A Genotypic Test for HIV-1 Tropism Combining Sanger Sequencing with Ultradeep Sequencing Predicts Virologic Response in Treatment-Experienced Patients

A tropism test is required prior to initiation of CCR5 antagonist therapy in HIV-1 infected individuals, as these agents are not effective in patients harboring CXCR4 (X4) coreceptor-using viral variants. We developed a clinical laboratory-based genotypic tropism test for detection of CCR5-using (R5) or X4 variants that utilizes triplicate population sequencing (TPS) followed by ultradeep sequencing (UDS) for samples classified as R5. Tropism was inferred using the bioinformatic algorithms geno2pheno_[coreceptor] and PSSM_x4r5. Virologic response as a function of tropism readout was retrospectively assessed using blinded samples from treatment-experienced subjects who received maraviroc (N = 327) in the MOTIVATE and A4001029 clinical trials. MOTIVATE patients were classified as R5 and A4001029 patients were classified as non-R5 by the original Trofile test. Virologic response was compared between the R5 and non-R5 groups determined by TPS, UDS alone, the reflex strategy and the Trofile Enhanced Sensitivity (TF-ES) test. UDS had greater sensitivity than TPS to detect minority non-R5 variants. The median log₁₀ viral load change at week 8 was −2.4 for R5 subjects, regardless of the method used for classification; for subjects with non-R5 virus, median changes were −1.2 for TF-ES or the Reflex Test and −1.0 for UDS. The differences between R5 and non-R5 groups were highly significant in all 3 cases (p<0.0001). At week 8, the positive predictive value was 66% for TF-ES and 65% for both the Reflex test and UDS. Negative predictive values were 59% for TF-ES, 58% for the Reflex Test and 61% for UDS. In conclusion, genotypic tropism testing using UDS alone or a reflex strategy separated maraviroc responders and non-responders as well as a sensitive phenotypic test, and both assays showed improved performance compared to TPS alone. Genotypic tropism tests may provide an alternative to phenotypic testing with similar discriminating ability.     

Correction of statistical miscalculation slightly alters conclusions about diversity effects for Douglass et al. (2008)

While most of the conclusions about diversity effects in Douglass, J.G., Duffy, J.E. & Bruno, J.F. [Ecol. Lett., 11, 2008, 1] are upheld, correction of a statistical miscalculation indicates that grazer diversity and predator diversity had combined effects on responses, but did not have interactive effects as initially reported.     

Stochastic modeling of aphid population growth with nonlinear, power-law dynamics

This paper develops a deterministic and a stochastic population size model based on power-law kinetics for the black-margined pecan aphid. The deterministic model in current use incorporates cumulative-size dependency, but its solution is symmetric. The analogous stochastic model incorporates the prolific reproductive capacity of the aphid. These models are generalized in this paper to include a delayed feedback mechanism for aphid death. Whereas the per capita aphid death rate in the current model is proportional to cumulative size, delayed feedback is implemented by assuming that the per capita rate is proportional to some power of cumulative size, leading to so-called power-law dynamics. The solution to the resulting differential equations model is a left-skewed abundance curve. Such skewness is characteristic of observed aphid data, and the generalized model fits data well. The assumed stochastic model is solved using Kolmogrov equations, and differential equations are given for low order cumulants. Moment closure approximations, which are simple to apply, are shown to give accurate predictions of the two endpoints of practical interest, namely (1) a point estimate of peak aphid count and (2) an interval estimate of final cumulative aphid count. The new models should be widely applicable to other aphid species, as they are based on three fundamental properties of aphid population biology.     

A radioimmunoprecipitation method in the serodiagnosis of HIV infection: the development of the optimal conditions for its performance and the evaluation of the possibilities for its use

The optimum conditions for using the method of radioimmunoprecipitation (RIP) for the detection of human immunodeficiency virus (HIV) in serum samples have been established. Out of several available cell lines persistently infected with HIV, specially selected line 17 has been chosen. The characteristic feature of this is the high and stable (under the conditions of prolonged cultivation) accumulation of virus-specific proteins in infected cells. The optimum conditions for making the test and its evaluation have also been established. The data of literature on the advantages of the method of RIP over such traditional methods as the enzyme immunoassay and immunoblotting have been confirmed. Thus, the presence of specific antibodies in several serum samples registered as false negative has been established. The intertypical reactivity of two serotypes of the virus, HIV-1 and HIV-2, has been studied. Cross reactivity of antibodies with respect to the HIV gene gag, but not with respect to viral glycoproteids, has been established. Ideas on the expediency and prospects of using RIP for the serological control of HIV infection are presented.     

Fine-scale substrate use by a small sit-and-wait predator

Substrate choice is one of the most important decisions thatsit-and-wait predators must make. Not only may it dictate theprey available but also the cover for the predator which mayconceal it from prey or its own predators. However, while ona particular substrate the behavior and use of that substratemay vary widely. When naïve, newly emerged crab spiderlingsMisumena vatia (Thomisidae) occupied flowering goldenrod Solidagocanadensis, their behavior differed markedly on inflorescenceswith relatively sparse and densely packed flower heads as wellas on experimentally thinned and unthinned inflorescences. Initially,the spiderlings most often hunted at the thinned sites and hidamong the dense flower heads at the unthinned sites, a differencethat disappeared in all broods tested after 2–3 h, possiblybecause of the growing hunger of the initially concealed individuals.Prey capture (dance flies) in the thinned sites initially significantlyexceeded that in unthinned sites but subsequently did not differ.However, spiderlings encountered their principal predator, thejumping spider Pelegrina insignis, significantly more oftenon unthinned than thinned inflorescences. Even though usagepatterns initially differed strikingly, spiderlings did notdiffer in their rates of quitting the two types of sites. Theseresults suggest a trade-off between foraging and predator avoidancethat changes in response to increasing hunger over time.     

Isolation and sequence analysis of cDNA for rat carboxypeptidase E [EC 3.4.17.10], a neuropeptide processing enzyme

Carboxypeptidase E (CPE) is the carboxypeptidase B-like enzyme associated with the biosynthesis of numerous peptide hormones and neurotransmitters. This enzyme has been previously purified to homogeneity from bovine tissues, and cDNA clones (non-full length) isolated from a bovine pituitary cDNA library. In the present study, cDNA encoding full-length rat CPE has been isolated and sequenced. Both the nucleotide and amino acid sequences of rat CPE show substantial homology with the bovine sequences. The bovine and rat nucleotide sequences are homologous within the entire coding region, as well as within several portions of the 3'-untranslated region. The predicted amino acid sequence of rat CPE is greater than 90% homologous with the bovine enzyme. Northern blot analyses indicate a single species of CPE mRNA approximately 2100 nucleotides in length to be present in many neural and endocrine tissues. High levels of CPE mRNA are present in rat hypothalamus, hippocampus, midbrain, striatum, and cerebral cortex; and moderate levels are present in the brain stem, cerebellum, heart, adrenal, and eye. Low levels are detected in testis and duodenum, but not in liver or thymus. This tissue-specific expression of CPE mRNA is consistent with the proposed role for this enzyme in the production of numerous peptide hormones and neurotransmitters.     

Variability of responses across training levels to maximal treadmill exercise

The variability of peak VO2 (ml/min, ml.kg-1.min-1), time on treadmill (TMILLTM), maximal heart rate (HRmax), respiratory exchange ratio at peak VO2 (Rmax), rate of respiration at peak VO2 (FREQ), and exercise-induced changes in plasma lactate concentration (LACDIF) was measured across three maximal treadmill runs in five highly trained, seven moderately trained, and five untrained males. No effect of training level on the variability of any of the parameters was found. Test-retest correlation coefficients for peak VO2 (r = 0.95, run 1 with run 2; r = 0.92, run 1 with run 3; r = 0.92, run 2 with run 3) were similar to previously reported values. Variance component distributions suggested that the underlying physiological mechanisms of response for peak VO2, TMILLTM, and HRmax were different from those of FREQ, Rmax, and LACDIF. Minimum detectable differences for peak VO2 (ml.kg-1.min-1, n = 5, minimum detectable within subject difference, 11.5%; minimum detectable among subject effects, 21.3%) indicated a need for careful attention to research design in future studies.     

Changes in the human mitochondrial genome after treatment of malignant disease

Mitochondrial DNA (mtDNA) is the only extrachromosomal DNA in human cells. The mitochondrial genome encodes essential information for the synthesis of the mitochondrial respiratory chain. Inherited defects of this genome are an important cause of human disease. In addition, the mitochondrial genome seems to be particularly prone to DNA damage and acquired mutations may have a role in ageing, cancer and neurodegeneration. We wished to determine if radiotherapy and chemotherapy used in the treatment of cancer could induce changes in the mitochondrial genome. Such changes would be an important genetic marker of DNA damage and may explain some of the adverse effects of treatment. We studied samples from patients who had received radiotherapy and chemotherapy for point mutations within the mtDNA control region, and for large-scale deletions. In blood samples from patients, we found a significantly increased number of point mutations compared to the control subjects. In muscle biopsies from 7 of 8 patients whom had received whole body irradiation as well as chemotherapy, the level of a specific mtDNA deletion was significantly greater than in control subjects. Our studies have shown that in patients who have been treated for cancer there is an increased level of mtDNA damage.