Evaluation of the validity of a maximum likelihood adaptive staircase procedure for measurement of olfactory detection threshold in mice

Threshold is defined as the stimulus intensity necessary for a subject to reach a specified percent correct on a detection test. MLPEST (maximum likelihood parameter estimation by sequential testing) is a method that is able to determine threshold accurately and more rapidly than many other methods. Originally developed for human auditory and visual tasks, it has been adapted for human olfactory and gustatory tests. In order to utilize this technique for olfactory testing in mice, we have adapted MLPEST methodology for use with computerized olfactometry as a tool to estimate odor detection thresholds. Here we present Monte Carlo simulations and operant conditioning data that demonstrate the potential utility of this technique in mice, we explore the ramifications of altering MLPEST test parameters on performance, and we discuss the advantages and disadvantages of using MLPEST compared to other methods for the estimation of thresholds in rodents. Using MLPEST, we find that olfactory detection thresholds in mice deficient for the cyclic nucleotide-gated channel subunit A2 are similar to those of wild-type animals for odorants the knockout animals are able to detect.     

Raman microspectroscopy as an identification tool within the phylogenetically homogeneous 'Bacillus subtilis' group

Vibrational methods have multiple advantages compared to more classic, chemotaxonomic and even molecular microbial tools for the identification of bacteria. Nevertheless, their definite breakthrough in diagnostic microbiology laboratories is determined by their identification potential. This paper reports on the profound evaluation of Raman spectroscopy to identify closely related species by means of 68 Bacillus strains that are assigned or closely related to the phylogenetically homogeneous ‘Bacillus subtilis’-group (sensu stricto). These strains were chosen to represent biological variation within the selected species and to create a realistic view on the possibilities of this technique

The evaluation resulted in 49/54 correct identifications at the species level for intern and 15/19 for extern testing. The correct identification of strains, which were not represented in the training set, supports the potential as an identification tool within the ‘B. subtilis group’. Considering the vague borderline between the species studied, Raman spectroscopy can be regarded here as a promising application for identifications at the species level.     

Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci?

A computer simulation study has been made of the accuracy of estimates of Theta = 4Nemu from a sample from a single isolated population of finite size. The accuracies turn out to be well predicted by a formula developed by Fu and Li, who used optimistic assumptions. Their formulas are restated in terms of accuracy, defined here as the reciprocal of the squared coefficient of variation. This should be proportional to sample size when the entities sampled provide independent information. Using these formulas for accuracy, the sampling strategy for estimation of Theta can be investigated. Two models for cost have been used, a cost-per-base model and a cost-per-read model. The former would lead us to prefer to have a very large number of loci, each one base long. The latter, which is more realistic, causes us to prefer to have one read per locus and an optimum sample size which declines as costs of sampling organisms increase. For realistic values, the optimum sample size is 8 or fewer individuals. This is quite close to the results obtained by Pluzhnikov and Donnelly for a cost-per-base model, evaluating other estimators of Theta. It can be understood by considering that the resources spent collecting larger samples prevent us from considering more loci. An examination of the efficiency of Watterson's estimator of Theta was also made, and it was found to be reasonably efficient when the number of mutants per generation in the sequence in the whole population is less than 2.5.     

Gene gain and gene loss in streptococcus: is it driven by habitat?

Bacterial genomes can evolve either by gene gain, gene loss, mutating existing genes, and/or by duplication of existing genes. Recent studies have clearly demonstrated that the acquisition of new genes by lateral gene transfer (LGT) is a predominant force in bacterial evolution. To better understand the significance of LGT, we employed a comparative genomics approach to model species-specific and intraspecies gene insertions/deletions (ins/del among 12 sequenced streptococcal genomes using a maximum likelihood method. This study indicates that the rate of gene ins/del is higher on the external branches and varies dramatically for each species. We have analyzed here some of the experimentally characterized species-specific genes that have been acquired by LGT and conclude that at least a portion of these genes have a role in adaptation.     

Robustness of coalescent estimators to between-lineage mutation rate variation

Data from HIV and from human neoplastic cells can show substantial between-lineage mutation rate variation even within a single population. Such variation may affect estimators of population quantities such as Theta = 4N(e)mu. Using simulated DNA data, I measured the effect of rate variation on recovery of Theta by the summary-statistic estimator of Watterson (Watterson GA. 1975. On the number of segregating sites in genetical systems without recombination. Theor Popul Biol. 7:256-276) and the coalescent maximum likelihood algorithm LAMARC (Kuhner MK. 2006. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics. Advance Access doi: 10.1093/bioinformatics/btk051). Watterson's estimator showed a downward bias, as expected, with high values of Theta. LAMARC's mean estimate was accurate for all tested values of Theta and rate variation except for a downward bias when rate variation was maximal (i.e., the slow rate was zero). LAMARC had consistently narrower confidence intervals (CIs) than Watterson's estimator. Both methods tended to reject the truth too often when rate variation was 8x or greater and independent among branches, as well as when variation was 4x or greater and correlated among branches. In the case of Watterson's estimate, this excess rejection was fully attributable to variation among genealogies in the amount of total branch length associated with the fast and slow rates. However, in the case of LAMARC, some excess rejection was still observed even when between-genealogy variation was taken into account. Both estimators are robust to modest rate variation; however, their use should be coupled with a statistical test to rule out extreme rate variation as the resulting CIs may not be reliable.     

Nanomechanics of Native Thick Filaments from Indirect Flight Muscles

During flight, the wings of Drosophila melanogaster beat nearly 200 times per second. The indirect flight muscle fibers that power this movement have evolved to resist the repetitive mechanical stress that results from the 5-ms wing beat cycle at a strain amplitude of 3.5%. In order to understand how this is achieved at the sarcomere level, we have analyzed the mechanical properties of native thick filaments isolated from indirect flight muscle. Single filaments adsorbed onto a solid support were manipulated in physiological buffer using an atomic force microscope. Images taken after the manipulation revealed that segments were stretched, on average, to 150%, with a maximum at 385% extension. The lateral-force-versus-displacement curve associated with each manipulation contained information about the bending and tensile properties of each filament. The bending process was dominated by shearing between myosin dimers and yielded a shear modulus between 3 and 13 MPa. Maximum tension along the stretched filaments was observed at ∼ 200% extension and varied between 8 and 17 nN. Based on current models of thick filament structure, these variations can be attributed to cross-links between myosin dimers distributed along the filament.     

Photosynthetic acclimation to CO2 enrichment related to ribulose-1,5-bisphosphate carboxylation limitation in wheat

Net photosynthetic rate (P _N) measured at the same CO₂ concentration, the maximum in vivo carboxylation rate, and contents of ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBPCO) and RuBPCO activase were significantly decreased, but the maximum in vivo electron transport rate and RuBP content had no significant change in CO₂-enriched [EC, about 200 μmol mol⁻¹ above the ambient CO₂ concentration (AC)] wheat leaves compared with those in AC grown wheat leaves. Hence photosynthetic acclimation in wheat leaves to EC is largely due to RuBP carboxylation limitation.     

<Emphasis Type="Italic">Interleukin13</Emphasis> haplotypes and susceptibility of Iranian women to breast cancer

Interleukin-13 (IL-13) is a TH2 cytokine with direct and indirect immunoregulatory functions on cancer cells. The cytokine has been reported to have some polymorphic variations at the gene level associated with some immune related diseases including asthma and allergy. In the present study, association of three IL13 gene polymorphisms at positions −1512 A/C and −1055 C/T in the promoter and +2044 G/A in exon-4 was investigated in Iranian women with breast cancer and healthy controls. Genotyping of IL13 gene polymorphisms were performed by PCR–RFLP methods. Serum level of IL-13 was assessed by ELISA. Haplotypes were constructed from genotypic data using Arlequin 3.1 software package. Haplotype analysis revealed higher frequency of a three-locus haplotype, ACA (−1512A/−1055C/+2044A), in normal women than breast cancer patients (P < 0.025). Haplotype CCA, from the other hand, was observed with more frequency among patients than controls (P < 0.03). No statistically significant differences were found in the frequency of genotypes and alleles between patients and control group. No association was observed between investigated genotypes and other prognostic factors including tumor type, lymph node involvement and tumor size. IL-13 serum level was undetectable in both patients and control subjects. Despite observing no association between breast cancer and the single SNPs, results of this investigation suggest that the presence of CCA haplotype of IL13 gene may be associated with susceptibility of Iranian women to breast cancer.     

Effect of roughage level in a total mixed ration on feed intake, ruminal fermentation patterns and chewing activity of early-weaned calves with ad libitum access to grass hay

In this study, two total mixed rations (TMR, based on dry ingredients) consisting (per kg dry matter (DM)) of 300 or 400 g finely chopped hay mixture of grass and alfalfa (H30 versus H40) were compared concerning their effects on dry matter intake (DMI), ruminal fermentation patterns and chewing activity of early-weaned (8 weeks milk-fed) calves. Ten ruminally cannulated male German Holstein calves were randomly assigned to two dietary treatments (n = 5) and observed from an age of 8–15 weeks. One group received the H30 (11.3 MJ metabolizable energy (ME)/kg DM) and the other the H40 (10.7 MJ ME/kg DM) TMR. All calves received grass hay (9.0 MJ ME/kg DM) separately. Water, TMR and hay were offered ad libitum twice daily (08:00 and 16:00 h). Rumen fluid was collected via cannula at an age of 9, 11, 13 and 15 weeks, twice weekly just prior to as well as 1, 3, 5 and 7 h after morning feeding. Chewing activity was recorded by a special head collar. As the calves aged DMI increased rapidly congruent with the recommended range for weaned calves. Because of the differing energy supply, calves receiving the H30 TMR were heavier than calves receiving the H40 TMR (139 kg versus 123 kg, P=0.007). During the trial ruminal pH of all calves were within the target range (6.2 ± 0.5), indicating physiological ruminal fermentation patterns. Daily mean ruminal pH was uninfluenced by treatment, however at an age of 13 and 15 weeks H30 showed a higher short chain fatty acid (SCFA) level than H40 (P=0.098; P=0.036). At an age of 15 weeks H30 showed a critical decrease in ruminal pH (3 h after feeding: 5.7) corresponding to a higher ruminal SCFA concentration (148.2 mmol/L, P=0.007). Chewing activity was well developed at an early age due to an increasing DMI after weaning. At an age of 15 weeks chewing activity (per day: 613–743 min total chewing; 358–418 min rumination) was similar to that of adult cows. In summary, feeding a dry TMR consisting per kg DM of 300–400 g hay to early-weaned calves can be recommended for a successful calf rearing up to an age of 15 weeks.     

Effects of Agave salmiana Otto Ex Salm-Dyck silage as forage on ruminal fermentation and growth in goats

Ensiling of Agave salmiana Otto Ex Salm-Dyck, a widespread plant in Mexico, as a viable preservation method to create a potential animal feed resource for ruminants was investigated. Fresh A. salmiana with 205 g dry matter (DM)/kg and wilted alfalfa with 602 g DM/kg were ensiled in combinations (DM:DM) of 1000:0, 500:500 and 350:650, to evaluate feeding value of agave:alfalfa silages on ruminal fermentation and growth of goats. Chemical composition and in situ ruminal disappearance of three total mixed rations (TMRs), which included 240 g/kg DM of each silage (1000:0, 500:500 and 350:650) were determined. The TMR were used to assess ruminal fermentation and growth of 15 goats (20 ± 2.2 kg body weight (BW)). Silage pH (≤4), lactate (>25 g/kg DM) and ammonia (<50 g/kg total N) concentrations indicate that silage quality was good. Lactic acid was the main acid in all silages, acetic acid concentrations were relatively low, and butyrate was only detected in only the 1000:0 agave:alfalfa silage. Potential DM disappearance of the TMR increased quadratically as the amount of alfalfa included in the silage mixture increased. The BW gain and feed efficiency were not changed by treatment, even though DM intake decreased and aNDF intake increased linearly as the amount of alfalfa included in the silage mixture increased. Ruminal pH and butyrate increased, and ammonia N, lactate and propionate decreased linearly as alfalfa proportion of alfalfa in the silage mixture was increased. The TMR ingredient selectivity by the goats may have limited goat performance when alfalfa was included in agave silage mixtures. Because the agave:alfalfa blend improved nutritional quality, ruminal digestibility and intake of agave silage, alfalfa inclusion may improve nutritional characteristics of agave plants silages for ruminants.