Determination of bacterial cell number and cell volume by means of flow cytometry, transmission electron microscopy, and epifluorescence microscopy

Comparative measurements of bacterial total counts and volumes of flow cytometry (FCM), transmission electron (TEM), and epifluorescence microscopy (EFM), were undertaken during a four week mesocosm experiment. Total counts of bacteria measured by TEM, EFM, and FCM were in the range of 1 · 10⁶−6 cells ml⁻¹, 1 · 10⁶−3 · 10¹⁶ cells ml⁻¹, and 5 · 10⁵ cells ml⁻¹ respectively. The mean volume of the bacterial community, measured by means of EFM and TEM, increased from 0.12–0.15 μm³ at the start of the experiment to 0.39–0.53 μm³ at the end. Generally, there was good agreement between the two methods and regression analyses gave r = 0.87 (p < < 0.01) for cell volume and r = 0.97 (p < < 0.01) for cell number. DAPI stained bacteria with volumes less than 0.2 μm³ were not detected by flow cytometry and these were generally an order of magnitude lower than counts made by TEM and EFM. For samples where the mean bacterial cell volume was longer than 0.3 μm³, all three methods were in agreement both with respect to counts and volume estimates.     

Cultivation and preservation of vinegar bacteria

Ten strains of acetic acid bacteria were investigated for their characteristics of growth and metabolism. The strains were identified as those presently in use for industrial vinegar production in southern Germany. At the time of isolation from industrial acetators the total concentrations, i.e. acetic acid (w/v) plus ethanol (v/v), of the fermenting vinegars were 6.1–14.9%. The applicability of a previously described method for starter preparation was examined for the various isolates as well as for the type strains of species of the genera Gluconobacter and Acetobacter. Isolates from cider or wine vinegar fermentations grew readily in RAE-medium to total counts of >1×10⁹ cells ml⁻¹. For the cultivation of strains isolated from spirit vinegar fermentations AE-medium proved most suitable. Cultures of these strains exhibited lag phases of 2–5 days and grew up to total counts of <1×10⁹ cells ml⁻¹. All type strains could be grown on RAE-agar. The use of 20% malt extract as cryo-protectant was effective for the preservation of all strains. Upon revitalization the cultures were suitable as inoculum for starting fermentations in pilot acetators. 16S rRNA-targeted oligonucleotide probes were constructed which were species specific for Gluconobacter oxydans or Acetobacter aceti or group specific for Acetobacter europaeus/Acetobacter xylinum. The probes hybridized with the DNA of the respective type strains. Four isolates were allotted to A. europaeus/A. xylinum applying the group specific probe. The DNA of six of the Acetobacter sp. hybridized with none of the probes.     

Occurrence of singlet oxygen oxygenation of oleic acid and linoleic acid in the skin of live mice

To assess the contribution of singlet molecular oxygen [O₂ (¹Δ_g)] to lipid peroxidation in vivo, this study combined gas chromatography-mass spectrometry with thin layer chromatography to analyse peroxidized lipids in the skin of hairless mice. Hydroxyoctadecenoate isomers and unconjugated hydroxyoctadecadienoate isomers derived from peroxidized oleic acid and linoleic acid, respectively, which are specific to O₂ (¹Δ_g)-dependent oxygenation, were detected in the skin of live mice under ordinary feeding conditions. Short-term ultraviolet A (UVA)-irradiation of the skin in vivo elevated levels of the unconjugated hydroxyoctadecadienoate isomers significantly, whereas the irradiation of skin homogenate in vitro increased levels of all isomers derived from both O₂ (¹Δ_g) and free radical-dependent oxygenation to a much greater extent. This is the first report to demonstrate the occurrence of O₂ (¹Δ_g)-specific oxygenation of unsaturated fatty acids in living animals.     

基于胃含物和碳、氮稳定同位素研究浙江南部近海蓝圆鲹的摄食生态

蓝圆鲹是浙江南部近海的重要经济鱼类。本文根据2020年5月、8月、11月和2021年1月在浙江南部近海进行的底拖网调查,应用胃含物分析和碳氮稳定同位素分析对浙江南部近海蓝圆鲹的摄食习性进行研究。结果表明: 浙江南部近海蓝圆鲹δ¹³C平均值为(-16.55±0.60)‰,范围为-17.76‰～-15.25‰,与叉长呈显著负相关;蓝圆鲹δ¹⁵N平均值为(11.76±0.88)‰,范围为9.06‰～13.03‰,与叉长呈显著正相关。根据δ¹⁵N值计算浙江南部近海蓝圆鲹的平均营养级为3.89±0.26。胃含物分析表明,浙江南部近海蓝圆鲹的主要饵料类群为鱼类、虾类、蟹类、头足类、多毛类和小型甲壳类。稳定同位素分析表明,虾类对浙江南部近海蓝圆鲹的营养贡献率最高(40%～84%),其次为多毛类、小型甲壳类、蟹类、头足类和鱼类。蓝圆鲹的摄食习性有明显的生长变化,随着蓝圆鲹叉长的增加,其倾向于摄食更高营养级的饵料生物。     

共生真菌对兰科植物种间杂交后代种子萌发的效应

石斛属(Dendrobium)植物在种子共生萌发过程中与真菌有着较为专一的共生关系, 为探讨这种共生关系在种间杂交后代上的进化和适应, 深入理解兰科植物和真菌共生关系的形成机制, 该研究利用能有效促进铁皮石斛(Dendrobium officinale)和齿瓣石斛(D. devonianum)种子萌发形成幼苗, 并具有较强专一性的胶膜菌属(Tulasnella)真菌SSCDO-5和瘤菌根菌属(Epulorhiza)真菌FDd1, 开展真菌对铁皮石斛和D. tortile种间杂交种子萌发效应的研究。结果表明, 在真菌与种子共生培养68天时, SSCDO-5菌株和FDd1菌株都能有效地促进杂交种子形成原球茎和幼苗, 两个接菌处理之间无显著差异, 来源于铁皮石斛的SSCDO-5菌株不但没有表现出优势, 反而在杂交石斛幼苗形成率上低于来源于齿瓣石斛的FDd1菌株(SSCDO-5: (22.13 ± 6.62)%; FDd1: (29.53 ± 5.51)%); SSCDO-5菌株和铁皮石斛在幼苗形成和发育阶段的共生专一性并没有在杂交后代上得到遗传或表现, 或者说是杂交打破了这种专一性的共生关系, 使得杂交后代能够和不同的真菌建立新的共生关系。该结果不支持关于共生真菌专一性是石斛属植物杂交后代形成的重要限制因素的假设, 推测石斛属植物在幼苗分化和发育阶段与真菌这种专一性的共生关系是在适应特定生态环境的过程中形成和建立的。     

Development and field application of a quantitative method for examining natural assemblages of protists with oligonucleotide probes.

A fluorescent in situ hybridization method that uses rRNA-targeted oligonucleotide probes for counting protists in cultures and environmental water samples is described. Filtration, hybridization, and enumeration of fixed cells with biotinylated eukaryote-specific probes and fluorescein isothiocyanate-conjugated avidin were performed directly on 0.4-microns-pore-size polycarbonate filters of Transwell cell culture inserts (Costar Corp., Cambridge, Mass.). Counts of various species of cultured protists by this probe hybridization method were not significantly different from counts obtained by the 4',6-diamidino-2-phenylindole (DAPI) and acridine orange (AO) staining methods. However, counts of total nanoplankton (TNAN) based on probe hybridizations in several field samples and in samples collected from a mesocosm experiment were frequently higher than TNAN counts obtained by staining with DAPI or AO. On the basis of these results, 25 to 70% of the TNAN determined with probes were not detectable by DAPI or AO staining. The underestimation of TNAN abundances in samples stained with DAPI or AO was attributed to the existence of small nanoplanktonic cells which could be detected with probes but not DAPI or AO and the difficulty associated with distinguishing DAPI- or AO-stained protists attached to or embedded in aggregates. We conclude from samples examined in this study that enumeration of TNAN with oligonucleotide probes provides estimates of natural TNAN abundances that are at least as high as (and in some cases higher than) counts obtained with commonly employed fluorochrome stains. The quantitative in situ hybridization method we have described here enables the direct enumeration of free-living protists in water samples with oligonucleotide probes. When combined with species-specific probes, this method will enable quantitative studies of the abundance and distribution of specific protistan taxa.     

Genetic evidence against a morphologically suggestive conspecificity of Dermacentor reticulatus and D. marginatus (Acari: Ixodidae)

Dermacentor reticulatus and D. marginatus exhibit overlapping phenotypes. The possibility of conspecificity was investigated on the nucleotide level by comparing DNA sequences of the second internal transcribed spacer (ITS 2) of the rDNA gene. The inter-specific polymorphism was more than 20-times greater than the intra-specific polymorphism of 3 D. reticulatus strains of different geographic origins. Furthermore, the degree of polymorphisms between D. reticulatus and D. marginatus was found to be of the same order of magnitude as that between D. andersoni and D. variabilis, for which separate species status is accepted. These genomic findings do not support a possible conspecificity of D. reticulatus and D. marginatus.     

Genetic analysis of mortality in murine angiostrongyliasis costaricensis using SMXA recombinant inbred mouse strains

The SMXA recombinant inbred mouse strain set was produced by systematic inbreeding from the F2 generation of a cross between two progenitor inbred strains, A/J and SM/J, which differed markedly with respect to the patterns of infection with Angiostrongylus costaricensis. We have applied this set to genetic analysis of mouse susceptibility to this nematode infection. The mortality was variable among substrains of the SMXA RI strains, indicating the involvement of multiple genes. Linkage analysis showed several chromosomal regions closely linked to mortality; chromosome 6 (D6Rik86, 87; P0.001), 10 (D10Rik66–D10Mit12; P=0.0058), 13 (D13Rik79, 80; P=0.0096) and 17 (D17Mit28–D17Rik76; P=0.0088).     

金钟藤入侵群落的种间联结及生态位特征

金钟藤(Decalobanthus boisianus)是林业有害植物, 其暴发生长和扩散对森林生态系统造成了严重破坏。本文以海南岛48个金钟藤典型分布群落为研究对象, 用方差比率法和贡献定律法探究群落的稳定性; 用χ ²统计量、联结系数(AC)、共同出现百分率(PC)、Ochiai指数和Dice指数分析金钟藤与伴生物种的种间联结关系; 用生态位宽度、生态位相似性系数和生态位重叠指数研究群落中各物种的生态位特征, 以期为金钟藤生物防治的植物物种筛选提供借鉴。结果表明: (1)金钟藤所在48个群落共有156种伴生植物, 其中大戟科、茜草科、桑科、无患子科和樟科植物占优势; (2)群落中优势物种呈正联结关系, 植物种类累积倒数百分比与累积相对频度交点坐标为(44.53, 55.47), 远离稳定交点坐标(20, 80), 说明群落处于不稳定状态; (3)金钟藤与芳槁润楠(Machilus suaveolens)、黄椿木姜子(Litsea variabilis)、岭南山竹子(Garcinia oblongifolia)、显脉杜英(Elaeocarpus dubius)、鸭脚木(Schefflera octophylla)和银柴(Aporusa dioica)都紧密关联, 说明金钟藤与这些物种的资源利用方式较相似; (4)金钟藤的生态位宽度最大, 与伴生物种间的生态位重叠度较高, 但伴生物种间的生态位重叠度较低。金钟藤的入侵导致群落处于不稳定状态, 并与伴生物种间存在激烈的竞争关系。因此, 建议在金钟藤已入侵的群落中大量栽种芳槁润楠、黄椿木姜子、显脉杜英、鸭脚木和银柴, 以遏制其蔓延; 大量栽种翻白叶树(Pterospermum heterophyllum)、海南菜豆树(Radermachera hainanensis)、九节(Psychotria rubra)和肉实树(Sarcosperma laurinum)用于金钟藤入侵群落的植被恢复。     

Lack of effect of the nematophagous fungus Duddingtonia flagrans on the development of the dung beetle, Aphodius constans

The nematode-trapping fungus Duddingtonia flagrans may be used as a biological control agent of gastro-intestinal nematode larvae of ruminants by feeding the hosts with fungal spores. This trial was intended to search an eventual detrimental impact of the presence of spores of D. flagrans in high numbers in goat feces on the common dung beetle, Aphodius constans (Coleoptera: Aphodiidae). A. constans eggs were settled in feces derived from grazing goats fed spores at daily dose rates of 0, 0.25 × 10⁶, 0.5 × 10⁶ or 10⁶ spores/kg BW. At the end of the incubation period, the number of adults that have emerged from eggs were counted and compared between dose rates. No difference in emergence rate between treatments can be seen. The presence of D. flagrans spores in goat feces, even in large numbers, did not alter the development of A. constans.     

Dual staining of natural bacterioplankton with 4',6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA sequences.

A method for quantifying eubacterial cell densities in dilute communities of small bacterioplankton is presented. Cells in water samples were stained with 4',6-diamidino-2-phenylindole (DAPI), transferred to gelatin-coated slides, and hybridized with rhodamine-labeled oligonucleotide probes specific for kingdom-level 16S rRNA sequences. Between 48 and 69% of the cells captured on membrane filters were transferred to gelatin-coated slides. The number of DAPI-stained cells that were visualized with eubacterial probes varied from 35 to 67%. Only 2 to 4% of these cells also fluoresced following hybridization with a probe designed to target a eukaryotic 16S rRNA sequence. Between 0.1 and 6% of the bacterioplankton in these samples were autofluorescent and may have been mistaken as cells that hybridized with fluorescent oligonucleotide probes. Dual staining allows precise estimates of the efficiency of transfers of cells to gelatin films and can be used to measure the percentage of the total bacterioplankton that also hybridize with fluorescent oligonucleotide probes, indicating specific phylogenetic groups.     

A novel means to develop strain-specific DNA probes for detecting bacteria in the environment.

A simple means to develop strain-specific DNA probes for use in monitoring the movement and survival of bacteria in natural and laboratory ecosystems was developed. The method employed amplification of genomic DNA via repetitive sequence-based PCR (rep-PCR) using primers specific for repetitive extragenic palindromic (REP) elements, followed by cloning of the amplified fragments. The cloned fragments were screened to identify those which were strain specific, and these were used as probes for total genomic DNA isolated from microbial communities and subjected to rep-PCR. To evaluate the utility of the approach, we developed probes specific for Burkholderia cepacia G4 and used them to determine the persistence of the strain in aquifer sediment microcosms following bioaugmentation. Two of four probes tested were found to specifically hybridize to DNA fragments of the expected sizes in the rep-PCR fingerprint of B. cepacia G4 but not to 64 genetically distinct bacteria previously isolated from the aquifer. One of these probes, a 650-bp fragment, produced a hybridization signal when as few as 10 CFU of B. cepacia G4 were present in a mixture with 10(6) CFU nontarget strains, indicating that the sensitivity of these probes was comparable to those of other PCR-based detection methods. The probes were used to discriminate groundwater and microcosm samples that contained B. cepacia G4 from those which did not. False-positive results were obtained with a few samples, but these were readily identified by using hybridization to the second probe as a confirmation step. The general applicability of the method was demonstrated by constructing probes specific to three other environmental isolates.     

大型枝角类蚤状溞对小型热带湖泊浮游植物群落影响的研究

2006年4月10日至2006年4月22日,采用原位吊瓶实验的方法,在暨南大学校园明湖中进行了大型枝角类蚤状溞(Daphnia pulex)对浮游植物种群变化和群落结构影响的实验。实验初期,明湖浮游植物群落的组成是以飞燕角甲藻(Ceratium hirundinella)和单角盘星藻(Pediastrum simplex)为优势种。在室内将蚤状溞培养至体长2mm以上,将蚤状溞加入到装满湖水的4.5L的透明瓶中,设置4个梯度:0ind(A,对照),10ind.(B),20ind(C)和30ind(D),每个梯度有3个平行,将实验瓶置于水表层50cm处。12d后实验结束,不同处理之间的浮游植物种群数量和组成有了明显的差异。与对照组相比,飞燕角甲藻和颗粒直链藻(Meclosira granulata)密度在实验组B、C和D中下降明显;小环藻(Cyclotella)和栅藻(Scenedesmus)等小型浮游植物在牧食压力比较大的C和D瓶中密度低于对照组,而在牧食压力相对较低的B瓶中,它们的密度高于对照组,这可能是由于蚤状溞加速了水体的营养盐循环反过来促进这些小型浮游植物的生长。处理组中绿藻门的盘星藻数量没有明显的下降,这与盘星藻不能被浮游动物直接滤食有关。实验结果表明蚤状溞对浮游植物的群落数量和组成的影响程度与其自身的种群密度密切相关,也与浮游植物群落结构有关。由于飞燕角甲藻是一种细胞较大的种类,蚤状溞对它的抑制作用主要是通过机械伤害作用实现的。     

Identification of rat cell lines that preferentially express insulin-like growth factor binding proteins rlGFBP-1, 2, or 3.

The bioavailability and action of the insulin-like growth factors (IGFs) are determined by specific IGF-binding proteins (IGFBP) to which they are complexed. Complementary DNA clones have been isolated that encode three related IGFBPs: human IGFBP-1 (hIGFBP-1), human IGFBP-3 (hIGFBP-3), and rat IGFBP-2 (rIGFBP-2). IGFBP-1 and IGFBP-3 are regulated differently in human plasma, suggesting that they have different functions. In order to study the molecular basis of the regulation of the different IGFBPs, we have identified a panel of rat cell lines that express a single predominant binding protein and developed an assay strategy to distinguish the different binding proteins. Proteins in conditioned medium were examined by ligand blotting, and by immunoprecipitation and immunoblotting using antibodies to rIGFBP-2 and hIGFBP-1; RNAs were hybridized to cDNA probes for rIGFBP-2 and hIGFBP-1. 1) C6 glial cells and B104 neuroblastoma cells express an approximately 40 kilodalton (kDa) glycosylated binding protein that most likely represents rIGFBP-3, the binding subunit of the 150 kDa IGF: binding protein complex in adult rat serum. The C6 and B104 binding proteins do not react with antibodies to rIGFBP-2, and RNAs from C6 and B104 cells do not hybridize to cDNA probes for rIGFBP-2 or hIGFBP-1. 2) BRL-3A, Clone 9, and TRL 12-15 cell lines derived from normal rat liver express rIGFBP-2, a 30 kDa nonglycosylated IGF-binding protein that is recognized by antibodies to rIGFBP-2 but not by antibodies to hIGFBP-1. RNAs from these cells hybridize to a rIGFBP-2 cDNA probe, but not to a hIGFBP-1 probe. 3) H35 rat hepatoma cells express a 30 kDa nonglycosylated IGFBP that is presumptively identified as rIGFBP-1. It does not react with antibodies to rIGFBP-2, but is recognized by polyclonal and monoclonal antibodies to hIGFBP-1. RNA from H35 cells hybridizes to a hIGFBP-1 cDNA probe, but not to a rIGFBP-2 probe. Expression of rIGFBP-1 by the H35 cell line has enabled us to establish and validate specific assays for this protein that allow us to study its regulation in intact rats. Identification of a panel of rat cell lines expressing specific IGFBPs should be useful in elucidating the molecular mechanisms of IGFBP regulation.     

Chloroplast DNA and the determination of species status in the Disa tripetaloides complex (Orchidaceae), and its relationships to three species Racemosae, section Disa

Disa cardinalis and three populations within the D. tripetaloides species complex contain variation in their chloroplast DNA (cpDNA) variability. All four taxa possessed unique cpDNAs and sequence divergence values ranged from 0.34 to 1.03%. A phylogeny of these genomes was reconstructed, along with the genomes of three other species, D. racemosa, D. uniflora and D. venosa, all of which are also section Disa and series RAcemosae, to determine the relationship of these closely related species to the D. tripetaloides complex. A phylogeny of the taxa using morphological data was also reconstructed. Outgroup comparison was made with D. sagittalis, a member of section Coryphaea. Although the molecular and morphological data were not completely congruent, both data types revealed D. cardinalis, rather than D. tripetaloides ssp. aurata, to be more closely allied with D. tripetaloides ssp. tripetaloides, suggesting that D. tripetaloides ssp. aurata should be elevated to species rank. Additionally, the high sequence divergence observed between the Natal and Cape populations, coupled with their geographical isolation and alternate flowering seasons, suggests that these two D. tripetaloides ssp. tripetaloides populations may, in fact, be more appropriately ranked as subspecies.     

A novel DNA microarray design for accurate and straightforward identification of Escherichia coli safety and laboratory strains

Escherichia coli K-12, B, C and W strains and their derivates are declared in biological safety guidelines as risk group 1 organisms as they are unable to colonise the human gut.

Differentiation and identification of these safety strains is mainly based on pulsed-field gel electrophoresis (PFGE), phage sensitivity tests or PCR-based methods. However, these methods are either tedious and time consuming (phage sensitivity, PFGE) or based on single specific fragments (PCR) or patterns (PFGE) lacking additional information for further differentiation of the strains.

In the current study, subtractive hybridisation techniques were applied to detect specific DNA fragments which were used to design a microarray (chip) for accurate and simple identification of these organisms, and to differentiate them from other E. coli strains. The chip can be used to identify E. coli safety strains and monitor them during ongoing experiments for changes in their genome and culture purity. The hybridisation layout of the microarray was arranged in such a way that the respective lineages of safety strains could be easily identified as distinct letters (K, B, C or W). Differentiation of single strains or subtyping was possible with further probes. In addition, a set of probes targeting genes coding for common virulence factors has been included, both to differentiate safety strains from pathogenic variants and to make sure that no transfer of these genes happens during handling or storage. The reliability of the approach has been tested on a comprehensive selection of E. coli laboratory strains and pathogenic representatives.     

Detection of Campylobacter jejuni in poultry samples using an enzyme-linked immunoassay coupled with an enzyme electrode.

An enzyme-linked immunoassay coupled with a tyrosinase modified enzyme electrode was used for rapid detection of Campylobacter jejuni. The immunomagnetic separation (IMS) method was investigated to achieve optimal isolation of C. jejuni cells. Eight types of beads with three different sizes and function groups were coated with anti-C. jejuni to isolate C. jejuni from the sample solution. Bead size and coating methods were found to be major factors that influenced the capture efficacy. Streptavidin-labeled beads (2.8 μm) provided the greatest capture ability. Three blocking reagents were tested to minimize non-specific binding. Bovine serum albumin (BSA) showed the best blocking capability. Two IMS formats were tested. Competitive immunoassay cut the detection time to 1.5 h, but the detection limit was relatively high (10⁶ CFU/ml). This system was evaluated using C. jejuni pure culture and poultry samples inoculated with C. jejuni. This detection method for C. jejuni could be completed within 2.5 h and had a detection limit of 2.1×10⁴ CFU/ml. No significant difference was found between pure culture samples and poultry samples (P>0.01). A linear relationship was found between C. jejuni cell numbers and the peak current ratio in a range of 10²–10⁷ CFU/ml (R²=0.94).     

Algal colonization in urchin barrens: defense by association during recruitment of the brown alga Agarum cribrosum

We investigated the process whereby juveniles of the kelp Agarum cribrosum escape grazing by the green sea urchin, Strongylocentrotus droebachiensis, on urchin barrens in the rocky subtidal zone in the Mingan Islands, northern Gulf of St. Lawrence. The highest recruitment of juvenile A. cribrosum occurred under the canopy of the large filamentous phaeophyte Desmarestia viridis, where urchin densities were markedly reduced, compared to the surrounding area. This pattern of distribution appeared to be related to the wave-induced sweeping motion of D. viridis, although currents may modify the back and forth motion of the alga by pushing the canopy towards a specific direction, thereby allowing urchins to invade the non-swept areas. The density of juveniles under D. viridis plants increased with plant size and increasing proximity to the holdfast. Living under D. viridis slightly reduced the growth rate of the A. cribrosum juveniles, but this loss in growth was clearly outweighed by the gain in protection from sea urchin grazing. The time scale over which D. viridis provides protection is in the order of months, as D. viridis is an annual alga that disappears in early autumn. This defensive association of juvenile A. cribrosum with D. viridis is possibly a successional step leading to the formation of mature stands of A. cribrosum.