Balkans’ Asteraceae Species as a Source of Biologically Active Compounds for the Pharmaceutical and Food Industry

Herbal drugs are a useful source of different bioactive compounds. Asteraceae species, as the most widespread vascular plants, can be used both as food and as medicine due to the great diversity of recorded chemical components – different phenolic compounds, terpenes, carotenoids, vitamins, alkaloids, etc. The Balkan Peninsula is characterized by great diversity of plants from Asteraceae family, including presence of rare and endemic species. In this review, results of the survey of chemical composition and biological activity, mainly focusing on antioxidant, antimicrobial and anticancer effects of selected Balkans’ Asteraceae species were provided. In addition, information on edible plants from Asteraceae family is presented, due to growing interest for the so‐called ‘healthy diet’ and possible application of Balkans’ Asteraceae species as food of high nutritional value or as a source of functional food ingredients.     

Utility of pairwise mtDNA genetic distances for predicting cross-species microsatellite amplification and polymorphism success in fishes

In many studies involving microsatellites cross-species amplification, primers designed for one (source) species are used to amplify homologous loci in related (target) species. However, it is not clear how closely related the species must be to attain significant success. Genetic divergence is a clear and easy way to assess similarity between species and provides an accurate measure of their evolutionary distance. Eight Mediterranean target species of the family Serranidae were analysed using twelve primers developed for Serranus cabrilla. Additionally, two mitochondrial genes (12S rRNA and 16S rRNA) were chosen on the basis of their extensive use in phylogenetic and evolutionary analyses to compute genetic divergence between the species. Significant negative correlations were found between genetic divergence and both cross-species amplification and maintained polymorphism of microsatellite markers, which could be generalized by gathering information from different fish studies. The success of obtaining amplifiable and polymorphic microsatellite loci can be a priori approximated knowing the mtDNA genetic divergence between a given source and target species using our inferred regression equations. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Detection heterogeneity in underwater visual‐census data

This study shows how capture–mark–recapture (CMR) models can provide robust estimates of detection heterogeneity (sources of bias) in underwater visual‐census data. Detection biases among observers and fish family groups were consistent between fished and unfished reef sites in Kenya, even when the overall level of detection declined between locations. Species characteristics were the greatest source of detection heterogeneity and large, highly mobile species were found to have lower probabilities of detection than smaller, site‐attached species. Fish family and functional‐group detectability were also found to be lower at fished locations, probably due to differences in local abundance. Because robust CMR models deal explicitly with sampling where not all species are detected, their use is encouraged for studies addressing reef‐fish community dynamics.     

Genetic evaluation of remnant and translocated shiners,Notropis heterodon and Notropis heterolepis

Population and conservation genetics of two freshwater fish species, Notropis heterodon and Notropis heterolepis, were evaluated in north‐eastern Illinois, U.S.A., where both species have severely declined. Fishes were sampled from two remnant populations occurring in small glacial lakes (source samples) and from two man‐made ponds that had been stocked with fishes from those same lakes (sanctuary samples). The goal was to obtain information that would help inform conservation programme planning to reintroduce sanctuary fishes to areas where both species are extirpated. Microsatellite data showed that the two species were genetically quite distinct and there was no evidence of hybridization in either source or sanctuary samples. Within each species, source and sanctuary samples had moderate levels of heterozygosity and were not significantly different from each other. Many alleles observed in the source samples, however, were not detected in the sanctuary samples, indicating that translocation had resulted in reduced allelic diversity of the sanctuary samples. Sibship analysis indicated that full and half sibs occurred within source‐lake samples, thus reducing the effective population size of the reintroduced stock. Taken together, these results suggest that source‐lake stocks rather than sanctuary stocks are more appropriate for future reintroductions of both species in their native range, unless sanctuary populations can be established with hundreds of fishes. Also, fishes should be harvested from multiple locations in source lakes to avoid over‐representation of family groups.     

Phylogenetic study of the species within the family Streptomycetaceae

Species of the genus Streptomyces, which constitute the vast majority of taxa within the family Streptomycetaceae, are a predominant component of the microbial population in soils throughout the world and have been the subject of extensive isolation and screening efforts over the years because they are a major source of commercially and medically important secondary metabolites. Taxonomic characterization of Streptomyces strains has been a challenge due to the large number of described species, greater than any other microbial genus, resulting from academic and industrial activities. The methods used for characterization have evolved through several phases over the years from those based largely on morphological observations, to subsequent classifications based on numerical taxonomic analyses of standardized sets of phenotypic characters and, most recently, to the use of molecular phylogenetic analyses of gene sequences. The present phylogenetic study examines almost all described species (615 taxa) within the family Streptomycetaceae based on 16S rRNA gene sequences and illustrates the species diversity within this family, which is observed to contain 130 statistically supported clades, as well as many unsupported and single member clusters. Many of the observed clades are consistent with earlier morphological and numerical taxonomic studies, but it is apparent that insufficient variation is present in the 16S rRNA gene sequence within the species of this family to permit bootstrap-supported resolution of relationships between many of the individual clusters.     

不同种源和家系白千层芳香油组分及含量初探

本文利用从澳大利亚引进的白千层芳香油树种天然种子进行繁育,并对生长期为18个月的白千层枝叶进行含油量测定,分析不同种源、家系白千层芳香油组分及含量,选择和推广具有经济开发价值的白千层优良品种。     

Complete genome sequence of Mahella australiensis type strain (50-1 BON)

Mahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella, which belongs to the family Thermoanaerobacteraceae. The species is of interest because it differs from other known anaerobic spore-forming bacteria in its G+C content, and in certain phenotypic traits, such as carbon source utilization and relationship to temperature. Moreover, it has been discussed that this species might be an indigenous member of petroleum and oil reservoirs. This is the first completed genome sequence of a member of the genus Mahella and the ninth completed type strain genome sequence from the family Thermoanaerobacteraceae. The 3,135,972 bp long genome with its 2,974 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Surrogates in marine benthic investigations ‐ which taxonomic unit to target?

Although the identification of organisms to the levelof species is the ideal in studies of marinemacrobenthos, there are situations where such a finelevel of taxonomic discrimination may be eitherimpossible or unwarranted, for example when much thefauna is undescribed, or if the task for which samplesare collected does not require them to be identifiedto the species level. The idea that abundances ofhigher taxa, or particular groups of organisms, may beused as surrogates for the total fauna in such studiesis explored in this paper using data from theNorwegian sector of the North Sea. The generalconclusion is that, in surveys of soft sedimentmacrofauna in disturbed areas of the North Sea wherepollution imposes simple spatial gradients on thebenthic communities, little information aboutinter-sample relationships is lost using data based onfamily, polychaete species, or polychaete familyabundances, rather than species abundances. In morepristine areas where spatial patterns are determinedby a number of processes, correlations betweencalculated diversity indices and similarity in faunalpatterns between species and family abundances arestill very high, but less so for polychaete species orpolychaete family abundances. This suggests thatidentification to the level of family may besatisfactory in many routine monitoring surveys,andidentification of only the polychaetes, either to thelevel of species or family, may also be a possiblealternative if there are clear disturbance gradientsin the survey area. Polychaetes are of importance indisturbed areas because the group contains tolerantand intolerant species, and in undisturbed areasbecause within the taxon species have a greater rangeof trophic and reproductive strategies than withinother taxa. Ultimately it is the distribution ofspecies, their identities, and their interactions witheach other and with the environment, that are ofinterest. The use of surrogates is likely to be mostadvantageous if it is only the extent of pollutioneffects from a discrete source that matters, andspecies level baseline studies have already beencompleted.     

黑颈鹤越冬期间植物性食物的显微分析

黑颈鹤与草海越冬期间共取食４７种植物。莎草科植物是主要食物,占７６．５４％,栽培植物仅占２．１４％。植物地一块茎是黑颈鹤取食的主要部位,占３５．１４％,其次为秆状茎,花果和叶。块状戏几乎全来自莎草科植物。酸模的种子占全部花果类食物２７．５４％。比重很大,尤其在越冬前期。我们还对５种主要食物植物或其部位进行了方差分析,得出的结论是食物的性差异是主要的,且非常显著。     

Pervasive purifying selection characterizes the evolution of I2 homologs

We sampled 384 sequences related to the Solanum pimpinellifolium (=Lycopersicon pimpinellifolium) disease resistance (R) gene 12 from six species, potato, S. demissum, tomato, eggplant, pepper, and tobacco. These species represent increasing phylogenetic distance from potato to tobacco, within the family Solanaceae. Using sequence data from the nucleotide binding site (NBS) region of this gene, we tested models of gene family evolution and inferred patterns of selection acting on the NBS gene region and I2 gene family. We find that the I2 family has diversified within the family Solanaceae for at least 14 million years and evolves through a slow birth-and-death process requiring approximately 12 million years to homogenize gene copies within a species. Analyses of selection resolved a general pattern of strong purifying selection acting on individual codon positions within the NBS and on NBS lineages through time. Surprisingly, we find nine codon positions strongly affected by positive selection and six pairs of codon positions demonstrating correlated amino acid substitutions. Evolutionary analyses serve as bioinformatic tools with which to sort through the vast R gene diversity in plants and find candidates for new resistance specificities or to identify specific amino acid positions important for biochemical function. The slow birth-and-death evolution of I2 genes suggests that some NBS-leucine rich repeat-mediated resistances may not be overcome rapidly by virulence evolution and that the natural diversity of R genes is a potentially valuable source for durable resistance.     

MALDI-TOF mass spectrometry is a fast and reliable platform for identification and ecological studies of species from family Rhizobiaceae

Family Rhizobiaceae includes fast growing bacteria currently arranged into three genera, Rhizobium, Ensifer and Shinella, that contain pathogenic, symbiotic and saprophytic species. The identification of these species is not possible on the basis of physiological or biochemical traits and should be based on sequencing of several genes. Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae. In this work we evaluated the suitability of Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for this purpose. Firstly, we evaluated the capability of this methodology to differentiate among species of family Rhizobiaceae including those closely related and then we extended the database of MALDI Biotyper 2.0 including the type strains of 56 species from genera Rhizobium, Ensifer and Shinella. Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences. The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies.     

ITS2 barcode for identifying the officinal rhubarb source plants from its adulterants

Officinal rhubarb, the dried root and rhizome of Rheum officinale Baill., Rh. palmatum L., and Rh. tanguticum (Maxim. ex Regel) Maxim. ex Balf. of Polygonaceae family, is one of the most well-known and important traditional Chinese medicines. The growing herbal market has led to the introduction of adulterants, and difficulties in morphological based discrimination has also resulted in concerns over consumer safety. ITS2 as a potential barcode was employed to discriminate officinal rhubarb sampled from the entire distribution range and its adulterants. The minimum K2P interspecific distance between officinal rhubarb source plants and the adulterants were higher than the maximum K2P intraspecific distance within the officinal rhubarb source plants. When the phylogenetic trees were constructed by neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian methods, all Rheum species were grouped into one clade, while Polygonum and Rumex species were clustered in another clade. In the Rheum clade, all the officinal rhubarb source plants constituted a distinct subclade, while other Rheum species formed other subclades. Our results suggested that the ITS2 region is a more suitable and accurate DNA barcode for distinguishing officinal rhubarb source plants from their adulterants.     

The Fossil Record of the Solanaceae Revisited and Revised—The Fossil Record of Rhamnaceae Enhanced

Solanaceae is a large cosmopolitan family of angiosperms that includes some 92–100 genera and 2300–2500 species. It has been the object of a great deal of attention because of its economic importance as a food source (tomatoes, potatoes, peppers), because it includes tobacco, and is source of drugs (alkaloids). However its fossil history has been elusive with relatively few seemingly reliable reports throughout Tertiary times and no solid bases for molecular dating models to pinpoint important events in its diversification and evolution. While the great diversity found within the family makes it difficult to find morphological characters that define it, in general, the flowers have an overall distinctive morphology with some diagnostic morphological characters. Thus, as is often the case, flowers are potentially the most reliable indicators of the family in the fossil record. There have been a number of reports of flowers representing Solanaceae in the Tertiary. Yet, we report here that upon reinvestigation only one taxon remains as a plausible representative of the family while one of the most notable and frequently cited fossil Solanaceae from the Tertiary of North America is clearly a member of the family Rhamnaceae consistent with the fossil leaf record.     

Do Rapoport's rule,the mid‐domain effect or the source–sink hypotheses predict bathymetric patterns of polychaete richness on the Pacific coast of South America?

Aim We evaluated the bathymetric gradient of benthic polychaete species richness from the Chilean coast, as well as its possible underlying causes. We tested three possible hypotheses to explain the richness gradient: (1) Rapoport's effect; (2) the mid‐domain effect (MDE); and (c) the source–sink hypothesis. Location South‐eastern Pacific coast of Chile. Methods The bathymetric gradient in richness was evaluated using the reported ranges of bathymetric distribution of 498 polychaete species, from the intertidal to abyssal zone (c. 4700 m). Rapoport's effect was evaluated by examining the relationship between bathymetric mid‐point and bathymetric range extent, and species richness and depth. The MDE was tested using the Monte Carlo simulation program. The source–sink hypothesis was tested through nestedness analysis. Results Species richness shows significant exponential decay across the bathymetric gradient. The pattern is characterized by a high presence of short‐ranged species on the continental shelf area; while only a few species reach abyssal depths, and they tend to show extremely wide bathymetric ranges. Our simulation analyses showed that, in general, the pattern is robust to sampling artefacts. This pattern cannot be reproduced by the MDE, which predicts a parabolic richness gradient. Rather, results agree with the predictions of Rapoport's effect. Additionally, the data set is significantly nested at species, genus and family levels, supporting the source–sink hypothesis. Main conclusions The sharp exponential decay in benthic polychaete richness across the bathymetric gradient supports the general idea that abyssal environments should harbour fewer species than shallower zones. This pattern may be the result of colonization–extinction dynamics, characterized by abyssal assemblages acting as ‘sinks’ maintained mainly by shallower ‘sources’. The source–sink hypothesis provides a conceptual and methodological framework that may shed light on the search for general patterns of diversity across large spatial scales.     

Novel universal primers establish identity of an enormous number of animal species for forensic application

This study describes a polymerase chain reaction (PCR)‐based approach, which without knowing the history of a forensic sample, is able to reveal whether the source of the sample is human or animal, and, if animal, which of the 221 animal species included in the study, simply by using one set of novel primers to amplify and sequence the PCR amplicons. The primers described in this study universally amplify a specific segment of mitochondrial cytochrome b sequence from a sample of unknown origin and delineate its identity to the level of family, genus and species. Because these primers are universal, this approach can be applied to an enormous number of other species, which are not included in the study, and could be an ultimate solution for the identification of species for forensic application.     

Whole Plastome Sequences from Five Ginger Species Facilitate Marker Development and Define Limits to Barcode Methodology

Plants from the Zingiberaceae family are a key source of spices and herbal medicines. Species identification within this group is critical in the search for known and possibly novel bioactive compounds. To facilitate precise characterization of this group, we have sequenced chloroplast genomes from species representing five major groups within Zingiberaceae. Generally, the structure of these genomes is similar to the basal angiosperm excepting an expansion of 3 kb associated with the inverted repeat A region. Portions of this expansion appear to be shared across the entire Zingiberales order, which includes gingers and bananas. We used whole plastome alignment information to develop DNA barcodes that would maximize the ability to differentiate species within the Zingiberaceae. Our computation pipeline identified regions of high variability that were flanked by highly conserved regions used for primer design. This approach yielded hitherto unexploited regions of variability. These theoretically optimal barcodes were tested on a range of species throughout the family and were found to amplify and differentiate genera and, in some cases, species. Still, though these barcodes were specifically optimized for the Zingiberaceae, our data support the emerging consensus that whole plastome sequences are needed for robust species identification and phylogenetics within this family.     

东北地区早春蜜源植物传粉昆虫多样性研究

为了揭示蜜源植物与传粉昆虫的关系,科学的保护和利用传粉昆虫资源,本研究选取东北地区早春常见蜜源植物柳树Salix、延胡索Corydalis和银莲花Anemone为研究对象,对其传粉昆虫种类和访花行为进行调查,分析不同蜜源植物的传粉昆虫种类、优势类群、多样性和访花行为。结果表明：东北地区早春蜜源植物传粉昆虫共采集726头,隶属于5目14科53种,其中膜翅目4科35种,双翅目5科13种,鳞翅目3科3种,同翅目1科 1种,鞘翅目1科1种。柳树的优势传粉昆虫为蜂类,延胡索的优势传粉昆虫为熊蜂类,银莲花的优势传粉昆虫为蝇类。延胡索的传粉昆虫多样性、均匀度和丰富度均最高。蜜蜂对柳树单位时间内访花次数和单花停留时间最高,为94.33次和18.90 s。熊蜂对延胡索单位时间内访花次数和单花停留时间最高,为76.42次和15.37 s,熊蜂在采集延胡索花时有明显的盗蜜行为,该行为有利于其它传粉昆虫生存。东北地区保护生物多样性和传粉昆虫资源,应结合蜜源植物保护,可在早春时期补种柳树、延胡索和银莲花,并合理搭配,为传粉昆虫提供良好食物源和栖息地。     

DNA barcoding of some medicinally important plant species of Lamiaceae family in India

Molecular Biology Reports - Several species of the Lamiaceae family are the primary source of bioactive aromatic oils and secondary metabolites, having broader applications in the cosmetics,...     

Complete genome sequence of Cellulomonas flavigena type strain (134)

Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of the genus Cellulomonas of the actinobacterial family Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for their ability to degrade cellulose and hemicellulose, particularly with regard to the use of biomass as an alternative energy source. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the genus Cellulomonas, and next to the human pathogen Tropheryma whipplei the second complete genome sequence within the actinobacterial family Cellulomonadaceae. The 4,123,179 bp long single replicon genome with its 3,735 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Characterization of a TOL-like plasmid from Alcaligenes eutrophus that controls expression of a chromosomally encoded p-cresol pathway.

Strains of all 18 species of the family Rhodospirillaceae (nonsulfur photosynthetic bacteria) were studied for their comparative nitrogen-fixing abilities. All species, with the exception of Rhodocyclus purpureus, were capable of growth with N2 as the sole nitrogen source under photosynthetic (anaerobic) conditions. Most rapid growth on N2 was observed in strains of Rhodopseudomonas capsulata. Within the genus Rhodopseudomonas, the species R. capsulata, R. sphaeroides, R. viridis, R. gelatinosa, and R. blastica consistently showed the highest in vivo nitrogenase rates (with the acetylene reduction technique); nitrogenase rates in other species of Rhodopseudomonas and in most species of Rhodospirillum were notably lower. Chemotrophic (dark microaerobic) nitrogen fixation occurred in all species with the exception of one strain of Rhodospirillum fulvum; oxygen requirements for dark N2 fixation varied considerably among species and even within strains of the same species. We conclude that the capacity to fix molecular nitrogen is virtually universal among members of the Rhodospirillaceae but that the efficacy of the process varies considerably among species.