Relationships Among Species Traits: Separating Levels Of Response And Identifying Linkages To Abundance

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/117076/1/ecy20038411.pd

Benefits of using biosolid nutrients in Australian agriculture - a national perspective.

Increased nutrient levels in inland waterways have led to algal blooms and eutrophication in many agricultural regions. To ensure fertiliser inputs are managed more effectively, the source of contamination needs to be tracked and identified. Point sources could include inorganic fertilisers, livestock excreta, or more recently biosolids. The presence of faecal indicator microorganisms has been widely used to identify the presence of faeces, however, these methods cannot distinguish between human and animals samples. This study investigated PCR amplification as a molecular method to distinguish biosolids from livestock faeces of biosolids, cattle, sheep, poultry and kangaroo. This was achieved using published priming sequences and restriction site profiling of amplified DNA across the 16S rRNA gene of anaerobic gastrointestinal bacteria Bacteroides spp and Bifidobacteria spp. Preliminary investigation showed that of the three Bacteroides spp primer pairs investigated, two were useful for cow faecal material; though at lower annealing temperatures were also applicable to biosolids and sheep faecal material. The third primer pair was specific only for biosolids. All three primer pairs were unable to PCR-amplify Bacteroides spp sequences in faecal material of kangaroo. Of the three Bifidobacteria spp primer pairs, one was useful for sheep faecal material; though at lower annealing temperature was also applicable to biosolids and cow and kangaroo faecal material. The Bifidobacterium angulatum specific primer pair enabled the PCR detection of anaerobes only in biosolids and faecal material of kangaroo. The third, a Bifidobacterium catenulatum specific primer pair was suitable for faecal material of cow and at lower annealing temperatures was also applicable to the sample from sheep. Varying degrees of success were observed in faecal material from other animals. Generally, biosolids tested positive for Bacteroides and Bfidobacteria with all primers except for those specific for B. angulatum. For some primer sets, PCR amplification alone could not differentiate biosolids from other faecal samples. The serial dilution of water contaminated by a range of livestock excreta and biosolids is being examined further to enable the sensitivity of this method to be applied in the field.Soil acidification is an increasing problem throughout many agricultural regions in Australia typically on lighter-textured soils that have a low buffering capacity to changes in soil pH and/or that may be naturally acidic. Crops and pastures grown on acidic soils are subject to problems such as aluminium toxicity (particularly in the subsoil), nodulation failure in legumes and a reduced availability of some nutrients. Lime and dolomite are products that are commonly applied to neutralise soil acidity and improve plant productivity with application rates often determined by their neutralising value and particle size of the product, and the pH buffering capacity (lime requirement) of the soil. To investigate the effect of lime amended biosolids (LAB) as a product for neutralising soil acidity and for improving crop growth, four rates of LAB (0, 5, 10 and 15 t DS/ha) and four equivalent rates of lime product (0, 2.3, 4.6 and 6.7 t/ha) were applied to an acidic red/brown sandy loam in the central wheatbelt of Western Australia. In addition, one rate of dewatered biosolids cake (DBC) at 7 t DS/ha was included to enable comparison to be made to this product. The experiment was conducted over three years and sown to wheat (Triticum aestivum), canola (Brassica napus) and then wheat in 2005, 2006 and 2007, respectively. Plants were sampled at 8 weeks and at harvest to determine the effect of LAB, lime and DBC on crop growth, nutrient uptake and grain yield. Samples of surface soil (0-10 cm) were collected and analysed at harvest for pH and major nutrients. Soil pH increased significantly with increasing rates of LAB or lime at the end of the first year, with similar values recorded between equivalent values of lime product. There was no significant change in soil pH following the addition of the DBC treatment. No further changes in soil pH had occurred by the end of the second year. The growth of both wheat and canola in the first two years was affected to a greater extent by nutrients (typically nitrogen) in the LAB than by the reduction in soil acidity. Measurements on wheat yield in the third year of the experiment and changes in soil pH in the surface (0-10 cm) and subsoil (10-20 cm) will provide further information as to the long term effects of LAB in agriculture and allow recommendations to be made regarding best practise land application rates

Interaction of preimplantation factor with the global bovine endometrial transcriptome

Preimplantation factor (PIF) is an embryo derived peptide which exerts an immune modulatory effect on human endometrium, promoting immune tolerance to the embryo whilst maintaining the immune response to invading pathogens. While bovine embryos secrete PIF, the effect on the bovine endometrium is unknown. Maternal recognition of pregnancy is driven by an embryo-maternal cross talk, however the process differs between humans and cattle. As many embryos are lost during the early part of pregnancy in cattle, a greater knowledge of factors affecting the embryo-maternal crosstalk, such as PIF, is needed to improve fertility. Therefore, for the first time, we demonstrate the effect of synthetic PIF (sPIF) on the bovine transcriptome in an ex vivo bovine endometrial tissue culture model. Explants were cultured for 30h with sPIF (100nM) or in control media. Total RNA was analysed via RNA-sequencing. As a result of sPIF treatment, 102 genes were differentially expressed compared to the control (Padj<0.1), although none by more than 2-fold. The majority of genes (78) were downregulated. Pathway analysis revealed targeting of several immune based pathways. Genes for the TNF, NF-κB, IL-17, MAPK and TLR signalling pathways were down-regulated by sPIF. However, some immune genes were demonstrated to be upregulated following sPIF treatment, including C3. Steroid biosynthesis was the only over-represented pathway with all genes upregulated. We demonstrate that sPIF can modulate the bovine endometrial transcriptome in an immune modulatory manner, like that in the human endometrium, however, the regulation of genes was much weaker than in previous human work

Effects of biosolids application on pasture and grape vines in south-eastern Australia

Biosolids were applied to a pasture and a vineyard in south-eastern Australia. At both sites, soil Cd, Cu, and Zn concentrations linearly increased with biosolids application rates although not to the extent of exceeding soil quality guidelines. Biosolids marginally increased soil C and N concentrations at the pasture site but significantly increased P concentrations. With lower overall soil fertility at the vineyard, biosolids increased C, N, and P concentrations. At neither site did biosolids application affect soil microbial endpoints. Biosolids increased pasture production compared to the unfertilised control but had little effect on grape production or quality. Interestingly, over the 3-year trial, there was no difference in pasture production between the biosolids treated plots and plots receiving inorganic fertiliser. These results suggest that biosolids could be used as a fertiliser to stimulate pasture production and as a soil conditioner to improve vineyard soils in this regio

Modelling the toxicity of copper and zinc to wheat and other crops and incorporation of the results into a proposed framework to derive biosolids guidelines

The application of biosolids to land can have both beneficial and detrimental environmentaleffects. The positive effects can arise from nutrients and organic carbon in the biosolids whilethe negative effects generally arise because of the contamination associated with biosolids(e.g. Broos et al., 2006; Heemsbergen et al., 2006; McLaughlin et al., 2006) but can also arisedue to excessive ammonia (Whatmuff et al., 2006). Therefore, any regulatory guidelinesdeveloped to manage the land application of biosolids must be able to enhance the beneficialeffects and minimise the deleterious effects

Genetic diversity within and between British and Irish breeds: the maternal and paternal history of native ponies.

The UK and Ireland have many native pony breeds with historical and cultural importance as well as being a source of uncharacterized genetic diversity. However, there is a lack of comprehensive research investigating their genetic diversity and phylogenetic interrelationships. Many studies contain a limited number of pony breeds or small sample sizes for these breeds. This may result in erroneous grouping of pony breeds that otherwise have intricate interrelationships with each other and are not evaluated correctly when placed as a token subset of a larger dataset. This is the first study that specifically investigates the genetic diversity within and between British and Irish native pony breeds using large sample numbers from locations of their native origin. This study used a panel of microsatellite markers and sequence analysis of the mitochondrial control region to analyze the genetic diversity within and between 11 pony breeds from Britain and Ireland. A large dataset was collected (a total of 485 animals were used for mtDNA analysis and 450 for microsatellite analysis), and previously published data were used to place the British and Irish ponies in a global context. The native ponies of Britain and Ireland were found to have had a complex history, and the interrelationships between the breeds were revealed. Overall, high levels of genetic diversity were maintained in native breeds, although some reduction was evident in small or isolated populations (Shetland, Carneddau, and Section C). Unusual mitochondrial diversity distribution patterns were apparent for the Carneddau and Dartmoor, although among breeds and global haplogroups there was a high degree of haplotype sharing evident, well-represented within British and Irish ponies. Ancestral maternal diversity was maintained by most populations, particularly the Fells and Welsh ponies, which exhibited rare and ancient lineages. The maternal and paternal histories of the breeds are distinct, with male-biased crossings between native breeds, and other shared influences, likely Arabs and Thoroughbreds, are apparent. The data generated herein provide valuable information to guide and implement the conservation of increasingly rare native genetic resources

Characterization of an Ex Vivo Equine Endometrial Tissue Culture Model Using Next-Generation RNA-Sequencing Technology

SIMPLE SUMMARY: Notwithstanding extensive research into fertility problems in mares, pregnancy rates have remained low mainly because of endometrial inflammation (endometritis). In the field of equine research, endometrial explants have been used to carry out in vitro studies of the mare’s endometrium. However, there has been no wide-ranging assessment of relative stability of this model over time. The aim of this study was to perform an in-depth transcriptomic assessment of endometrial explants over a culture period of 72 h and assess if they are representative of the whole mare. Explants at 24 h demonstrated significant changes when compared to biopsies at 0 h as expected. Even though gene expression changes were seen between 24 and 48 h of culture, prior to this window changes were dominated by the effects of explanting and culture and subsequently, transcription was generally compromised. Our results, therefore have defined the optimal period when explants can be used to study equine endometritis and how the endometrium is modulated during inflammation. It highlights the use of abattoir derived samples to understand the physiology and pathophysiology of the equine endometrium, negating the need to collect repeated uterine biopsies from living mares. ABSTRACT: Persistent mating-induced endometritis is a major cause of poor fertility rates in the mare. Endometritis can be investigated using an ex vivo equine endometrial explant system which measures uterine inflammation using prostaglandin F(2α) as a biomarker. However, this model has yet to undergo a wide-ranging assessment through transcriptomics. In this study, we assessed the transcriptomes of cultured endometrial explants and the optimal temporal window for their use. Endometrium harvested immediately post-mortem from native pony mares (n = 8) were sampled (0 h) and tissue explants were cultured for 24, 48 and 72 h. Tissues were stored in RNALater, total RNA was extracted and sequenced. Differentially expressed genes (DEGs) were defined using DESeq2 (R/Bioconductor). Principal component analysis indicated that the greatest changes in expression occurred in the first 24 h of culture when compared to autologous biopsies at 0 h. Fewer DEGs were seen between 24 and 48 h of culture suggesting the system was more stable than during the first 24 h. No genes were differentially expressed between 48 and 72 h but the low number of background gene expression suggested that explant viability was compromised after 48 h. ESR1, MMP9, PTGS2, PMAIP1, TNF, GADD45B and SELE genes were used as biomarkers of endometrial function, cell death and inflammation across tissue culture timepoints. STRING assessments of gene ontology suggested that DEGs between 24 and 48 h were linked to inflammation, immune system, cellular processes, environmental information processing and signal transduction, with an upregulation of most biomarker genes at 24 h. Taken together our observations indicated that 24–48 h is the optimal temporal window when the explant model can be used, as explants restore microcirculation, perform wound healing and tackle inflammation during this period. This key observation will facilitate the appropriate use of this as a model for further research into the equine endometrium and potentially the progression of mating-induced endometritis to persistent inflammation between 24 and 48 h

Exploring the Life Course Perspective in Maternal and Child Health through Community-Based Participatory Focus Groups: Social Risks Assessment

Little is known about the patterns of risk factors experienced by communities of color and how diverse community contexts shape the health trajectory of women from the early childhood period to the time of their pregnancies. Thus, we conducted a focus group study to identify social risks over the life course that contribute to maternal and child health from the perspective of community members residing in low income urban areas. Ten community-based participatory focus groups were conducted with residents from selected communities in Tampa, Florida, from September to November 2013. We used the life course perspective to illuminate and explain the experiences reported by the interviewees. A total of 78 residents participated in the focus groups. Children and adolescents’ health risks were childhood obesity, lack of physical activity, and low self-esteem. Women’s health risks were low self-esteem, low educational level, low health literacy, inadequate parenting skills, and financial problems. Risks during pregnancy included stress, low self-esteem, inadequate eating patterns, lack of physical activity, healthcare issues, lack of social support, and lack of father involvement during pregnancy. Multiple risk factors contribute to maternal and child health in low income communities in Tampa Bay. The intersection of risk factors in different life periods suggest possible pathways, cumulative, and latent effects, which must be considered in future longitudinal studies and when developing effective maternal and child health programs and policies