Isolation and characterization of actinobacteria ectosymbionts from Acromyrmex subterraneus brunneus (Hymenoptera, Formicidae)

The ectosymbiont actinobacterium Pseudonocardia was isolated from the integument of Acromyrmex leaf-cutter ants and seems to play a crucial role in maintaining asepsis of the nest. Currently, there has been an intensive search for Pseudonocardia associated with several attine species, but few studies have indicated that other actinobacteria may be associated with these ants as well. We therefore characterized the culturable actinobacteria community associated with the integument of the fungus-growing ant Acromyrmex subterraneus brunneus Forel, 1893 (Hymenoptera: Formicidae). Ectosymbionts were isolated using four different media and characterized by morphological and molecular (16S rDNA) methods. A total of 20 strains were isolated, of which 17 were characterized as Streptomyces spp., and one isolate each as Pseudonocardia, Kitassatospora and Propionicimonas. Unlike other Acromyrmex species, A. subterraneus brunneus is associated with a diversity of actinobacteria. Even though Pseudonocardia is present on this leaf-cutting ant`s integument, the number and diversity of Streptomyces spp. found differs from those of previous studies with other attine ants and suggest that different culturing approaches are needed to characterize the true diversity of microbes colonizing the integument of attine ants. Moreover, understanding the diversity of the culturable actinobacteria associated with A. subterraneus brunneus should increase our knowledge of the evolutionary relationship of this intricate symbiotic association. (C) 2010 Elsevier GmbH. All rights reserved.

Identification of microsatellites markers associated with yield components and quality parameters in sugarcane

Marker assisted selection depends on the identification of tightly linked association between marker and the trait of interest. In the present work, functional (EST-SSRs) and genomic (gSSRs) microsatellite markers were used to detect putative QTLs for sugarcane yield components (stalk number, diameter and height) and as well as for quality parameters (Brix, Pol and fibre) in plant cane. The mapping population (200 individuals) was derived from a bi-parental cross (IACSP95-3018 x IACSP93-3046) from the IAC Sugarcane Breeding Program. As the map is under construction, single marker trait association analysis based on the likelihood ratio test was undertaken to detect the QTLs. Of the 215 single dose markers evaluated (1:1 and 3:1), 90 (42%) were associated with putative QTLs involving 43 microsatellite primers (18 gSSRs and 25 EST-SSRs). For the yield components, 41 marker/trait associations were found: 20 for height, 6 for diameter and 15 for stalk number. An EST-SSRs marker with homology to non-phototropic hypocotyls 4 (NPH4) protein was associated with a putative QTL with positive effect for diameter as also with a negative effect for stalk number. In relation to the quality parameters, 18 marker trait associations were found for Brix, 19 for Pol, and 12 for fibre. For fibre, 58% of the QTLs detected showed a negative effect on this trait. Some makers associated with QTLs with a negative effect for fibre showed a positive effect for Pol, reflecting the negative correlation generally observed between these traits.

Evaluation of algorithms used to order markers on genetic maps

When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results. Heredity (2009) 103, 494-502; doi:10.1038/hdy.2009.96; published online 29 July 2009

Random regression models to estimate test-day milk yield genetic parameters Holstein cows in Southeastern Brazil

A total of 152,145 weekly test-day milk yield records from 7317 first lactations of Holstein cows distributed in 93 herds in southeastern Brazil were analyzed. Test-day milk yields were classified into 44 weekly classes of DIM. The contemporary groups were defined as herd-year-week of test-day. The model included direct additive genetic, permanent environmental and residual effects as random and fixed effects of contemporary group and age of cow at calving as covariable, linear and quadratic effects. Mean trends were modeled by a cubic regression on orthogonal polynomials of DIM. Additive genetic and permanent environmental random effects were estimated by random regression on orthogonal Legendre polynomials. Residual variances were modeled using third to seventh-order variance functions or a step function with 1, 6,13,17 and 44 variance classes. Results from Akaike`s and Schwarz`s Bayesian information criterion suggested that a model considering a 7th-order Legendre polynomial for additive effect, a 12th-order polynomial for permanent environment effect and a step function with 6 classes for residual variances, fitted best. However, a parsimonious model, with a 6th-order Legendre polynomial for additive effects and a 7th-order polynomial for permanent environmental effects, yielded very similar genetic parameter estimates. (C) 2008 Elsevier B.V. All rights reserved.

Winter-feeding systems for gestating sheep II. Effects on feedlot performance, glucose tolerance, and carcass composition of lamb progeny

Mature pregnant crossbred ewes (n = 90) were used in a randomized complete block design experiment and were assigned to 1 of 3 winter-feeding systems differing in primary feed source: haylage (HL), limit-fed corn (CN), or limit-fed dried distillers grains (DDGS). Effects of these winter-feeding strategies on postweaning progeny performance were determined. Lamb progeny (n = 96) were weaned at 61 +/- 4 d of age and fed a common high-concentrate diet. Lambs were assigned to feedlot pen (n = 18) based on dam mid-gestation pen. Growth rate, DMI, and ADG were determined for the first 40 d of the finishing period. At 96 +/- 4 d of age, 1 wether lamb was randomly selected from each pen (n = 18) for a glucose tolerance test. The experiment was terminated, and lambs were slaughtered individually when they were determined to have achieved 0.6-cm 12th-rib fat thickness. After a 24-h chill, carcass data were collected and a 2.54-cm chop was removed from each lamb from the LM posterior to the 12th rib for ether extract analysis. Additional carcass measurements of bone, muscle, and fat from the shoulder, rack, loin, and leg were collected on 35 carcasses. At weaning, lamb BW was not different among treatments, whereas final BW tended to be greater (P = 0.09) for lambs from ewes fed DDGS and CN during gestation than from those fed HL. Overall lamb growth rate from birth to slaughter was not different among treatments. Lambs from ewes fed DDGS vs. CN or HL tended to have a greater initial insulin response (P = 0.09). Dressing percent was less (P = 0.04) in lambs from ewes fed DDGS, but no difference (P = 0.16) was detected in HCW among treatments. As expected, 12th rib fat thickness was similar among treatments, whereas LM area was largest to smallest (P = 0.05) in lambs from ewes fed CN, HL, and DDGS, respectively. Proportion of internal fat tended to be greatest to smallest (P = 0.06) in lambs from ewes fed DDGS, CN, and HL, respectively. Calculated boneless trimmed retail cuts percentage was less (P = 0.04) in lambs from ewes fed DDGS than CN or HL. Loin muscle weight as a percentage of wholesale cut tended (P = 0.10) to be greater in lambs from ewes fed CN and HL than DDGS, whereas other muscle, bone, and fat weights and proportions were similar (P > 0.24) among treatments. Prepartum diet during mid to late gestation of ewes altered postnatal fat and muscle deposition and may be associated with alterations in insulin sensitivity of progeny.

Parameterization and Evaluation of Predictions of DSSAT/CANEGRO for Brazilian Sugarcane

The DSSAT/CANEGRO model was parameterized and its predictions evaluated using data from five sugarcane (Sacchetrum spp.) experiments conducted in southern Brazil. The data used are from two of the most important Brazilian cultivars. Some parameters whose values were either directly measured or considered to be well known were not adjusted. Ten of the 20 parameters were optimized using a Generalized Likelihood Uncertainty Estimation (GLUE) algorithm using the leave-one-out cross-validation technique. Model predictions were evaluated using measured data of leaf area index (LA!), stalk and aerial dry mass, sucrose content, and soil water content, using bias, root mean squared error (RMSE), modeling efficiency (Eff), correlation coefficient, and agreement index. The Decision Support System for Agrotechnology Transfer (DSSAT)/CANEGRO model simulated the sugarcane crop in southern Brazil well, using the parameterization reported here. The soil water content predictions were better for rainfed (mean RMSE = 0.122mm) than for irrigated treatment (mean RMSE = 0.214mm). Predictions were best for aerial dry mass (Eff = 0.850), followed by stalk dry mass (Eff = 0.765) and then sucrose mass (Eff = 0.170). Number of green leaves showed the worst fit (Eff = -2.300). The cross-validation technique permits using multiple datasets that would have limited use if used independently because of the heterogeneity of measures and measurement strategies.

Positive selection on an acrosomal sperm protein, M7 lysin, in three species of the mussel genus Mytilus

Marine invertebrate sperm proteins are particularly interesting because they are characterized by positive selection and are likely to be involved in prezyogotic isolation and, thus, speciation. Here, we present the first survey of inter and intraspecific variation of a bivalve sperm protein among a group of species that regularly hybridize in nature. M7 lysin is found in sperm acrosomes of mussels and dissolves the egg vitelline coat, permitting fertilization. We sequenced multiple alleles of the mature protein-coding region of M7 lysin from allopatric populations of mussels in the Mytilus edulis species group (M. edulis, M. galloprovincialis, and M. trossulus). A significant McDonald-Kreitman test showed an excess of fixed amino acid replacing substitutions between species, consistent with positive selection. In addition, Kolmogorov-Smirnov tests showed significant heterogeneity in polymorphism to divergence ratios for both synonymous variation and combined synonymous and non-synonymous variation within M. galloprovincialis. These results indicate that there has been adaptive evolution at M7 lysin and, furthermore, shows that positive selection on sperm proteins can occur even when post-zygotic reproductive isolation is incomplete.

Sampling phylogenetic tree space with the generalized Gibbs sampler

The generalized Gibbs sampler (GGS) is a recently developed Markov chain Monte Carlo (MCMC) technique that enables Gibbs-like sampling of state spaces that lack a convenient representation in terms of a fixed coordinate system. This paper describes a new sampler, called the tree sampler, which uses the GGS to sample from a state space consisting of phylogenetic trees. The tree sampler is useful for a wide range of phylogenetic applications, including Bayesian, maximum likelihood, and maximum parsimony methods. A fast new algorithm to search for a maximum parsimony phylogeny is presented, using the tree sampler in the context of simulated annealing. The mathematics underlying the algorithm is explained and its time complexity is analyzed. The method is tested on two large data sets consisting of 123 sequences and 500 sequences, respectively. The new algorithm is shown to compare very favorably in terms of speed and accuracy to the program DNAPARS from the PHYLIP package.

Birds - their importance to visitors to an Australian rainforest

Lamington National Park in Queensland, Australia is noted for its rainforest and is part of Australia’s fourteen World Heritage listed properties but no systematic study has been done of the importance of birds to its visitors. This study rectifies this situation. It is based on data from survey forms handed to visitors at an important site in this park and completed by visitors following their visit. This yielded 622 useable replies. These enabled us to establish the comparative importance of birds as an attraction to this site. Furthermore, logit regression is used to analyze and to identify factors that increase the likelihood of a visitor saying that birds are an important attraction. In addition, the relative importance to visitors of various attributes of birds at this site is established. These attributes include hearing birds, diversity of birds, seeing lots of birds, presence of rare birds, presence of brightly colored birds and physical contact with birds. Logit regression analysis is used to isolate independent variables that increase or decrease the likelihood that visitors find diversity of birds, brightly colored birds or physical contact with birds at this site to be important. For example, factors such as the level of education of visitors, their gender, knowledge of birds and conservation attitudes are statistically significant influences.

Birds in an Australian rainforest: Their attraction for visitors and visitors' ecological impacts

Lamington National Park in Queensland, Australia is noted for its rainforest and is part of the World Heritage listed property but prior to this work, no systematic study has been done of the importance of birds to its visitors. This study is based on data from survey forms handed to visitors at an important site in the park and completed by visitors following their visit. It yielded 622 useable responses. These enabled us to establish the comparative importance of birds as an attraction to this site for this sample of visitors. Furthermore, logit regression is used to target analysis and to identify factors that increase the likelihood of a visitor saying that birds are an important attraction. In addition, the relative importance to visitors of various attributes of birds at this site is established. These attributes include hearing birds, diversity of birds, seeing lots of birds, presence of rare birds, presence of brightly coloured birds and physical contact with birds. Logit regression analysis is used to isolate independent variables that increase or decrease the likelihood that visitors find diversity of birds, brightly coloured birds or physical contact with birds at this site to be important. For example, factors such as the level of education of visitors, their gender, knowledge of birds and conservation attitudes and statistically significant influences. As a result of the analysis potential conflicts between different types of park visitors in relation to human interaction with birds are identified. Some potential ecological implications of human interactions with birds are modelled and discussed, and their economic conservation and biodiversity consequences are considered

Minocycline and oral pigmentation

Minocycline is a semisynthetic tetracycline used in the treatment of inflammatory acne because of its broad spectrum of activity, less common development of resistant organisms, and its anti-inflammatory effects. A number of adverse reactions are reported, including skin and oral pigmentation. This paper details the pharmacology of minocycline and describes the pigmentation and likely mechanisms active in both hard and soft tissues. Oral pigmentation usually involves the hard tissues only and presents typically as a discrete band occupying the central zone of the alveolar mucosa and palate. As with other sites, it may persist following withdrawal of the drug. Early recognition by the dental practitioner may allow an alternative form of therapy to be sought, minimizing the likelihood of a longterm aesthetic problem.

On the mechanism of microbial cell disruption in high-pressure homogenisation

The tensions produced in the wall of a rigid, thin-walled, liquid-filled sphere as it moves with an axisymmetric straining flow are examined. This problem has not been previously addressed. A generalised correlation for the maximum wall tension, expressed in dimensionless form as a Weber number (We), is developed in terms of the acceleration number (Ac) and Reynolds number (Re) of the straining flow. At low Reynolds number We is dominated by viscous forces, while inertial forces due to internal pressure gradients caused by sphere acceleration dominate at higher Re. The generalised correlation has been used to examine the case of a typical yeast cell (a thin-walled, liquid-filled sphere) passing through a typical high-pressure homogeniser (a straining-flow device). At 56 MPa homogenising pressure, a 6 mu m yeast cell experiences tensions in the inertially dominated regime (Re = 100). The correlation gives We = 0.206, corresponding to a maximum wall tension of 8 Nm(-1). This is equivalent to an applied compressive force of 150 mu N and compares favourably with the force required to break yeast cells under compressive micromanipulation (40-90 mu N). Inertial forces may therefore be an important and previously unrecognised. mechanism of microbial cell disruption during high-pressure homogenisation. Further work is required to examine the likelihood of cell deformation in the high-strain-rate short-residence-time environment of the homogeniser, and the effect that such deformation may have on the contribution of inertial forces to disruption. (C) 1998 Published by Elsevier Science Ltd. All rights reserved.

Distinguishing species and populations of Rhipicephaline ticks with its 2 ribosomal RNA

Most populations and some species of ticks of the genera Boophilus (5 spp.) and Rhipicephalus (ca. 75 spp.) cannot be distinguished phenotypically. Moreover, there is doubt about the validity of species in these genera. I studied the entire second internal transcribed spacer (ITS 2) rRNA of 16 populations of rhipicephaline ticks to address these problems: Boophilus,microplus from Australia, Kenya, South Africa and Brazil (4 populations); Boophilus decoloratus from Kenya; Rhipicephalus appendiculatus from Kenya, Zimbabwe and Zambia (7 populations); Rhipicephalus zambesiensis from Zimbabwe (3 populations); and Rhipicephalus evertsi from Kenya. Each of the 16 populations had a unique ITS 2, but most of the nucleotide variation occurred among species and genera. ITS 2 rRNA can be used to distinguish the populations and species of Boophilus and Rhipicephalus studied here. Little support was found for the hypothesis that B. microplus from Australia and South Africa are different species. ITS 2 appears useful for phylogenetic inference in the Rhipicephalinae because in genetic distance, maximum likelihood, and maximum parsimony analyses, most branches leading to species had >95% bootstrap support. Rhipicephalus appendiculatus and R, zambeziensis are closely related, yet their ITS 2 sequences could be distinguished unambiguously. This lends weight to a previous proposal that Rhipicephalus sanguineus and Rhipicephalus turanicus, and Rhipicephalus pumlilio and Rhipicephalus camicasi, respectively, are conspecific, because each of these pairs of species had identical sequences for ca. 250 bp of ITS 2 rRNA.

Critical values for unit root and cointegration test statistics - the use of response surface equations

This note considers the value of surface response equations which can be used to calculate critical values for a range of unit root and cointegration tests popular in applied economic research.

Predictors of local recurrence after treatment of ductal carcinoma in situ - A meta-analysis

lBACKGROUND. Management of patients with ductal carcinoma in situ (DCIS) is a dilemma, as mastectomy provides nearly a 100% cure rate but at the expense of physical and psychologic morbidity. It would be helpful if we could predict which patients with DCIS are at sufficiently high risk of local recurrence after conservative surgery (CS) alone to warrant postoperative radiotherapy (RT) and which patients are at sufficient risk of local recurrence after CS + RT to warrant mastectomy. The authors reviewed the published studies and identified the factors that may be predictive of local recurrence after management by mastectomy, CS alone, or CS + RT. METHODS. The authors examined patient, tumor, and treatment factors as potential predictors for local recurrence and estimated the risks of recurrence based on a review of published studies. They examined the effects of patient factors (age at diagnosis and family history), tumor factors (sub-type of DCIS, grade, tumor size, necrosis, and margins), and treatment (mastectomy, CS alone, and CS + RT). The 95% confidence intervals (CI) of the recurrence rates for each of the studies were calculated for subtype, grade, and necrosis, using the exact binomial; the summary recurrence rate and 95% CI for each treatment category were calculated by quantitative meta-analysis using the fixed and random effects models applied to proportions. RESULTS, Meta-analysis yielded a summary recurrence rate of 22.5% (95% CI = 16.9-28.2) for studies employing CS alone, 8.9% (95% CI = 6.8-11.0) for CS + RT, and 1.4% (95% CI = 0.7-2.1) for studies involving mastectomy alone. These summary figures indicate a clear and statistically significant separation, and therefore outcome, between the recurrence rates of each treatment category, despite the likelihood that the patients who underwent CS alone were likely to have had smaller, possibly low grade lesions with clear margins. The patients with risk factors of presence of necrosis, high grade cytologic features, or comedo subtype were found to derive the greatest improvement in local control with the addition of RT to CS. Local recurrence among patients treated by CS alone is approximately 20%, and one-half of the recurrences are invasive cancers. For most patients, RT reduces the risk of recurrence after CS alone by at least 50%. The differences in local recurrence between CS alone and CS + RT are most apparent for those patients with high grade tumors or DCIS with necrosis, or of the comedo subtype, or DCIS with close or positive surgical margins. CONCLUSIONS, The authors recommend that radiation be added to CS if patients with DCIS who also have the risk factors for local recurrence choose breast conservation over mastectomy. The patients who may be suitable for CS alone outside of a clinical trial may be those who have low grade lesions with little or no necrosis, and with clear surgical margins. Use of the summary statistics when discussing outcomes with patients may help the patient make treatment decisions. Cancer 1999;85:616-28. (C) 1999 American Cancer Society.