Lateral drift correction in time-laps images by the particle-tracking algorithm

In long-term time-laps imaging of living cells, a significant lateral drift of the fluorescently labeled structures is often observed due to many reasons including superfusion of solution, temperature gradients, bolus addition of pharmacological agents and cell motility. We have detected lateral drift in long-term time-laps confocal imaging by tracking fluorescent puncta, which represent single exocytotic vesicles expressing synaptopHluorin (spH), a pH sensitive green fluorescence protein. Following the initial increase in fluorescence intensity due to alkalinization of vesicle lumen, the spH fluorescent puncta dimmed, which may be attributed to the resealing of the fusion pore and subsequent slow reacidification of the vesicle, or alternatively the dimming may be due to a significant lateral drift of the vesicle out of the region of interest (ROI). We identified and compensated the lateral drift by tracking particles present in the confocal images, without any additional mechanical and/or optical hardware components. The peak of the Gaussian two-dimensional (2D) curve fitted to the fluorescent particle intensity profile was recorded as the X and Y coordinates of the vesicle in each frame. The resulting coordinates of vesicle positions were averaged and rounded to the nearest pixel value, which was used to correct the drift in the time-laps images. In drift corrected time-laps images, the vesicle remained enclosed by the ROI, and the time dependent changes of spH fluorescence intensity averaged from the ROI remained at a constant level, revealing that endocytosis with subsequent slow reacidification of vesicles was an unlikely event.     

The annexins of Dictyostelium

Annexins are a highly conserved ubiquitous family of Ca2+- and phospholipid-binding proteins present in nearly all eukaryotic cells. Analysis of the Dictyostelium genome revealed the presence of two annexin genes, the annexin C1 gene (nxnA) giving rise to two isoforms of 47 and 51 kDa (previously synexin), and the annexin C2 gene (nxnB) coding for a 56-kDa protein with 33% sequence identity to annexin C1. Annexin C2 is expressed at very low and constant levels throughout development. Quantification by real-time PCR indicated that it is present in about 35-fold lower amounts compared to annexin C1. We have used a GFP-tagged annexin C2 to study its cellular distribution and dynamics. In cell fractionation studies, annexin C2 cofractionates with annexin C1 and is enriched in the 100,000 g pellet. Like annexin C1, GFP-AnxC2 stains the plasma membrane. In addition it is present in the perinuclear region and overlaps to some degree with the Golgi apparatus, whereas annexin C1 is present on intracellular membranes resembling endosomal membranes and in the nucleus. Annexin C2 is not observed in the nucleus. An annexin C1 mutant (SYN-) which shows a defect during multicellular development can be rescued by full-length annexin C1, whereas overexpression of GFP-AnxC2 did not rescue the developmental defect The data support the concept that annexins, although having a highly conserved structure, participate in different functions in a cell.     

Species–area relationships across four trophic levels – decreasing island size truncates food chains

That larger areas will typically host more diverse ecological assemblages than small ones has been regarded as one of the few fundamental ‘laws’ in ecology. Yet, area may affect not only species diversity, but also the trophic structure of the local ecological assemblage. In this context, recent theory on trophic island biogeography offers two clear‐cut predictions: that the slope of the species–area relationship should increase with trophic rank, and that food chain length (i.e. the number of trophic levels) should increase with area. These predictions have rarely been verified in terrestrial systems. To offer a stringent test of key theory, we focused on local food chains consisting of trophic specialists: plants, lepidopteran herbivores, and their primary and secondary parasitoids. For each of these four trophic levels, we surveyed species richness across a set of 20 off‐shore continental islands spanning a hundred‐fold range in size. We then tested three specific hypotheses: that species richness is affected by island size, that the slope of the species–area curve is related to trophic rank, and that such differences in slope translate into variation in food chain length with island size. Consistent with these predictions, estimates of the species–area slope steepened from plants through herbivores and primary parasitoids to secondary parasitoids. As a result of the elevated sensitivity of top consumers to island size, food chain length decreased from large to small islands. Since island size did not detectably affect the ratio between generalists and specialists among either herbivores (polyphages vs oligophages) or parasitoids (idiobionts vs koinobionts), the patterns observed seemed more reflective of changes in the overall number of nodes and levels in local food webs than of changes in their linking structure. Overall, our results support the trophic‐level hypothesis of island biogeography. Per extension, they suggest that landscape modification may imperil food web integrity and vital biotic interactions.     

Continuous testing system for Baeyer-Villiger biooxidation using recombinant Escherichia coli expressing cyclohexanone monooxygenase encapsulated in polyelectrolyte complex capsules

An original strategy for universal laboratory testing of Baeyer-Villiger monooxygenases based on continuous packed-bed minireactor connected with flow calorimeter and integrated with bubble-free oxygenation is reported. Model enantioselective Baeyer-Villiger biooxidations of rac-bicyclo[3.2.0]hept-2-en-6-one to corresponding lactones (1R,5S)-3-oxabicyclo-[3.3.0]oct-6-en-3-one and (1S,5R)-2-oxabicyclo-[3.3.0]oct-6-en-3-one as important chiral synthons for the synthesis of bioactive compounds were performed in the minireactor equipped with a column packed with encapsulated recombinant cells Escherichia coli overexpressing cyclohexanone monooxygenase. The cells were encapsulated in polyelectrolyte complex capsules formed by reaction of oppositely charged polymers utilizing highly reproducible and controlled encapsulation process. Encapsulated cells tested in minireactor exhibited high operational stability with 4 complete substrate conversions to products and 6 conversions above 80% within 14 repeated consecutive biooxidation tests. Moreover, encapsulated cells showed high enzyme stability during 91 days of storage with substrate conversions above 80% up to 60 days of storage. Furthermore, usable thermometric signal of Baeyer-Villiger biooxidation obtained by flow calorimetry using encapsulated cells was utilized for preparatory kinetic study in order to guarantee sub-inhibitory initial substrate concentration for biooxidation tests.     

High-level functional expression of a fungal xylose isomerase: the key to efficient ethanolic fermentation of xylose by Saccharomyces cerevisiae?

Evidence is presented that xylose metabolism in the anaerobic cellulolytic fungus Piromyces sp. E2 proceeds via a xylose isomerase rather than via the xylose reductase/xylitol-dehydrogenase pathway found in xylose-metabolising yeasts. The XylA gene encoding the Piromyces xylose isomerase was functionally expressed in Saccharomyces cerevisiae. Heterologous isomerase activities in cell extracts, assayed at 30 degrees C, were 0.3-1.1 micromol min(-1) (mg protein)(-1), with a Km for xylose of 20 mM. The engineered S. cerevisiae strain grew very slowly on xylose. It co-consumed xylose in aerobic and anaerobic glucose-limited chemostat cultures at rates of 0.33 and 0.73 mmol (g biomass)(-1) h(-1), respectively.     

Language Metaphors of Life

We discuss the difference between formal and natural languages, and argue that should the language metaphor have any foundation, it’s analogy with natural languages that should be taken into account. We discuss how such operation like reading, writing, sign, interpretation, etc., can be applied in the realm of the living and what can be gained, by such an approach, in order to understand the phenomenon of life.     

Masterpiece of epigenetic engineering – how Toxoplasma gondii reprogrammes host brains to change fear to sexual attraction

The protozoan parasite Toxoplasma gondii is known to induce specific behavioural changes in its intermediate hosts, including humans, that are believed to increase the chance of its successful transmission to the definitive host, the cat. The most conspicuous change is the so‐called fatal attraction phenomenon, the switch from the mice's and rats’ natural fear of the smell of cats toward an attraction to this smell. The mechanism of this manipulation activity is unknown; however, many indices suggest that changes in the concentrations of dopamine and testosterone are involved. In this issue of Molecular Ecology, Hari Dass & Vyas ( 2014 ) present results of a study showing that, by hypomethylation of certain regulatory elements of key gene, Toxoplasma is able to reprogramme the brain's genetic machinery in such a way that cat odour activates and changes the wiring of the medial amygdala circuits responsible for sexual behaviour. This study delivers the first clear evidence of a parasite's ability to use sophisticated epigenetic engineering techniques for the manipulation of the phenotype of its infected host.     

The elemental composition, the microfibril angle distribution and the shape of the cell cross-section in Norway spruce xylem

Relationships between the elemental composition, the microfibril angle (MFA) distribution and the average shape of the cell cross-section of irrigated-fertilised and untreated Norway spruce (Picea abies [L.] Karst.) earlywood were studied. Sample material was obtained from Flakaliden, Sweden. The elemental composition was studied by determining the relative mass fractions of the elements P, S, Cl, K, Ca and Mn by X-ray fluorescence and by determining the mass absorption coefficients for X-rays. X-ray diffraction was used to determine the MFA distribution and the average shape of the cell cross-section. The latter was also determined by light microscopy. In transition from juvenile wood to mature wood, a decrease of the mode of the MFA distribution from 13°–24° to 3°–6° was connected to a change in the shape of the cell cross-section from circular to rectangular. The irrigation-fertilisation treatment caused no change in the MFA distribution or in the shape of the cell cross-section, whereas the mass absorption coefficient was higher and the density was smaller in irrigated-fertilised wood. Larger proportion of the elements S, Cl and K, but smaller proportion of the element Mn, were observed due to the treatment. The results indicate that the shape of the cell cross-section or the MFA distribution are not directly linked to the growth rate of tracheids or to the nutrient-element content in the xylem and only show notable changes as a function of the cambial age.