The possibilities and challenges of <Emphasis Type="Italic">in vitro</Emphasis> methods for plant conservation

Seed-based methods are generally the most efficient for propagating and storing plant germplasm, but these methods are not always adequate, and some species can benefit from in vitro methods for conservation. For species that produce few or no seeds in the wild, plants may be propagated in vitro, and in vitro shoot tips can provide material for cryostorage when seeds are not available or are recalcitrant. In vitro propagated plants may also serve as subjects for research, without depleting the genetic resources of the species. Clonal plants can be used to test out suitable habitat and can be used for basic research on endangered species, without disturbing the wild population. Despite the effectiveness of widely used techniques, however, there are still species that resist initiation into culture or that may be difficult to root or acclimatise. Similarly, tissue cryopreservation methods may be restrained by cost, particularly in maintaining multiple genotypes of many species. Maintaining such genotypes in vitro is also costly and runs the risk of loss or change over time. Examples of the successful use of in vitro methods will illustrate the variety of applications of these techniques, but costs and specific challenges will also be discussed to help define areas where further research is needed to realise the potential of in vitro methods as a tool for conservation.     

An improved method for monitoring cell death in cell suspension and leaf disc assays using evans blue

Cell viability or cell death is an important variable to monitor in many studies of host/pathogen interactions. However for studies that focus on events within the first few hours of the interaction, many of the viability assays currently being used are either too laborious and time consuming or measure the cell's temporary metabolic state rather than irreversible cell death. Evans blue has proven over the years to be a dependable stain for microscopic determination of cell death. We have used this stain to develop a spectrophotometric procedure that allows rapid, reproducible quantification of the stain retained by dead cells. This spectrophotometric procedure was used to compare plant/bacteria interactions involving either soybean/Pseudomonas syringae pv. glycinea or tobacco/P. syringae pv. syringae. Relative increases in cell death during these interactions in suspension cell systems were measured by both the spectrophotometric and microscopic technique and found to be similar. The spectrophotometric procedure was also adapted for leaf disc assays.Abbreviations HR hypersensitive response - SDS sodium dodecyl sulfate     

‘Yeast Mail’: A Novel Saccharomyces Application (NSA) to Encrypt Messages

The universal genetic code is used by all life forms to encode biological information. It can also be used to encrypt semantic messages and convey them within organisms without anyone but the sender and recipient knowing, i.e., as a means of steganography. Several theoretical, but comparatively few experimental, approaches have been dedicated to this subject, so far. Here, we describe an experimental system to stably integrate encrypted messages within the yeast genome using a polymerase chain reaction (PCR)‐based, one‐step homologous recombination system. Thus, DNA sequences encoding alphabetical and/or numerical information will be inherited by yeast propagation and can be sent in the form of dried yeast. Moreover, due to the availability of triple shuttle vectors, Saccharomyces cerevisiae can also be used as an intermediate construction device for transfer of information to either Drosophila or mammalian cells as steganographic containers. Besides its classical use in alcoholic fermentation and its modern use for heterologous gene expression, we here show that baker's yeast can thus be employed in a novel Saccharomyces application (NSA) as a simple steganographic container to hide and convey messages.     

Association mapping of quantitative resistance for <Emphasis Type="Italic">Leptosphaeria maculans</Emphasis> in oilseed rape (<Emphasis Type="Italic">Brassica napus</Emphasis> L.)

Stem canker caused by the fungus Leptosphaeria maculans is a major disease of Brassica napus. Quantitative resistance factors appear to be important components for effective and durable control of this pathogen. Quantitative trait loci (QTL) for stem canker resistance have previously been identified in the Darmor variety. However, before these QTL can be used in marker-assisted selection (MAS) to breed resistant varieties, they must be validated in a wide range of genetic backgrounds. We used an association mapping approach to confirm the markers located within the QTL previously identified in Darmor and establish their usefulness in MAS. For this, we characterized the molecular diversity of an oilseed rape collection of 128 lines showing a large spectrum of responses to infection by L. maculans, using 72 pairs of primers for simple sequence repeat and other markers. We used different association mapping models which either do or do not take into account the population structure and/or family relatedness. In all, 61 marker alleles were found to be associated with resistance to stem canker. Some of these markers were associated with previously identified QTL, which confirms their usefulness in MAS. Markers located in regions not harbouring previously identified QTL were also associated with resistance, suggesting that new QTL or allelic variants are present in the collection. All of these markers associated with stem canker resistance will help identify accessions carrying desirable alleles and facilitate QTL introgression.     

Recognition and clinical significance of mechanisms of bacterial resistance to beta-lactams

Resistance to beta-lactams may be difficult to recognize. This is due to the difficulty in detecting these resistances, when the routine tests performed in diagnostic laboratories are interpreted in the usual manner. Since failure to recognize this type of resistance may have serious consequences for the patient, it is essential that it be detected when present. For the detection of methicillin resistance ofStaphylococcus aureus a standardized method using either a medium containing 5% NaCl or a low incubation temperature is advocated. Methicillin resistance ofS. epidermidis can only be recognized reliably by means of a quantitative test and incubation for 42–48 h. Resistance ofHaemophilus influenzae to ampicillin may be intrinsic or it may be caused by a TEM beta-lactamase; a beta-lactamase test should be used to detect the latter type of resistance. Inducible cephalosporinase may be responsible for the rapid development of resistance of some bacterial species to cefamandole, even during therapy. If a stable beta-lactamase production is attained by mutation, resistance to other beta-lactams will usually be present as well. Routine induction tests should be performed for all isolates of species ofEnterobacter, Serratia, Citrobacter andProteus, indole-positive. The same type of ‘hidden’ resistance may be present inPseudomonas aeruginosa, with regard to cefotaxime and other third-generation cephalosporins. Beta-lactamase-positiveNeisseria gonorrhoeae can easily be recognized by a beta-lactamase test. In addition, the results of diffusion tests allow one to distinguish between beta-lactamase-positive and beta-lactamase-negative strains. Recognition of those strains ofN. gonorrhoeae having a decreased susceptibility to penicillin is only possible when well-standardized quantitative tests are used.     

Nestmate recognition in the leaf-cutting antAtta laevigata

Summary We tested matureAtta laevigata colonies in the field to see if the ants used queen substances, environmental odours (in this case odours produced by the nest's fungi), an odour produced by each individual, or a gestalt odour (resulting from odours distributed between nestmates) as a discrimination signal for nestmate recognition. We found that nestmate recognition inA. laevigata appears to be largely based on an odour produced by each nestmate which appears to be concentrated in the head, although other odours may also be used. We found no evidence of genetic relatedness influencing the discrimination ability, nor did ants respond differently to neighbors in comparison to non-neighbors.     

Global metabolic profiling of plant cell wall polysaccharide degradation by Saccharophagus degradans

Plant cell wall polysaccharides can be used as the main feedstock for the production of biofuels. Saccharophagus degradans 2–40 is considered to be a potent system for the production of sugars from plant biomass due to its high capability to degrade many complex polysaccharides. To understand the degradation metabolism of plant cell wall polysaccharides by S. degradans, the cell growth, enzyme activity profiles, and the metabolite profiles were analyzed by gas chromatography‐time of flight mass spectrometry using different carbon sources including cellulose, xylan, glucose, and xylose. The specific activity of cellulase was only found to be significantly higher when cellulose was used as the sole carbon source, but the xylanase activity increased when xylan, xylose, or cellulose was used as the carbon source. In addition, principal component analysis of 98 identified metabolites in S. degradans revealed four distinct groups that differed based on the carbon source used. Furthermore, metabolite profiling showed that the use of cellulose or xylan as polysaccharides led to increased abundances of fatty acids, nucleotides and glucuronic acid compared to the use of glucose or xylose. Finally, intermediates in the pentose phosphate pathway seemed to be up‐regulated on xylose or xylan when compared to those on glucose or cellulose. Such metabolic responses of S. degradans under plant cell wall polysaccharides imply that its metabolic system is transformed to more efficiently degrade polysaccharides and conserve energy. This study demonstrates that the gas chromatography‐time of flight mass spectrometry‐based global metabolomics are useful for understanding microbial metabolism and evaluating its fermentation characteristics. Biotechnol. Bioeng. 2010; 105: 477–488. © 2009 Wiley Periodicals, Inc.     

Marker‐based estimates of relatedness and inbreeding coefficients: an assessment of current methods

Inbreeding (F) of and relatedness (r) between individuals are now routinely calculated from marker data in studies in the fields of quantitative genetics, conservation genetics, forensics, evolution and ecology. Although definable in terms of either correlation coefficient or probability of identity by descent (IBD) relative to a reference, they are better interpreted as correlations in marker‐based analyses because the reference in practice is frequently the current sample or population whose F and r are being estimated. In such situations, negative estimates have a biological meaning, a substantial proportion of the estimates are expected to be negative, and the average estimates are close to zero for r and equivalent to F_IS for F. I show that although current r estimators were developed from the IBD‐based concept of relatedness, some of them conform to the correlation‐based concept of relatedness and some do not. The latter estimators can be modified, however, so that they estimate r as a correlation coefficient. I also show that F and r estimates can be misleading and become biased and marker dependent when a sample containing a high proportion of highly inbred and/or closely related individuals is used as reference. In analyses depending on the comparison between r (or F) estimates and a priori values expected under ideal conditions (e.g. for identifying genealogical relationship), the estimators should be used with caution.     

Amplified fragment length polymorphism (AFLP) fingerprinting of symbiotic fungi cultured by the fungus-growing ant Cyphomyrmex minutus

A PCR-based fingerprinting technique based on amplified fragment length polymorphisms (AFLP) is used to screen symbiotic fungi of the fungus-growing ant Cyphomyrmex minutus for genetic differences. AFLP fingerprints reveal several fungal ‘types’ that (a) represent distinct clones propagated vegetatively by the ant, or (b) correspond to free-living fungi that may be acquired by the ant. Fungal types identified by AFLP fingerprints correspond to vegetative-compatibility groups established previously, suggesting that vegetative compatibility can be used as a crude indicator of genetic differences between fungi of C. minutus.     

SPORE MORPHOLOGY IN THE GENUS BRUCHIA SCHWAEGR. (MUSCI)

Scanning electron microscopy observations of the spores of Bruchia have resulted in the recognition of four spore types based on the ornamentation of the distal spore surface: warty or verrucate, pitted, reticulate, and spinose. The proximal surface of the spores of all species, except B. brevipes, is characterized by a central aperture region surrounded by a triangular murus or rows of spinae forming a triangle and 1 or 2 smooth or verrucate collars. The ornamentation patterns observed are considered to be characteristic for the genus. Spore morphology alone can rarely be used to distinguish species but in conjunction with certain other characteristics, it is an important taxonomic feature. Spore morphology is a major characteristic used to define the limits of the highly variable species B. flexuosa (spinose spores) and to distinguish it from the closely related species B. texana (reticulate spores). Variations in ornamentation patterns within the genus support the recognition of two subgenera (subgenus Bruchia and subgenus Sporledera). Spore morphology also supports the close relationship between Bruchia and Trematodon and is sufficient to eliminate several questionable taxa from the genus.     

External structures used during attachment and sperm transfer in tubificids (Annelida,Oligochaeta)

The genital region of seven species of Tubificidae has been studied by SEM (Scanning Electron Microscopy). The form and the position of penial and spermathecal chaetae, male and spermathecal pores and other special structures have been examined. Peristodrilus montanus shows a special system to hold the partner: the penial chaetae anchor in an elaborated structure of the body wall formed between the spermathecal pores, the `anchorage bridge'. Protuberodrilus tourenqui has a long glandular porophore with the male pores at the tip, allowing contact with the spermathecal pores which are located in deep, close to the mid-ventral line of the body. The grooved and strongly curved penial chaetae of Rhyacodrilus falciformis seem to be used both for attachment and for sperm transfer, entering into the lateral spermathecal pores. The embrace of the partners, as suggested by observations on Psammoryctides barbatus, Potamothrix bavaricus, Potamothrix hammoniensis and Potamothrix heuscheri, seems to be another important mechanism to fix contact between male and spermathecal pores and allow sperm transfer. The spermathecal chaetae could be interpreted as piercing chaetae with a chemical or mechanical stimulating role. Sensitive cilia near the penial chaetae seem to be used by the three rhyacodrilines studied to find the correct anchorage place. There is a great variety of structures which appear to be used for attachment and sperm transfer in tubificids, and consequently their role in the evolution of the whole family may be profound.     

A newEscherichia coli: Bacteroides shuttle vector,pRRI207, based on theBacteroides ruminicola plasmid replicon pRRI2

A 3.4kb cryptic plasmid, pRRI2, was isolated fromBacteroides ruminicola 223/M2/7 and used as the basis for a newBacteroides/Escherichia shuttle vector. Constructs were made incorporating pRRI2, aBacteroides erythromycin/clindamycin resistance marker and theE. coli pUC8-derived vector pHG165. One of these, pRRI207 (11 kb), was capable of introduction into strains belonging to four different species ofBacteroides (B. uniformis, B. distasonis, B. thetaiotaomicron, orB. ruminicola) either by conjugal transfer fromE. coli or by electrotransformation. pRRI207 carries several unique restriction sites derived from the pUC8 multiple cloning site. Only one of sixB. ruminicola strains tested was used successfully as a recipient for pRRI207, indicating that further modifications to transfer procedures or marker genes may be needed for wider application in this species.     

A method for generating precise gene deletions and insertions in Escherichia coli

A simple and general method for disrupting chromosomal genes and introducing insertions is described. This procedure involves eliminating wild-type bacterial genes and introducing mutant alleles or other insertions at the original locus of the wild-type gene. To demonstrate the utility of this approach, the tig gene of Escherichia coli was replaced by homologous recombination with a cassette containing the chloramphenicol resistance gene and the sacB gene. The cassette was then removed and the tig mutant alleles were moved into the native tig location. Sequencing and Western blotting results demonstrated that insertions or deletions can be introduced precisely in E. coli using our approach. Our system does not require extra in vitro manipulations such as restriction digestion or ligation, and does not require use of specific plasmids or strains which are used to prevent false positive transformants caused by template plasmid transformation. This technique can be used widely in bacterial genome analysis.     

Advances in molecular detection of Aspergillus: an update

Filamentous cosmopolitan fungi of the genus Aspergillus can be harmful in two ways, directly they can be opportunistic pathogens causing aspergillosis and indirectly due to aflatoxin production on food products which can lead to aflatoxicosis. Therefore, a number of methods have been proposed so far for detection of the fungi with lowest possible concentration at the earliest. Molecular methods such as PCR and/or in combination with certain techniques have been found to be useful for Aspergillus detection. We discuss here various technologies that have emerged in recent years and can possibly be used for the molecular detection of Aspergillus in an efficient way. These methods like RSIC, C-probe, and inversion probe with pyrosequencing or direct ss/dsDNA detection have been used for the identification of fungal or bacterial pathogens and thus formulate a ‘gold standard’ for Aspergillus detection.     

Wool-degrading <Emphasis Type="Italic">Bacillus</Emphasis> isolates: extracellular protease production for microbial processing of fabrics

Wool is a natural animal fiber commonly used in fabrics, but requires physical and chemical processing treatment for such applications. With the aim of developing new woollen textile products using environmentally friendly treatments, proteolytic bacteria were isolated from raw wool samples of Merino sheep and screened for wool-degrading activity. Two isolates were identified as Bacillus megaterium L4 and Bacillus thuringiensis L11 by 16S rRNA gene sequence analysis. Both isolates grew on a minimal medium using wool-fiber or wool-fabric as sole carbon and nitrogen sources. Bacterial growth was correlated with extracellular protease activity, and maximal protease production was in early stationary phase. The exoprotease produced by L11 was found to be a thermo-tolerant metalloprotease stabilized by calcium or magnesium, and had optimum activity at pH 7.0 and temperature at 40°C. During bacterial growth the wool-fiber lost weight, but it did not show changes in diameter. When wool-fabric was used instead of wool-fiber weight loss and non-shrinking was found. These are encouraging results for textile processing that should be useful for development of new textile products by direct microbial processing. A potential alternative that could be suggested from our study would be to treat wool with wool-degrading microorganisms in order to develop environmentally friendly processes.     

Tools for chloroplast transformation in Chlamydomonas: expression vectors and a new dominant selectable marker

Reverse-genetic studies of chloroplast genes in the green alga Chlamydomonas reinhardtii have been hampered by the paucity of suitable selectable markers for chloroplast transformation. We have constructed a series of vectors for the targeted insertion and expression of foreign genes in the Chlamydomonas chloroplast genome. Using these vectors we have developed a novel selectable marker based on the bacterial gene aphA-6, which encodes an aminoglycoside phosphotransferase. The aphA-6 marker allows direct selection for transformants on medium containing either kanamycin or amikacin. The marker can be used to inactivate or modify specific chloroplast genes, and can be used as a reporter of gene expression. The availability of this marker now makes possible the serial transformation of the chloroplast genome of Chlamydomonas. Received: 26 October 1999 / Accepted: 28 December 1999     

An individual-based model for competingDrosophila populations

An individual-based model forDrosophila is formulated, based on competition amongst larvae consuming the same batch of food. The predictions of the model are supported by data for single speciesDrosophila populations reared in the laboratory. The model is used to build a simple discrete model for the dynamics ofDrosophila populations that are kept over a number of generations. The dynamics of a single species is shown to give either a stable equilibrium or fluctuations which can be periodic or chaotic. When the dynamics of a species in the absence of the other is periodic or chaotic, we found coexistence or two alternative states, on neither of which the species can coexist.     

Development of the magnetic capture system for recovery of Xiphinema americanum

Xiphinema americanum is listed as a quarantine nematode by The European Plant Protection Organisation because of its ability to transmit quarantine viruses. Detection of this nematode in soil samples, or in mixed nematode samples extracted from soil, is therefore of paramount importance. We recently described the use of magnetic beads (Dynabeads) in combination with probes such as lectins or antibodies for recovery of small endoparasitic nematodes including Meloidogyne spp. and Globodera rostochiensis from mixed nematode samples. Here we show that magnetic capture can be used with much larger nematodes such as X. americanum. We describe lectins and antisera that bind to the surface of this nematode and show that the antisera can be used in the Dynabeads system to recover and enrich X. americanum from mixed nematode samples.     

The Comparative Discriminating Abilities of Lipases in Different Media and Their Application in Fatty Acid Enrichment

The generally held belief that the selectivity of lipase can be changed by changing the media from aqueous to non-aqueous was tested by monitoring the rates of hydrolysis, ester synthesis and transesterification with a range of fatty acid mono-esters. Although the absolute rates of reaction varied, hydrolysis was by far the most rapid of the three, the relative rates for the fatty acids used were similar in all three reaction types. The selectivity of the five enzymes used appeared to remain unchanged irrespective of the type of reaction, i.e. hydrolysis of p-nitrophenyl esters, direct ester synthesis with butanol and fatty acid or transesterification with butyl butyrate and fatty acid, and could not be changed by changing water activity. This principle was applied to screen for suitable lipases which could be used to increase the gamma linolenic acid content of a fatty acid mixture. Enzymes could be selected by measuring the rate of hydrolysis of a range of P-nitrophenyl esters.     

替加环素与5种抗生素对多重耐药鲍曼不动杆菌体外联合药敏实验的研究

分析亚胺培南、头孢哌酮-舒巴坦、头孢曲松、左氧氟沙星、庆大霉素5种临床常用鲍曼不动杆菌治疗的抗生素单用和分别与替加环素联用的体外敏感性实验的研究,以期发现较好的联合用药方案,为临床合理使用抗生素提供用药参考。采用微量肉汤稀释法测定5种抗生素对鲍曼不动杆菌的MIC值,再采用棋盘法测定5种抗生素分别与替加环素联用MIC值,并计算FIC指数。结果显示,替加环素与亚胺培南、头孢哌酮舒巴坦、左氧氟沙星、头孢曲松具有协同和相加作用,替加环素与庆大霉素具有拮抗作用。临床在选择抗生素治疗鲍曼不动杆菌所引起的重症感染时,可根据该药敏实验结果与亚胺培南或头孢哌酮舒巴坦或左氧氟沙星或头孢曲松与替加环素联合使用,但应避免与庆大霉素联合使用。