Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitrogen supply and demand in Australian agriculture

The supply of and demand for nitrogen by whole industries and individual crops is discussed in relation to changes in farming systems, particularly the relative importance of fertiliser and biologically fixed nitrogen. The use of fertiliser nitrogen (N) in Australia has grown at an annual rate of 14% since the early 1990s, after growing at half that rate since the 1950s. The accelerated growth occurred during a period when world demand has been almost constant. Most of the additional demand has been for the dryland cereal and canola industries of southern Australia, where crops previously obtained almost all their N from mineralisation of soil organic matter and the residues of legume pastures. The most likely reasons for the belated increase in use of fertiliser N in Australia are to replace the supply from pasture residues as the area of pasture decreased and to satisfy the increased demand of cereals following break crops and of the break crops themselves, particularly canola. For a dryland cereal, there is a problem of matching soil N supply with an unpredictable N demand. For winter cereals in Australia, crop N demand is poorly synchronised with soil N supply. The time of greatest demand is normally during the stem-elongation phase when the crop is growing fastest. For crops targeted for high-protein grain, there is an even greater demand around the flowering phase. The peak N demand for well-managed crops growing with no water limitations exceeds the capacity of the soil to supply N from mineralisation at the time, so additional N is required to meet the shortfall, either from fertiliser or mineral N retained in the soil from earlier mineralisation. Predicting the optimum supply of fertiliser N at sowing is difficult in cases where N demand is influenced by variable rainfall. Topdressing and banding fertiliser offer prospects for more closely matching N supply and demand for dryland crops. The future role of legumes in supplying residual N is discussed in relation to the trend towards continuous cropping.
Biochemical Characterization of a Type II Diacylglycerol Acyltransferase from Claviceps purpurea

Claviceps purpurea, a fungal pathogen, of ergot diseases in agriculturally important cereal crops, produces high levels of glycerides containing ricinoleic acid (12hydroxyoctadec-cis-9-enoic acid) in its sclerotia. A fatty acid hydroxylase (CpFAH) involved in the biosynthesis of ricinoleic acid was recently identified from C. purpurea. This research describes the biochemical characterization of a type II diacylglycerol acyltransferase (CpDGAT2) involved in the assembly of this fatty acid into triglycerides from C. purpurea. Expression of CpDGAT2 in a quadruple mutant Saccharomyses cerevisiae H1246, in which all four triacylglycerol (TG) biosynthesis genes (DGA1, LOR1, ACAT1 and ACAT2) were disrupted, restored the ability of the mutant to synthesize TGs in vivo. In vitro enzymatic assays of microsomal preparations of the transformants indicated that CpDGAT2 preferentially use ricinoleic acid over linoleic acid, oleic acid and linolenic acids as acyl donor, and 1,2-dioleoyl-sn-glycerol over 1,2-dipalmitoyl-sn-glycerol as acyl acceptor. CpDGAT2 did not show any activities for the formation of wax esters and estolides when 1-hexadecanol and triricinolein were used as acyl acceptors. Co-expression of CpFAH and CpDGAT2 in yeast resulted in increased accumulation of ricinoleic acids compared to expression of CpFAH along with the yeast native DGAT2 (ScDGA1) or expression of CpFAH alone. Northern blot analysis indicated that CpFAH is solely expressed in sclerotium cells and no transcripts of this gene were detected in mycelium and conidium cells. CpDGAT2 is more widely expressed in cell types examined except for conidiospores where the expression is low. The highest expression of CpDGAT2 was detected in 20 day-old sclerotium cells where the highest levels of ricinoleate glycerides are accumulated.
Pituitary Gonadotroph Estrogen Receptor-α Is Necessary for Fertility in Females

Estrogens play a central role in regulating female reproduction throughout the reproductive axis, and the pituitary is one of the major targets of estrogen action. We hypothesized that estrogen receptor α (ERα) mediates estrogen action in the pituitary gonadotroph. To test this hypothesis, we generated a mouse line with a selective ERα deletion in the gonadotropin α-subunit (αGSU)-expressing pituitary cells (pituitary-specific ERα knockout; ERαflox/flox αGSUcre). Although the ERαflox/flox αGSUcre female mice maintain a basal level of serum LH and FSH and their ovulatory capacity is comparable to that in controls, they do not display regular estrous cycles and are infertile, indicating a potential disorder in regulating LH and/or FSH secretion. The ERαflox/flox αGSUcre female mice express equivalent levels of LHβ and αGSU mRNA compared with wild-type mice as determined by microarray analysis. Taken together, these findings indicate that pituitary gonadotroph ERα carries out the effects of estrogens with regard to estrous cyclicity and ultimately fertility.
Drought effects on yield and its components in Indian mustard (Brassica juncea L.)

Effects of drought on yield and yield components were investigated during the spring season 2000-2001 by growing 14 Indian mustard genotypes under irrigated and rain-fed conditions at Bharatpur and Jobner. A disease and pest management schedule was followed when required. The drought susceptibility index (DSI) for seed yield and component characteristics was calculated to characterize the relative tolerance of genotypes. Plant height, primary branches, secondary branches per plant, 1000-seed weight and seed yield were reduced under rain-fed conditions. The top five genotypes at 13haratpur that showed tolerance to moisture stress for seed yield, as indicated by their lowest DSI, were, in descending order PSR-20, PRO-97024, JMMWR-941, IS-1787 and PCR-7, whereas at Jobner these were JMMWR-941, RC-1446, PSR-20, RH-819 and 'Varuna'. Of these, PSR-20 and JMMWR-941 were among the top six at both locations. These genotypes also showed relatively low DSI for one or more characteristics, such as primary branches per plant, secondary branches per plant, harvest index and seed : husk ratio. Genotypes with the lowest DSI, particularly for seed yield at both locations, would serve as useful donors in the breeding programme for improving the drought tolerance of existing Indian mustard cultivars.
Daminozide, Root Pruning, Trunk Scoring, and Trunk Ringing Effects on Fruit Ripening and Storage Behavior of `McIntosh' Apple

A midsummer foliar daminozide (DZ) application (750 mg a.i./liter) to 'Macspur McIntosh'/M.7 apple trees (Malus domestics Borkh.) reduced preharvest drop and retarded flesh firmness loss and starch hydrolysis when tested at harvest; DZ also reduced fruit ethylene production at harvest and after 19 weeks of storage at 0.5C. Root pruning at full bloom (May) resulted in increased soluble solids concentration (SSC) and firmer flesh and less starch hydrolysis at harvest, but not consistently each year. Full-bloom root pruning reduced the incidence of stem-cavity browning and brown core, but again not each year. Full-bloom root pruning did not influence ethylene evolution at harvest but did reduce post-storage ethylene evolution in two of three seasons. Full-bloom root pruning generally was less effective than DZ in altering fruit behavior, while root pruning later than full bloom had virtually no effect. Trunk scoring or ringing increased SSC and retarded loss of flesh firmness before harvest and following storage, but had little effect on starch hydrolysis. Scoring or ringing decreased incidence of some disorders and reduced post- storage ethylene evolution, although these treatments had little effect on ethylene production at harvest. Trunk scoring influenced some fruit characteristics more strongly than DZ. Fruit size was not affected by any treatment in any year. Chemical name used: butanedioic acid mono (2,2 -dimethylhydrazide) (daminozide). Midsummer daminozide (DZ, Uniroyal Chemical, Middle- bury, Corm.) sprays have been widely used on 'McIntosh' apple for control of preharvest drop, fruit maturation, and problems of quality deterioration during and after storage (Edgerton and Blanpied, 1970; Forshey, 1970; Greene et al., 1977; Looney, 1975a, 1975b; Miller and Lougheed, 1971; Williams et al.,
Dissecting the molecular basis of foot-and-mouth disease virus evolution

Foot-and-mouth disease virus (FMDV) causes the most contagious transboundary disease of animals, affecting both wild and domestic cloven-hoofed animals. Similarly to other RNA viruses, FMDV is highly variable as a result of the inherent low fidelity of the viral RNA-dependent RNA polymerase. The accumulation of this variability and relatedness between FMDV sequences was used to provide evidence for modes of transmission (fomite) as well as a constant clock rate across two FMDV topotypes (~8.70 x 10-3 substitutions/site/year), during the 1967 UK FMD epidemic, using full genome consensus sequencing. However, during an epidemic, virus replicates within multiple animals, where it is also replicating and evolving within different tissues and cells. Each scale of evolution, from a single cell to multiple animals across the globe, involves evolutionary processes that shape the viral diversity generated below the level of the consensus. During this PhD project, next-generation sequencing (NGS) was used to dissect the fine scale viral population diversity of FMDV. Collaboration with the Institute of Biodiversity, Animal Health and Comparative Medicine at the University of Glasgow provided the specialist bioinformatic and statistical capabilities required for the analysis of NGS datasets. As part of this collaboration, a new systematic approach was developed to process NGS data and distinguish genuine mutations from artefacts. Additionally, evolutionary models were applied to this data to estimate parameters such as the genome-wide mutation rate of FMDV (upper limit of 7.8 x 10-4 per nt). Analysis of the mutation spectra generated from a clonal control study established a mutation frequency threshold of 0.5% above which there can be confidence that 95% of mutations are real in the sense that they are present in the sampled virus population. This threshold, together with an optimized protocol, was used for the more extensive investigation of within and between host viral population dynamics during transmission. Analysis of mutation spectra and site-specific mutations revealed that intra-host bottlenecks are typically more pronounced than inter-host bottlenecks. NGS analysis has distinguished between the population structure of multiple samples taken from a single host, which may provide the means to reconstruct both intra- and inter-host transmission routes in the future. A more sophisticated understanding of viral diversity at its finest scales could hold the key to the better understanding of viral pathogenesis and, therefore development of effective and sustainable disease treatment and control strategies.
Shading and the growth and photosynthetic responses of Ammannia coccinnea

The effects of shade on the growth and CO 2 exchange rate (CER) of Ammannia coccinnea Wild. , a noxious weed in water-seeded rice, were determined under glasshouse conditions. Shade substantially reduced A. coccinnea growth when imposed early and maintained throughout the growing season. However, plants transferred from full light to 18% or 50% sunlight 30 or 45 days after seeding had only slightly less dry weight than unshaded plants. Constant shade reduced growth severely (94%). In contrast, plants that were shaded for 45 days and then placed in full light largely recovered from the effects of shading by final harvest. The ability of A. coccinnea to reduce the effects of shade appears related to increased partitioning to leaves, increased specific leaf area and decreased dark respiration rates. The ability of the weed to recover from shade appears related to its ability to greatly increase CER in new leaves in response to increased light. Plasticity in A. coccinnea morphology and physiology appears to explain its persistence in California rice fields and suggests that management strategies that rely on shade alone may not improve control of this weed.
A Brief History of Marine Bio-Invasions in South Africa

Marine species have been introduced continuously into South Africa for more than 400 years, since the arrival of the first European explorers. Various waves of introduction can be identified over this period, each associated with a different mix of vectors. Early wooden vessels carried specialized wood-boring species, a rich external fouling community, plus semi-terrestrial species associated with dry ballast. Modern steel vessels continue to import fouling species, despite the use of anti-fouling paints, and may ply new routes, bringing additional introductions from novel locations. More modern waves of introduction are associated with use of ballast water and with marine aquaculture. Research on marine bio-invasions in South Africa has a short history, marked by a rapid rate of discovery of introductions. Some 86 marine species are currently regarded as introduced to the region, with a further 39 considered cryptogenic, but this number is increasing rapidly. Moreover, many taxa and regions still remain inadequately explored, indicating that the current list remains far from complete. The reasons for under-reporting of introduced populations are discussed and include lack of sample coverage, misidentification of aliens as native species and erroneous redescriptions of aliens as new, indigenous species. However, the lack of taxonomic expertise across large sections of the biota remains the greatest impediment to progress.
Proportion of copepod biomass declines with decreasing salinity in the Baltic Sea

The biomass ratio of copepoda/cladocera decreased in the Northern Baltic Archipelago Sea (SW Finland) in concert with a decrease in the seawater salinity during the 1980s. There also was an increase in freshwater run-off from the watershed of the Baltic Proper. Seawater salinity correlated negatively with freshwater run-off with a time lag of several years. The abundance percentages of most dominant zooplankton species correlated significantly with salinity, either positively (large neritic copepods), or negatively (freshwater cladocerans). All data sets together indicate a close connection between the functioning of the pelagic Baltic Sea ecosystem and large-scale weather patterns over the run-off area.
Genetic diversity, population structure and conservation implication of the endemic Sumatran lowland dipterocarp tree species (Shorea javanica)

Shorea javanica is an economically important dammar-producing tree, endemic to tropical lowland forest in Sumatra and Java, Indonesia. Total population size, however, is very limited and endangered. We sequenced three non-coding regions of chloroplast DNA and three nuclear genes, and genotyped seven microsatellite loci in six populations representing the current species distribution. There was no variation in the chloroplast DNA regions, except for one unique indel polymorphism. Mean silent site nucleotide diversity across three nuclear regions was 0.0011, which is much smaller than those of common dipterocarp species. Expected mean population heterozygosity in the microsatellite loci was 0.423, and the total heterozygosity was 0.477. These results show genetic variation in S. javanica is extremely low at both population and species levels. Genetic differentiation among populations was moderate (FST = 0.064 for nuclear genes and FST {ENA} = 0.076 for microsatellite loci), but this result is essentially caused by one isolated population in Oku. We suggest that conservation efforts should focus on promoting connectivity and augmenting population size across the species range. Ex-situ conservation should also be considered to provide insurance against catastrophic events and to facilitate for reintroduction. Key words: Shorea javanica, repong dammar, chloroplast DNA, nuclear genes, microsatellite markers.
Relationships between Height, Diameter and Weight Distributions of Chenopodium album Plants in Stands: Effects of Dimension and Allometry

Abstract Frequency distributions of height (H), stem diameter (D) and dry weight (W) of Chenopodium album plants in even-aged monocultures at the initial plant densities of 400, 800 and 1200 plants m -2 (400-, 800- and 1200-plots) were compared. The height distributions at the end of the growing season were bimodal for the 400-plot but L-shaped for the 800- and 1200-plots. The distributions of diameter and dry weight were L-shaped for all the plots. When the size measures were expressed on the log scale so as to eliminate effects of the differences in dimension, frequency distributions of log W and log H for the 400-plot were bimodal. In contrast, the log D distributions were bell-shaped for all the plots. To elucidate factors responsible for the differences in frequency distributions among log size measures, we examined allometric relationships between log size measures. They were all non-linear all non-linear mainly because the allometric relationships were markedly different between the plants forming the upper-most leaf layer ('upper' plants) and the suppressed plants ('lower' plants). A striking feature was that the heights of the 'upper' plants were almost uniform in spite of their varied diameters. Continuous monitoring of growth of the individual plants in the stand revealed that the height of the 'upper' plants became uniform just after the canopy closure, at about 30 d after emergence, and that uniform growth in height of these plants continued for about 70 d until the end of the growing season. On the other hand, growth of the suppressed 'lower' plants terminated at various stages before flowering. The 'height convergence' of the 'upper' plants was thus identified as a key factor for the segregation of the plants into the two groups of distinctly different allometries. Since the segregation of the plants into 'upper' and 'lower' plants was reflected in their dry weights, frequency distributions of log W were similar to those of log H. The bell-shaped distributions of log D were attributed to the overlapping of the diameters of slender 'upper' plants with those of larger 'lower' plants. Significance of 'height convergence' is discussed.
The role of carbohydrate storage and redistribution in the source‐sink relations of wheat and barley during grain filling — a review

SUMMARY Two types of source contribute photosynthate for grain filling in wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), current photosynthate transferred directly to the grain and photosynthate redistributed from reserve pools in vegetative tissues. Reserve pools provide the substrate needed to maintain transport and the supply of assimilate to grains during the dark period of the diurnal cycle and during the latter part of grain filling, when the photosynthetic apparatus is senescing and the rate of dry matter accumulation of grains exceeds the rate of dry matter accumulation of the total crop. In addition reserve pools provide a means by which the current rates of photosynthate production and of photosynthate use in grain filling are allowed to proceed (at least in part) independently from each other. There is evidence that all photosynthetic organs (leaves, glumes and exposed portion of the peduncle) contain one or more diurnal carbohydrate storage pools. Diurnal storage of sucrose seems to be much more important than the transient storage of starch. There is little evidence for fructan pools serving a role as a net source of carbon during the dark period of the diurnal cycle. However, fructan is the most important longer-term reserve carbohydrate of vegetative tissues. Fructan accumulation occurs mainly in the extended internodes and leaf sheaths and usually terminates within three weeks following anthesis, after which fructan is gradually lost until grain maturity. The accumulation and loss of fructan are greatly influenced by environmental conditions and treatments that alter the longer-term balance between photosynthate production by the plant and photosynthate use in grain filling. Observations are consistent with the view that fructan accumulation in expanded vegetative tissue is not competitive with grain filling, but the fructan pools accept surplus photosynthate during periods of low demand by grains and provide photosynthate during longer-term deficits in current photosynthate production. Even under optimal conditions for photosynthesis it is likely that half or more of the photosynthate in mature grains is temporarily deposited in one or more reserve pools before being transferred to the grain. Neither the efficiency of reserve utilization in grain filling nor its potential variability in different genotypes and environments are known. Also, very little is known about the mechanisms that control the partitioning of photosynthate between the grain and reserve pools and the allocation to different types of reserve pools. Future progress in the understanding of photosynthesis-yield relationships will likely depend to a great extent on improved knowledge of the controls that govern photosynthate deposition and redistribution in the different pools of reserve carbohydrate.
Species Diversity, Antifungal Susceptibility, and Virulence Attributes of Candida Colonising the Oral Cavities of Adult Diabetic Patients

Oral candidiasis is a common occurrence in diabetic patients. Species of Candida isolated from these infections and their virulence pattern undergo changes over time and require periodic assessments. Objective of this study was to determine changes in the spectrum of Candida species colonizing oral cavity, their antifungal susceptibility patterns, and virulence attributes, in adult diabetic patients. Oral swabs were collected from 100 patients with diabetes mellitus (DM) and an equal number of healthy controls. Specimens were cultured for Candida and species were identified, according to standard protocols. Of 100 diabetic patients, 42 were colonized by yeasts with C. albicans as the predominant species (51%). Non-Candida albicans Candida (NCAC) species accounted for 47% of the specimens, with C. tropicalis being the commonest. Among healthy controls, 23 were colonized by Candida species, of which C. albicans was predominant. Results obtained indicate that C. albicans continues to be the predominant species in oral cavities of diabetic patients. Candidal carriage was significantly associated with duration of diabetes and fasting blood sugar levels. Virulence attributes, proteinase and phospholipase secretion, and biofilm formation were significantly higher in DM group.