Monitoring vegetation change caused by trampling: a study in the Cairngorms,Scotland

Summary

A study was made in the Cairngorms, Scotland to make recommendations for a monitoring scheme capable of detecting changes in the vegetation caused by recreational pressure following the development of a funicular railway. Four methods were used in field trials to assess percentage cover of plant species and gravel, rock and bare ground, where appropriate, in two vegetation types (open and closed). The methods used were visual estimates in 50 × 40 cm quadrats (Q), the mean of visual estimates in twenty 10 × 10 cm sub-quadrats of the 50 × 40 cm quadrats (Q₂₀), a modified point intercept method (RL) and photography. Variances between observers and between-quadrats were estimated for the different methods. The sampling design for detecting change was based on a model of variance, constructed from field trial data.

Between-observer and between-quadrat variances were related to mean percentage cover and approximated to a binomial distribution. The between-quadrat variance was larger than observer variance. The Q₂₀ method achieved appreciably better precision than the other methods. Analysis of half of the 10 × 10 cmsub-quadrats (1/2Q₂₀) selected in a checker board design achieved a relative efficiency of 78% compared with the Q₂₀. This result suggests that comparable precision to the Q₂₀ method could be achieved by choosing about 14 sub-quadrats in a larger quadrat, thus saving some time. Variation between quadrats also suggested that the Q₂₀ method was the one of choice for maximising precision. The precision of the photographic method was based on fewer data points, so is less accurate than other estimates.

Minimum sample sizes were estimated for detecting a 10% relative change of a species in open vegetation with 30% cover (i.e. a change from 30% to <27 or to >33% cover). With a 10 % Type II error rate and 5 % Type I error rate the minimum sample sizes were 47 quadrats for Q, 18 for Q ₂₀, 43 for RL, and 23 for the means of ten 10 × 10 cm sub-quadrats in open vegetation.

The most time-efficient field recording appeared to be the use of Q despite the required sample size being 2.6 times higher than that of Q₂₀. The far lower time requirement per quadrat, however, compensated for the higher numbers. The number of quadrats would depend on the specified change in percentage cover and on the statistical significance level used. For example, to detect a 10% absolute change in cover (i.e. from 30% to either <20 % or >40 % cover) at 95 % probability the net effective recording time is estimated at 5 h per vegetation type while to detect a 5 % change at 99 % probability would require c. 25 h. Larger samples may be required for other species or for species with a low initial cover.     

Effects of aortic irregularities on blood flow

Anatomic aortic anomalies are seen in many medical conditions and are known to cause disturbances in blood flow. Turner syndrome (TS) is a genetic disorder occurring only in females where cardiovascular anomalies, particularly of the aorta, are frequently encountered. In this study, numerical simulations are applied to investigate the flow characteristics in four TS patient- related aortic arches (a normal geometry, dilatation, coarctation and elongation of the transverse aorta). The Quemada viscosity model was applied to account for the non-Newtonian behavior of blood. The blood is treated as a mixture consisting of water and red blood cells (RBC) where the RBCs are modeled as a convected scalar. The results show clear geometry effects where the flow structures and RBC distribution are significantly different between the aortas. Transitional flow is observed as a jet is formed due to a constriction in the descending aorta for the coarctation case. RBC dilution is found to vary between the aortas, influencing the WSS. Moreover, the local variations in RBC volume fraction may induce large viscosity variations, stressing the importance of accounting for the non-Newtonian effects.     

The mycobiome of Australian tree hollows in relation to the Cryptococcus gattii and C. neoformans species complexes

Cryptococcosis is a fungal infection caused by members of the Cryptococcus gattii and C. neoformans species complexes. The C. gattii species complex has a strong environmental association with eucalypt hollows (particularly Eucalyptus camaldulensis), which may present a source of infection. It remains unclear whether a specific mycobiome is required to support its environmental survival and growth. Conventional detection of environmental Cryptococcus spp. involves culture on differential media, such as Guizotia abyssinica seed agar. Next‐generation sequencing (NGS)‐based culture‐independent identification aids in contextualising these species in the environmental mycobiome. Samples from 23 Australian tree hollows were subjected to both culture‐ and amplicon‐based metagenomic analysis to characterize the mycobiome and assess relationships between Cryptococcus spp. and other fungal taxa. The most abundant genera detected were Coniochaeta, Aspergillus, and Penicillium, all being commonly isolated from decaying wood. There was no correlation between the presence of Cryptococcus spp. in a tree hollow and the presence of any other fungal genus. Some differences in the abundance of numerous taxa were noted in a differential heat tree comparing samples with or without Cryptococcus‐NGS reads. The study expanded the known environmental niche of the C. gattii and C. neoformans species complexes in Australia with detections from a further five tree species. Discrepancies between the detection of Cryptococcus spp. using culture or NGS suggest that neither is superior per se and that, rather, these methodologies are complementary. The inherent biases of amplicon‐based metagenomics require cautious interpretation of data through consideration of its biological relevance.     

Main chain NMR assignments of subtilisin Sbt70 in its prodomain-bound state

Main chain assignments are described for a 266-residue subtilisin mutant, Sbt70, in its 35 kDa complex with an N-terminal prodomain. The assignments provide the basis for understanding how the prodomain assists folding of subtilisin at a residue-specific level.     

Metabolic profile and quantification of deoxyribose synthesis pathways in HepG2 cells

Traditional tracer studies of cell proliferation fail to distinguish between label enrichment due to increased DNA repair versus DNA replication. We used the emerging stable (non-radiating) isotope-based dynamic metabolic profiling technique on HepG2 cells to determine synthesis pathways of nucleic acids from glucose and rates of proliferation using CG-MS assay of RNA and DNA enrichment. Comparing the isotopic enrichment curve in DNA with the theoretical curve based on cell growth, we observed that the measured tracer enrichment was significantly higher, indicating that surplus label was acquired during DNA repair. In particular, after the first duplication (3 days), 80.13% of the total enrichment observed corresponds to duplication and 19.87% corresponds to DNA repair as calculated from the [1, 2-¹³C₂]-glucose incorporation curve. Our data indicate contemporary measurements of cell proliferation rates relying on tracer incorporation may be overestimated. ¹³C label was distributed between m1 (m1/Σm = 80) and m2 (m2/Σm = 14) of deoxyribose, indicating that most of the glucose carbon was acquired via direct glucose oxidation in the pentose cycle. The stable isotope technique distinguishes rates of DNA synthesis and repair via the oxidative and non-oxidative pentose cycle, separately, in one test, without inhibition of either process. The contribution of DNA repair in malignant cells to isotope accumulation in deoxyribose remains to be investigated.     

Fungal transformation of natural and synthetic cobalt-bearing manganese oxides and implications for cobalt biogeochemistry

Manganese oxide minerals can become enriched in a variety of metals through adsorption and redox processes, and this forms the basis for a close geochemical relationship between Mn oxide phases and Co. Since oxalate-producing fungi can effect geochemical transformation of Mn oxides, an understanding of the fate of Co during such processes could provide new insights on the geochemical behaviour of Co. In this work, the transformation of Mn oxides by Aspergillus niger was investigated using a Co-bearing manganiferous laterite, and a synthetic Co-doped birnessite. A. niger could transform laterite in both fragmented and powder forms, resulting in formation of biomineral crusts that were composed of Mn oxalates hosting Co, Ni and, in transformed laterite fragments, Mg. Total transformation of Co-doped birnessite resulted in precipitation of Co-bearing Mn oxalate. Fungal transformation of the Mn oxide phases included Mn(III,IV) reduction by oxalate, and may also have involved reduction of Co(III) to Co(II). These findings demonstrate that oxalate-producing fungi can influence Co speciation in Mn oxides, with implications for other hosted metals including Al and Fe. This work also provides further understanding of the roles of fungi as geoactive agents which can inform potential applications in metal bioremediation, recycling and biorecovery.     

Expression profiles of BRCA1 splice variants in asynchronous and in G1/S synchronized tumor cell lines

Disrupting the function of the BRCA1 gene by mechanisms other than germline mutations is suspected to occur in cases of sporadic breast/ovarian cancers. Using ribonuclease protection assay and multiplex RT-PCR, we examined the change of the total BRCA1 mRNA pool and the expression profile of four predominant BRCA1 splice variants in asynchronous and in G1/S synchronized tumor cell populations compared to normal breast cells. Experiments were carried out on MCF-7 and MDA-MB-231 breast cancer, OVCAR-5 ovarian cancer, and K562 leukemia cell lines. The ratio of the full length, the delta(11q), the delta(9,10), and the delta(9,10,11q) BRCA1 isoforms showed different expression patterns in the examined breast and ovarian tumor cell lines as compared to the leukemia cell line. This observation raises the possibility that the dysregulation of alternative splicing of the BRCA1 gene could be involved in tumor formation in the breast and the ovary, even in the absence of germline mutations.