holocene population expansion event. In contrast, genetic variation and structuring were high in P. chalcographus indicating a longer and more complex evolutionary history. This was estimated to be five times older than I. typographus, beginning during the last Pleistocene glacial maximum over 100 000 years ago. Although the expansions of P. chalcographus haplogroups also date to the Holocene or just prior to its onset, we show that these occurred from at least three geographically separated glacial refugia. Overall, these results suggest that the much longer evolutionary history of P. chalcographus greatly influenced the levels of phylogeographic subdivision among lineages and may have led to the evolution of different life-history traits which in turn have affected genetic structure and resulted in an advantage over the more aggressive I. typographus.     

Comparative and evolutionary genomics of Yersinia pestis

Yersinia pestis is the causative agent of plague, causing three human plague pandemics in history. Comparative and evolutionary genomics of Y. pestis are extensively discussed in this review. Understanding the genomic variability and the adaptive evolution of Y. pestis from the genomic point of view will contribute greatly to plague detection, identification, control and prevention.     

Diversity of plant evolutionary lineages promotes arthropod diversity

Large‐scale habitat destruction and climate change result in the non‐random loss of evolutionary lineages, reducing the amount of evolutionary history represented in ecological communities. Yet, we have limited understanding of the consequences of evolutionary history on the structure of food webs and the services provided by biological communities. Drawing on 11 years of data from a long‐term plant diversity experiment, we show that evolutionary history of plant communities – measured as phylogenetic diversity – strongly predicts diversity and abundance of herbivorous and predatory arthropods. Effects of plant species richness on arthropods become stronger when phylogenetic diversity is high. Plant phylogenetic diversity explains predator and parasitoid richness as strongly as it does herbivore richness. Our findings indicate that accounting for evolutionary relationships is critical to understanding the severity of species loss for food webs and ecosystems, and for developing conservation and restoration policies.     

Evidence for Golgi bodies in proposed 'Golgi-lacking' lineages

Golgi bodies are nearly ubiquitous in eukaryotic cells. The apparent lack of such structures in certain eukaryotic lineages might be taken to mean that these protists evolved prior to the acquisition of the Golgi, and it raises questions of how these organisms function in the absence of this crucial organelle. Here, we report gene sequences from five proposed 'Golgi-lacking' organisms (Giardia intestinalis, Spironucleus barkhanus, Entamoeba histolytica, Naegleria gruberi and Mastigamoeba balamuthi). BLAST and phylogenetic analyses show these genes to be homologous to those encoding components of the retromer, coatomer and adaptin complexes, all of which have Golgi-related functions in mammals and yeast. This is, to our knowledge, the first molecular evidence for Golgi bodies in two major eukaryotic lineages (the pelobionts and heteroloboseids). This substantiates the suggestion that there are no extant primitively 'Golgi-lacking' lineages, and that this apparatus was present in the last common eukaryotic ancestor, but has been altered beyond recognition several times.     

A highly efficient electroporation system for transformation of Yersinia

The various pathogenic Yersinia species are not readily and efficiently transformed by classical methods. For this reason, the electroporation technique was applied for genetic transformation of these species. Using optimal conditions, we were able to transform the six Yersinia strains studied with the two most widely used groups of plasmids: pSU2718 (a pACYC184 derivative) and pK19 (a pUC19 derivative). Only Yersinia enterocolitica (Y. e.) serotype 0:8 gave poor results (less than 5 x 10(2) transformants/microgram) DNA). Electrical transformation of the other species resulted in high efficiencies, up to 10(5) transformants/microgram DNA for Y. e. serotypes 0:3 and 0:9, 10(6) for Y. pseudotuberculosis and 10(7) for Y. pestis. The results varied for each strain with the type of plasmid used. Neither the introduced foreign plasmid nor the resident 72-kb virulence plasmid underwent detectable deletions. Transformation was most efficient with supercoiled DNA, decreasing by one and four orders of magnitude for relaxed circular and linearized plasmids, respectively. The ability to easily and efficiently transfer plasmid DNA via electroporation will greatly facilitate the application of recombinant DNA technology for direct cloning and analysis of significant genes into Yersinia.     

Genome-wide screens to identify genes of human pathogenic Yersinia species that are expressed during host infection

An obvious goal in the study of bacteria that cause human disease is to identify the bacterial genes required for growth within the host. Historically, this has presented a significant technological challenge. However, with this goal in mind, the in vivo expression technology (IVET) and signature-tagged mutagenesis (STM) techniques were developed during the 1990s. These techniques have been used to identify virulence genes in the three human pathogenic Yersinia species, Y. enterocolitica, Y. pseudotuberculosis and Y. pestis, using variations of their mouse models of infection. In this review, each of these studies is described individually, including the pertinent details of how each was done, and a brief discussion of the genes identified. In addition, the results of these IVET and STM screens are compared, and the striking lack of overlap between the genes identified is discussed. Most of these studies were only recently published, which means that there have been few follow-up studies on some of the novel virulence genes identified. However, the Y. enterocolitica hreP, rscR and psp genes have become the subject of further studies, which are also summarized here. Finally, I briefly describe the use of the genome-wide (but not in vivo) technology, subtractive hybridization, to identify Yersinia virulence genes.