Isolation and description of a non-motile,fusiform, stalked bacterium,a representatieve of a new genus

A single strain representing the fusiform group of caulobacters first described by Henrici and Johnson has been isolated from a freshwater pond. Like the genusCaulobacter this is a chemo-organotrophic bacterium that has one polar prostheca, a stalk in the sense that its apical holdfast permits the cell to attach to solid substrates. Fine structure studies reveal, however, that the prostheca of this organism contains typical cellular constituents, not the membranous material found in the stalks ofCaulobacter andAsticcacaulis. The organism also differs from the other caulobacters in having no motile stage and no dimorphic life cycle (both daughter cells are stalked at the time of division). Because only one strain has been isolated no nomenclatural proposals are made, but sufficient evidence is presented to indicate that this is a representative of a new genus of the Schizomycetes.     

Do light intensity,temperature and photoperiod affect the entrapment of mites on glandular hairs of cultivated tomatoes?

The effects of plant growth conditions (light intensity, temperature and photoperiod) on the proportion of spider mites (Tetranychus urticae) and predatory mites (Phytoseiulus persimilis) entrapped by type VI trichomes were investigated in the cultivated tomato Lycopersicon esculentum. Trichomes released sticky substances showing rapid hardening when the trichome head was ruptured by contact with mites. Adult individuals of both species of mites were immobilized by exudates in a higher percentage on leaf stalks from plants grown in the light (160 einsteins cm^-2s^-1) than on leaf stalks from plants grown in the shade (50 einsteins cm^-2 s^-1). Leaf stalks from plants grown in the light showed bigger trichome heads. More predatory mites were also entrapped on the leaf stalks from plants grown at 18°C (65% RH) as compared to the ones grown at 24°C (60% RH), whereas trichome heads were bigger under the former conditions. Contrary to leaf stalks, leaflet areas, through differences in trichome density and size, showed no diffences in predator and spider mite entrapment. Trichome head size was probably related to mite entrapment. It is also hypothesised that temperature increase might influence predator entrapment through effects on trichome quality.     

Genetic analysis of agronomic traits in a cross between sugarcane (Saccharum officinarum L.) and its presumed progenitor (S. robustum Brandes & Jesw. ex Grassl)

Saccharum robustum Brandes & Jesw. ex Grassl has been suggested as the immediate progenitor species of cultivated sugarcane (S. officinarum L.) [4]. Chromosome pairing and assortment in these two species were previously studied by genetic analysis of single-dose DNA markers in parents in and 44 F₁ progeny of a cross between euploid, meiotically regular 2n=80S. officinarum LA Purple andS. robustum Mol 5829 [2]. This same population was subsequently clonally propagated and evaluated in replicated trials for quantitative traits important to sugarcane breeders. Numbers of stalks, tasseled stalks, and stalks with smut, and the average diameter of two stalks were determined one day prior to harvest. At harvest, plant material from each plot was weighed and evaluated for pol (sucrose content) and fiber percentages. Clones were significantly different (P<0.01) for all traits analyzed. Associations of 83 single-dose arbitrarily primed PCR genetic markers with quantitative trait loci (QTL) of recorded traits was determined by single-factor ANOVA, and multiple regression. QTL analysis revealed markers significantly (P<0.05) associated with the expression of each trait analyzed. Markers associated with QTL after multiple regression were tested for digenic linear × linear epistatic interactions. The various multilocus models explained between 23% and 58% of the total phenotypic variation and 32% and 76% of the genotypic variation for the various traits. Digenic interactions were uncommon. Implications for marker-assisted selection in sugarcane and sugarcane domestication are discussed.     

A novel cost-effective technology to convert sucrose and homocelluloses in sweet sorghum stalks into ethanol

Background

Sweet sorghum is regarded as a very promising energy crop for ethanol production because it not only supplies grain and sugar, but also offers lignocellulosic resource. Cost-competitive ethanol production requires bioconversion of all carbohydrates in stalks including of both sucrose and lignocellulose hydrolyzed into fermentable sugars. However, it is still a main challenge to reduce ethanol production cost and improve feasibility of industrial application. An integration of the different operations within the whole process is a potential solution.

Results

An integrated process combined advanced solid-state fermentation technology (ASSF) and alkaline pretreatment was presented in this work. Soluble sugars in sweet sorghum stalks were firstly converted into ethanol by ASSF using crushed stalks directly. Then, the operation combining ethanol distillation and alkaline pretreatment was performed in one distillation-reactor simultaneously. The corresponding investigation indicated that the addition of alkali did not affect the ethanol recovery. The effect of three alkalis, NaOH, KOH and Ca(OH)₂ on pretreatment were investigated. The results indicated the delignification of lignocellulose by NaOH and KOH was more significant than that by Ca(OH)₂, and the highest removal of xylan was caused by NaOH. Moreover, an optimized alkali loading of 10% (w/w DM) NaOH was determined. Under this favorable pretreatment condition, enzymatic hydrolysis of sweet sorghum bagasse following pretreatment was investigated. 92.0% of glucan and 53.3% of xylan conversion were obtained at enzyme loading of 10 FPU/g glucan. The fermentation of hydrolyzed slurry was performed using an engineered stain, Zymomonas mobilis TSH-01. A mass balance of the overall process was calculated, and 91.9 kg was achieved from one tonne of fresh sweet sorghum stalk.

Conclusions

A low energy-consumption integrated technology for ethanol production from sweet sorghum stalks was presented in this work. Energy consumption for raw materials preparation and pretreatment were reduced or avoided in our process. Based on this technology, the recalcitrance of lignocellulose was destructed via a cost-efficient process and all sugars in sweet sorghum stalks lignocellulose were hydrolysed into fermentable sugars. Bioconversion of fermentable sugars released from sweet sorghum bagasse into different products except ethanol, such as butanol, biogas, and chemicals was feasible to operate under low energy-consumption conditions.

     

A new method for the determination of microbial activity and critical logP in the presence of organic solvents

A new method to determine microbial activity and critical logP of an organism in the presence of organic solvents has been developed which involves direct contact with a solvent, and a measurement of the developing colony size. This technique has been used to estimate the critical logP of Alcaligenes xylosoxidans Y234, and, although the critical logP for this organism is 3.5, solvents with logP values of up to 4.5 can still reduce microbial activity by up to 55% of the uninhibited amount.     

Observations on the fine structure of the endophyte of the root nodules of alnus glutinosa (L.) gaertn.

Summary Electron micrographs have been prepared showing different stages in the development of the endophyte in Alnus glutinosa root nodules. Although the complete life cycle of the organism has not yet been worked out it is concluded that it is an Actinomycete. The organism can exist as a septate, branching filament of diameter 0.7–1.0 . However, under certain conditions within the nodule, the endophyte can form spherical sub-divided vesicles 4–5 in diameter and it is suggested that these vesicles are analogous to sporangia. Yet again under other conditions the organism fragments to form bacteroids. It would appear that the different forms of the organism are associated with different seasons of the year and with different metabolic patterns, of particular interest in this connection is the fixation of nitrogen which is associated with the nodule symbiosis.     

Trends in the functional morphology and sensorimotor control of feeding behavior in salamanders: An example of the role of internal dynamics in evolution

Organisms are self-producing and self-maintaining, or autopoietic systems. Therefore, the course of evolution and adaptation of an organism is strongly determined by its own internal properties, whatever role external selection may play. The internal properties may either act as constraints that preclude certain changes or they open new pathways: the organism canalizes its own evolution. As an example the evolution of feeding mechanisms in salamanders, especially in the lungless salamanders of the family Plethodontidae, is discussed. In this family a large variety of different feeding mechanisms is found. The authors reconstruct this evolutionary process as a series of bifurcation points of either constraints or opportunities forming a sequence of preconditions for the formation of a high-speed projectile tongue characteristic of tropical salamanders. Furthermore, it is shown how parallel evolution of seemingly unrelated domains within an organism such as respiratory physiology, life history biology and pattern of ontogeny has rather direct relevance to the feeding biology, thus demonstrating that organisms always evolve as wholes.     

Studies of two strains of Actinopolyspora halophila,an extremely halophilic actinomycete

Actinopolyspora halophila is an extremely halophilic actinomycete requiring a minimum salt concentration of 12% (w/v) for growth in liquid media at 37°C. During antibiotic sensitivity testing of the organism, an erythromycin-resistant phenotypic variant designated A. halophila ER, was isolated. This strain was approximately 60-fold more resistant to erythromycin than the wild-type strain, and, moreover, was capable of growth in 6% sodium chloride. Optimal growth of both strains in liquid media was observed in 20% salt.After resuspension in water for up to 20 days, the organism exhibited good growth in fresh salt-containing media. Cultures resuspended in salt-containing media, however, were subject to extensive cellular autolysis.In addition to resistance to -lactam antibiotics which was mediated by cellular and exocellular -lactamases, the organism was insensitive to all other tested antibiotics except amakacin, chloramphenicol, kanamycin, gentamycin, naladixic acid, streptomycin, and tetracycline. No plasmids were detected in either strain. A. halophila possessed high cellular levels of catalase, -lactamase, and -glucosidase. A variety of exocellular enzymes including protease, -lactamase, xylanase, and carboxymethyl cellulase, were secreted maximally into growth media containing 15% NaCl.Issued as NRCC 25148     

Occurrence of mycotic granules in mouse tissues infected with an acid-fast organism

Summary An acid-fast organism has been consistently isolated from blood and tumor tissue of Swiss mice implanted with Sarcoma 180. The organism is pathogenic to mice. Swiss mice treated with cortisone prior to infection died within a week. Lesions similar to granules vermiculaires described byLangeron in connection with fungus infections (mycetomas) were produced in spleen, liver and kidney of mice that developed these acute infections.     

Isolation and characterization of a strictly xylan-degrading Dictyoglomus from a man-made,thermophilic anaerobic environment

A thermophilic, strictly anaerobic eubacterium which utilized an unusually limited range of substrates was isolated from a sludge and pulp sample from a paperpulp cooling tank at a paper-board factory in Finland. The organism grew only with beech wood or oat spelt xylan; no growth occurred with soluble sugars, other polysaccharides, peptone, or yeast extract. The organism was rod-shaped, long (up to 20 m), thin (0.3 m), gramnegative, and in late-exponential and stationary phase cultures formed ball of yarn like structures; endospores were not observed and the organism was not motile. The organism grew fastest (=0.08 – 0.09 h^-1) at 65 to 75°C and pH 6.5 to 8.4, with a maximum growth temperature between 75 and 80°C and an upper pH limit near 9. During growth on beech xylan the isolate produced only acetate, H₂, and CO₂ as fermentation products. The guanine + cytosine (G+C) content of the isolates cellular DNA was 34%. The unusual morphology of the isolate is characteristic of the genus Dictyoglomus, and the limited substrate range, higher G+C ratio, and different fermentation products indicated that the isolate was a new species in that genus.     

Characterization of a new methylotrophic strain,Methylomonas clara

Summary The organism examined was identified as an obligate methylotroph and as an organism of type I, because it has some characteristics of this group: methanol is utilized via the hexulose phosphate pathway, the enzymes glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, malate dehydrogenase, and isocitrate dehydrogenase (both NAD- and NADP-specific) could be detected, whereas the citric acid cycle is incomplete (in particular -ketoglutarate dehydrogenase could not be found). Furthermore, the organism is able to fix nitrogen. In contrast, there are some different characteristics: carbon dioxide can be fixed in connection with methanol. There is no formate dehydrogenase, and formaldehyde dehydrogenase can be induced by different culture conditions. Moreover, the GC content (49.2%) is distinctly lower than normal, and the hexulose phosphate synthase shows a higher activity with NAD as cosubstrate than with NADP. Carbon is not metabolized via the Embden-Meyerhoff-Parnaß pathway, but via the Entner-Doudoroff pathway. In the disk test, the organism is resistant to some antibiotics: chloramphenicol, fusidic acid, methicillin and lincomycin. A partial resistance can be observed with penicillin, neomycin, novobiocin, and cloxacillin.     

Towards classifying species in systems biology papers using text mining

Background

In recent years high throughput methods have led to a massive expansion in the free text literature on molecular biology. Automated text mining has developed as an application technology for formalizing this wealth of published results into structured database entries. However, database curation as a task is still largely done by hand, and although there have been many studies on automated approaches, problems remain in how to classify documents into top-level categories based on the type of organism being investigated. Here we present a comparative analysis of state of the art supervised models that are used to classify both abstracts and full text articles for three model organisms.

Results

Ablation experiments were conducted on a large gold standard corpus of 10,000 abstracts and full papers containing data on three model organisms (fly, mouse and yeast). Among the eight learner models tested, the best model achieved an F-score of 97.1% for fly, 88.6% for mouse and 85.5% for yeast using a variety of features that included gene name, organism frequency, MeSH headings and term-species associations. We noted that term-species associations were particularly effective in improving classification performance. The benefit of using full text articles over abstracts was consistently observed across all three organisms.

Conclusions

By comparing various learner algorithms and features we presented an optimized system that automatically detects the major focus organism in full text articles for fly, mouse and yeast. We believe the method will be extensible to other organism types.

     

Limited overlap of the community of bees and wasps (Hymenoptera: Aculeata) nesting in reed galls with those nesting in other cavities

Hymenopterans occurring in wetlands represent specific community with bioindicative characters but poorly understood nesting biology. We have studied the nesting preferences of these insects in ten reed beds—five represented by natural wetlands, and the other five localized to anthropogenic sites. We reared the hymenopterans from trap-nests consisting of reed stalks and goldenrod stems, which were installed at the localities through the nesting season, and compared them with quantitative data of hymenopterans reared from reed galls collected at the same localities. Most of the species that nested in reed galls accepted the reed stalk traps but not vice versa. Some of the species that accepted both these nesting resources strongly differed in their frequency of use of these two nesting resources. Moreover, the species composition differed substantially between goldenrod stems and either reed stalks or reed galls. The digger wasp Pemphredon fabricii was eudominant in reed galls with higher abundance at anthropogenic sites, while it was also observed in reed stalks but in much lower numbers. Hylaeus pectoralis was frequent in reed galls at both habitat types and only one individual was reared from reed stalks. Trypoxylon deceptorium was quite numerous in reed galls but much more frequent in reed stalks. Species unknown from reed galls (Psenulus pallipes, Hylaeus confusus, Gymnomerus laevipes) were numerous in reed stalks. We experimentally confirmed that P. fabricii and H. pectoralis show high preference of reed galls and are dependent on these nesting resources. The available evidence suggests that the management of both natural and anthropogenic sites needs to implement tools preserving reed beds, especially the terrestrial ones with reed galls.     

An electron microscope study of the cell surface ofCytophaga johnsonii and some observations on related organisms

The cell surface of a non-fruiting myxobacterium,Cytophaga johnsonii, was investigated by electron optical techniques. Negative staining revealed an irregularly undulating surface topography and the presence of strands of material arising from the cells. Replicas of freeze-dried cells and thin sections confirmed the uneven nature of the surface and showed that, in contrast to eubacteria, the cell was surrounded by an envelope of amorphous, electron-translucent material contained within a crenated, outer, unit membrane. This material could be extruded as long strands. It is considered that this envelope of material represents the slime layer of the organism.The appearance of the slime layer at various stages in the growth of the organism was followed by negative staining and the image of the organism presented by negative staining was compared to that given byMyxococcus xanthus andFlavobacterium aquatile.     

An airlift-recycle fermenter for microbial desulfurization of coal

Summary An airlift-external recycle fermenter has been constructed and used for the removal of pyritic sulfur from coal samples (4% initial total sulfur) by the thermophilic, sulfur oxidizing organism Sulfolobus acidocaldarius. The airlift fermenter behaved as a well mixed reactor. Approximately, 30% of initial pyritic sulfur has been removed from a 5% coal slurry of ~125 particle size, at a maximum rate of 1.8 mg S/l.h.     

Soil silicon amendments increase resistance of sugarcane to stalk borer Eldana saccharina Walker (Lepidoptera: Pyralidae) under field conditions

Background and aims

Soil amendment with silicon (Si) can significantly increase resistance of susceptible sugarcane cultivars grown in pots to stalk borer Eldana saccharina (Lepidoptera: Pyralidae). This study tested the hypothesis that a single application of silicate can increase resistance to E. saccharina and increase yield in field-grown sugarcane.

Methods

Two Si materials (Calmasil® and Slagment® at 4 and 8 t/ha) were applied at planting to a field trial extending over three successive crops and incorporating three sugarcane cultivars varying in borer susceptibility.

Results

Both materials, especially Slagment, significantly increased soil, leaf and stalk Si content, but leaf Si levels seldom exceeded 0.5 %. Silicon treatment significantly reduced percent stalks bored in all three crops and stalk length bored in the second ratoon crop, but did not affect borer numbers per 100 stalks (E/100) or increase cane or sucrose yield. Borer damage and E/100 were significantly and consistently reduced in the resistant cultivar.

Conclusions

We argue that if leaf Si% in field sugarcane can be elevated to or exceed 0.8 %, using materials that release Si slowly, substantial reductions in stalk damage and sucrose loss could be achieved in susceptible cultivars in low-Si soils.     

Discussion: Screening-off and Visibility to Selection

Philosophers have used the probabilistic relation of screening-off to explicate concepts in the theories of causation and explanation. Brandon has used screening-off relations in an attempt to reconstruct an argument of Mayr and Gould that natural selection acts at the level of the organism. I argue that Brandons reconstruction is unsuccessful.     

Selective induction of β-glucosidase in Trichoderma reesei by xylan

Summary In Trichoderma reesei, QM 9414, -glucosidase can be selectively induced by xylan. At a concentration of 0.5% xylan in the growth medium, the yield of -glucosidase is 3 times more than in cellulose medium suggesting that the synthesis of this enzyme in this organism is under an independent regulatory control.     

An in vitro oxidative stress test for determining pollutant tolerance in algae

An in vitro oxidative stress test has been developed to assess pollutant tolerance in freshwater algae using Euglena gracilis as the test organism and FeSO₄ and NaCl as the pollutants. The test evaluates free radical-mediated oxidative stress through the concomitant application of three biochemical assays: (1) the non-invasive, gas chromatographic-volatile headspace analysis of hydroxyl radicals (OH) using dimethyl-sulphoxide as a radical trap; (2) the spectroscopic determination of total antioxidant activity; (3) a fluorescent microscopy viability test. In vitro pollutant testing was devised to simulate contaminant loadings that impact urban retention ponds. E. gracilis was found to be tolerant to FeSO₄ (2–10% (w/v)) and NaCl (10–5000 ppm) as indicated by high positive viabilities (ca. 100%) and low, or no OH production, as compared to controls. Total antioxidant activity increased with increasing pollutant loading suggesting that the organism has the capacity to enhance antioxidant defence in response to pollutant stress. This in vitro test provides a new approach to monitor the effects of water quality on the biological components of urban and/or polluted aquatic ecosystems. It also has a potential application in the identification of putative algal phytoremediators.     

Thiobacillus strain Q,a chemolithoheterotrophic sulphur bacterium

The physiological properties of an organism isolated from a selective chemostat enrichment using acetate and thiosulphate as the limiting substrates, provisionally called Thiobacillus Q, were investigated. Although the organism made up 85% of the community in the enrichment culture, its expected chemolithotrophic nature was not apparent in batch experiments. The growth yield was not enhanced by the addition of thiosulphate to an acetate containing mineral medium, even though up to 50% of the thiosulphate was oxidized. Under acetate limitation in the chemostat, there was a linear increase in yield with thiosulphate addition up to a concentration of 7 mM. Higher thiosulphate concentrations resulted in loss of thiosulphate oxidizing capacity and a decrease in the biomass to the level obtained with acetate alone. This loss may be due to the presence of inhibitory (50–100 M) levels of sulphite which is probably produced as an intermediate of the biological thiosulphate oxidation. Experiments with sulphide showed that Thiobacillus Q could also use it as an additional energy source. The complete lack of autotrophic growth, both in batch and chemostat experiments, together with the absence of even very low amounts of the key enzymes of the Calvin cycle demonstrated that this organism is a typical chemolithoheterotroph. Although this organism has provisionally been placed in the genus Thiobacillus, standard taxonomic procedures showed a close relationship with Pseudomonas alcaligenes. This study stresses the importance of quantitative chemostat studies in establishing the role of inorganic oxidations in energy metabolism and in the understanding of the role of heterotrophic sulphur oxidation in natural environments.