ScanLag: High-throughput Quantification of Colony Growth and Lag Time

Growth dynamics are fundamental characteristics of microorganisms. Quantifying growth precisely is an important goal in microbiology. Growth dynamics are affected both by the doubling time of the microorganism and by any delay in growth upon transfer from one condition to another, the lag. The ScanLag method enables the characterization of these two independent properties at the level of colonies originating each from a single cell, generating a two-dimensional distribution of the lag time and of the growth time. In ScanLag, measurement of the time it takes for colonies on conventional nutrient agar plates to be detected is automated on an array of commercial scanners controlled by an in house application. Petri dishes are placed on the scanners, and the application acquires images periodically. Automated analysis of colony growth is then done by an application that returns the appearance time and growth rate of each colony. Other parameters, such as the shape, texture and color of the colony, can be extracted for multidimensional mapping of sub-populations of cells. Finally, the method enables the retrieval of rare variants with specific growth phenotypes for further characterization. The technique could be applied in bacteriology for the identification of long lag that can cause persistence to antibiotics, as well as a general low cost technique for phenotypic screens.     

Male-biased investment during chick rearing in the Griffon Vulture Gyps fulvus

Capsule: In Griffon Vultures Gyps fulvus both parents take part in all parenting tasks but males take a significantly larger part of the burden.     

Independent axes of genetic variation and parallel evolutionary divergence of opercle bone shape in threespine stickleback

Evolution of similar phenotypes in independent populations is often taken as evidence of adaptation to the same fitness optimum. However, the genetic architecture of traits might cause evolution to proceed more often toward particular phenotypes, and less often toward others, independently of the adaptive value of the traits. Freshwater populations of Alaskan threespine stickleback have repeatedly evolved the same distinctive opercle shape after divergence from an oceanic ancestor. Here we demonstrate that this pattern of parallel evolution is widespread, distinguishing oceanic and freshwater populations across the Pacific Coast of North America and Iceland. We test whether this parallel evolution reflects genetic bias by estimating the additive genetic variance-covariance matrix (G) of opercle shape in an Alaskan oceanic (putative ancestral) population. We find significant additive genetic variance for opercle shape and that G has the potential to be biasing, because of the existence of regions of phenotypic space with low additive genetic variation. However, evolution did not occur along major eigenvectors of G, rather it occurred repeatedly in the same directions of high evolvability. We conclude that the parallel opercle evolution is most likely due to selection during adaptation to freshwater habitats, rather than due to biasing effects of opercle genetic architecture.     

Comparative oogenesis in cardinal fishes (Apogonidae,Perciformes), with special focus on the adaptive structures of the egg envelopes

The present study compares gonad structure and oogenesis in 30 species of cardinal fish (Apogonidae) from the Indo-Pacific region. In all of the species studied the ovaries are bilobed, with each lobe possessing ovigerous lamellae whose numbers and dimensions increase concomitantly with growth of the fish and reproductive stage, and correlate with the total dimensions of the particular species. In species of the genus Siphamia, the ovarian lobes are associated with a fat body that is not found in species of the other genera studied. Some of the species studied (Siphamia spp.; Archamia spp.) demonstrate group-synchronized maturation of eggs, possibly with only one spawn per reproduction season. However, most of the Apogon spp., and other genera, have unsynchronized cycles, a characteristic of multiple spawners. The various stages of previtellogenic and vitellogenic development are similar in the different species, but differ in timing and dimensions of the oocytes around which the morphogenesis of the egg envelope (chorion) and follicle begins. Differentiation of the egg envelope and follicle cells parallels the vitellogenic stages of egg development. The number of eggs was found to correlate positively with the length of the body and ovary of the fish, whereas egg diameter was found to correlate negatively with body length. The surface of the egg envelope bears ridges that form patterns of various types, whose structures and dimensions seem to be species-specific, and which in most species converge upon the single micropyle on the animal pole. The exposed ridge mazes include a special fibrous web that anchors in the micropyle. The production and importance of these ridges, as well as the correlations between egg numbers per spawn, egg dimensions, and the oral dimensions of the paternal male, are discussed.     

Oral cancer,cigarette smoke and mitochondrial 18 kDa translocator protein (TSPO) — In vitro,in vivo,salivary analysis

Oral cancer features high rates of mortality and morbidity, and is in dire need for new approaches. In the present study we analyzed 18 kDa translocator protein (TSPO) expression in oral (tongue) cancer tumors by immunohistochemistry. We also assayed TSPO binding in human tongue cancer cell lines and in the cellular fraction of saliva from tongue cancer patients, heavy cigarette smokers, and non-smoking healthy people as controls. Concurrently, TSPO protein levels, cell viability, mitochondrial membrane potential (Δψ_m), and general protein levels were analyzed. TSPO expression could be significantly enhanced in oral cancer tumors, compared to unaffected adjacent tissue. We also found that five-year survival probability dropped from 65% in patients with TSPO negative tumors to 7% in patients with highly expressed TSPO (p < 0.001). TSPO binding capacity was also pronounced in the human oral cancer cell lines SCC-25 and SCC-15 (3133 ± 643 fmol/mg protein and 6956 ± 549 fmol/mg protein, respectively). Binding decreased by 56% and 72%, in the SCC-25 and SCC-15 cell lines, respectively (p < 0.05) following CS exposure in cell culture. In the cellular fraction of saliva of heavy smokers TSPO binding was lower than in non-smokers (by 53%, p < 0.05). Also the cellular fraction of saliva exposed to CS in vitro showed decreased TSPO binding compared to unexposed saliva (by 30%, p < 0.001). Interestingly, oral cancer patients also displayed significantly lower TSPO binding in the cellular fraction of saliva compared to healthy controls (by 40%, p < 0.01). Our results suggest that low TSPO binding found in the cellular fraction of saliva may depend on genetic background as well as result from exposure to CS. We suggest that this may be related to a predisposition for occurrence of oral cancer.     

Anticipating future conditions via trajectory sensitivity

Plants are known to be highly responsive to environmental heterogeneity and normally allocate more biomass to organs that grow in richer patches. However, recent evidence demonstrates that plants can discriminately allocate more resources to roots that develop in patches with increasing nutrient levels, even when their other roots develop in richer patches. Responsiveness to the direction and steepness of spatial and temporal trajectories of environmental variables might enable plants to increase their performance by improving their readiness to anticipated resource availabilities in their immediate proximity. Exploring the ecological implications and mechanisms of trajectory-sensitivity in plants is expected to shed new light on the ways plants learn their environment and anticipate its future challenges and opportunities.Key words: Gradient perception, phenotypic plasticity, anticipatory responses, plant behavior, plant learningNatural environments present organisms with myriad challenges of surviving and reproducing under changing conditions.¹ Depending on its extent, predictability and costs, environmental heterogeneity may select for various combinations of genetic differentiation and phenotypic plasticity.^2–6 However, phenotypic plasticity is both limited and costly.⁷ One of the main limitations of phenotypic plasticity is the lag between the perception of the environment and the time the products of the plastic responses are fully operational.⁷ For instance, the developmental time of leaves may significantly limit the adaptive value of their plastic modification due to mismatches between the radiation levels and temperatures prevailing during their development and when mature and fully functional.^8,9 Accordingly, selection is expected to promote responsiveness to cues that bear information regarding the probable future environment.^9,10Indeed, anticipatory responses are highly prevalent, if not universal, amongst living organisms. Whether through intricate cerebral processes, such as in vertebrates, nervous coordination, as in Echinoderms,¹¹ or by relatively rudimentary non-neural processes, such as in plants¹² and bacteria,¹³ accumulating examples suggest that virtually all known life forms are able to not only sense and plastically respond to their immediate environment but also anticipate probable future conditions via environmental correlations.¹⁰Perhaps the best known example of plants'' ability to anticipate future conditions is their responsiveness to spectral red/far-red cues, which is commonly tightly correlated with future probability of light competition.¹⁴ Among others, plants have been shown to respond to cues related to anticipated herbivory^15,16 and nitrogen availability.¹⁷ Imminent stress is commonly anticipated by the perception of a prevailing stress. For example, adaptation to anticipated severe stress was demonstrated to be inducted by early priming by sub-acute drought,¹⁸ root competition¹⁹ and salinity.²⁰Future conditions can also be anticipated by gradient perception: because resource and stress levels are often changing along predictable spatial and temporal trajectories, spatio-temporal dynamics of environmental variables might convey information regarding anticipated growth conditions (Fig. 1). For example, the order of changes in day length, rather than day length itself, are known to assist plants in differentiating fall from spring and thus avoid blooming in the wrong season.²¹ In addition, responsiveness to environmental gradients as such, i.e., sensitivity to the direction and steepness of environmental trajectories, independently from the stationary levels of the same factors, has been demonstrated in higher organisms, such as the perception of acceleration in contrast to velocity;²² and the dynamics of skin temperature in contrast to stationary skin temperature;²³ where the adaptive value of the second-order derivatives of environmental factors is paramount. Similar perception capabilities have also been demonstrated in rudimentary life forms such as bacteria (reviewed in refs. ¹³ and ²⁴) and plants.^25,26 Specifically, perception of environmental trajectories might assist organisms to both anticipate future conditions and better utilize the more promising patches in their immediate environment.^27,28Open in a separate windowFigure 1Trajectory sensitivity in plants. The hypothetical curves depict examples of spatio-temporal trajectories of resource availability, which might be utilized by plants to increase foraging efficiency in newly-encountered patches. When young or early-in-the-season (segment 1–2), plants are expected to allocate more resources to roots that experience the most promising (steepest increases or shallowest decreases) resource availabilities (e.g., allocating more resources to organs in INC-1 than INC-2). In addition, plants are predicted to avoid allocation to roots experiencing decreasing trajectories (DEC, segment 1–2); although temporarily more abundant with resources, such DEC patches are expected to become poorer than alternative patches in the longer run (segment 2–3).²⁹ However, responsiveness to environmental trajectories is only predicted where the expected period of resource uptake is relatively long, e.g., when plants are still active in segment 2–3, a stipulation which might not be fulfilled in e.g., short-living annuals with life span shorter than segment 1–2.In a recent study, Pisum plants have been demonstrated to be sensitive to temporal changes in nutrient availabilities. Specifically, plants allocated greater biomass to roots growing under dynamically-improving nutrient levels than to roots that grew under continuously higher, yet stationary or deteriorating, nutrient availabilities.²⁹ Allocation to roots in poorer patches might seem maladaptive if only stationary nutrient levels are accounted for, and indeed-almost invariably, plants are known to allocate more resources to organs that experience higher (non-toxic) resource levels (reviewed in ref. ³³). Accordingly, the new findings suggest that rather than merely responding to the prevailing nutrient availabilities, root growth and allocation are also responsive to trajectories of nutrient availabilities (Fig. 1).¹⁰Although Shemesh et al.²⁹ demonstrated trajectory-sensitivity of individual roots to temporal gradient of nutrient availabilities, it is likely that this sensitivity helps plants sense spatial gradients, whereby root tips perceive changes in growth conditions as they move through space.³⁴ Interestingly, because the trajectory-sensitivity was observed when whole roots were subjected to changing nutrient levels, it is likely that trajectory sensitivity in roots is based on the integration of sensory inputs perceived by yet-to-be-determined parts of the root over time, i.e., temporal sensitivity/memory (e.g. reviewed in ref. ³⁵), rather than on the integration of sensory inputs at different locations on the same individual roots (i.e., spatial sensitivity).Besides the direction of change, it is hypothesized that plants are also sensitive to the steepness of environmental trajectories (Fig. 1). This might be especially crucial in short-living annuals, which are expected to only be responsive to trajectories steep enough to be indicative of changes in growth conditions before the expected termination of the growth season (Fig. 1).Studying responsiveness to environmental variability is pivotal for understanding the ecology and evolution of any living organism. However, until recently most attention has been given to the study of responses to stationary spatial and temporal heterogeneities in growth conditions. Exploring the ecological implications and mechanisms of trajectory sensitivity in plants is expected to shed new light on the ways plants learn their immediate environment and anticipate its future challenges and opportunities.     

Magnetosome dynamics in magnetotactic bacteria.

Diffusive motions of the magnetosomes (enveloped Fe3O4 particles) in the magnetotactic bacterium Aquaspirillum magnetotacticum result in a very broad-line Mössbauer spectrum (T approximately 100 mm/s) above freezing temperatures. The line width increases with increasing temperature. The data are analyzed using a bounded diffusion model to yield the rotational and translational motions of the magnetosomes as well as the effective viscosity of the material surrounding the magnetosomes. The results are [theta 2] l/2 less than 1.5 degrees and [x2] 1/2 less than 8.4 A for the rotational and translational motions, respectively, implying that the particles are fixed in whole cells. The effective viscosity is 10 cP at 295 K and increases with decreasing temperature. Additional Fe3+ material in the cell is shown to be associated with the magnetosomes. Fe2+ material in the cell appears to be associated with the cell envelope.     

Whole-genome immunoinformatic analysis of F. tularensis: predicted CTL epitopes clustered in hotspots are prone to elicit a T-cell response

The cellular arm of the immune response plays a central role in the defense against intracellular pathogens, such as F. tularensis. To date, whole genome immunoinformatic analyses were limited either to relatively small genomes (e.g. viral) or to preselected subsets of proteins in complex pathogens. Here we present, for the first time, an unbiased bacterial global immunoinformatic screen of the 1740 proteins of F. tularensis subs. holarctica (LVS), aiming at identification of immunogenic peptides eliciting a CTL response. The very large number of predicted MHC class I binders (about 100,000, IC(50) of 1000 nM or less) required the design of a strategy for further down selection of CTL candidates. The approach developed focused on mapping clusters rich in overlapping predicted epitopes, and ranking these "hotspot" regions according to the density of putative binding epitopes. Limited by the experimental load, we selected to screen a library of 1240 putative MHC binders derived from 104 top-ranking highly dense clusters. Peptides were tested for their ability to stimulate IFNγ secretion from splenocytes isolated from LVS vaccinated C57BL/6 mice. The majority of the clusters contained one or more CTL responder peptides and altogether 127 novel epitopes were identified, of which 82 are non-redundant. Accordingly, the level of success in identification of positive CTL responders was 17-25 fold higher than that found for a randomly selected library of 500 predicted MHC binders (IC(50) of 500 nM or less). Most proteins (ca. 2/3) harboring the highly dense hotspots are membrane-associated. The approach for enrichment of true positive CTL epitopes described in this study, which allowed for over 50% increase in the dataset of known T-cell epitopes of F. tularensis, could be applied in immunoinformatic analyses of many other complex pathogen genomes.