Letter: Molecular symmetry axes and subunit interfaces in certain dehydrogenases

A right-handed orthogonal set of axes P, Q, R has been denned coincident with the three different molecular 2-fold axes of lactate dehydrogenase. The four different symmetry-related subunits can then be color-coded red, yellow, green and blue to identify the three different subunit contacts made by any one subunit to the remaining three others. This nomenclature has been extended to soluble malate dehydrogenase and will facilitate the comparison of dehydrogenases with related ternary and quaternary structures.     

The endemic bovids from Sardinia and the Balearic Islands: State of the art

Bovids are not so common in endemic insular faunas and are mainly recorded in Southeast Asia, Japan and some Mediterranean islands. In the Western Mediterranean, endemic bovids have been recorded during the late Miocene in the Tusco-Sardinian palaeobioprovince (Baccinello-Cinigiano basin, South Tuscany, and Fiume Santo, north-western Sardinia). In the latest Neogene and Quaternary, bovids showing highly endemic features were restricted to the Balearic Islands and Sardinia, while Bovini only slightly reduced in size were present on Pianosa, Malta and Sicily. On Sardinia, the richest bovid sample comes from Monte Tuttavista (Orosei), where at least three species have been identified: Asoletragus genthry, Nesogoral aff. N. melonii, and Nesogoral sp. 2. On Mallorca (Balearic Islands) six chronospecies belonging to the Myotragus endemic phylogenetic lineage have been described, spreading in age from the Early Pliocene to the Holocene. For decades, a close phylogenetic relationship between Nesogoral and Myotragus has been widely accepted by scholars. Morphological and biometrical differences shown by Balearic and Sardinian bovids have generally been regarded as the result of the evolution into two different island ecological systems, characterized by different inter and intra-guild selection pressures. Indeed, the more diversified environment of Sardinia, as well as the presence of other large mammals (similar-sized competitors belonging to the same guild and a running predator), increased the interspecific competition, forcing Sardinian bovids to exploit different resources and to occupy different niches, while Myotragus exploited under a monopoly regime the supply of resources available for large herbivores on the Eastern Balearic Islands. Nonetheless, new data suggest that Nesogoral and Myotragus possibly originated from different taxa.     

Larch chromosomal mosaicism

Karyological study of larch population members from different parts of the Larix olgensis L. Henry areal in the Primorskii krai has been carried out. The main amount of chromosomes for larch as n = 12 (2n = 24) has been confirmed. Mixoploidy was observed in all studied populations. The difference of individuals from the larch areal based on the cell amount with a different level of ploidity has been found in the population of L. olgensis locus classicus and both L. sibirica and L. gmelinii, which is probably a consequence of their hybrid nature.     

Mitotic Recombination in the Heterochromatin of the Sex Chromosomes of DROSOPHILA MELANOGASTER

The frequency of spontaneous and X-ray-induced mitotic recombination involving the Y chromosome has been studied in individuals with a marked Y chromosome arm and different XY compound chromosomes. The genotypes used include X chromosomes with different amounts of X heterochromatin and either or both arms of the Y chromosome attached to either side of the centromere. Individuals with two Y chromosomes have also been studied. The results show that the bulk of mitotic recombination takes place between homologous regions.     

Chemoenzymatic preparation of a biologically active naphthoquinone from Tabebuia impetiginosa using lipases or alcohol dehydrogenases

Cancer chemopreventive agent (S)-5-hydroxy-2-(1-hydroxyethyl)naphtho[2,3-b]furan-4,9-dione and its counterpart (R)-acetate have been obtained through a lipase-catalyzed transesterification process in organic solvent. Candida antarctica lipase B and Pseudomonas cepacia lipase have demonstrated their potential as excellent biocatalysts for the production of enantiomerically pure compounds under mild reaction conditions. At the same time different commercially available alcohol dehydrogenases have been tested in the bioreduction of the corresponding naphthoquinone in an aqueous system. Biologically active (S)-alcohol has been isolated in enantiopure form with different conversion values depending on the biocatalyst employed and the reaction conditions.     

Description of the type-series of Palaeocryptonyx donnezani Depéret, 1892 (Aves: Phasianidae) with the selection of a lectotype

We have re-examined the original type-series of Palaeocryptonyx donnezani Depéret, 1892 housed in the Laboratoire de Géologie de Lyon, Université Claude-Bernard Lyon 1 (France), and have selected a lectotype and paralectotypes. P. donnezani is the type species of the extinct genus Palaeocryptonyx, known from six species from different European Neogene and Pleistocene fossil localities. The species have been compared with different medium-sized Phasianidae species on the basis of our own study and data from the literature. The systematic position of P. donnezani has been questioned, because it has been misplaced in the extant genera Alectoris and Coturnix, but our analysis confirms its validity and its attribution to a separate genus; hence we also confirm the validity of the genus Palaeocryptonyx.     

Genetic basis of the variability of nitrate reduction trait in Yersinia pestis strains

The genetic basis of the varying ability to reduce nitrate in strains belonging to different biovars and subspecies of plague-causing microbe has been investigated and the inability to reduce nitrate observed in different intraspecies groups of Yersinia pestis has been shown to stem from mutations in different genes involved in the expression of this trait. The absence of denitrifying activity in strains of altaica and hissarica subspecies was not due to a mutation at position 613 of the periplasmic reductase napA observed in the strains of the biovar medievalis of the main subspecies, but rather was due to a mutation in the sequence encoding the nitrate-binding domain of the ABC transporter protein SsuA; a thymine insertion (+T) was detected at position 302 from the start of the ssuA gene. Five strains of biovar antiqua isolated at different times in Mongolia, China, and Africa were shown to lack the ability to reduce nitrate. A PCR test targeting two chromosomal regions containing deletions of 19 and 24 bp in size has been developed for the identification of strains of the biovar medievalis. This test can be combined with the test for the marker mutation in the napA gene for a more reliable detection of Y. pestis strains belonging to this biovar.     

Molecular epidemiology of cryptosporidiosis: An update

Molecular tools have been developed to detect and differentiate Cryptosporidium at the species/genotype and subtype levels. These tools have been increasingly used in characterizing the transmission of Cryptosporidium spp. in humans and animals. Results of these molecular epidemiologic studies have led to better appreciation of the public health importance of Cryptosporidium species/genotypes in various animals and improved understanding of infection sources in humans. Geographic, seasonal and socioeconomic differences in the distribution of Cryptosporidium spp. in humans have been identified, and have been attributed to differences in infection sources and transmission routes. The transmission of C. parvum in humans is mostly anthroponotic in developing countries, with zoonotic infections play an important role in developed countries. Species of Cryptosporidium and subtype families of C. hominis have been shown to induce different clinical manifestations and have different potential to cause outbreaks. The wide use of a new generation of genotyping and subtyping tools in well designed epidemiologic studies should lead to a more in-depth understanding of the epidemiology of cryptosporidiosis in humans and animals.     

On the Complexity of the Saccharomyces bayanus Taxon: Hybridization and Potential Hybrid Speciation

Although the genus Saccharomyces has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is S. bayanus, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (bayanus and uvarum), which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the S. bayanus taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequence data, and based on the S. bayanus var. bayanus reference strain NBRC 1948, a hypothetical pure S. bayanus was reconstructed for these genes that showed alleles with similarity values lower than 97% with the S. bayanus var. uvarum strain CBS 7001, and of 99–100% with the non S. cerevisiae portion in S. pastorianus Weihenstephan 34/70 and with the new species S. eubayanus. Among the S. bayanus strains under study, different levels of homozygosity, hybridization and introgression were found; however, no pure S. bayanus var. bayanus strain was identified. These S. bayanus hybrids can be classified into two types: homozygous (type I) and heterozygous hybrids (type II), indicating that they have been originated by different hybridization processes. Therefore, a putative evolutionary scenario involving two different hybridization events between a S. bayanus var. uvarum and unknown European S. eubayanus-like strains can be postulated to explain the genomic diversity observed in our S. bayanus var. bayanus strains.     

Foliar appendages in certain species ofSalvia (studies inLamiaceae VI)

Foliar appendages of eight species ofSalvia L. have been studied. Eleven types of non glandular and five types of glandular appendages have been observed. They have been classified under three major categories: (1) glandular capitate; (2) non glandular filiform and (3) non glandular capitate. Five new types of trichomes have been reported fromLamiaceae for the first time. On the basis of trichome types different species ofSalvia can be identified. A tentative key has been presented.     

A multigene phylogeny demonstrates that Tuber aestivum and Tuber uncinatum are conspecific

For almost 2 centuries it has been disputed whether Tuber aestivum and Tuber uncinatum constitute two different species of truffles. Molecular markers have been applied previously to contribute to resolving this question, coming to different conclusions. In this study, we address this question by analyzing the genetic structure of truffles assigned to either of the two putative species from a geographically broad sampling across Europe. We used an approach involving multigene phylogenies and coalescent analyses of nine regions from five genes. All tests conducted supported the conspecificity of Tuber aestivum and Tuber uncinatum.     

Alcaloïdes steroidiques du Malouetia Brachyloba et du M. Heudelotii

Malouetine and funtumafrine C have been isolated from the leaves of Malouetia brachyloba, indicating that this species is not very different from M. bequaertiana. Five conanine derivatives have been extracted from the leaves of M. heudelotii, a species which does not contain any alkaloid with a quaternary ammonium function.     

Interpopulation differences in hemocyte DNA-comet parameters of snail Lymnaea stagnalis from regions with different environmental loads

Research on hemocytes of snail Lymnaea stagnalis from regions with different environmental loads has been carried out by comet assay. Significant interpopulation differences in hemocyte DNA-comet parameters and sensitivity of hemocyte genetic material to external damaging factors (heavy-metal Sr, in particular) have been revealed by means of software analysis of hemocyte DNA-comet images. Two snail populations are characterized by high genetic identity; therefore, the different proliferative activity in the hemocytes of snail Lymnaea stagnalis from different ecological zones revealed by comet assay may be considered as an indicator of the intensity of damaging effects and environmental quality.     

Sexual dimorphism and polymorphism in a Callovian Phlycticeras (Ammonoidea) assemblage of Kutch, India

An assemblage of Phlycticeras Hyatt from a precisely dated zone of Middle Callovian in Kutch, India has been analyzed. Systematic study reveals that this sample can be divided into two size groups. The larger set shows different adult modifications leading to ornamental polymorphism. Polymorphs are very similar, if not identical, to different chronospecies of Europe, which range between Middle to Upper Callovian. They are grouped under well-known Phlycticeras polygonium (Zieten). The group of smaller specimens on the other hand, strongly resembles a species, which has been previously described as Phlycticeras schaumburgi (Waagen) from the younger Upper Callovian horizons in Kutch. It has a peculiar ‘rooster’-like septicarinate keel in the venter near adult aperture. Phlycticeras-Oecoptychius have been considered as a possible dimorphic pair since long, but here shown to have many inconsistencies to support these views. Instead, sexual dimorphism is explored within Phlycticeras and P. polygonium-P. schaumburgi is proposed as possible antidimorphs. A similar association is found in different stratigraphic assemblages of Europe. Interestingly these two morphs show parallel evolutionary changes within the Phlycticeras genus.     

Pollen morphology of the Phyllanthus species occurring in the continental United States

Twelve native United States species have been examined. The pollen grains could be divided into five pollen types based on sexine ornamentation, aperture structure, sexine/nexine ratio and sexine 1/sexine 2 ratio. Within these types it was often possible to distinguish the grains of the different species. Two groups of types have been recognized based on the similarities in ornamentation. One group, consisting of the Phyllanthus amarus type, the P. tenellus type and the P. urinaria type, is characterized by the Tilia structure, whereas the second group of types, comprising the P. caroliniensis type and the P. liebmannianus type are microreticulate. The postulation that different subgenera show different pollen types is true in general, but there is one exception: P. niruri, taxonomically belonging to the subgenus Phyllanthus, has pollen grains of the P. caroliniensis type, a type also comprising species from the subgenus Isoclades.     

Identification of Bacterial Strains Isolated from the Mediterranean Sea Exhibiting Different Abilities of Biofilm Formation

The Mediterranean Sea has rarely been investigated for the characterization of marine bacteria as compared to other marine environments such as the Atlantic or Pacific Ocean. Bacteria recovered from inert surfaces are poorly studied in these environments, when it has been shown that the community structure of attached bacteria can be dissimilar from that of planktonic bacteria present in the water column. The objectives of this study were to identify and characterize marine bacteria isolated from biofilms developed on inert surfaces immersed in the Mediterranean Sea and to evaluate their capacity to form a biofilm in vitro. Here, 13 marine bacterial strains have been isolated from different supports immersed in seawater in the Bay of Toulon (France). Phylogenetic analysis and different biological and physico-chemical properties have been investigated. Among the 13 strains recovered, 8 different genera and 12 different species were identified including 2 isolates of a novel bacterial species that we named Persicivirga mediterranea and whose genus had never been isolated from the Mediterranean Sea. Shewanella sp. and Pseudoalteromonas sp. were the most preponderant genera recovered in our conditions. The phenotypical characterization revealed that one isolate belonging to the Polaribacter genus differed from all the other ones by its hydrophobic properties and poor ability to form biofilms in vitro. Identifying and characterizing species isolated from seawater including from Mediterranean ecosystems could be helpful for example, to understand some aspects of bacterial biodiversity and to further study the mechanisms of biofilm (and biofouling) development in conditions approaching those of the marine environment.     

The Choice of PCR Primers Has Great Impact on Assessments of Bacterial Community Diversity and Dynamics in a Wastewater Treatment Plant

Assessments of bacterial community diversity and dynamics are fundamental for the understanding of microbial ecology as well as biotechnological applications. We show that the choice of PCR primers has great impact on the results of analyses of diversity and dynamics using gene libraries and DNA fingerprinting. Two universal primer pairs targeting the 16S rRNA gene, 27F&1492R and 63F&M1387R, were compared and evaluated by analyzing the bacterial community in the activated sludge of a large-scale wastewater treatment plant. The two primer pairs targeted distinct parts of the bacterial community, none encompassing the other, both with similar richness. Had only one primer pair been used, very different conclusions had been drawn regarding dominant phylogenetic and putative functional groups. With 27F&1492R, Betaproteobacteria would have been determined to be the dominating taxa while 63F&M1387R would have described Alphaproteobacteria as the most common taxa. Microscopy and fluorescence in situ hybridization analysis showed that both Alphaproteobacteria and Betaproteobacteria were abundant in the activated sludge, confirming that the two primer pairs target two different fractions of the bacterial community. Furthermore, terminal restriction fragment polymorphism analyses of a series of four activated sludge samples showed that the two primer pairs would have resulted in different conclusions about community stability and the factors contributing to changes in community composition. In conclusion, different PCR primer pairs, although considered universal, target different ranges of bacteria and will thus show the diversity and dynamics of different fractions of the bacterial community in the analyzed sample. We also show that while a database search can serve as an indicator of how universal a primer pair is, an experimental assessment is necessary to evaluate the suitability for a specific environmental sample.     

In silico analysis of PHB gene family in maize

Prohibitins (PHBs) are highly conserved proteins in species ranging from prokaryotes to eukaryotes. Plant PHBs have been implicated in various cellular processes including development, senescence and stress responses. Although PHBs have been investigated in several plant species including Arabidopsis and tobacco, no systematic gene family analysis has been carried in maize. In the present study, 16 putative PHB genes have been identified. Analysis of the conserved protein motifs and gene structures has revealed high levels of conservation within the phylogenetic subgroups. Published microarray database showed that most maize PHB genes exhibited different expression levels in different tissues and developmental stages. Cis-elements analysis showed that ZmPHB2 and ZmPHB12 may play important roles in plant development. Taken together, we provide a comprehensive bioinformatics analysis of the PHB gene family in maize genome and our data provide an important foundation for further functional study of this gene family in maize.