Salmonella enterica Burden in Harvest-Ready Cattle Populations from the Southern High Plains of the United States

Our objectives were to quantify the Salmonella enterica burdens in harvest-ready cattle and to identify specific at-risk populations of cattle most likely to harbor multiply resistant S. enterica. Hide swabs were collected in abattoirs from three cohorts of cattle (feedlot origin cattle that had achieved desirable harvest characteristics and dairy- and beef-type cows harvested because of poor productivity). Feces were collected from two cohorts housed in feedlots (cattle that had achieved desirable harvest characteristics and animals identified for salvage recovery because of poor productivity). Facilities were visited on four occasions over a 12-month period. Salmonella enterica isolates were recovered, and organisms were quantified using standard microbiological methodologies. Susceptibility to antimicrobial drugs and serotype were determined for one S. enterica isolate per sample. Salmonella enterica was recovered from 55.6% of 1,681 samples. The prevalences on hides and in feces were 69.6% and 30.3%, respectively. The concentrations of S. enterica organisms averaged (as determined by the most probable number technique) 1.82 log₁₀/100 cm² of hides and 0.75 log₁₀/g of feces. None of the isolates recovered from cattle that had achieved desirable harvest characteristics were resistant to four or more drugs. For isolates recovered from animals with poor productivity characteristics, 6.5% were resistant to four or more drugs. Twenty-two serovars were identified, with the most common being Salmonella enterica serovar Anatum (25.5%), Salmonella enterica serovar Montevideo (22.2%), and Salmonella enterica serovar Cerro (12.5%). High-level resistance, i.e., resistance to four or more drugs, was clustered within a few relatively uncommon serovars. These results demonstrate that even though S. enterica isolates are readily recoverable from harvest-ready cattle, multiply resistant variants are rare and are associated with specific serovars in cattle harvested because of poor productivity characteristics.     

Issues affecting the measurement of disturbance response patterns in herbaceous vegetation – A test of the intermediate disturbance hypothesis

The 'intermediate disturbance hypothesis' (IDH) predicts maximum species diversity at intermediate levels of disturbance. Disturbance levels are measured by intensity or frequency of disturbance or by the time since disturbance. The IDH has been tested over a wide range of studies and communities with results either accepting or rejecting the hypothesis. The objectives of this study were to determine how observed disturbance response patterns for the same herbaceous plant community are influenced by modelling techniques, particularly in relation to the expression of disturbance gradients, choice of species diversity indices, and time of assessment since disturbance. Response patterns were examined using a multi-factorial disturbance experiment involving grazing (absent and present); fire (absent and present); soil cultivation (none, 5 and 20 cm); and amendment (none, fertiliser, and fertiliser plus clover seeds). Generalized linear models with a b-spline function were used to define response patterns for five different disturbance gradients over a 24-month period using three indices of diversity. Seven basic disturbance response models were recognized ranging from the classical IDH bell-shaped pattern through increasing or decreasing trends, to a no-change model with increasing levels of disturbance. Only 6.7% of all models were consistent with the IDH. The no-change model was found in nearly half the cases investigated and increased in occurrence with time since disturbance. The choice of the disturbance intensity gradient, the species diversity index used and the time of assessment after disturbance significantly influenced the frequency of occurrence of the disturbance response models observed. Consequently, the responses of vegetation to disturbance gradients show many patterns depending on how they are defined and modelled rather than the simple bell-shaped curve as predicted by the IDH, but the ecological mechanisms supporting some of these patterns need to be further investigated.     

Patterns of Dolphin Bycatch in a North-Western Australian Trawl Fishery

The bycatch of small cetaceans in commercial fisheries is a global wildlife management problem. We used data from skippers'' logbooks and independent observers to assess common bottlenose dolphin (Tursiops truncatus) bycatch patterns between 2003 and 2009 in the Pilbara Trawl Fishery, Western Australia. Both datasets indicated that dolphins were caught in all fishery areas, across all depths and throughout the year. Over the entire datasets, observer reported bycatch rates (n = 52 dolphins in 4,124 trawls, or 12.6 dolphins/1,000 trawls) were ca. double those reported by skippers (n = 180 dolphins in 27,904 trawls, or 6.5 dolphins/1,000 trawls). Generalised Linear Models based on observer data, which better explained the variation in dolphin bycatch, indicated that the most significant predictors of dolphin catch were: (1) vessel - one trawl vessel caught significantly more dolphins than three others assessed; (2) time of day – the lowest dolphin bycatch rates were between 00:00 and 05:59; and (3) whether nets included bycatch reduction devices (BRDs) - the rate was reduced by ca. 45%, from 18.8 to 10.3 dolphins/1,000 trawls, after their introduction. These results indicated that differences among vessels (or skippers'' trawling techniques) and dolphin behavior (a diurnal pattern) influenced the rates of dolphin capture; and that spatial or seasonal adjustments to trawling effort would be unlikely to significantly reduce dolphin bycatch. Recent skipper''s logbook data show that dolphin bycatch rates have not declined since those reported in 2006, when BRDs were introduced across the fishery. Modified BRDs, with top-opening escape hatches from which dolphins might escape to the surface, may be a more effective means of further reducing dolphin bycatch. The vulnerability of this dolphin population to trawling-related mortality cannot be assessed in the absence of an ongoing observer program and without information on trawler-associated dolphin community size, broader dolphin population size and connectivity with adjacent populations.     

Diverse intracellular signalling systems used by growth hormone-releasing hormone in regulating voltage-gated Ca2+ or K channels in pituitary somatotropes

Influx of Ca2+ via Ca2+ channels is the major step triggering exocytosis of pituitary somatotropes to release growth hormone (GH). Voltage-gated Ca2+ and K+ channels, the primary determinants of the influx of Ca2+, are regulated by GH-releasing hormone (GHRH) through G-protein-coupled intracellular signalling systems. Using whole-cell patch-clamp techniques, the changes of the Ca2+ and K+ currents in primary cultured ovine and human somatotropes were recorded. Growth hormone-releasing hormone (10 nmol/L) increased both L- and T-type voltage-gated Ca2+ currents. Inhibition of the cAMP/protein kinase A (PKA) pathway by either Rp-cAMP or H89 blocked this increase in both L- and T-type Ca2+ currents. Growth hormone-releasing hormone also decreased voltage-gated transient (IA) and delayed rectified (IK) K+ currents. Protein kinase C (PKC) inhibitors, such as calphostin C, chelerythrine or downregulation of PKC, blocked the effect of GHRH on K+ currents, whereas an acute activation of PKC by phorbol 12, 13-dibutyrate (1 micromol/L) mimicked the effect of GHRH. Intracellular dialysis of a specific PKC inhibitor (PKC19-36) also prevented the reduction in K+ currents by GHRH. It is therefore concluded that GHRH increases voltage-gated Ca2+ currents via cAMP/PKA, but decreases voltage-gated K+ currents via the PKC signalling system. The GHRH-induced alteration of Ca2+ and K+ currents augments the influx of Ca2+, leading to an increase in [Ca2+]i and the GH secretion.     

An effect of shade on the boron requirement for leaf blade elongation in black gram (Vigna mungo L. Hepper)

The present experiment was undertaken to examine whether shading affects the critical boron (B) concentration for leaf blade elongation in black gram. Six days after germination (D6), black gram seedlings were transferred to 8 pairs of pots containing basal nutrient solution: one pot of each pair contained 1 M H₃BO₃ and the other 10 M H₃BO₃. On D10, one day after the emergence of the first trifoliolate leaf blade (TF₁) and one day before the emergence of TF₂, four pairs of pots were shaded, decreasing the light intensity they received in the glasshouse to about 35% of full sunlight compared with 70% received by the unshaded plants. The response to B supply of dry matter (DM) and elongation rate (LBER) of TF₂ were less pronounced in shaded than in unshaded plants. Critical B concentrations for LBER in TF₂ of black gram were 10 mg B kg^-1DM in shaded and 15 mg B unshaded plants, suggesting that shading may have decreased the B requirement for LBER. Thus the present results suggest that light may need to be considered when setting critical values for the diagnosis of B deficiency in black gram.     

Calcium and Nodulation in Subterranean Clover (Trifolium subterraneum L.)

From a study of the effects of Ca ions on the nodulation of subterranean clover in flowing culture solutions it is concluded that root infection or nodule initiation has a higher Ca requirement than either nodule development or host plant growth in the presence of fixed nitrogen.     

MitoScape: A big-data,machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data

The growing number of next-generation sequencing (NGS) data presents a unique opportunity to study the combined impact of mitochondrial and nuclear-encoded genetic variation in complex disease. Mitochondrial DNA variants and in particular, heteroplasmic variants, are critical for determining human disease severity. While there are approaches for obtaining mitochondrial DNA variants from NGS data, these software do not account for the unique characteristics of mitochondrial genetics and can be inaccurate even for homoplasmic variants. We introduce MitoScape, a novel, big-data, software for extracting mitochondrial DNA sequences from NGS. MitoScape adopts a novel departure from other algorithms by using machine learning to model the unique characteristics of mitochondrial genetics. We also employ a novel approach of using rho-zero (mitochondrial DNA-depleted) data to model nuclear-encoded mitochondrial sequences. We showed that MitoScape produces accurate heteroplasmy estimates using gold-standard mitochondrial DNA data. We provide a comprehensive comparison of the most common tools for obtaining mtDNA variants from NGS and showed that MitoScape had superior performance to compared tools in every statistically category we compared, including false positives and false negatives. By applying MitoScape to common disease examples, we illustrate how MitoScape facilitates important heteroplasmy-disease association discoveries by expanding upon a reported association between hypertrophic cardiomyopathy and mitochondrial haplogroup T in men (adjusted p-value = 0.003). The improved accuracy of mitochondrial DNA variants produced by MitoScape will be instrumental in diagnosing disease in the context of personalized medicine and clinical diagnostics.     

The effects of burning on the understorey composition of 11–13 year-old rehabilitated bauxite mines in Western Australia – Vegetation characteristics

Alcoa of Australia Limited has been rehabilitating bauxite mines in the jarrah (Eucalyptus marginata) forest of Western Australia for more than 30 years. Mines rehabilitated in the early 1980s using out-dated methods have built up substantial fuel loads that may be reduced through prescribed burning. The vegetation response of 11–13 year-old rehabilitated bauxite mines to fire regimes differing in intensity and season over the first two years of post-burn succession is compared to the native jarrah forest. A total of 243 species from 137 genera and 56 families were identified in the native forest reference sites and in the 11–13 year-old rehabilitated areas before and after burning. The vegetation of the pre-burn rehabilitated areas was very different to that of the native jarrah forest. While total live plant cover, Acacia density, non-native eucalypt seedling density, weed density and the evenness index were similar between the two areas, total plant density, live Acacia cover, the proportion of weeds, native species numbers and diversity were significantly different. However, the greatest difference between the vegetation of the pre-burn rehabilitated sites and the native jarrah forest was the higher dominance of seeding species (plants killed by fire) in rehabilitated areas. In contrast, native jarrah forest was dominated by resprouting species (plants that survive fire). Burning the rehabilitated sites was successful in making the areas more similar to the forest in terms of total plant density, live Acacia cover and native species numbers but decreased their similarity in terms of live plant cover, Acacia density, non-native eucalypt seedling density, weed density and evenness. The vegetation response of the rehabilitated areas to different seasons of burning showed that autumn burning led to a greater increase in plant establishment than spring burning. Autumn burning also resulted in an undesirable increase in the density of non-native eucalypt seedlings that was not observed following spring burning. Although burning these 11–13 year-old rehabilitated sites will increase similarity to the native forest, it is unlikely that they will resemble the native jarrah forest without further management intervention.     

Microhabitat distribution of juvenile Penaeus merguiensis de Man and other epibenthic crustaceans within a mangrove forest in subtropical Australia

The distribution of juvenile Penaeus (Fenneropenaeus) merguiensis de Man and other epibenthic crustaceans in different microhabitats within a riverine mangrove forest was examined in subtropical eastern Australia. Catches in vegetated and cleared microhabitats were compared at sites located in mangroves on the creek edge (1-2 m into the forest) and the inner forest (a further 14-22 m into the forest). Crustaceans were sampled using 3×3 m lift nets that were activated at the top of spring flood tides between March and May 2000. The abundance of P. merguiensis in the adjacent creek was also monitored during both high and low tides using a small beam trawl. A large size range of P. merguiensis was caught in the mangrove forest (2-13.5 mm carapace length) and the maximum density recorded was 1 prawn m⁻². Catches of P. merguiensis were significantly higher at the creek edge than at the inner forest sites. Catches did not differ significantly between vegetated and cleared microhabitats, but catches were highly variable within microhabitats. This result was attributed to the very high activity levels of P. merguiensis and suggests that detecting differences between microhabitats used by prawns in the field would require a large number of samples. Substantial numbers of Acetes sibogae australis (Hansen), Macrobrachium novaehollandiae (de Man) and Metapenaeus bennettae (Racek and Dall) also entered the forest and catches of these species followed a similar pattern to those for P. merguiensis, i.e. catches were higher at the creek edge than the inner forest, did not differ between microhabitats and were highly variable within a microhabitat.