Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds

To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.

Comportamento higroscópico de partes aéreas de pimenta-de-macaco (Piper aduncum L.)

Isotermas de dessorção de pimenta-de-macaco foram determinadas pelo método gravimétrico estático nas temperaturas de 35, 45 e 55 ºC, com umidade relativa variando de 5,5-81%. Três modelos matemáticos foram aplicados para analisar os dados experimentais. O modelo de GAB modificado apresentou o melhor ajuste aos dados experimentais. O calor isostérico e a entropia diferencial foram determinados pela aplicação das equações de Clausius-Clapeyron e Gibbs-Helmholtz, respectivamente. O calor isostérico e a entropia da isoterma de dessorção apresentaram comportamento similar. A teoria da compensação entalpia-entropia foi aplicada às isotermas indicando que o mecanismo de dessorção de umidade das partes aéreas de pimenta-de-macaco é controlado pela entalpia.

Attitudes, Confidence, and Achievement of High-Ability Fifth Grade Math Students

In this action research study of my fifth grade high-ability mathematics class, I investigated student attitudes of mathematics and their confidence in mathematics. Student achievement was compared to two different confidence scales to identify a relationship between confidence and achievement. Six boys and eleven girls gave their consent to the study. I discovered there seems to be a connection between confidence and achievement and that boys are generally more confident than girls. Most students liked math and were comfortable sharing answers and methods of solving problems with other students. As a result of this study I plan to use my survey and interview questions at the beginning of the school year with my new class in order to assess their attitudes and confidence in math. I can use this information to identify potential struggles and better plan for student instruction.

AN OVERVIEW OF DEPREDATING BIRD DAMAGE CONTROL IN CALIFORNIA

To many people, California is synonomous with Disneyland, freeways, Los Angeles smog, Yosemite, the California missions, or for you bird aficionados, the California Condor. But do you think about California when you eat strawberry shortcake? You should -- California leads the nation in strawberry production. How about artichokes? California produces over 98% of the artichokes raised in the United States. Dates? California produces over 99% of the dates in the United States. Yes, California is all of these, and it is much more. California may well be the most diverse state in the United States. Within its 100.2 million acres, California has the lowest place in the U.S. in Death Valley and one of the highest mountains with Mt. Whitney. Because California is such a diverse state and has a wide variety of micro- climates, it supports a uniquely diverse agriculture. Agriculture uses only about 36 million acres of its total 100.2 million acres, and most of the cash return from crops is produced on 8,6 million acres that are irrigated. California produces about 250 crops and livestock commodities (excluding nursery crops) and provides the U.S. with about 25% of its table foods. California leads the nation in the production of 46 commercial crops and livestock commodities; its farmers and ranchers marketed $8.6 billion of crop and livestock products in 1975, and the state’s harvested farm production in 1975 set a new record at 51.1 million tons. HISTORY OF BIRD PROBLEMS Records such as this are not achieved without some risk. Crops growing in Cali- fornia have always had competition from many types of vertebrate pests. The wide variety of crops grown in California and the varied climates and situations in which they are grown has resulted in many different species of birds damaging crops. Birds have compet- ed with man for his crops since the dawn of agriculture. McAtee (1932) cited examples of bird damage that occurred in a wide variety of crops in California during the early 1900s. During the 1920s, many requests for Information and relief from damage caused by a wide variety of birds, culminated in the assignment, in May 1929, of two biologists, S. E. Piper and Johnson Neff, of the former U.S. Bio- logical Survey, to initiate field studies in California. In cooperation with the Cali- fornia Department of Food and Agriculture and County Agricultural Commissioners, the study was to determine the problems and devise control procedures relative to bird depredations. Piper and Neff found such damage as Horned Larks pulling sprouting crops, House Finches disbudding deciduous fruit trees and devouring mature fruit. Blackbirds were a problem in the rice crop. Early controls were varied and, for the most part, lacked effectiveness. Flagging of fields was common to deter Horned Larks. Windmill devices were tried to frighten birds. Shooting to kill birds was common; scarecrows were.used. The six-year study brought forth the basis of most of the depredating bird control techniques still in use in California. At the end of the study, these two biologists compiled a book called “Procedure and Methods in Controlling Birds Injurious to Crops in California.” This was and still is the “Bible” for bird damage control techniques used in California. The thorough investigations conducted by these biologists resulted in techniques that have remained valid in California for over 40 years.

In vitro Metabolism of Grandisin, a Lignan with Anti-chagasic Activity

Tetrahydrofuran lignans represent a well-known group of phenolic compounds capable of acting as antiparasitic agents. In the search for new medicines for the treatment of Chagas disease, one promising compound is grandisin which has shown significant activity on trypomastigote forms of Trypanosoma cruzi. In this work, the in vitro metabolism of grandisin was studied in the pig cecum model and by biomimetic phase I reactions, aiming at an ensuing a preclinical pharmacokinetic investigation. Although grandisin exhibited no metabolization by the pig microbiota, one putative metabolite was formed in a biomimetic model using Jacobsen catalyst. The putative metabolite was tested against T. cruzi revealing loss of activity in comparison to grandisin.

Dillapiole as Antileishmanial Agent: Discovery, Cytotoxic Activity and Preliminary SAR Studies of Dillapiole Analogues

In this paper, the isolation of dillapiole (1) from Piper aduncum was reported as well as the semi-synthesis of two phenylpropanoid derivatives [di-hydrodillapiole (2), isodillapiole (3)], via reduction and isomerization reactions. Also, the compounds' molecular properties (structural, electronic, hydrophobic, and steric) were calculated and investigated to establish some preliminary structureactivity relationships (SAR). Compounds were evaluated for in vitro antileishmanial activity and cytotoxic effects on fibroblast cells. Compound 1 presented inhibitory activity against Leishmania amazonensis (IC50?=?69.3 mu M) and Leishmania brasiliensis (IC50?=?59.4 mu M) and induced cytotoxic effects on fibroblast cells mainly in high concentrations. Compounds 2 (IC50?=?99.9 mu M for L. amazonensis and IC50?=?90.5 mu M for L. braziliensis) and 3 (IC50?=?122.9 mu M for L. amazonensis and IC50?=?109.8 mu M for L. brasiliensis) were less active than dillapiole (1). Regarding the molecular properties, the conformational arrangement of the side chain, electronic features, and the hydrophilic/hydrophobic balance seem to be relevant for explaining the antileishmanial activity of dillapiole and its analogues.

High-throughput sequencing of black pepper root transcriptome

Background: Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host's root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. Results: The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant's root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. Conclusions: This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.

Depression, fatigue, and health-related quality of life in head and neck cancer patients: a prospective pilot study

To assess the prevalence of depression and fatigue symptoms in head and neck cancer patients during radiotherapy treatment and relate them symptoms with these patients' quality of life. This is a prospective study. The Beck Depression Inventory (BDI), Piper Fatigue Scale-revised and Functional Assessment Cancer Therapy Head and Neck (FACT-H&N) were applied to 41 head and neck cancer patients at three times: at the start of treatment (T1), approximately 15 days after the start of treatment (T2) and at the end of treatment (T3), approximately 30 days after the start of the radiotherapy. The mean BDI and PIPER increased during the radiotherapy treatment. BDI scores did not demonstrate the presence of depression, although the number of symptoms increased, and the presence of fatigue rose as treatment advanced. The mean FACT H&N decreased in the middle and at the end of treatment, indicating worsening in these patients' Quality of Life. Depression and fatigue symptoms increased during radiotherapy treatment, while QoL levels decreased. This demonstrates that these symptoms are strongly correlated and that their presence negatively influenced QoL. At the start of treatment, nurses need to advise patients and plan care, offering interventions to decrease these symptoms and improve QoL.

Electrophysiological Responses of the Naupactus bipes Beetle to Essential Oils from Piperaceae Species

Electrophysiological responses based on electroantennographic detection (GC-EAD) and electroantennography (EAG) analysis of Naupactus bipes beetles (Germar, 1824) (Coleoptera: Curculionidae: Brachycerinae) were used to test volatile oils of Piper gaudichaudianum, P. regnellii and P. hispidum. In the EAG experiments, female and male beetles showed significant EAG response to the three volatile oils of Piper species, with the females' responses slightly higher than the males'. The experiments with GC-EAD revealed that some terpenoids (namely, alpha-pinene, beta-pinene, myrcene, alpha-copaene and germacrene) present in the leaf essential oils of the Piper species are perceptible to female and male beetles.

Secondary metabolites isolated from Piper chimonantifolium and their antifungal activity

In this study, the CH2Cl2 extract from leaves of Piper chimonantifolium was subjected to several chromatographic separation procedures to afford one chromene (gaudichaudianic acid) as a major compound as well as two flavonoids (dihydrooroxylin and pinocembrin) and three steroids (sitosterol, sitosteryl palmitate and stigmasterol). The structures of all determined compounds were characterised by spectrometric analysis, mainly mass spectrometry and NMR, as well as their optical properties. This article describes the first phytochemical study of the leaves of P. chimonantifolium and an evaluation of the antifungal activity of its major compounds.

Chemical constituents from three medicinal plants: Piper renitens, Siparuna guianensis and Alternanthera brasiliana

Chemical study of three medicinal plants: from leaves of Piper renitens (Miq.) Yunck, Piperaceae, and Siparuna guianensis Aubl., Siparunaceae, and from flowers of Alternanthera brasiliana (L.) Kuntze, Amaranthaceae, resulted in isolation of nine compounds: three steroids, β-sitosterol, stigmasterol from P. renitens and sitosterol-3-O-β-D-glucopyranoside from A. brasiliana, the diterpene kaurane ent-kauran-16α,17-diol from P. renitens, two derivatives kaempferol-methylether, kumatakenine (kaempferol-3,7-dimethylether) and kaempferol-3,7,3'-trimethylether from S. guianensis and three flavones, crysoeriol (5,7,4'-trihydroxy-3'-methoxyflavone), tricin (5,7,4'-trihydroxy-3',5'-dimethoxyflavone) and 7-O-β-D-glucopyranoside-5,4'-dihydroxy-3'-methoxyflavone from A. brasiliana. Compounds structures were determinate using 1D and 2D ¹H NMR and 13C spectral data, mass and IR spectra, comparing with literature data.

Contractile performance of adult ventricular rat cardiomyocytes is not directly jeopardized by NO/cGMP-dependent induction of pro-apoptotic pathways

The activation of NO/cGMP pathways can induce pro-apoptotic pathways in cardiomyocytes although only a small number of cardiomyocytes fulfill the criteria of apoptosis. The same pathways reduce the contractile performance of cardiomyocytes. In the present study, we tested the hypothesis that exposure of cells to NO/cGMP for 24 h decrease their contractile performance due to an activation of pro-apoptotic pathways. Experiments were performed on freshly isolated and cultured adult ventricular rat cardiomyocytes. Cells were incubated with 8-bromo-cyclo-GMP (100 nmol/L-1 micromol/L), the NO donor SNAP (1 nmol/L-100 micromol/L), or the guanylyl cyclase activator YC-1 (3 micromol/L). Cell shortening, contraction and relaxation velocities, and diastolic cell lengths were determined at beating frequencies of 0.5, 1, and 2 Hz 24 h later. The activation of pro-apoptotic pathways was determined by staining of cardiomyocytes with an antibody directed against active caspase-3 and quantification of the number of apoptotic cells (annexin staining). Caspase-3 activation and an increase in the number of apoptotic cells was observed, but only at the highest concentrations tested (8-bromo-cyclo-GMP: 1-10 mmol/L; SNAP: 1-100 micromol/L). At these concentrations, none of the drugs decreased the mean cell shortening of cardiomyocytes. However, at concentrations lower than those required for induction of apoptotic cell death, the diastolic cell lengths and sarcomere lengths increased but cell shortening decreased. In conclusion, low concentrations of either NO or cGMP cause a desensitization of myofibrils, as indicated by elongated cell shapes, increased sarcomere lengths and reduced load-free cell shortening. High concentrations of NO/cGMP induce caspase-3 activation and increase the number of cells fulfilling the criteria of apoptotic cell death but did not impair cell function. Therefore, induction of apoptotic cell death per se seems not to contribute to the loss of contractile efficiency on the cellular level.

Recombinant human erythropoiesis-stimulating agents and mortality in patients with cancer: a meta-analysis of randomised trials

BACKGROUND: Erythropoiesis-stimulating agents reduce anaemia in patients with cancer and could improve their quality of life, but these drugs might increase mortality. We therefore did a meta-analysis of randomised controlled trials in which these drugs plus red blood cell transfusions were compared with transfusion alone for prophylaxis or treatment of anaemia in patients with cancer. METHODS: Data for patients treated with epoetin alfa, epoetin beta, or darbepoetin alfa were obtained and analysed by independent statisticians using fixed-effects and random-effects meta-analysis. Analyses were by intention to treat. Primary endpoints were mortality during the active study period and overall survival during the longest available follow-up, irrespective of anticancer treatment, and in patients given chemotherapy. Tests for interactions were used to identify differences in effects of erythropoiesis-stimulating agents on mortality across prespecified subgroups. FINDINGS: Data from a total of 13 933 patients with cancer in 53 trials were analysed. 1530 patients died during the active study period and 4993 overall. Erythropoiesis-stimulating agents increased mortality during the active study period (combined hazard ratio [cHR] 1.17, 95% CI 1.06-1.30) and worsened overall survival (1.06, 1.00-1.12), with little heterogeneity between trials (I(2) 0%, p=0.87 for mortality during the active study period, and I(2) 7.1%, p=0.33 for overall survival). 10 441 patients on chemotherapy were enrolled in 38 trials. The cHR for mortality during the active study period was 1.10 (0.98-1.24), and 1.04 (0.97-1.11) for overall survival. There was little evidence for a difference between trials of patients given different anticancer treatments (p for interaction=0.42). INTERPRETATION: Treatment with erythropoiesis-stimulating agents in patients with cancer increased mortality during active study periods and worsened overall survival. The increased risk of death associated with treatment with these drugs should be balanced against their benefits. FUNDING: German Federal Ministry of Education and Research, Medical Faculty of University of Cologne, and Oncosuisse (Switzerland).

Guineensine is a novel inhibitor of endocannabinoid uptake showing cannabimimetic behavioral effects in BALB/c mice

High-content screening led to the identification of the N-isobutylamide guineensine from Piper nigrum as novel nanomolar inhibitor (EC50 = 290 nM) of cellular uptake of the endocannabinoid anandamide (AEA). Noteworthy, guineensine did not inhibit endocannabinoid degrading enzymes fatty acid amide hydrolase (FAAH) or monoacylglycerol lipase (MAGL) nor interact with cannabinoid receptors or fatty acid binding protein 5 (FABP5), a major cytoplasmic AEA carrier. Activity-based protein profiling showed no inhibition of serine hydrolases. Guineensine also inhibited the cellular uptake of 2-arachidonoylglycerol (2-AG). Preliminary structure–activity relationships between natural guineensine analogs indicate the importance of the alkyl chain length interconnecting the pharmacophoric isobutylamide and benzodioxol moieties for AEA cellular uptake inhibition. Guineensine dose-dependently induced cannabimimetic effects in BALB/c mice shown by strong catalepsy, hypothermia, reduced locomotion and analgesia. The catalepsy and analgesia were blocked by the CB1 receptor antagonist rimonabant (SR141716A). Guineensine is a novel plant natural product which specifically inhibits endocannabinoid uptake in different cell lines independent of FAAH. Its scaffold may be useful to identify yet unknown targets involved in endocannabinoid transport.

The effect of thyroxine and triiodothyronine on fatigue, depression, and memory in a hypothyroid population

Background. This study was planned at a time when important questions were being raised about the adequacy of using one hormone to treat hypothyroidism instead of two. Specifically, this trial aimed to replicate prior findings which suggested that substituting 12.5 μg of liothyronine for 50 μg of levothyroxine might improve mood, cognition, and physical symptoms. Additionally, this trial aimed to extend findings to fatigue. ^ Methods. A randomized, double-blind, two-period, crossover design was used. Hypothyroid patients stabilized on levothyroxine were invited to participate. Thirty subjects were recruited and randomized. Sequence one received their standard levothyroxine dose in one capsule and placebo in another during the first six weeks. Sequence two received their usual levothyroxine dose minus 50 μg in one capsule and 10 μg of liothyronine in another. At the end of the first six week period, subjects were crossed over. T tests were used to assess carry-over and treatment effects. ^ Results. Twenty-seven subjects completed the trial. The majority of completers had an autoimmune etiology. Mean baseline levothyroxine dose was 121 μg/d (±26.0). Subjects reported small increases in fatigue as measured by the Piper Fatigue Scale (0.9, p = 0.09) and in symptoms of depression measured by the Beck Depression Inventory-II (2.3, p = 0.16) as well as the General Health Questionnaire-30 (4.7, p = 0.14) while treated with substitution treatment. However, none of these differences was statistically significant. Measures of working memory were essentially unchanged between treatments. Thyroid stimulating hormone was about twice as high during substitution treatment (p = 0.16). Free thyroxine index was reduced by 0.7 (p < 0.001), and total serum thyroxine was reduced by 3.0 (p < 0.001) while serum triiodothyronine was increased by 20.5 (p < 0.001) on substitution treatment. ^ Conclusions. Substituting an equivalent amount of liothyronine for a portion of levothyroxine in patients with hypothyroidism does not decrease fatigue, symptoms of depression, or improve working memory. However, due to changes in serum hormone levels and small increments in fatigue and depression symptoms on substitution treatment, a question was raised about the role of T3 in the serum. ^