Low genetic diversity in the vulnerable Goitred Gazelle,Gazella subgutturosa (Cetartiodactyla: Bovidae), in Iran: potential genetic consequence of recent population declines

The Goitered Gazelle, Gazella subgutturosa, is the most widespread gazelle species in the Middle East and central Asia inhabiting desert and semi-desert habitats. Today it is threatened and its geographic range and population size have experienced significant decline in the last decades. In Iran, the remnant populations are confined to fragmented habitats. We aimed to characterise genetic diversity and phylogenetic status of the populations of Goitered Gazelle in Central Iran and to evaluate the potential effect of a historic population bottleneck on the genetic variation of today’s population. We used noninvasive sampling to uncover structure and level of genetic variation in a fragment of the cytochrome-b gene from 170 samples. Genealogical analyses were performed using HKY+I model and phylogenetic trees reconstructed using Bayesian inference and maximum likelihood. We found extremely low levels of genetic variation, with altogether only five haplotypes in samples from different populations. Overall haplotype diversity was 0.081 and nucleotide diversity 0.0003. The mean observed mismatch between any two sequences was 0.093 with the largest peak for small numbers. The mismatch distribution fit the model of population expansion and suggested that gazelles had experienced a sudden expansion. An unrooted median-joining network analysis of mtDNA haplotypes showed a star-like structure which few mutations steps separating the haplotypes from other regions. Our findings strengthen the urgency of preserving the species’ genetic diversity to prevent local extinction.     

Denitrification and N2O emissions from a UK pasture soil following the early spring application of cattle slurry and mineral fertiliser

Total denitrification and nitrous oxide (N₂O) losses were measured from three contrasting dairy management systems representing good commercial practice (system 1), production maintained but with reduced N losses (system 2); and nitrate leaching less than 50 mg L^-1 but with reduced production (system 3). Measurements were made following mineral fertiliser application and from two plot experiments where four treatments were applied: control, NH₄NO₃ at 60 kg N ha^-1, cattle slurry applied to the surface (equivalent to 45 kg N ha^-1), and cattle slurry injected. Despite low soil temperatures (<6 °C) and low rainfall (<3 mm), total denitrification and N₂O losses peaked at 56 and 16 g N ha^-1 d^-1, respectively. Total denitrification losses decreased: system 1 system 2 > system 3, whereas N₂O losses decreased: system 2 > system 3 > system 1. Total denitrification losses tended to decrease with decreasing fertiliser application rate, whereas fertiliser application rate was not the sole determinant of the N₂O loss. The system 3 field was injected with cattle slurry for 2 yr, system 2 received some slurry by injection and system 1 received slurry to the surface. Thus, the amount, timing and method of previous cattle slurry application was important in determining the loss following subsequent fertiliser application. For the plot experiments, total denitrification and N₂O losses decreased in the order: slurry injected > mineral fertiliser > slurry applied to the surface > control for 5 days following application. However, 16 and 19 days after application, N₂O losses above the control were measured from plots that had received cattle slurry. It was inferred that the application of cattle slurry to the pasture soil stimulated greater N₂O production and increased losses over a longer time period compared with mineral fertiliser additions.     

Oxidative damage to ferritin by 5-aminolevulinic acid

5-Aminolevulinic acid (ALA), a heme precursor overproduced in various porphyric disorders, has been implicated in iron-mediated oxidative damage to biomolecules and cell structures. From previous observations of ferritin iron release by ALA, we investigated the ability of ALA to cause oxidative damage to ferritin apoprotein. Incubation of horse spleen ferritin (HoSF) with ALA caused alterations in the ferritin circular dichroism spectrum (loss of a alpha-helix content) and altered electrophoretic behavior. Incubation of human liver, spleen, and heart ferritins with ALA substantially decreased antibody recognition (51, 60, and 28% for liver, spleen, and heart, respectively). Incubation of apoferritin with 1-10mM ALA produced dose-dependent decreases in tryptophan fluorescence (11-35% after 5h), and a partial depletion of protein thiols (18% after 24h) despite substantial removal of catalytic iron. The loss of tryptophan fluorescence was inhibited 35% by 50mM mannitol, suggesting participation of hydroxyl radicals. The damage to apoferritin had no effect on ferroxidase activity, but produced a 61% decrease in iron uptake ability. The results suggest a local autocatalytic interaction among ALA, ferritin, and oxygen, catalyzed by endogenous iron and phosphate, that causes site-specific damage to the ferritin protein and impaired iron sequestration. These data together with previous findings that ALA overload causes iron mobilization in brain and liver of rats may help explain organ-specific toxicities and carcinogenicity of ALA in experimental animals and patients with porphyria.     

Conformational stability and normal coordinate analyses for 1-halovinyl azides CH<Subscript>2</Subscript>=CX–NNN (X is F,Cl and Br)

The conformational behavior of 1-halovinyl azides CH2=CX-NNN (X=F, Cl and Br) were investigated by DFT-B3LYP and ab initio MP2 calculations with the 6-311++G** basis set. The molecules were predicted to exist predominantly in the trans (the vinyl CH2=CH- and the azide -NNN groups are trans to each other) conformation. The relative energy between cis and trans were calculated to decrease in order: bromide>chloride>fluoride. Full optimization was performed at the ground and transition states in the molecule at both MP2 and B3LYP levels. The barrier to internal rotation around the C-N single bond in the three molecules was calculated to be about 4-5 kcal mol(-1). The vibrational frequencies were computed at the DFT-B3LYP level and the calculated infrared and Raman spectra of the cis- trans mixture of the three molecules were plotted. Complete vibrational assignments were made on the basis of normal coordinate calculations for both stable conformers of the three molecules.     

Sterols and steryl esters in some Brassica and Sinapis seeds

The qualitative and quantitative composition of sterols in the free form and esterified to fatty acids was studied in seed oils from Brassica napus, B. campestris, B..iuncea, B. nigra, Sinapis alba and S. aruefisis (Brassica kaber). Sitosterol, followed by campesterol, predominated in both the free and the esterified sterols. The free sterols were richer in brassicasterol (ca 10–20%) than the steryl esters (3–10%). Small amounts of δ⁵-avenasterol and δ⁷-stigmastenol were also found in the Brassica oils, often more in the esterified than in the free form. The quantity of sterols was studied only in Brassica campestris, which had ca 0.3 % in the free as well as in the esterified form. In Sinapis alba, ca 10% of the sterols in the free form and 20 % in the esterified sterols were δ⁵-avenasterol. This compared to only a few per cent in both the free and esterified sterols in the Brassica oils. Similarly, ca 2 % of cholesterol was found among the sterols of Sinapis alba but only traces in the Brassica oils. The similarity of sterol compositions among the cultivated brassicas and wild mustard (Sinapis arvensis), and the specific characteristics of the sterols in white mustard (Sinapis alba) adds further weight to the suggestion that wild mustard should be treated as Brassica kaber and strengthens the generic separation of Sinapis alba.     

Direct observation of cell wall structure in living plant tissues by solid-state C NMR spectroscopy

Solid-state ¹³C nuclear magnetic resonance (NMR) spectra of the following intact plant tissues were recorded by the crosspolarization magic-angle spinning technique: celery (Apium graveolens L.) collenchyma; carob bean (Ceratonia siliqua L.), fenugreek (Trigonella foenum-graecum L.), and nasturtium (Tropaeolum majus L.) endosperm; and lupin (Lupinus polyphyllus Lindl.) seed cotyledons. All these tissues had thickened cell walls which allowed them to withstand the centrifugal forces of magic angle spinning and which, except in the case of lupin seeds, dominated the NMR spectra. The celery collenchyma cell walls gave spectra typical of dicot primary cell walls. The carob bean and fenugreek seed spectra were dominated by resonances from galactomannans, which showed little sign of crystalline order. Resonances from β(1,4′)-d galactan were visible in the lupin seed spectrum, but there was much interference from protein. The nasturtium seed spectrum was largely derived from a xyloglucan, in which the conformation of the glucan core chain appeared to be intermediate between the solution form and solid forms of cellulose.     

Coefficients of digestibility and nutritional values of geophytes and tubers eaten by southern African mole-rats (Rodentia: Bathyergidae)

Subterranean rodents have high energy requirements when they are excavating their burrows. This study investigates the energy available to, and the efficiency with which it can be extracted by, four species of bathyergid mole-rats fed natural diets ranging from the underground storage organs of geophytes to grass roots and leaves.
The digestibility coefficients of geophytes ranged from 53% for the fibrous tuber of the gemsbok cucumber to 95–7% for corms and bulbs. One species, Bathyergus suillus whose diet consists of over 80% grass, had a digestibility coefficient of 87% on an all grass diet.
All species had similar coefficients of digestibility of > 90% when fed on a uniform diet of sweet potato.
Bulbs and corms had a low fibre content (3–3–4%), high calorific value (15–16kJ/g) and high digestibility coefficients (95–7–96%) and on this diet the mole-rats maintained their body mass. Food of lower digestibility tended to have a high fibre content (8–2–45%) and, with the exception of B. suillus , although the mole-rats consumed a greater quantity of food, they lost mass. The sweet potato had a low fibre content (4–1 %) but was energetically very similar to bulbs and corms (15–5 kJ/g).
Geophytes which have low fibre contents are generally small (1–20 g), whereas geophytes with high fibre contents are much larger (30–2000 g) and often occur in more arid zones.     

Disease-associated pathophysiologic structures in pediatric rheumatic diseases show characteristics of scale-free networks seen in physiologic systems: implications for pathogenesis and treatment

Background

Tamoxifen (TAM) is a well characterized breast cancer drug and selective estrogen receptor modulator (SERM) which also has been associated with a small increase in risk for uterine cancers. TAM's partial agonist activation of estrogen receptor has been characterized for specific gene promoters but not at the genomic level in vivo.Furthermore, reducing uncertainties associated with cross-species extrapolations of pharmaco- and toxicogenomic data remains a formidable challenge.

Results

A comparative ligand and species analysis approach was conducted to systematically assess the physiological, morphological and uterine gene expression alterations elicited across time by TAM and ethynylestradiol (EE) in immature ovariectomized Sprague-Dawley rats and C57BL/6 mice. Differential gene expression was evaluated using custom cDNA microarrays, and the data was compared to identify conserved and divergent responses. 902 genes were differentially regulated in all four studies, 398 of which exhibit identical temporal expression patterns.

Conclusion

Comparative analysis of EE and TAM differentially expressed gene lists suggest TAM regulates no unique uterine genes that are conserved in the rat and mouse. This demonstrates that the partial agonist activities of TAM extend to molecular targets in regulating only a subset of EE-responsive genes. Ligand-conserved, species-divergent expression of carbonic anhydrase 2 was observed in the microarray data and confirmed by real time PCR. The identification of comparable temporal phenotypic responses linked to related gene expression profiles demonstrates that systematic comparative genomic assessments can elucidate important conserved and divergent mechanisms in rodent estrogen signalling during uterine proliferation.     

Greenbeards in yeast: an undergraduate laboratory exercise to teach the genetics of cooperation

Recent years have seen a dramatic increase in our understanding of the social behaviour of microbes. Here, we take advantage of these developments to present an undergraduate laboratory exercise that uses the cooperative flocculating behaviour of yeast (Saccharomyces sp.) to introduce the concept of inclusive fitness and teach the genetics of cooperation. Students generate their own data using co-cultures of various yeast strains and perform statistical analyses to test whether kin selection or greenbeard effects determine the cooperative flocculating behaviour. The lab has run successfully for two consecutive years in a second year course with some 1, 200 students per year at the University of Toronto, Canada. We discuss the benefits of using microbes to teach social evolution, describe the set-up and learning outcomes of the laboratory exercise, and then outline possible extension and variants of the lab. In addition to providing students with the opportunity to use a model organism to study social behaviour, students are also taught common laboratory skills, such as replica plating and sterile techniques. Ultimately, while the genetics of cooperation has traditionally been taught through computer simulations and evolutionary games, this exercise demonstrates a way to experimentally introduce the topic.     

Trypanosoma brucei: a survey of pyrimidine transport activities

Purine uptake has been studied in many protozoan parasites in the last few years, and several of the purine transporters have been cloned. In contrast, very little is known about the salvage of preformed pyrimidines by protozoa, and no pyrimidine transporters have been cloned, yet chemotherapy based on pyrimidine nucleobases and nucleosides has been as effective as purine antimetabolites in the treatment of infectious and neoplastic disease. Here, we surveyed the presence of pyrimidine transporters in Trypanosoma brucei brucei. We could not detect any mediated uptake of thymine, thymidine or cytidine, but identified a very high-affinity transporter for cytosine, designated C1, with a K(m) value of 0.048+/-0.009 microM. We also confirmed the presence of the previously reported U1 uracil transporter and found it capable of mediating uridine uptake as well, with a K(m) of 33+/-5 microM. A higher-affinity U2 uridine transporter (K(m)=4.1+/-2.1 microM) was also identified, but efficiency of the C1 and U2-mediated transport was low. Pyrimidine antimetabolites were tested as potential trypanocidal agents and only 5-fluorouracil was found to be effective. This drug was efficiently taken up by bloodstream forms of T. b. brucei.