Next generation restoration metrics: Using soil eDNA bacterial community data to measure trajectories towards rehabilitation targets.

In post-mining rehabilitation, successful mine closure planning requires specific, measurable, achievable, relevant and time-bound (SMART) completion criteria, such as returning ecological communities to match a target level of similarity to reference sites. Soil microbiota are fundamentally linked to the restoration of degraded ecosystems, helping to underpin ecological functions and plant communities. High-throughput sequencing of soil eDNA to characterise these communities offers promise to help monitor and predict ecological progress towards reference states. Here we demonstrate a novel methodology for monitoring and evaluating ecological restoration using three long-term (>25 year) case study post-mining rehabilitation soil eDNA-based bacterial community datasets. Specifically, we developed rehabilitation trajectory assessments based on similarity to reference data from restoration chronosequence datasets. Recognising that numerous alternative options for microbiota data processing have potential to influence these assessments, we comprehensively examined the influence of standard versus compositional data analyses, different ecological distance measures, sequence grouping approaches, eliminating rare taxa, and the potential for excessive spatial autocorrelation to impact on results. Our approach reduces the complexity of information that often overwhelms ecologically-relevant patterns in microbiota studies, and enables prediction of recovery time, with explicit inclusion of uncertainty in assessments. We offer a step change in the development of quantitative microbiota-based SMART metrics for measuring rehabilitation success. Our approach may also have wider applications where restorative processes facilitate the shift of microbiota towards reference states.

MATRILINEAL, a sperm-specific phospholipase, triggers maize haploid induction.

Sexual reproduction in flowering plants involves double fertilization, the union of two sperm from pollen with two sex cells in the female embryo sac. Modern plant breeders increasingly seek to circumvent this process to produce doubled haploid individuals, which derive from the chromosome-doubled cells of the haploid gametophyte. Doubled haploid production fixes recombinant haploid genomes in inbred lines, shaving years off the breeding process. Costly, genotype-dependent tissue culture methods are used in many crops, while seed-based in vivo doubled haploid systems are rare in nature and difficult to manage in breeding programmes. The multi-billion-dollar maize hybrid seed business, however, is supported by industrial doubled haploid pipelines using intraspecific crosses to in vivo haploid inducer males derived from Stock 6, first reported in 1959 (ref. 5), followed by colchicine treatment. Despite decades of use, the mode of action remains controversial. Here we establish, through fine mapping, genome sequencing, genetic complementation, and gene editing, that haploid induction in maize (Zea mays) is triggered by a frame-shift mutation in MATRILINEAL (MTL), a pollen-specific phospholipase, and that novel edits in MTL lead to a 6.7% haploid induction rate (the percentage of haploid progeny versus total progeny). Wild-type MTL protein localizes exclusively to sperm cytoplasm, and pollen RNA-sequence profiling identifies a suite of pollen-specific genes overexpressed during haploid induction, some of which may mediate the formation of haploid seed. These findings highlight the importance of male gamete cytoplasmic components to reproductive success and male genome transmittance. Given the conservation of MTL in the cereals, this discovery may enable development of in vivo haploid induction systems to accelerate breeding in crop plants.

Characterization of an oncolytic herpes simplex virus drug candidate.

The structural integrity and conformational stability of a genetically modified live, oncolytic herpes simplex virus (o-HSV) were investigated across a wide pH (5.5-8.0) and temperature (10°C-87.5°C) range. A combination of circular dichroism, intrinsic and extrinsic fluorescence, and static light scattering results was visualized using an empirical phase diagram approach to provide a global assessment of physical stability. Distinct phases were identified including the native state of the virus, an intermediate phase that could represent gradual swelling and/or shedding of the viral envelope, and a highly disrupted, aggregated phase. The nature of these altered forms of the virus was further evaluated by transmission electron microscopy and viral plaque assays. The effect of freeze-thaw (F/T) stress on o-HSV was also examined. After one F/T cycle, a loss of infectious virus titers was observed. In addition, the monomeric virus particle concentration decreased during F/T stress, whereas there was a concurrent increase in larger particles (2-10 µm). The comprehensive biophysical characterization of viral stability conducted in this study identified major degradation events leading to loss of infectivity of o-HSV and represents an important step toward stabilization of the virus against thermal and F/T stresses.

Off-Stream Watering Systems and Partial Barriers as a Strategy to Maximize Cattle Production and Minimize Time Spent in the Riparian Area.

A study was conducted in 2009 at two locations in Manitoba (Killarney and Souris), Canada to determine the impact of off-stream waterers (OSW) with or without natural barriers on (i) amount of time cattle spent in the 10 m buffer created within the riparian area, referred to as the riparian polygon (RP), (ii) watering location (OSW or stream), and (iii) animal performance measured as weight gain. This study was divided into three 28-day periods over the grazing season. At each location, the pasture-which ranged from 21.0 ha to 39.2 ha in size-was divided into three treatments: no OSW nor barriers (1CONT), OSW with barriers along the stream bank to deter cattle from watering at the stream (2BARR), and OSW without barriers (3NOBARR). Cattle in 2BARR spent less time in the RP in Periods 1 (p = 0.0002), 2 (p = 0.1116), and 3 (p < 0.0001) at the Killarney site compared to cattle in 3NOBARR at the same site. Cattle in 2BARR at the Souris site spent more time in the RP in Period 1 (p < 0.0001) and less time in Period 2 (p = 0.0002) compared to cattle in 3NOBARR. Cattle did use the OSW, but not exclusively, as watering at the stream was still observed. The observed inconsistency in the effectiveness of the natural barriers on deterring cattle from the riparian area between periods and locations may be partly attributable to the environmental conditions present during this field trial as well as difference in pasture size and the ability of the established barriers to deter cattle from using the stream as a water source. Treatment had no significant effect (p > 0.05) on cow and calf weights averaged over the summer period. These results indicate that the presence of an OSW does not create significant differences in animal performance when used in extensive pasture scenarios such as those studied within the present study. Whereas the barriers did not consistently discourage watering at the stream, the results provide some indication of the efficacy of the OSW as well as the natural barriers on deterring cattle from the riparian area.