A surface energy spectral study on the bone heterogeneity and beam obliquity using the flattened and unflattened photon beams

Aim

Using flattened and unflattened photon beams, this study investigated the spectral variations of surface photon energy and energy fluence in the bone heterogeneity and beam obliquity.

Background

Surface dose enhancement is a dosimetric concern when using unflattened photon beam in radiotherapy. It is because the unflattened photon beam contains more low-energy photons which are removed by the flattening filter of the flattened photon beam.

Materials and methods

We used a water and bone heterogeneity phantom to study the distributions of energy, energy fluence and mean energy of the 6 MV flattened and unflattened photon beams (field size = 10 cm × 10 cm) produced by a Varian TrueBEAM linear accelerator. These elements were calculated at the phantom surfaces using Monte Carlo simulations. The photon energy and energy fluence calculations were repeated with the beam angle turned from 0° to 15°, 30° and 45° in the water and bone phantom.

Results

Spectral results at the phantom surfaces showed that the unflattened photon beams contained more photons concentrated mainly in the low-energy range (0–2 MeV) than the flattened beams associated with a flattening filter. With a bone layer of 1 cm under the phantom surface and within the build-up region of the 6 MV photon beam, it is found that both the flattened and unflattened beams had slightly less photons in the energy range <0.4 MeV compared to the water phantom. This shows that the presence of the bone decreased the low-energy photon backscatters to the phantom surface. When both the flattened and unflattened photon beams were rotated from 0° to 45°, the number of photon and mean photon energy increased. This indicates that both photon beams became more hardened or penetrate when the beam angle increased. In the presence of bone, the mean energies of both photon beams increased. This is due to the absorption of low-energy photons by the bone, resulting in more beam hardening.

Conclusions

This study explores the spectral relationships of surface photon energy and energy fluence with bone heterogeneity and beam obliquity for the flattened and unflattened photon beams. The photon spectral information is important in studies on the patient''s surface dose enhancement using unflattened photon beams in radiotherapy.     

Measurement and comparison of head scatter factor for 7 MV unflattened (FFF) and 6 MV flattened photon beam using indigenously designed columnar mini phantom

Aim

To measure and compare the head scatter factor for 7 MV unflattened and 6 MV flattened photon beam using a home-made designed mini phantom.

Background

The head scatter factor (Sc) is one of the important parameters for MU calculation. There are multiple factors that influence the Sc values, like accelerator head, flattening filter, primary and secondary collimators.

Materials and methods

A columnar mini phantom was designed as recommended by AAPM Task Group 74 with high and low atomic number material for measurement of head scatter factors at 10 cm and d_max dose water equivalent thickness.

Results

The Sc values measured with high-Z are higher than the low-Z mini phantoms observed for both 6MV-FB and 7MV-UFB photon energies. Sc values of 7MV-UFB photon beams were smaller than those of the 6MV-FB photon beams (0.6–2.2% (Primus), 0.2–1.4% (Artiste) and 0.6–3.7% (Clinac iX (2300CD))) for field sizes ranging from 10 cm × 10 cm to 40 cm × 40 cm. The SSD had no influence on head scatter for both flattened and unflattened beams. The presence of wedge filters influences the Sc values. The collimator exchange effects showed that the opening of the upper jaw increases Sc irrespective of FF and FFF.

Conclusions

There were significant differences in Sc values measured for 6MV-FB and unflattened 7MV-UFB photon beams over the range of field sizes from 10 cm × 10 cm to 40 cm × 04 cm. Different results were obtained for measurements performed with low-Z and high-Z mini phantoms.     

Analysis of physical parameters and determination of inflection point for Flattening Filter Free beams in medical linear accelerator

Background

Medical Linear accelerators manufactured without flattening filters are increasing popular in recent days. The removal of flattening filter results in increased dose rate, reduced mean energy, reduction in head leakage and lateral scattering, which have shown advantageous when used for special treatment procedures.

Aim

This study aims to analyze physical parameters of FFF beams and to determine the inflection point for standardizing the beam flatness and penumbra.

Materials and methods

The beam profiles and depth dose patterns were measured using Radiation Field Analyzer (RFA) with 0.13 cc cylindrical ion chamber. The beam energy characteristics, head scatter factor (Sc) were obtained for 6FFF and 10FFF beams and compared with 6 MV and 10 MV photons, respectively. The symmetry and stability of unflattened regions were also analyzed. In addition, the study proposes a simple physical concept for obtaining inflection point for FFF beams and results were compared using the Akima spline interpolation method. The inflection point was used to determine the field size and penumbra of FFF beams.

Results

The Sc varied from 0.922 to 1.044 for 6FFF and from 0.913 to 1.044 for 10FFF with field sizes from 3 cm × 3 cm to 40 cm × 40 cm which is much less than FF beams. The obtained value of field size and penumbra for both simple physical concept and Akima spline interpolation methods is within the ±1.0 mm for the field size and ±2 mm penumbra. The results indicate that FFF beams reduce Sc compared with FF beams due to the absence of a flattening filter.

Conclusion

The proposed simple method to find field size and penumbra using inflection point can be accepted as it is closely approximated to mathematical results. Stability of these parameters was ascertained by repeated measurements and the study indicates good stability for FFF beam similar to that of FF beams.     

Radiotherapy dose enhancement using BNCT in conventional LINACs high-energy treatment: Simulation and experiment

Aim

To employ the thermal neutron background that affects the patient during a traditional high-energy radiotherapy treatment for BNCT (Boron Neutron Capture Therapy) in order to enhance radiotherapy effectiveness.

Background

Conventional high-energy (15–25 MV) linear accelerators (LINACs) for radiotherapy produce fast secondary neutrons in the gantry with a mean energy of about 1 MeV due to (γ, n) reaction. This neutron flux, isotropically distributed, is considered as an unavoidable undesired dose during the treatment. Considering the moderating effect of human body, a thermal neutron fluence is localized in the tumour area: this neutron background could be employed for BNCT by previously administering ¹⁰B-Phenyl-Alanine (¹⁰BPA) to the patient.

Materials and methods

Monte Carlo simulations (MCNP4B-GN code) were performed to estimate the total amount of neutrons outside and inside human body during a traditional X-ray radiotherapy treatment.Moreover, a simplified tissue equivalent anthropomorphic phantom was used together with bubble detectors for thermal and fast neutron to evaluate the moderation effect of human body.

Results

Simulation and experimental results confirm the thermal neutron background during radiotherapy of 1.55E07 cm⁻² Gy⁻¹.The BNCT equivalent dose delivered at 4 cm depth in phantom is 1.5 mGy-eq/Gy, that is about 3 Gy-eq (4% of X-rays dose) for a 70 Gy IMRT treatment.

Conclusions

The thermal neutron component during a traditional high-energy radiotherapy treatment could produce a localized BNCT effect, with a localized therapeutic dose enhancement, corresponding to 4% or more of photon dose, following tumour characteristics. This BNCT additional dose could thus improve radiotherapy, acting as a localized radio-sensitizer.     

A calibration method for patient specific IMRT QA using a single therapy verification film

Aim

The aim of the present study is to develop and verify the single film calibration procedure used in intensity-modulated radiation therapy (IMRT) quality assurance.

Background

Radiographic films have been regularly used in routine commissioning of treatment modalities and verification of treatment planning system (TPS). The radiation dosimetery based on radiographic films has ability to give absolute two-dimension dose distribution and prefer for the IMRT quality assurance. However, the single therapy verification film gives a quick and significant reliable method for IMRT verification.

Materials and methods

A single extended dose rate (EDR 2) film was used to generate the sensitometric curve of film optical density and radiation dose. EDR 2 film was exposed with nine 6 cm × 6 cm fields of 6 MV photon beam obtained from a medical linear accelerator at 5-cm depth in solid water phantom. The nine regions of single film were exposed with radiation doses raging from 10 to 362 cGy. The actual dose measurements inside the field regions were performed using 0.6 cm³ ionization chamber. The exposed film was processed after irradiation using a VIDAR film scanner and the value of optical density was noted for each region. Ten IMRT plans of head and neck carcinoma were used for verification using a dynamic IMRT technique, and evaluated using the gamma index method with TPS calculated dose distribution.

Results

Sensitometric curve has been generated using a single film exposed at nine field region to check quantitative dose verifications of IMRT treatments. The radiation scattered factor was observed to decrease exponentially with the increase in the distance from the centre of each field region. The IMRT plans based on calibration curve were verified using the gamma index method and found to be within acceptable criteria.

Conclusion

The single film method proved to be superior to the traditional calibration method and produce fast daily film calibration for highly accurate IMRT verification.     

Pretreatment verification of dose calculation and delivery by means of measurements with PLEXITOM™ phantom

Aim

To validate a pretreatment verification method of dose calculation and dose delivery based on measurements with Metaplex PTW phantom.

Background

The dose-response relationships for local tumor control and radiosensitive tissue complications are strong. It is widely accepted that an accuracy of dose delivery of about 3.5% (one standard deviation) is required in modern radiotherapy. This goal is difficult to achieve. This paper describes our experience with the control of dose delivery and calculations at the ICRU reference point.

Materials and methods

The calculations of dose at the ICRU reference point performed with the treatment planning system CMS XiO were checked by measurements carried out in the PLEXITOM™ phantom.All measurements were performed with the ion chamber positioned in the phantom, at the central axis of the beam, at depth equivalent to the radiological depth (at gantry zero position). The source-to-phantom surface distance was always set to keep the source-to-detector distance equal to the reference point depth defined in the ICRU Report 50 (generally, 100 cm). The dose was measured according to IAEA TRS 398 report for measurements in solid phantoms. The measurement results were corrected with the actual accelerator''s output factor and for the non-full scatter conditions. Measurements were made for 111 patients and 327 fields.

Results

The average differences between measurements and calculations were 0.03% (SD = 1.4%), 0.3% (SD = 1.0%), 0.1% (SD = 1.1%), 0.6% (SD = 1.8%), 0.3% (SD = 1.5%) for all measurements, for total dose, for pelvis, thorax and H&N patients, respectively. Only in 15 cases (4.6%), the difference between the measured and the calculated dose was greater than 3%. For these fields, a detailed analysis was undertaken.

Conclusion

The verification method provides an instantaneous verification of dose calculations before the beginning of a patient''s treatment. It allows to detect differences smaller than 3.5%.     

Energy dependence of radiochromic dosimetry films for use in radiotherapy verification

Aim

The purpose of the study was to examine the energy dependence of Gafchromic EBT radiochromic dosimetry films, in order to assess their potential use in intensity-modulated radiotherapy (IMRT) verifications.

Materials and methods

The film samples were irradiated with doses from 0.1 to 12 Gy using photon beams from the energy range 1.25 MeV to 25 MV and the film response was measured using a flat-bed scanner. The samples were scanned and the film responses for different beam energies were compared.

Results

A high uncertainty in readout of the film response was observed for samples irradiated with doses lower than 1 Gy. The relative difference exceeds 20% for doses lower than 1 Gy while for doses over 1 Gy the measured film response differs by less than 5% for the whole examined energy range. The achieved uncertainty of the experimental procedure does not reveal any energy dependence of Gafchromic EBT film response in the investigated energy range.

Conclusions

Gafchromic EBT film does not show any energy dependence in the conditions typical for IMRT but the doses measured for pre-treatment plan verifications should exceed 1 Gy.     

Comparison of dosimetric variation between prostate IMRT and VMAT due to patient's weight loss: Patient and phantom study

Aim

This study compared the dosimetric impact between prostate IMRT and VMAT due to patient''s weight loss.

Background

Dosimetric variation due to change of patient''s body contour is difficult to predict in prostate IMRT and VMAT, since a large number of small and irregular segmental fields is used in the delivery.

Materials and methods

Five patients with prostate volumes ranging from 32.0 to 86.5 cm³ and a heterogeneous pelvis phantom were used for prostate IMRT and VMAT plans using the same set of dose–volume constraints. Doses in IMRT and VMAT plans were recalculated with the patient''s and phantom''s body contour reduced by 0.5–2 cm to mimic size reduction. Dose coverage/criteria of the PTV and CTV and critical organs (rectum, bladder and femoral heads) were compared between IMRT and VMAT.

Results

In IMRT plans, increases of the D99% for the PTV and CTV were equal to 4.0 ± 0.1% per cm of reduced depth, which were higher than those in VMAT plans (2.7 ± 0.24% per cm). Moreover, increases of the D30% of the rectum and bladder per reduced depth in IMRT plans (4.0 ± 0.2% per cm and 3.5 ± 0.5% per cm) were higher than those of VMAT (2.2 ± 0.2% per cm and 2.0 ± 0.6% per cm). This was also true for the increase of the D5% for the right femoral head in a patient or phantom with size reduction due to weight loss.

Conclusions

VMAT would be preferred to IMRT in prostate radiotherapy, when a patient has potential to suffer from weight loss during the treatment.     

Against the odds: complete outcrossing in a monoecious clonal seagrass Posidonia australis (Posidoniaceae)

Background and Aims

Seagrasses are marine, flowering plants with a hydrophilous pollination strategy. In these plants, successful mating requires dispersal of filamentous pollen grains through the water column to receptive stigmas. Approximately 40 % of seagrass species are monoecious, and therefore little pollen movement is required if inbreeding is tolerated. Outcrossing in these species is further impacted by clonality, which is variable, but can be extensive in large, dense meadows. Despite this, little is known about the interaction between clonal structure, genetic diversity and mating systems in hydrophilous taxa.

Methods

Polymorphic microsatellite DNA markers were used to characterize genetic diversity, clonal structure, mating system and realized pollen dispersal in two meadows of the temperate, monoecious seagrass, Posidonia australis, in Cockburn Sound, Western Australia.

Key Results

Within the two sampled meadows, genetic diversity was moderate among the maternal shoots (R = 0·45 and 0·64) and extremely high in the embryos (R = 0·93–0·97). Both meadows exhibited a highly clumping (or phalanx) structure among clones, with spatial autocorrelation analysis showing significant genetic structure among shoots and embryos up to 10–15 m. Outcrossing rates were not significantly different from one. Pollen dispersal distances inferred from paternity assignment averaged 30·8 and 26·8 m, which was larger than the mean clone size (12·8 and 13·8 m).

Conclusions

These results suggest highly effective movement of pollen in the water column. Despite strong clonal structure and moderate genetic diversity within meadows, hydrophilous pollination is an effective vector for completely outcrossed offspring. The different localized water conditions at each site (highly exposed conditions vs. weak directional flow) appear to have little influence on the success and pattern of successful pollination in the two meadows.     

Visualization of embolism formation in the xylem of liana stems using neutron radiography

Background and Aims

Cold neutron radiography was applied to directly observe embolism in conduits of liana stems with the aim to evaluate the suitability of this method for studying embolism formation and repair. Potential advantages of this method are a principally non-invasive imaging approach with low energy dose compared with synchrotron X-ray radiation, a good spatial and temporal resolution, and the possibility to observe the entire volume of stem portions with a length of several centimetres at one time.

Methods

Complete and cut stems of Adenia lobata, Aristolochia macrophylla and Parthenocissus tricuspidata were radiographed at the neutron imaging facility CONRAD at the Helmholtz-Zentrum Berlin für Materialien und Energie, with each measurement cycle lasting several hours. Low attenuation gas spaces were separated from the high attenuation (water-containing) plant tissue using image processing.

Key results

Severe cuts into the stem were necessary to induce embolism. The formation and temporal course of an embolism event could then be successfully observed in individual conduits. It was found that complete emptying of a vessel with a diameter of 100 µm required a time interval of 4 min. Furthermore, dehydration of the whole stem section could be monitored via decreasing attenuation of the neutrons.

Conclusions

The results suggest that cold neutron radiography represents a useful tool for studying water relations in plant stems that has the potential to complement other non-invasive methods.     

Duration of xylogenesis in black spruce lengthened between 1950 and 2010

Background and Aims

Reconstructions have identified the 20th century as being uniquely warm in the last 1000 years. Changes in the phenology of primary meristems converged toward increases in length of the growing season. Has the phenology of secondary meristem changed during the last century, and to what extent?

Methods

Timings of wood formation in black spruce, Picea mariana, were monitored for 9 years on a weekly timescale at four sites in the boreal forest of Quebec, Canada. Models for assessing xylem phenology were defined and applied to reconstruct onset, ending and duration of xylogenesis between 1950 and 2010 using thermal thresholds on chronologies of maximum and minimum temperatures.

Key Results

All sites exhibited increasing trends of both annual and May–September temperatures, with the greatest changes observed at the higher latitudes. Phenological events in spring were more affected than those occurring in autumn, with cambial resumptions occurring 0·5–0·8 d decade⁻¹ earlier. The duration of xylogenesis has lengthened significantly since 1950, although the models supplied wide ranges of variations, between 0·07 and 1·5 d decade⁻¹, respectively.

Conclusions

The estimated changes in past cambial phenology demonstrated the marked effects of the recent increase in temperature on the phenological traits of secondary meristems. In the long run, the advancement of cambial activity could modify the short time window for growth of boreal species and dramatically affect the dynamics and productivity of trees in these temperature-limited ecosystems.     

Gibberellin mediates the development of gelatinous fibres in the tension wood of inclined Acacia mangium seedlings

Background and Aims

Gibberellin stimulates negative gravitropism and the formation of tension wood in tilted Acacia mangium seedlings, while inhibitors of gibberellin synthesis strongly inhibit the return to vertical growth and suppress the formation of tension wood. To characterize the role of gibberellin in tension wood formation and gravitropism, this study investigated the role of gibberellin in the development of gelatinous fibres and in the changes in anatomical characteristics of woody elements in Acacia mangium seedlings exposed to a gravitational stimulus.

Methods

Gibberellin, paclobutrazol and uniconazole-P were applied to the soil in which seedlings were growing, using distilled water as the control. Three days after the start of treatment, seedlings were inclined at 45 ° to the vertical and samples were harvested 2 months later. The effects of the treatments on wood fibres, vessel elements and ray parenchyma cells were analysed in tension wood in the upper part of inclined stems and in the opposite wood on the lower side of inclined stems.

Key Results

Application of paclobutrazol or uniconazole-P inhibited the increase in the thickness of gelatinous layers and prevented the elongation of gelatinous fibres in the tension wood of inclined stems. By contrast, gibberellin stimulated the elongation of these fibres. Application of gibberellin and inhibitors of gibberellin biosynthesis had only minor effects on the anatomical characteristics of vessel and ray parenchyma cells.

Conclusions

The results suggest that gibberellin is important for the development of gelatinous fibres in the tension wood of A. mangium seedlings and therefore in gravitropism.     

The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum

Background

Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations of genes acquired from bacterial, animal and plant ancestors. Furthermore, they display both DNA methylation and gene silencing activities. Yet, the biogenesis and regulatory function of small RNAs (sRNAs) remain ill defined in diatoms.

Results

Here we report the first comprehensive characterization of the sRNA landscape and its correlation with genomic and epigenomic information in Phaeodactylum tricornutum. The majority of sRNAs is 25 to 30 nt-long and maps to repetitive and silenced Transposable Elements marked by DNA methylation. A subset of this population also targets DNA methylated protein-coding genes, suggesting that gene body methylation might be sRNA-driven in diatoms. Remarkably, 25-30 nt sRNAs display a well-defined and unprecedented 180 nt-long periodic distribution at several highly methylated regions that awaits characterization. While canonical miRNAs are not detectable, other 21-25 nt sRNAs of unknown origin are highly expressed. Besides, non-coding RNAs with well-described function, namely tRNAs and U2 snRNA, constitute a major source of 21-25 nt sRNAs and likely play important roles under stressful environmental conditions.

Conclusions

P. tricornutum has evolved diversified sRNA pathways, likely implicated in the regulation of largely still uncharacterized genetic and epigenetic processes. These results uncover an unexpected complexity of diatom sRNA population and previously unappreciated features, providing new insights into the diversification of sRNA-based processes in eukaryotes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-698) contains supplementary material, which is available to authorized users.     

Water stress-induced xylem hydraulic failure is a causal factor of tree mortality in beech and poplar

Background and Aims

Extreme water stress episodes induce tree mortality, but the physiological mechanisms causing tree death are still poorly understood. This study tests the hypothesis that a potted tree''s ability to survive extreme monotonic water stress is determined by the cavitation resistance of its xylem tissue.

Methods

Two species were selected with contrasting cavitation resistance (beech and poplar), and potted juvenile trees were exposed to a range of water stresses, causing up to 100 % plant death.

Key Results

The lethal dose of water stress, defined as the xylem pressure inducing 50 % mortality, differed sharply across species (1·75 and 4·5 MPa in poplar and beech, respectively). However, the relationships between tree mortality and the degree of cavitation in the stems were similar, with mortality occurring suddenly when >90 % cavitation had occurred.

Conclusions

Overall, the results suggest that cavitation resistance is a causal factor of tree mortality under extreme drought conditions.     

3D conformal hypofractionated radical radiotherapy in early glottic cancer

Aim

The purpose of this study was to evaluate acute and late toxicity and the locoregional control in patients treated with hypofractionated radical radiotherapy 2.25 Gy/fraction/day for early glottic carcinoma.

Materials and methods

A retrospective analysis was performed of 27 patients, stage T1–T2 N0 glottic squamous cell carcinoma, that underwent radical RT from April 2008 to October 2011. The mean age was 64.6 years (range 36–81). Seventeen patients were staged T1a, 3 patients T1b and 7 patients T2. All patients were 3D planned and treated in a 6 MV LINAC, 2.25 Gy/fraction/5 days per week, to a total dose between 63 Gy and 67.5 Gy. Biological Effective Dose (BED (α/β = 10)) ranged from 77.18 Gy to 82.69 Gy and EQD2 from 64.31 Gy to 68.91 Gy. Patients were evaluated in periodic follow-up. Toxicity was evaluated according to RTOG Toxicities Scales.

Results

With a median follow-time of 24.7 months (range 3.6–44.2 months), no evidence of locoregional recurrence was observed. The treatment was well tolerated and no unscheduled interruptions in treatments for toxicity were documented, with the median overall treatment time of 41 days (range 38–48). Only grades 1 and 2 acute toxicity were observed and no evidence of severe late toxicity.

Conclusion

The authors believe that this moderately hypofractionated scheme can provide a good locoregional control for T1–T2 glottic carcinomas with no increase of toxicity. As the limitation of this work is the reduced number of patients and the lack of long term follow-up, the authors hope to update this retrospective study in the future in order to improve the power of the results.     

Assessment of pharmacological activities of two medicinal plant of Bangladesh: Launaea sarmentosa and Aegialitis rotundifolia roxb in the management of pain,pyrexia and inflammation

Background

The current study aims at evaluating the analgesic, anti-pyretic and anti-inflammatory properties of methanolic extract of the stem, bark and leaves of Launaea sarmentosa and Aegialitis rotundifolia roxb.

Results

The AELS and AEAR extract presented a significant (***p < 0.001) dose dependent increase in reaction time in writhing method and showed inhibition of 63.1% and 57.1% respectively at the doses of 400 mg/kg body weight while standard drug showed (P < 0.001) inhibition of 69.23%. In tail immersion method, AELS and AEAR showed maximum time of tail retention at 30 min in hot water i.e. 6.93 sec and 6.54 sec respectively at highest doses of 400 mg/kg body weight than lower dose while standard pentazocine showed reaction time of 7.62 sec. The AELS and AEAR extract also exhibited promising anti-inflammatory effect as demonstrated by statistically significant inhibition of paw volume by 32.48% and 26.75% respectively at the dose of 400 mg/kg body weight while the value at the dose of 200 mg/kg body weight were linear to higher dose at the 3^rd hour of study. On the other hand, Standard indomethacin inhibited 40.13% of inflammation (***P < 0.001). In Cotton-pellet granuloma method, AELS and AEAR extract at the dose of 400 mg/kg body weight exhibited inhibition of inflammation of 34.7% and 29.1% respectively while standard drug showed (P < 0.001) inhibition of 63.22%. Intraperitoneal administration of AELS and AEAR showed dose dependent decrease in body temperature in brewer’s yeast induced hyperthermia in rats at both doses. However, AELS significantly decreased body temperature (***p < 0.001) at 400 mg/kg compared to control.

Conclusions

Present work propose that the methanolic extract of Launaea sarmentosa and Aegialitis rotundifolia roxb possesses dose dependent pharmacological action which supports its therapeutic use in folk medicine possibly mediated through the inhibition or blocking of release of prostaglandin and/or actions of vasoactive substances such as histamine, serotonin and kinins.     

Genome diversification within a clonal population of pandemic Vibrio parahaemolyticus seems to depend on the life circumstances of each individual bacteria

Background

New strains of Vibrio parahaemolyticus that cause diarrhea in humans by seafood ingestion periodically emerge through continuous evolution in the ocean. Influx and expansion in the Southern Chilean ocean of a highly clonal V. parahaemolyticus (serotype O3:K6) population from South East Asia caused one of the largest seafood-related diarrhea outbreaks in the world. Here, genomics analyses of isolates from this rapidly expanding clonal population offered an opportunity to observe the molecular evolutionary changes often obscured in more diverse populations.

Results

Whole genome sequence comparison of eight independent isolates of this population from mussels or clinical cases (from different years) was performed. Differences of 1366 to 217,729 bp genome length and 13 to 164 bp single nucleotide variants (SNVs) were found. Most genomic differences corresponded to the presence of regions unique to only one or two isolates, and were probably acquired by horizontal gene transfer (HGT). Some DNA gain was chromosomal but most was in plasmids. One isolate had a large region (8,644 bp) missing, which was probably caused by excision of a prophage. Genome innovation by the presence of unique DNA, attributable to HGT from related bacteria, varied greatly among the isolates, with values of 1,366 (ten times the number of highest number of SNVs) to 217,729 (a thousand times more than the number of highest number of SNVs).

Conclusions

The evolutionary forces (SNVs, HGT) acting on each isolate of the same population were found to differ to an extent that probably depended on the ecological scenario and life circumstances of each bacterium.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1385-8) contains supplementary material, which is available to authorized users.     

Recovery and fine structure variability of RGII sub-domains in wine (Vitis vinifera Merlot)

Background and Aims

Rhamnogalacturonan II (RGII) is a structurally complex pectic sub-domain composed of more than 12 different sugars and 20 different linkages distributed in five side chains along a homogalacturonan backbone. Although RGII has long been described as highly conserved over plant evolution, recent studies have revealed variations in the structure of the polysaccharide. This study examines the fine structure variability of RGII in wine, focusing on the side chains A and B obtained after sequential mild acid hydrolysis. Specifically, this study aims to differentiate intrinsic structural variations in these RGII side chains from structural variations due to acid hydrolysis.

Methods

RGII from wine (Vitis vinifera Merlot) was sequentially hydrolysed with trifluoroacetic acid (TFA) and the hydrolysis products were separated by anion-exchange chromatography (AEC). AEC fractions or total hydrolysates were analysed by MALDI-TOF mass spectrometry.

Key Results

The optimal conditions to recover non-degraded side chain B, side chain A and RGII backbone were 0·1 m TFA at 40 °C for 16 h, 0·48 m TFA at 40 °C for 16 h (or 0·1 m TFA at 60 °C for 8 h) and 0·1 m TFA at 60 °C for 16 h, respectively. Side chain B was particularly prone to acid degradation. Side chain A and the RGII GalA backbone were partly degraded by 0·1 m TFA at 80 °C for 1–4 h. AEC allowed separation of side chain B, methyl-esterified side chain A and non-methyl-esterified side chain A. The structure of side chain A and the GalA backbone were highly variable.

Conclusions

Several modifications to the RGII structure of wine were identified. The observed dearabinosylation and deacetylation were primarily the consequence of acidic treatment, while variation in methyl-esterification, methyl-ether linkages and oxidation reflect natural diversity. The physiological significance of this variability, however, remains to be determined.