Microbial sequences retrieved from environmental samples from seasonal Arctic snow and meltwater from Svalbard, Norway

16S rRNA gene (rrs) clone libraries were constructed from two snow samples (May 11, 2007 and June 7, 2007) and two meltwater samples collected during the spring of 2007 in Svalbard, Norway (79°N). The libraries covered 19 different microbial classes, including Betaproteobacteria (21.3%), Sphingobacteria (16.4%), Flavobacteria (9.0%), Acidobacteria (7.7%) and Alphaproteobacteria (6.5%). Significant differences were detected between the two sets of sample libraries. First, the meltwater libraries had the highest community richness (Chao1: 103.2 and 152.2) and Shannon biodiversity indices (between 3.38 and 3.59), when compared with the snow libraries (Chao1: 14.8 and 59.7; Shannon index: 1.93 and 3.01). Second, ∫-LIBSHUFF analyses determined that the bacterial communities in the snow libraries were significantly different from those of the meltwater libraries. Despite these differences, our data also support the theory that a common core group of microbial populations exist within a variety of cryohabitats.     

Nitrogen fixation in Arctic vegetation and soils from Svalbard,Norway

Nitrogen fixation was measured by the acetylene reduction method in a high Arctic ecosystem at Kongsfjorden, Spitsbergen (79°N, 12°E). The most important source of biologically fixed nitrogen was found in cyanobacteria either as free living colonies ofNostoc sp. in wet unvegetated or sparsely vegetated grounds or growing as epiphytes on bryophytes. Fixation associated with plant roots or in soil and peat samples had little or no significance for nitrogen input to the ecosystem. The ability to support an epiphytic flora of nitrogen-fixing cyanobacteria varied greatly between bryophyte species.Calliergon richardsonii andSanionia uncinata seemed especially well adapted for harbouring epiphytic cyanobacteria, but the extent of nitrogen fixation varied with the growing location. The rate of nitrogen fixation was greatly influenced by grazing by geese. In a geese-grazing area values were found with a maximum of 693.6±1.5 nmol C₂H₄ h⁻¹ g (dry weight)⁻¹ while the maximum value for ungrazed areas was 65.3±16.6 nmol C₂H₄ h⁻¹ g (dry weight)⁻¹. In the grazed area cyanobacteria were also found fixing nitrogen epiphytically on grass. The high plant productivity, supporting heavy grazing, clearly indicates an effective transfer of fixed nitrogen to the plant community. Under cliffs harbouring colonies of birds, the biological nitrogen fixation was inhibited by bird droppings.     

Genetic diversity in populations of Sphagnum capillifolium from the mountains of Bulgaria,and their possible refugial role

Abstract

Genetic diversity in eight populations of Sphagnum capillifolium from different Bulgarian mountains was investigated by means of isozyme electrophoresis. High levels of allelic diversity were found (H_S = 0.119), comparable to earlier estimates for northern European populations (H_S = 0.116). Strong differentiation among populations and a low number of widespread genotypes suggest a high degree of isolation and restricted gene flow between populations, which is consistent with generally small and scattered populations. The large proportion of distinguishable genotypes (mean 0.498) suggests high levels of out-crossing either currently or in the past. Introgression between S. capillifolium and S. rubellum, a species not found in Bulgaria, was suggested by the occurrence of rubellum-alleles in five populations from different mountains. This could be explained by an ancient hybridization event in a sympatric population. Based on (1) the high genetic diversity, (2) the fairly wide distribution of alien alleles, and (3) the isolated distribution of populations even within one mountain, a possible survival of S. capillifolium in the Balkan area during the Quaternary ice periods is hypothesized.     

Climate change impacts on wildlife in a High Arctic archipelago – Svalbard,Norway

The Arctic is warming more rapidly than other region on the planet, and the northern Barents Sea, including the Svalbard Archipelago, is experiencing the fastest temperature increases within the circumpolar Arctic, along with the highest rate of sea ice loss. These physical changes are affecting a broad array of resident Arctic organisms as well as some migrants that occupy the region seasonally. Herein, evidence of climate change impacts on terrestrial and marine wildlife in Svalbard is reviewed, with a focus on bird and mammal species. In the terrestrial ecosystem, increased winter air temperatures and concomitant increases in the frequency of ‘rain‐on‐snow’ events are one of the most important facets of climate change with respect to impacts on flora and fauna. Winter rain creates ice that blocks access to food for herbivores and synchronizes the population dynamics of the herbivore–predator guild. In the marine ecosystem, increases in sea temperature and reductions in sea ice are influencing the entire food web. These changes are affecting the foraging and breeding ecology of most marine birds and mammals and are associated with an increase in abundance of several temperate fish, seabird and marine mammal species. Our review indicates that even though a few species are benefiting from a warming climate, most Arctic endemic species in Svalbard are experiencing negative consequences induced by the warming environment. Our review emphasizes the tight relationships between the marine and terrestrial ecosystems in this High Arctic archipelago. Detecting changes in trophic relationships within and between these ecosystems requires long‐term (multidecadal) demographic, population‐ and ecosystem‐based monitoring, the results of which are necessary to set appropriate conservation priorities in relation to climate warming.     

Ploidy levels among species in the 'Oxalis tuberosa alliance' as inferred by flow cytometry

The 'Oxalis tuberosa alliance' is a group of Andean Oxalis species allied to the Andean tuber crop O. tuberosa Molina (Oxalidaceae), commonly known as 'oca'. As part of a larger project studying the origins of polyploidy and domestication of cultivated oca, flow cytometry was used to survey DNA ploidy levels among Bolivian and Peruvian accessions of alliance members. In addition, this study provided a first assessment of C-values in the alliance by estimating nuclear DNA contents of these accessions using chicken erythrocytes as internal standard. Ten Bolivian accessions of cultivated O. tuberosa were confirmed to be octoploid, with a mean nuclear DNA content of approx. 3.6 pg/2C. Two Peruvian wild Oxalis species, O. phaeotricha and O. picchensis, were inferred to be tetraploid (both with approx. 1.67 pg/2C), the latter being one of the putative progenitors of O. tuberosa identified by chloroplast-expressed glutamine synthetase data in prior work. The remaining accessions (from 78 populations provisionally identified as 35 species) were DNA diploid, with nuclear DNA contents varying from 0.79 to 1.34 pg/2C.     

On the inverse problem in flow cytometry recovering DNA distribution from FMF data

The problem of recovering DNA distribution from cytofluorometric experimental data was investigated. Theoretical analysis led to a convenient formulation of the problem and to uniqueness results for its solution. A minimization algorithm has been implemented to get the optimal estimate of G₁, S, G₂, and M phase percentages. This algorithm was tested in some experimental cases.     

DNA isolation by a rapid method from human blood samples: Effects of MgCl2, EDTA,storage time,and temperature on DNA yield and quality

The isolation of DNA from whole blood by a modified rapid method (RM) was tested using various detergents and buffer conditions. Extraction of DNA with either NP-40 or Triton X-100 gave a high yield of undegraded DNA in less than an hour. The concentration of magnesium ion in the buffers was critical to obtaining intact, high molecular weight (HMW) DNA. Greater than 10 mM MgCl₂ led to degradation. Addition of EDTA to the buffer inhibits this degradation. Preparation of DNA from blood stored at room temperature or incubated at 37°C for 24 hr resulted in the same amount and quality of DNA as from samples frozen at −70°C. DNA from blood samples that had undergone more than four freeze-thaw cycles was found to be partially degraded. The modified RM can be applied to extract DNA from as little as 10 μl of blood (340 ng of DNA) and from dried blood samples. DNA samples remained intact and undegraded for longer times when DNA was dissolved in higher concentrations of EDTA. This work was supported by grants from the Indiana Department of Mental Health and PHS RO1 AG10297.     

Chromosomal abnormalities and DNA image cytometry of haematological neoplasms in fine needle aspirates of lymph nodes

The current diagnostics of haematological neoplasms along with morphological analysis, immunophenotyping and molecular analysis inevitably includes cytogenetic analysis. In this work the possibility of cytomorphological subclassification of haematological neoplasms from lymph node fine needle aspirates was examined without depending upon the referential histological diagnosis and cytogenetic analysis. In addition, the feasibility of cytogenetic analysis of the material obtained by lymph node fine needle aspiration (FNA) was examined. By analysing the findings of cytogenetic analysis and DNA image cytometry, it was decided to examine the possibility of comparing the findings and supplementing diagnostic possibilities of these methods. In 15 cases cytological diagnoses and cytogenetic analysis of haematological neoplasms were performed on the material obtained by lymph node FNA. In 12 of 15 cases histological diagnosis was made separately. A good cytohistological correlation was available in 9 of 12 cases (75%). Cytomorphological diagnoses in 10 of 15 cases (76%) were confirmed by the finding of a specific chromosomal translocation. In two cases cytological diagnosis did not correlate with the histological diagnosis and was confirmed only with specific chromosomal translocations. The lymphocytes obtained by lymph node FNA were adequate material for cytogenetic analysis - in 15 of 18 (83%) cases mitoses in cell cultures were obtained. In 13 of 15 (87%) cases clonal chromosomal abnormalities were detected, whereas in 2 of 15 (13%) cases a normal karyotype was found. DNA image cytometry was performed on nine samples, whereas in six samples the material was not sufficient. Although a small number of samples was analysed in the cases with identical cytomorphological diagnoses, the analysed histograms regarding the DNA index values showed heterogeneity. In conclusion, a cell culture sampled by FNA of lymph nodes is an adequate method for the chromosomal analysis. The specific cytogenetic abnormality associated with cytological diagnosis provides an opportunity to make a definitive diagnosis and provides a powerful approach when reference diagnosis on biopsy material cannot be obtained.     

Energy intake and utilisation by nursing bearded seal (Erignathus barbatus) pups from Svalbard,Norway

In this study we measure energy intake via milk in nursing bearded seal (Erignathus barbatus) pups and determine how this energy is allocated into metabolism and storage of new tissues. This was accomplished using longitudinal mass gain records and the doubly labelled water technique on nursing pups in combination with cross-sectional data on changes in milk composition from bearded seal mothers. The pups (n=3) were all less than a week old at the start of the experiments. Pups gained 3.3±0.4 kg·day^-1 of which 50% was fat, 14% protein and 36% water. Average daily water influx for the pups was 69.5±9.0 ml · kg^-1· day^-1. Average CO₂ production during the study period was 0.99±0.10 ml·g^-1·h^-1, which corresponds to a field metabolic rate of 642±67 kJ·kg^-1· day^-1, or 6.0±0.5 times the predicted basal metabolic rate according to Kleiber (1975). The pups drank an average of 7.6±0.5 kg of milk daily. This corresponds to a daily energy intake of 154±8 MJ, 47±14% of which was stored as new body tissue. Despite this high energy intake bearded seal pups do not get as fat as do other nursing phocids. This is in part due to their larger body size but also due to their very active aquatic lifestyle and the lower and more consistent fat content of the milk compared to other phocid species. Bearded seal mothers forage during lactation and may also be involved in teaching their pups to feed independently. All these data suggest that the lactation strategy of bearded seals differs from the phocid norm.     

Nuclear DNA content of Solanum species grown in vitro, as determined by flow cytometry

The DNA relative content in nuclei from several Solanum species, which were used as partners for somatic hybridization, were determined using a flow cytometry method. The nuclei were isolated mechanically or via protoplasts from leaves of in vitro grown plants. In the case of S. nigrum as well as S. tuberosum cv. Bzura and dihaploid clone H8105, the nuclei were also obtained from suspension cultured cells by lysis of protoplasts. The source and the method of nuclei isolation affected the pattern of nuclear DNA in the genotypes studied. The mesophyll nuclei showed two distinct peaks on the DNA histograms, whereas the DNA peaks produced by cell suspension nuclei were broad and less distinct. The DNA content in the nuclei, calculated from the DNA histograms of the samples and a DNA standard historgam (Trout Red Blood Cells, having DNA content of 5.05 pg per nucleus), were much lower in mesophyll nuclei than in those obtained from the cell suspension for the same genotypes. The results are discussed in respect of the genetic instability of Solanum genotypes. The usefulness of a flow cytometry approach in somatic hybridization research is also discussed.     

Mitochondrial DNA diversity among four sympatric morphs of Arctic charr, Salvelinus alpinus L., from Thingvallavatn, Iceland

Restriction fragment length polymorphisms in mitochondrial DNA (mtDNA) were examined in progeny of four sympatric morphs of Arctic charr ( Salvelinus alpinus L.) from Thingvallavatn, Iceland. The mtDNA analysis with 46 hexanucleotide restriction enzymes indicates that the Thingvallavatn morphs are very closely related. Sequence divergence was less than 0.2% between any of the five clones detected. Although not significant, the topology of the mtDNA UPGMA dendogram was similar to that from a previous allozyme survey. Icelandic Arctic charr show greater affinity to charr from the British Isles than those from North America supporting their current taxonomic distinction.     

Southern and dot blot analysis of DNA from formalin-fixed,paraffin-embedded tissue samples from colonic carcinomas

Two extraction methods for the isolation of DNA from formalin-fixed, paraffin-embedded tissue samples from colonic carcinomas were compared. The processed DNAs were compared with DNAs from fresh specimens of the same tumors. The two extraction methods gave similar results. Formalin-fixation and paraffinembedding irreversibly denatured DNA and consequently decreased the extraction yield and interfered with the quantitative measurement of DNA. Southern blot and dot blot analysis of processed and native DNA was performed using a c-myc and an actin probe. The results show that for Southern analysis processed DNA can be used but, due to the generation of random breaks, the restriction fragments have to be small. Furthermore, the fixation-induced crosslinking of DNA appears to hamper hybridization. For these reasons processed DNA can be analyzed better by dot blot rather than Southern blot hybridization.     

Determination of ploidy level and nuclear DNA content in blueberry by flow cytometry

The technique of DNA flow cytometry was used to study variation in DNA content among different ploidy levels, as well as among diploid species, of Vaccinium section Cyanococcus. In a sample of plants of varying ploidy level, the relative fluorescence intensity (RFI) of nuclei stained with propidium iodide was a function of the number of chromosome sets (x), as represented by the linear equation RFI=3.7x-2.3 (r²=95%). The data indicated that DNA flow cytometry could be useful for the determination of ploidy level at the seedling stage in blueberry. They also suggest that conventional polyploid evolution has occurred in this section of the genus Vaccinium with an increase in nuclear DNA content concurrent with the increase in chromosome number. The nuclear DNA content of diploid species of Vaccinium section Cyanococcus was estimated from the relationship of the observed RFI to an internal known DNA standard (trout red blood cells). A nested analysis of variance indicated significant variation among species, as well as among populations within species, in nuclear DNA content, although this variation was small compared to the variation among ploidy levels. The variation in nuclear DNA content corresponded to the phylogenetic relationships among species determined from previous studies.     

Fluorometric determination of DNA in mammalian cell cultures by PicoGreen

An intercalating fluorochrome, PicoGreen, was assessed for its ability to determine the concentration of DNA in clarified mammalian cell culture broths containing monoclonal antibodies. Fluorescent signal suppression was ameliorated by sample dilution or by performing the assay above the pI of secreted IgG. The source of fluorescence in clarified culture broth was validated by incubation with RNase A and DNase I. At least 91.8% of fluorescence was attributable to nucleic acid and pre-digestion with RNase A was shown to be a requirement for successful quantification of DNA in such samples.     

Detection of hepatitis B virus in blood samples negative for surface antigen,by DNA probe hybridization assay

A DNA hybridization assay was developed using a cloned hepatitis B viral genome to detect the presence of infectious virions in human serum. The merit of this assay was to put in evidence virus particles in 7 out of 133 sera that were negative for surface antigen (HBsAg) using routine serological methods. The usefulness of this assay was confirmed by actual visualization of the virus under electron microscope. Some serum samples although positive for surface antigen, did not give a hybridization signal by dot blot assay and might indicate cases of acute hepatitis     

非损伤采样提取DNA技术在猫科动物调查中的应用

<正>猫科动物广泛分布于世界各地(Johnson et al.,2006),全球现存37种猫科动物,其中25种已被国际自然保护联盟(IUCN)列为濒危和易危,86%以上的种群数量处于下降或未知状态(IUCN Red List,2011)。我国有13种猫科动物,占世界种类的35%(王应祥,2003),其中属于国家一级保护的有4种,二级保护的有8种,然而,对这些珍稀物种的生态学研究并不充分(高耀亭,     

Diagnostic and prognostic significance of image cytometric DNA ploidy measurement in cytological samples of cervical squamous intraepithelial lesions

D. Demirel, N. Akyürek and I. Ramzy
Diagnostic and prognostic significance of image cytometric DNA ploidy measurement in cytological samples of cervical squamous intraepithelial lesions Objective: To study the DNA ploidy pattern of uterine cervical squamous intraepithelial lesions (SILs) and its diagnostic and prognostic significance. Methods: The study included 31 cases of SIL: 11 low‐grade (LSIL) and 20 high‐grade (HSIL). Feulgen–pararosaniline staining was performed on previously Papanicolaou‐stained smears and a DNA image cytometric study was performed. An internal reference was used to calibrate the samples. Results: All 31 cases of SIL, either LSIL or HSIL, were non‐diploid. Of the 11 cases of LSIL, four were tetraploid and seven were aneuploid, whereas, of the 20 cases of HSIL, four were tetraploid and 16 were aneuploid. Stemline aneuploidy was not a significant discriminator between LSIL and HSIL (P = 0.32). Based on single‐cell analysis, HSIL cases had significantly higher DNA content than LSIL cases (P < 0.01). When a mean of 30% or more was used for the 6c‐exceeding event (6cEE) value, the sensitivity and specificity to indicate HSIL were 83% and 64%, respectively, with a positive predictive value (PPV) of 81% and negative predictive value (NPV) of 65%. All HSIL cases were cervical intraepithelial neoplasia grade 2 or worse (CIN2+) on biopsy. In addition, cases which showed recurrence had more DNA content by single‐cell analysis than those with an indolent clinical behaviour: P = 0.04 and P = 0.03 for LSIL and HSIL, respectively. Conclusions: Image cytometric DNA analysis is a useful technique for diagnostic and prognostic purposes in uterine cervical SIL when appropriate ‘c’ values are used in single‐cell analysis. We propose that a >6c DNA content of 30% is useful as a cut‐off level for predicting cases with CIN2+ in DNA image cytometry of cervical smears.     

DNA quantification is technically feasible and of value in cervical smear samples: possible applications for determination of progression in low grade dyskaryosis

This study evaluates the feasibility of DNA analysis of cervical intraepithelial neoplasia III (CIN III) lesions on cervical smear and formalin-fixed paraffin-embedded tissue (FFPET) blocks with a view to extending this type of analysis to milder grades of dyskaryosis. DNA ploidy was determined by image analysis using a CAS 200 Image Analyser. Seventeen patients with a diagnosis of CIN III were studied. Results show that all smear and tissue samples were non-diploid with nine aneuploid and eight tetraploid lesions. In 6/7 patients whose smears and corresponding biopsies were examined there was complete agreement as to the DNA profile. We conclude that DNA quantification is technically feasible in archival, routinely prepared cervical smears. This technique should now be applied to CINI and CINII cervical smears to determine if it is of value in identifying those lesions that will progress to CIN III. This study is particularly timely with the possibility in the near future of estimation of ploidy by image analysis using instruments such as the Highly Optimized Microscope Environment (HOME) system.