Sample size for diversity studies in tetraploid alfalfa (<Emphasis Type="Italic">Medicago sativa</Emphasis>) based on codominantly coded SSR markers

The number of genotypes investigated per population is important for the reliability of diversity studies. The objective of this study was to determine the sample size for the identification of differences among populations of an outcrossing autotetraploid species, alfalfa (Medicago sativa), using codominantly coded SSR markers. One hundred and twenty genotypes from each of two closely related populations were analysed with two markers. Twenty random subsamples for each of three sample sizes (10, 20 and 40 genotypes) were built. Compared to the populations with 120 genotypes, alleles that were no longer present in subsamples with 40 genotypes were mainly rare, whereas abundant alleles were also excluded in subsamples with 10 genotypes. F _ST values for pairs of subsamples between the two populations were always significantly different based on 40 genotypes, whereas for 10 genotypes more than half of the pairs were not significantly different. We concluded that 40 genotypes are a reasonable sample size for diversity studies with closely related populations of tetraploid alfalfa investigated with SSR markers. Twenty genotypes may be an economical alternative for large scale studies, but 10 genotypes were a too low number for reliable results.     

Integrating functional diversity into tropical forest plantation designs to study ecosystem processes

? The elucidation of relationships between biodiversity and ecosystem processes has been limited by the definition of metrics of biodiversity and their integration into experimental design. Functional trait screening can strengthen the performance of these designs.

? We suggest the use of Rao’s quadratic entropy to measure both functional diversity and phylogenetic diversity of species mixtures proposed for an experimental design, and demonstrate how they can provide complementary information.

? We also present an index assessing the statistical performance of these independent variables in different experimental designs. Measurement of independent variables as continuous vs. discrete variables reduces statistical performance, but improves the model by quantifying species differences masked by group assignments.

? To illustrate these advances, we present an example from a tropical forest tree community in which we screened 38 species for nine functional traits. The proposed TropiDEP design is based on the relative orthogonality of two multivariate trait axes defined using principal component analysis.

? We propose that independent variables describing functional diversity might be grouped to calculate independent variables describing suites of different traits with potentially different effects on particular ecosystem processes. In other systems these axes may differ from those reported here, yet the methods of analysis integrating functional and phylogenetic diversity into experimental design could be universal.

     

Atomic-level characterization of the structural dynamics of proteins

Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.     

Long‐term outcome after implantation of a suprachoroidal cyclosporine drug delivery device in horses with recurrent uveitis

Objective To determine the long‐term efficacy, complications, and duration of effect of a cyclosporine (CsA) suprachoroidal implant (CSI) in horses with equine recurrent uveitis (ERU). Methods Horses with ERU were treated with a 6‐mm diameter, 25 mg, reservoir matrix CsA implant in the deep sclera adjacent to the suprachoroidal space. Horses with follow‐up >1 year were examined for frequency of uveitis episodes, complications, and vision at last recheck. Results Data from 151 eyes of 133 horses from the USA and Europe that had CsA devices implanted for ERU were reviewed. Follow‐up time ranged from 13 to 85 months after surgery, with a mean and median follow‐up time of 28.9 and 26.3 months, respectively. Overall, at last follow‐up 78.8% of eyes were considered visual and the overall mean frequency of uveitis episodes after CSI was 0.09 ± SD 0.08 episodes per month. The most common complications leading to vision loss at last follow‐up were persistent uveitis episodes (54%), glaucoma (22%), mature cataracts (16%), and retinal detachment (6%). Persistent uveitis episodes tended to be the highest cause of vision loss in horses with <24 months and >48 months of follow‐up. Conclusions This study demonstrated the long‐term maintenance of vision of horses with ERU implanted with a CSI. The increased vision loss related to uveitis episode of inflammation in eyes after the likely depletion of CsA from the CSI suggests that a repeat CSI may be required at or before 48 months after surgery.     

Detection of GTP-tubulin conformation in vivo reveals a role for GTP remnants in microtubule rescues

Microtubules display dynamic instability, with alternating phases of growth and shrinkage separated by catastrophe and rescue events. The guanosine triphosphate (GTP) cap at the growing end of microtubules, whose presence is essential to prevent microtubule catastrophes in vitro, has been difficult to observe in vivo. We selected a recombinant antibody that specifically recognizes GTP-bound tubulin in microtubules and found that GTP-tubulin was indeed present at the plus end of growing microtubules. Unexpectedly, GTP-tubulin remnants were also present in older parts of microtubules, which suggests that GTP hydrolysis is sometimes incomplete during polymerization. Observations in living cells suggested that these GTP remnants may be responsible for the rescue events in which microtubules recover from catastrophe.     

Nematode resistance in bananas: screening results on some wild and cultivated accessions of Musa spp.

Bananas cultivated for export all belong to Cavendish cultivars and are all recognized as very susceptible to nematodes, particularly to the burrowing nematode Radopholus similis and the lesion nematode Pratylenchus coffeae. Even if there have been many changes in the management of banana nematodes in large commercial banana plantations, chemical control still remains most often the last resort method to manage the nematodes, although the number of registered products is definitely declining. Therefore, nematode control though genetic improvement is gaining new interest worldwide. In this study, 55 banana accessions mostly diploids from the Musa acuminata genome group (AA) but including some triploid accessions (AAA), some diploids of the Musa balbisiana genome group (BB) and some interspecific hybrids (AAB, AB) were evaluated for resistance to four nematode species R. similis, P. coffeae, Meloidogyne incognita and M. arenaria. These experiments were conducted in a growth chamber under controlled conditions. All banana accessions were susceptible to nematode species, although many different levels of susceptibility were detected. This study confirmed the good resistance status to R. similis of some cultivars from the Pisang jari buaya and Pisang batuau subgroups and the partial resistance of 17 diploid accessions significantly different from the susceptible reference cv. Grande Naine. This study also showed that 12 diploid accessions exhibited a partial resistance to P. coffeae, including some usual or potential genitors belonging to the wild diploids subspecies burmannica (cvs. Long Tavoy 1 and 2) and burmannicoides (cv. Calcutta 4). No source of resistance to Meloidogyne spp. was found. These screening results, combining for the first time four nematode species, are discussed within the scope of banana breeding in order to produce parental diploid lines with single or combined nematode resistances and further develop triploids that can substitute existing susceptible commercial cultivars.     

Multiple Ebola virus transmission events and rapid decline of central African wildlife

Several human and animal Ebola outbreaks have occurred over the past 4 years in Gabon and the Republic of Congo. The human outbreaks consisted of multiple simultaneous epidemics caused by different viral strains, and each epidemic resulted from the handling of a distinct gorilla, chimpanzee, or duiker carcass. These animal populations declined markedly during human Ebola outbreaks, apparently as a result of Ebola infection. Recovered carcasses were infected by a variety of Ebola strains, suggesting that Ebola outbreaks in great apes result from multiple virus introductions from the natural host. Surveillance of animal mortality may help to predict and prevent human Ebola outbreaks.     

Pharmacokinetics and tissue fluid distribution of cephalexin in the horse after oral and i.v. administration

The purpose of this study was to determine the pharmacokinetics and tissue fluid distribution of cephalexin in the adult horse following oral and i.v. administration. Cephalexin hydrate (10 mg/kg) was administered to horses i.v. and plasma samples were collected. Following a washout period, cephalexin (30 mg/kg) was administered intragastrically. Plasma, interstitial fluid (ISF) aqueous humor, and urine samples were collected. All samples were analyzed by high-pressure liquid chromatography (HPLC). Following i.v. administration, cephalexin had a plasma half-life (t(1/2)) of 2.02 h and volume of distribution [V(d(ss))] of 0.25 L/kg. Following oral administration, the average maximum plasma concentration (C(max)) was 3.47 mug/mL and an apparent half-life (t(1/2)) of 1.64 h. Bioavailability was approximately 5.0%. The AUC(ISF):AUC(plasma) ratio was 80.55% which corresponded to the percentage protein-unbound drug in the plasma (77.07%). The t(1/2) in the ISF was 2.49 h. Cephalexin was not detected in the aqueous humor. The octanol:water partition coefficient was 0.076 +/- 0.025. Cephalexin was concentrated in the urine with an average concentration of 47.59 microg/mL. No adverse events were noted during this study. This study showed that cephalexin at a dose of 30 mg/kg administered orally at 8 h dosage intervals in horses can produce plasma and interstitial fluid drug concentrations that are in a range recommended to treat susceptible gram-positive bacteria (MIC < or = 0.5 microg/mL). Because of the low oral bioavailability of cephalexin in the horse, the effect of chronic dosing on the normal intestinal bacterial flora requires further investigation.